Biology subjects

Ravishankar, R.

Publications and source records attributed to Ravishankar, R..

8 recordsLinked to original sources

bioRxiv2026

A genetically encoded RhoG FRET biosensor reveals spatially compartmentalized RhoG-Rac1 signaling during cell protrusion

RhoG is a member of the Rho-family of small GTPases, and is closely related to the canonical Rac1 GTPase, implicated in membrane trafficking, dorsal ruffling, macropinocytosis, and cell protrusion, but its activity has been difficult to visualize directly in living cells with high spatial and temporal resolution. Here, we developed and validated a genetically encoded, single-chain Forster resonance energy transfer (FRET) biosensor for RhoG based on a C-terminal full-length RhoG and an intramolecular RhoG-binding domain derived from ELMO1. The biosensor showed a robust dynamic range when comparing constitutively active and inactive RhoG mutants, responded appropriately to regulation by RhoGDI, GAPs, and GEFs, and detected growth factor-stimulated RhoG activation in live cells. Imaging in mouse embryonic fibroblasts revealed dynamic RhoG activation at leading-edge protrusions, dorsal ruffles, and forming pinocytic and macropinocytic structures. To define the signaling relationship between RhoG and its closely related family member Rac1, we combined the RhoG biosensor with a near-infrared Rac1 FRET biosensor for simultaneous live-cell imaging. Morphodynamic mapping showed that both RhoG and Rac1 activities were positively coupled to edge protrusion, with strongest correlations near the leading-edge, but their direct coupling varied with distance from the edge, indicating partial spatial decoupling within protrusive regions. Inhibition of Src-family kinases altered RhoG dynamics, strongly suppressed Rac1 coupling to protrusion, and inverted the normal positive correlation between RhoG and Rac1 activities. Signaling microdomain analysis further showed that Src inhibition selectively prolonged Rac1 microdomain lifetimes without significantly affecting RhoG domains. Together, these results establish a new biosensor for direct visualization of RhoG activity and reveal that RhoG and Rac1 are coordinated but spatially and temporally distinct components of protrusion-associated signaling networks, with Src-family kinases playing a central role in maintaining their normal coupling.

cell biology↗

bioRxiv2026

ARHGAP20 organizes spatial Rap1-RhoA signaling coordination controlling adhesion dynamics during migration

Cell migration requires the precise coordination of signaling pathways that regulate cytoskeletal dynamics and adhesion turnover. Rho GTPase-activating proteins (RhoGAPs) play critical roles in shaping these processes by controlling the spatial and temporal activity of small GTPases. ARHGAP20 is a RhoA-specific GAP, a downstream target of the Ras-related GTPase Rap1, and has been implicated in cancer cell motility, yet its functional role in coordinating migration-associated signaling remains poorly understood. Here, we investigated the role of ARHGAP20 in cell migration and its impact on the coordination between adhesion- and contractility-associated signaling pathways regulated by Rap1A and RhoA respectively. Using loss-of-function approaches in MTLn3 cells, we show that depletion of ARHGAP20 impairs both directed and random migration, leading to reduced cell velocity and displacement, and increased cell adhesion. To explore the underlying signaling mechanisms, we developed a genetically encoded FRET biosensor to monitor Rap1A activity and combined it with a near-infrared RhoA biosensor to simultaneously analyze their spatiotemporal dynamics in living cells. We found that Rap1A and RhoA activities are negatively coordinated during leading-edge dynamics and that ARHGAP20 depletion enhances this local anticorrelation. To further define where ARHGAP20 regulates Rap1A-RhoA signaling, we applied a microdomain-based analytical framework to quantify local signaling clusters. This analysis revealed that ARHGAP20 selectively modulates Rap1A-RhoA coordination outside focal adhesion regions, while leaving signaling correlations and overlap within focal adhesions unchanged. Subcellular localization analyses further reveal that ARHGAP20 is largely excluded from focal adhesions but associates with microtubules, the endoplasmic reticulum, the Golgi apparatus, and multiple Rab-positive vesicular compartments, supporting a trafficking-dependent mechanism for its spatial targeting. Together, our results identify ARHGAP20 as a regulator of cell migration that modulates the coordination between Rap1A and RhoA signaling through intracellular vesicular trafficking, highlighting the GAPs role in organizing the spatial coupling between signaling pathways in adhesion-associated regions required for efficient cell migration.

