Biology subjects

Prabhu, S.

Publications and source records attributed to Prabhu, S..

11 recordsLinked to original sources

bioRxiv2026

PQBP1 couples HIV-1 capsid recognition to cGAS recruitment through conformational remodeling

Pattern recognition receptors (PRRs) must selectively engage pathogen-derived signals to potentiate inflammation and antimicrobial responses. Polyglutamine-binding protein 1 (PQBP1) acts upstream of cyclic GMP-AMP synthase (cGAS) during HIV-1 infection through the recognition of viral capsid. However, the mechanism by which capsid binding enables cGAS recruitment remains unclear. As an intrinsically disordered protein, PQBP1 samples an ensemble of conformational states whose distribution depends on ligand engagement. Here we show that capsid engagement shifts this population toward a conformation competent for cGAS binding. Capsid binding at the N-terminus of PQBP1 redistributes conformational sampling within the WW domain and distal polar-rich domain (PRD). Alanine substitutions within these capsid-responsive regions retain capsid binding yet disrupt infection-dependent cGAS recruitment, indicating that capsid binding and cGAS recruitment depend on distinct regions of PQBP1. Together, these findings define a mechanism by which HIV-1 capsid engagement remodels PQBP1 into a cGAS-competent state, coupling capsid recognition to innate immune activation. IMPORTANCEPolyglutamine-binding protein 1 (PQBP1) initiates innate immune detection of HIV-1 by recognizing the incoming viral capsid. We show that capsid engagement reshapes PQBP1 conformational dynamics, and we identify distal regions required for infection-dependent cGAS association. These findings provide a mechanistic framework for how pathogen recognition is coupled to downstream innate immune activation.

molecular biology↗

bioRxiv2026

Inhibition of Dot1L Histone Methyltransferase Expands Bone Injury-Responsive CXCL12⁺ Stromal Progenitors

Adult bone marrow contains a heterogeneous network of skeletal stromal and progenitor cells (SSPC) that maintain bone homeostasis, support the hematopoietic niche, and drive the regenerative responses to injury. Despite their central role in bone regeneration, the mechanisms that regulate injury-induced SSPC activation and fate transitions remain incompletely understood. Here we identify Disruptor of telomeric silencing 1 like (DOT1L), the sole histone methyltransferase responsible for H3K79 methylation, as a critical regulator that restrains stromal activation. Using complementary genetic, pharmacologic, single-cell transcriptomic and injury models, we show that either Prrx1 lineage Dot1L haploinsufficiency or acute pharmacological Dot1L inhibition promote SSPC expansion, but through distinct programs: haploinsufficiency drives the expansion of Cxcl12+ CAR cells, whereas acute pharmacologic inhibition enriches fibroblastic-like stromal states. Single Cell Regulatory Network Inference and Clustering (SCENIC) analysis identifies DOT1L as a stabilizer of homeostatic marrow-supportive transcriptional programs, whose disruption facilitates transition to injury responsive stromal states. Partial loss of Dot1L in the Prrx1 lineage enhances injury-induced intramedullary mineralization in vivo. Collectively, these findings establish DOT1L as a gatekeeper of the stromal progenitor state that restrains lineage commitment and restrains the magnitude of the SSPC response following injury.

