Biology subjects

Poudel, M.

Publications and source records attributed to Poudel, M..

3 recordsLinked to original sources

bioRxiv2026

SPIN: A Scalable Bioinformatics Pipeline for Screening Pathogenicity Related Host-Pathogen Protein INteractions Using AlphaFold3

Traditional experimental approaches have greatly advanced our understanding of protein-protein interactions (PPIs) that govern host susceptibility or resistance. Nonetheless, the molecular characterization of microbial effectors and their cognate host targets remains challenging in many economically important plant pathosystems. AlphaFold3 (AF3) has transformed structural biology by achieving near-experimental accuracy in protein structure and complex prediction. A bioinformatics pipeline SPIN (Screening Pathogenicity-Related Host/Pathogen Protein INteractions) was developed for large-scale prediction of interactions between the host and pathogen-secreted proteins. SPIN integrates three core modules: pathogen and host protein preprocessing using bioinformatics tools (SignalP6.0, OrthoFinder, CD-HIT), AF3-based interaction modeling, supported by automated input generation and output filtering. However, AF3 training bias toward mammalian proteins necessitated careful evaluation in plant systems. Benchmarking against experimentally validated plant PPIs revealed that derivative metrics emphasizing interfacial geometry and residue-level contact (ipSAE and pDockQ) provide superior discrimination compared to native global confidence measures (pTM and ipTM), particularly for proteins with intrinsically disordered regions. A multi-metric confidence scoring framework combining pLDDT, PAE, ipSAE, and pDockQ, improved prediction reliability by enhancing recall and reduced false positives through robust assessment of structural confidence and interface quality. For proof-of-concept, SPIN was applied to examine the molecular landscape underlying two economically important diseases of citrus (Citrus L.) caused by Candidatus Liberibacter asiaticus and Ca. Phytoplasma citri. Both pathogens are phloem-limited and cause distinct symptoms, citrus greening and witches broom, respectively. AF3-predicted interactome data revealed conserved host colonization strategies alongside disease-specific molecular mechanisms, demonstrating the utility of SPIN for dissecting and supporting mechanistic studies in plant-pathogen interactions.

genomics↗

bioRxiv2025

AKAP1 regulates mitochondrial and synaptic homeostasis to enable neuroprotection and repair in retinal ganglion cell degeneration

Glaucoma is a leading cause of irreversible blindness, characterized by progressive retinal ganglion cell (RGC) loss and optic nerve degeneration. Mitochondrial dysfunction plays a central role in this neurodegeneration, yet effective targeted therapies remain limited. Here, we identify the mitochondrial scaffold A-kinase anchoring protein 1 (AKAP1) as a critical regulator of RGC resilience and axon regeneration. AKAP1 expression is diminished in human glaucomatous retinas and experimental glaucoma models, correlating with elevated intraocular pressure, disrupted mitochondrial dynamics, oxidative stress, and synaptic instability. Restoration of AKAP1 via adeno-associated virus serotype 2-mediated gene therapy preserves RGC survival, promotes mitochondrial fusion and cristae integrity, enhances ATP production, and mitigates oxidative and apoptotic stress in mouse models of glaucoma and optic nerve injury. Transcriptomic profiling of AKAP1 knockout retinas reveals widespread dysregulation of mitochondrial and synaptic gene networks. Mechanistically, AKAP1 stabilizes synapses by promoting mitochondrial biogenesis, modulating calcium/calmodulin-dependent kinase II and synapsin phosphorylation, maintaining synaptophysin expression, and suppressing complement component C1q expression, thereby preventing early synaptic loss in glaucomatous neurodegeneration. Moreover, restoring AKAP1 expression facilitates axonal regeneration, preserves the central visual pathway, and maintains visual function. Collectively, these findings establish AKAP1 as a master regulator of mitochondrial and synaptic homeostasis and axonal regeneration and a promising therapeutic target for vision preservation in glaucomatous neurodegeneration. One Sentence SummaryAKAP1 protects retinal ganglion cells and preserves vision by restoring mitochondrial and synaptic health in experimental glaucoma models.

neuroscience↗

bioRxiv2025

Neoantigens and Stochastic Fluctuations Regulate T Cell Proliferation in Primary and Metastatic Malignant Brain Tumors

Brain cancer is one of the most aggressive forms of cancer in the central nervous system occurring as primary or metastatic tumors. Sequencing of resected tissues from glioblastoma (GBM) and brain metastases (BrMET) reveals high heterogeneity in neoantigens and T cell receptor (TCR) repertoires. Our analysis of published sequencing data in different spatial regions of tumors GBM and BrMET patients show the presence of T cell clones of sizes with a heavy right-tailed distribution spanning several orders of magnitude (e.g., 1 - 1000 cells) with a few (<10) large clone sizes and many small clones. We investigated how neoantigens in the tumor microenvironment (TME) drive T cell expansion in GBM and BrMET by developing a mechanistic mathematical model based on the interaction of T cells and the neoantigens that incorporates their stochastic proliferation in the immunosuppressive environment and trained it to predict the emergence of T cell clones in different spatial regions. The model accurately predicts the distribution of observed T cell clone sizes and reveals that the strength of interaction between TCR and neoantigen-MHC complex and stochastic T cell proliferation crucially regulates T cell expansion in the TME. It also suggests higher rate of T cell proliferation BrMET compared to GBM. An extended version of the model predicts the ability of individual neoantigens to generate T cell clones in the periphery in patients receiving personalized neoantigen vaccines. Our model may facilitate the discovery of improved peptide combinations in neoantigen vaccine studies. Significance StatementNeoantigen-driven T cell responses are key to immune defense against solid tumors. Multi-region sequencing of brain tumors reveals spatial heterogeneity in neoantigens and T cell repertoires. To understand whether neoantigen-driven T cell expansion underlies the TCR repertoire heterogeneities, we developed a stochastic, mechanistic model of T cell proliferation using published TCR and neoantigen data from primary and metastatic brain tumors. The model accurately predicts clone size distributions, showing faster T cell proliferation in metastases and stronger responses to clonal (shared) neoantigens than to private (region-specific) ones. The model is extended to describe T cell clonal expansion in the periphery in response to neoantigen vaccine in glioblastoma patients. This framework may help design optimal peptide combinations in neoantigen vaccine development.

cancer biology↗