cell biology↗

bioRxiv2026

Allosteric Biosensors Unravel GTPase-Effector Feedback

Fluorescent biosensors that report protein conformation in vivo have been invaluable for understanding how the spatio-temporal dynamics of signaling controls cells. However, for GTPases these biosensors report the activated conformation using reagents that block the binding of downstream proteins, generating dominant negative effects and altering normal cell physiology. We present here a generalizable design to make GTPase biosensors (AlloRac1 and AlloCdc42), in which a circularly permuted fluorescent protein is inserted into a conserved loop allosterically connected to the effector binding site, generating activity-dependent fluorescence without blocking ligand interactions. The Rac1 biosensor showed that effector interactions led to increased Rac1 activation, indicating an auto-regulatory positive feedback made visible by the new biosensor design. This feedback regulated the kinetics and localization of Rac1 activity, including Rac1 activity gradients that controlled motility. Feedback was generated through Rac1 interaction with the effector Pak1, which led to further activation of Rac1 by the guanine exchange factor {beta}-Pix. The new biosensor approach enables quantitative imaging of previously obscure spatio-temporal dynamics in GTPase regulation.

cell biology↗

bioRxiv2026

Modulation of Oncogenic KRAS Signaling by Branched Actin-driven Cell Membrane Protrusions

For over three decades, we have known that oncogenic RAS alters the actin cytoskeleton organization and cell surface morphology1,2. RAS activates the GTPase RAC1, which triggers the growth of branched actin networks to promote cell membrane protrusions3,4. In melanoma, the hyperactive RAC1 mutant, Rac1P29S, was recently shown to drive extended lamellipodia, which then empower cell proliferation through sequestration and localized inhibition of the merlin tumor suppressor5. This discovery illustrates cell morphological programs not only as outputs but also as regulators of human oncogenic signals. Hence, we wondered whether the pronounced branched actin-driven membrane protrusions (BAMPs) downstream of oncogenic RAS are not mere outputs of RAS signaling but rather an active component in mediating the oncogenic penetrance of RAS mutants. We used volumetric light sheet microscopy and biochemical approaches to investigate the role of BAMPs in regulating the molecular signaling of oncogenic KRAS in pancreatic and lung cancer models. We found that elevated BAMP formation regulated the interaction of oncogenic KRAS with downstream effectors, specifically with the RAC1 GEF TIAM1. This implies that BAMPs amplify their own upstream regulators in a positive feedback. This meritorious cycle upregulates cyclin D1 expression by inactivating the merlin tumor suppressor, independently of the mitogen activated protein kinase pathway (MAPK). In the absence of BAMPs, cells carrying oncogenic KRAS mutations are unable to attain their full penetrance in proliferation. Overall, this work unveils the long-overlooked role of branched actin-driven cell morphology in the functionalization of KRAS mutants as potent oncogenes.

cancer biology↗

bioRxiv2025

Phosphoinositide lipids have bidirectional and spatially distinct roles in filopodial dynamics

Neural circuits are assembled by filopodia, dynamic actin-rich protrusions that connect environment sensing with structural changes. Using rapid timelapse imaging and acute pharmacological perturbation in Xenopus laevis retinal ganglion cells, we reveal that phosphoinositide lipid conversions impose spatially distinct control over filopodial dynamics. The class I phosphoinositide 3-kinase (PI3K) inhibitor alpelisib and Oculocerebrorenal syndrome of Lowe protein/Inositol polyphosphate 5-phosphatase inhibitor YU142670 markedly reduced filopodial tip motility. Class II PI3K inhibitor PITCOIN4 and YU142670 curtailed base dynamics, indicating location-specific lipid requirements. Despite no detectable change in PI(4,5)P2, both alpelisib and YU142670 depleted PI(3,4)P2 at filopodial tips. Their co-application was non-additive, with partial alleviation of YU142670-induced stalling by alpelisib, consistent with networked control of lipid conversion and actin remodelling. Live imaging with a TAPP1-3xcPH probe combined with quantitative cross-correlation and Granger causality analysis showed that PI(3,4)P2 at filopodial tips both generates tip extension and responds to forward filopodial movement. Disrupting actin polymerisation rapidly erased tip PI(3,4)P2 prior to filopodial stalling. These findings define a vulnerable node with implications for neurodevelopmental miswiring.

cell biology↗

bioRxiv2025

Robust statistical assessment of Oncogenotype to Organotropism translation in xenografted zebrafish