cell biology↗

bioRxiv2024

Effects of Aging on the Immune and Periosteal Response to Fracture in Mice

Aging predisposes individuals to reduced bone mass and fragility fractures, which are costly and linked to high mortality. Understanding how aging affects fracture healing is essential for developing therapies to enhance bone regeneration in older adults. During the inflammatory phase of fracture healing, immune cells are recruited to the injury site as periosteal skeletal stem/progenitor cells (pSSPCs) rapidly proliferate and differentiate into osteochondral lineages, allowing for fibrocartilaginous callus formation and complete bone healing. Irrespective of age, how periosteal mesenchymal and immune cells interact during early fracture healing is incompletely understood, limiting our ability to potentially modulate these processes. To address this, we directly analyzed, in parallel, at a single-cell level, isolated murine CD45(+) and CD45(-) periosteal cells dissected from intact and fractured bones, collected three days after injury. Through comprehensive analysis, corroborated by bulk RNA-sequencing, flow cytometry, and histology, we found aging decreases pSSPCs proliferative, marked by a reduced expression of genes required for callus formation and an increased senescence signature. We found that the chemokine Cxcl9 was highly upregulated in aged intact Prrx1+ pSSPCs, predicted to interact with other pSSPCs directly, and associated with increased recruitment of CD8+ T cells at the fracture site three days after injury. Cell-to-cell communication analysis provided insight into the complexity of interactions among the many cell types regulating fracture healing and the impact of aging on these processes. Together, these results provide insight into age-induced alterations in fracture healing, informing the development of improved therapeutic approaches for fragility fractures.

cell biology↗

bioRxiv2024

Improved Methodology for Studying Postnatal Osteogenesis via Intramembranous Ossification in a Murine Bone Marrow Injury Model

Long bone injuries heal through either endochondral or intramembranous bone formation pathways. Unlike the endochondral pathway that requires a cartilage template, the process of intramembranous ossification involves the direct conversion of skeletal stem and progenitor cells (SSPCs) into bone-forming osteoblasts. There are limited surgical methods to model this process in experimental mice. Here, we have improved upon a bone marrow injury model in mice to facilitate the study of bone repair via intramembranous ossification and to assess postnatal regulators of osteogenesis. This method is highly reproducible and user-friendly, and it allows temporal assessment of new bone formation in a short period (3-7 days post-injury) using {micro}CT and frozen section histology. Furthermore, the contributions of SSPCs and mature osteoblasts can be readily assessed using a combination of fluorescent reporter mice and this intramembranous bone marrow injury model. In clinical contexts, intramembranous bone formation is relevant for healing critical size defects, stress fractures, cortical defects, trauma from tumor resections, and joint replacements. SUMMARYThe murine bone marrow injury model is a useful tool to study postnatal osteogenesis through intramembranous ossification. This simplified surgical protocol describes the bone marrow ablation procedure for downstream assessment of new bone formation and cellular responses following injury.

cell biology↗

bioRxiv2024

Non-Invasive Brain Mapping Localizes Essential Language Function in Surgical Glioma Patients

IntroductionGlioma patients with tumors near critical language regions present significant clinical challenges. Surgeons often lack the tools to understand how each unique surgical approach may impact linguistic ability, leading to subjective decisions and unpredictable outcomes. ObjectiveWe aim to develop an approach that uses data-driven preoperative brain mapping to quantitatively predict the impact of planned resections on long-term language function. MethodsThis study included 79 consecutive patients undergoing resection of language-eloquent gliomas. Patients underwent preoperative navigated transcranial magnetic stimulation (nTMS) language mapping to identify language-positive sites ("TMS points") and their associated white matter tracts ("TMS tracts") as well as formal language evaluations pre and postoperatively. The resection of regions identified by preoperative mapping was correlated with persistent postoperative language deficits (PLDs). ResultsThe resection of TMS points did not predict PLDs. However, a TMS point subgroup defined by white matter connectivity significantly predicted PLDs (OR=8.74, p<.01) and exhibited a canonical group-level anatomical distribution of cortical language sites. TMS-derived tracts recapitulated normative group-level patterns of white matter connectivity defined by the Human Connectome Project (HCP). Subcortical resection of TMS tracts predicted PLDs independently of cortical resection (OR=60, p<.001). The resected TMS tract segments in patients with PLDs co-localized with normative, language-associated subcortical pathways, in contrast to the resected TMS tract segments in non-aphasic patients (p<.05). Accordingly, resecting patient- specific co-localizations between TMS tracts and normative tracts in native space predicted PLDs with an accuracy of 94% (OR=134, p<.001). Co-localization between individualized and normative tracts precisely predicted the linguistic performance of a patient intraoperatively in response to direct electrophysiological stimulation of subcortical brain. ConclusionThis study outlines a data-driven brain mapping approach that provides surgical insight by preoperatively predicting the impact of individual glioma resection on long-term language function. Key PointsO_LIWhite matter connectivity determines the long-term functionality of cortical language sites mapped by TMS. C_LIO_LILong-term deficits in language processing result from resecting individualized subcortical regions within language-associated white matter tracts. C_LIO_LINon-invasive TMS language mapping combined with routine preoperative imaging can predict language outcomes of individual surgical approaches with an accuracy of 94%. C_LI

neuroscience↗

bioRxiv2023

SignEEG v1.0 : Multimodal Electroencephalography and Signature Database for Biometric Systems

Handwritten signatures in biometric authentication leverage unique individual characteristics for identification, offering high specificity through dynamic and static properties. However, this modality faces significant challenges from sophisticated forgery attempts, underscoring the need for enhanced security measures in common applications. To address forgery in signature-based biometric systems, integrating a forgery-resistant modality, namely, noninvasive electroencephalography (EEG), which captures unique brain activity patterns, can significantly enhance system robustness by leveraging multimodalitys strengths. By combining EEG, a physiological modality, with handwritten signatures, a behavioral modality, our approach capitalizes on the strengths of both, significantly fortifying the robustness of biometric systems through this multimodal integration. In addition, EEGs resistance to replication offers a high-security level, making it a robust addition to user identification and verification. This study presents a new multimodal SignEEG v1.0 dataset based on EEG and hand-drawn signatures from 70 subjects. EEG signals and hand-drawn signatures have been collected with Emotiv Insight and Wacom One sensors, respectively. The multimodal data consists of three paradigms based on mental, & motor imagery, and physical execution: i) thinking of the signatures image, (ii) drawing the signature mentally, and (iii) drawing a signature physically. Extensive experiments have been conducted to establish a baseline with machine learning classifiers. The results demonstrate that multimodality in biometric systems significantly enhances robustness, achieving high reliability even with limited sample sizes. We release the raw, pre-processed data and easy-to-follow implementation details.

neuroscience↗

bioRxiv2023

AutophagyNet: High-resolution data source for the analysis of autophagy and its regulation

Autophagy is a highly-conserved catabolic process eliminating dysfunctional cellular components and invading pathogens. Autophagy malfunction contributes to disorders such as cancer, neurodegenerative and inflammatory diseases. Understanding autophagy regulation in health and disease has been the focus of the last decades. We previously provided an integrated database for autophagy research, the Autophagy Regulatory Network (ARN). For the last seven years, this resource has been used by thousands of users. Here, we present a new and upgraded resource, AutophagyNet. It builds on the previous database but contains major improvements to address user feedback and novel needs due to the advancement in omics data availability. AutophagyNet contains updated interaction curation and integration of over 280,000 experimentally verified interactions between core autophagy proteins and their protein, transcriptional and post-transcriptional regulators as well as their potential upstream pathway connections. AutophagyNet provides annotations for each core protein about their role: 1) in different types of autophagy (mitophagy, xenophagy, etc.); 2) in distinct stages of autophagy (initiation, elongation, termination, etc); 3) with subcellular and tissue-specific localization. These annotations can be used to filter the dataset, providing customizable download options tailored to the users needs. The resource is available in various file formats (e.g., CSV, BioPAX and PSI-MI), and data can be analyzed and visualized directly in Cytoscape. The multi-layered regulation of autophagy can be analyzed by combining AutophagyNet with tissue- or cell type-specific using (multi-)omics datasets (e.g. transcriptomic or proteomic data). The resource is publicly accessible at http://autophagynet.org.

bioinformatics↗

bioRxiv2022

Doublet microtubule inner junction protein FAP20 recruits tubulin to the microtubule lattice