Organotropism results from the functional versatility of metastatic cancer cells to survive and proliferate in diverse microenvironments. This adaptivity can originate in clonal variation of the spreading tumor and is often empowered by epigenetic and molecular reprogramming of cell regulatory circuits. Related to organotropic colonization of metastatic sites are environmentally-sensitive, differential responses of cancer cells to therapeutic attack. Accordingly, understanding the organotropic profile of a cancer and probing the underlying driver mechanisms are of high clinical importance. However, determining systematically the organotropism of one cancer versus the organotropism of another cancer, potentially with the granularity of comparing the same cancer type between patients or tracking the evolution of a cancer in a single patient for the purpose of personalized treatment, has remained very challenging. It requires a host organism that allows observation of the spreading pattern over relatively short experimental times. Moreover, organotropic patterns often tend to be statistically weak and superimposed by experimental variation. Thus, an assay for organotropism must give access to statistical powers that can separate meaningful heterogeneity, i.e., heterogeneity that determines organotropism, from meaningless heterogeneity, i.e., heterogeneity that causes experimental noise. Here we describe an experimental workflow that leverages the physiological properties of zebrafish larvae for an imaging-based assessment of organotropic patterns over a time-frame of 3 days. The workflow incorporates computer vision pipelines to automatically integrate the stochastic spreading behavior of a particular cancer xenograft in tens to hundreds of larvae allowing subtle trends in the colonization of particular organs to emerge above random cell depositions throughout the host organism. We validate our approach with positive control experiments comparing the spreading patterns of a metastatic sarcoma against non-transformed fibroblasts and the spreading patterns of two melanoma cell lines with previously established differences in metastatic propensity. We then show that integration of the spreading pattern of xenografts in 40 - 50 larvae is necessary and sufficient to generate a Fish Metastatic Atlas page that is representative of the organotropism of a particular oncogenotype and experimental condition. Finally, we apply the power of this assay to determine the function of the EWSR1::FLI1 fusion oncogene and its transcriptional target SOX6 as plasticity factors that enhance the adaptive capacity of metastatic Ewing sarcoma.

cancer biology↗

bioRxiv2023

A Humanized Yeast System for Evaluating the Protein Prenylation of a Wide Range of Human and Viral CaaX Sequences

The C-terminal CaaX sequence (cysteine-aliphatic-aliphatic-any of several amino acids) is subject to isoprenylation on the conserved cysteine and is estimated to occur in 1-2% of proteins within yeast and human proteomes. Recently, non-canonical CaaX sequences in addition to shorter and longer length CaX and CaaaX sequences have been identified that can be prenylated. Much of the characterization of prenyltransferases has relied on the yeast system because of its genetic tractability and availability of reporter proteins, such as the a-factor mating pheromone, Ras GTPase, and Ydj1 Hsp40 chaperone. To compare the properties of yeast and human prenyltransferases, including the recently expanded target specificity of yeast farnesyltransferase, we have developed yeast strains that express human farnesyltransferase or geranylgeranyltransferase-I in lieu of their yeast counterparts. The humanized yeast strains display robust prenyltransferase activity that functionally replaces yeast prenyltransferase activity in a wide array of tests, including the prenylation of a wide variety of canonical and non-canonical human CaaX sequences, virus encoded CaaX sequences, non-canonical length sequences, and heterologously expressed human proteins HRas and DNAJA2. These results reveal highly overlapping substrate specificity for yeast and human farnesyltransferase, and mostly overlapping substrate specificity for GGTase-I. This yeast system is a valuable tool for further defining the prenylome of humans and other organisms, identifying proteins for which prenylation status has not yet been determined. Summary StatementWe report yeast engineered to express human prenylation enzymes with which prenylation can be investigated for established and novel CaaX sequences associated with proteins involved in human disease.

biochemistry↗

bioRxiv2022

Therapeutic Interruption of T Cell Development Generates High-Affinity T Cells That Escape Exhaustion and Improve Cancer Immunotherapy

Availability of effective anti-tumor T cells is limited by cancer immunoediting, which depletes neoantigens, and central tolerance, which eliminates developing T cells with high-affinity T cell receptors (TCRs) against tumor self-antigens. Remaining tumor-reactive T cells are often exhausted after immune checkpoint blockade (ICB). Whether endogenous T cells with high- affinity TCRs against tumor self-antigens can be generated to circumvent exhaustion and reject neoantigen-poor tumors is unclear. We show that transiently interrupting central tolerance through RANKL blockade unleashes T cells possessing TCRs with self-reactive features that enable ICB to reject poorly immunogenic tumors. Upon recognition of tumor self-antigens, these T cells exhibit enhanced TCR signaling, enrichment in NFAT/AP-1 genes, and lymph node priming. Consequently, memory-precursor T cells against tumor self-antigens are generated, avoid exhaustion, and become effector-memory cells with transcriptional features associated with clinical ICB response. Thus, interrupting central tolerance provides T cells with tumor- directed autoreactivity that avoid exhaustion and improve immunotherapy.

immunology↗