Motility of organisms involves beating of cilia and flagella that are composed of doublet microtubules. The doublets are made of A- and B-tubules that fuse together at two junctions. Among these, the outer junction is made of tripartite tubulin connections, while the inner junction contains distinct non-tubulin elements. The latter includes Flagellar-associated protein 20 (FAP20) and Parkin co-regulated gene protein (PACRG) that together link the A- and B- tubules at the inner junction. While the structures of doublet microtubules reveal molecular details, their assembly is poorly understood and examining proteins at the junctions can provide important clues. In this study, we purified recombinant FAP20 and characterized its effects on microtubule dynamics by TIRF microscopy. Using in vitro reconstitution and cryo-electron microscopy, we conclusively show that FAP20 recruits free tubulin to the existing microtubule, where it mediates flexible lateral interactions between the microtubule lattice and tubulin dimers. Our structure of microtubule:FAP20:tubulin complex partially resembles the inner junction architecture, further providing insights into assembly steps involved in closure of B- tubule in a doublet microtubule.

biophysics↗

bioRxiv2022

Regenerating aggregates of hydra display unique cytoskeletal organisation that is absent in a regeneration-deficient strain

Hydra has the unique ability to regenerate from aggregates of dissociated single cells that lack positional information. We compared two strains of hydra, a strain of hydra that was capable of regenerating from aggregates and a strain of hydra that was deficient in this type of regeneration. We observed unique actin cytoskeletal arrangements that were present in the regenerates of regeneration-competent strain but not in the regeneration-deficient strain. Concomitantly, the regeneration-deficient strain failed to organise the extracellular cytoskeleton of laminin and collagen between ectodermal and endodermal epithelial cells. These interesting preliminary observations highlight the importance of the cytoskeletal organisation in regeneration of hydra and suggest that regeneration from the aggregates of dissociated cells through de novo patterning requires correct structural organisation of cytoskeletal elements.

zoology↗

bioRxiv2021

An intranasally administrated SARS-CoV-2 beta variant subunit booster vaccine prevents beta variant viral replication in rhesus macaques

Emerging of SARS-CoV-2 variants and waning of vaccine/infection-induced immunity poses threats to curbing the COVID-19 pandemic. An effective, safe, and convenient booster vaccine will be needed. We hypothesized that a variant-modified mucosal booster vaccine might induce local immunity to prevent SARS-CoV-2 infection at the port of entry. The beta-variant is hardest to cross-neutralize. Herein we assessed the protective efficacy of an intranasal booster composed of beta variant-spike protein S1 with IL-15 and TLR agonists in previously immunized macaques. The macaques were first vaccinated with Wuhan strain S1 with the same adjuvant. One year later, negligibly detectable SARS-CoV-2-specific antibody remained. Nevertheless, the booster induced vigorous humoral immunity including serum- and bronchoalveolar lavage (BAL)-IgG, secretory nasal- and BAL-IgA, and neutralizing antibody against the original strain and/or beta variant. Beta-variant S1-specifc CD4+ and CD8+ T cell responses were also elicited in PBMC and BAL. Following SARS-CoV-2 beta variant challenge, the vaccinated group demonstrated significant protection against viral replication in the upper and lower respiratory tracts, with almost full protection in the nasal cavity. The fact that one intranasal beta-variant booster administrated one year after the first vaccination provoked protective immunity against beta variant infections may inform future SARS-CoV-2 booster design and administration timing.

immunology↗

bioRxiv2018

Caring without sharing: Meta-analysis 2.0 for massive genome-wide association studies

Genome-wide association studies have been effective at revealing the genetic architecture of simple traits. Extending this approach to more complex phenotypes has necessitated a massive increase in cohort size. To achieve sufficient power, participants are recruited across multiple collaborating institutions, leaving researchers with two choices: either collect all the raw data at a single institution or rely on meta-analyses to test for association. In this work, we present a third alternative. Here, we implement an entire GWAS workflow (quality control, population structure control, and association) in a fully decentralized setting. Our iterative approach (a) does not rely on consolidating the raw data at a single coordination center, and (b) does not hinge upon large sample size assumptions at each silo. As we show, our approach overcomes challenges faced by meta-studies when it comes to associating rare alleles and when case/control proportions are wildly imbalanced at each silo. We demonstrate the feasibility of our method in cohorts ranging in size from 2K (small) to 500K (large), and recruited across 2 to 10 collaborating institutions.

bioinformatics↗