Biology subjects

Narayana, V. K.

Publications and source records attributed to Narayana, V. K..

8 recordsLinked to original sources

bioRxiv2026

Temporal phosphoproteomics reveals rapid restoration of kinase signaling by Glycyrrhiza glabra in a rotenone-induced Parkinson disease model

Parkinsons disease is a progressive neurodegenerative disorder associated with mitochondrial dysfunction, oxidative stress, impaired autophagy, and dysregulated cellular signaling pathways. Although Glycyrrhiza glabra has been reported to exhibit neuroprotective properties, the early phosphorylation-mediated signaling mechanisms underlying its protective effects remain poorly understood. In this study, we employed a Tandem Mass Tag (TMT)-based temporal quantitative phosphoproteomic approach to investigate early signaling events associated with Glycyrrhiza glabra-mediated neuroprotection in a rotenone-induced in vitro PD model. Differentiated IMR-32 neuronal cells were treated with rotenone alone or in combination with Glycyrrhiza glabra extract, and phosphoproteomic alterations were analyzed at 2, 5, 15, and 30 minutes using liquid chromatography coupled with tandem mass spectrometer. Temporal phosphoproteomic analysis identified 6,424 phosphopeptides corresponding to 2,368 phosphoproteins and 5,468 phosphorylation sites. Comparative analysis revealed extensive phosphorylation rewiring induced by rotenone and restoration of several dysregulated phosphorylation events following Glycyrrhiza glabra co-treatment. More than 130 phosphoproteins and multiple kinase-associated signaling pathways were dynamically regulated across the temporal conditions. Kinase enrichment analysis identified restoration of several critical kinases, including AKT1, MTOR, MAPK1/3, PRKACA, PRKCD, and GSK3A/B, which are associated with neuronal survival, stress adaptation, and autophagy. Integrated pathway and kinase-substrate interaction analyses further revealed enrichment of AMPK signaling, FOXO signaling, receptor tyrosine kinase signaling, RNA processing, and cell-cycle regulatory pathways. Notably, several spliceosome-associated phosphoproteins demonstrated dynamic phosphorylation changes during the early neuroprotective response. Collectively, this study provides a detailed temporal phosphoproteomic landscape of early signaling events associated with Glycyrrhiza glabra-mediated neuroprotection and highlights kinase-driven signaling pathways that may represent potential therapeutic targets in Parkinsons disease.

neuroscience↗

bioRxiv2025

Hematopoietic stem cell conditioned media induces excessive mitochondrial fission via Drp-1 to target colorectal cancer

Mitochondria, often referred to as the "powerhouses of the cell," are particularly crucial in cancer cells due to their high energy demands. Mitochondrial fusion-fission dynamics play a critical role in regulating signaling pathways and metabolic activities in colorectal cancer (CRC) cells. Increased mitochondrial fission drives metabolic reprogramming, enabling CRCs to proliferate, metastasize, and resist chemotherapy. Paradoxically, excessive fission induces mitochondria-mediated apoptosis. Our previous studies have shown that hematopoietic stem cell-derived conditioned media (CM) modulate the apoptosis pathway and mitochondrial bioenergetics of cancer stem cells by altering the cancer microenvironment. In this study, We found that HSCs-CM facilitates excessive fission in colorectal cancer cells by modulating Drp-1 and concurrently activating the PINK1-Parkin mitophagy pathway and intrinsic apoptosis, leading to loss of viability of these cells. Moreover, proteomics data showed that HSCs-CM dysregulated the electron transport chain complexes, with an exceptionally high degree of dysregulation of complexes III and IV. Metabolomics revealed dysregulation of critical metabolites, RNA sequencing revealed dysregulation of transcripts, and proteomics revealed dysregulation of proteins, involved in mitochondrial bioenergetics and the autophagy pathway in CRCs treated with CM. Taken together, our studies reveal the therapeutic potential of HSC-conditioned media for treating colorectal cancer. HighlightsO_LIHematopoietic stem cell-derived conditioned media (HSC-CM) induces excessive mitochondrial fission in colorectal cancer (CRC) cells by upregulating Drp-1, thereby activating the intrinsic apoptotic pathway. C_LIO_LIExcessive fission and bioenergetic dysfunction caused by HSC-CM result in loss of mitochondrial membrane potential and elevated reactive oxygen species production. C_LIO_LIHSC-CM severely disrupts the electron transport chain in CRC cells, precipitating an energy crisis and engaging the PINK1-mediated mitophagy pathway. C_LI SummaryHematopoietic stem cell-derived conditioned media (HSC-CM) compromises mitochondrial dynamics by inducing excessive fission in colorectal cancer (CRC) cells through upregulation of Drp-1 and its associated protein complex. The resulting hyperfission leads to severe mitochondrial dysfunction, characterised by a loss of mitochondrial membrane potential, decreased ATP production, and disrupted electron transport chain complexes. This bioenergetic crisis and overproduction of reactive oxygen species ultimately trigger intrinsic apoptosis and engage the mitophagy pathway, leading to loss of CRC cell viability.

cancer biology↗

bioRxiv2024

SpaMTP: Integrative Statistical Analysis and Visualisation of Spatial Metabolomics and Transcriptomics data.

The ability to spatially measure multi-modal data provides an unprecedented opportunity to comprehensively explore molecular regulation at transcriptional, translational and metabolic levels to acquire insights on cellular activities underpinning health and disease. However, there is currently a lack of analytical tools to integrate complementary information across different spatial-omics data modalities, particularly with respect to spatial metabolomics data, which is becoming increasingly invaluable. We introduce SpaMTP, a versatile software that implements an end-to-end integrative analysis of spatial metabolomics and transcriptomics data. Based in R, SpaMTP bridges processing functionalities for metabolomics data from Cardinal with user-friendly cell-centric analyses implemented in Seurat. Furthermore, SpaMTPs comprehensive analysis pipeline covers (1) automated mass-to-charge ratio (m/z) metabolite annotation; (2) a wide range of metabolite-gene based downstream statistical analyses including differential expression, pathway analysis, and correlation analysis; (3) integrative spatial-omics analysis; and (4) a suite of visualisation functions. For flexibility and interoperability, SpaMTP includes various functions for data import/export and object conversion, enabling seamless integration with other R and Python packages. We demonstrated the utility of SpaMTP to draw new biological understandings through analysing two biological system. We believe this software and implemented methods will be broadly utilised in spatial multi-omics and spatial metabolomics analyses.

bioinformatics↗

bioRxiv2024

An integrative spatial multi-omic workflow for unified analysis of tumor tissue

Combining molecular profiling with imaging techniques has advanced the field of spatial biology, offering new insights into complex biological processes. Focusing on diffuse IDH-mutated low-grade glioma, this study presents a workflow for Spatial Multi-omics Integration, SMINT, specifically combining spatial transcriptomics and spatial metabolomics. Our workflow incorporates both existing and custom-developed computational tools to enable cell segmentation and registration of spatial coordinates from both modalities to a common coordinate framework. During our investigation of cell segmentation strategies, we found that nuclei-only segmentation, while containing only 40% of segmented cell transcripts, enables accurate cell type annotation, but does not account for multinucleated cells. Our integrative workflow including cell-morphology segmentation identified distinct cellular neighborhoods at the infiltrating edge of gliomas, which were enriched in multinucleated and oligodendrocyte-lineage tumor cells, that may drive tumor invasion into the normal cortical layers of the brain. HighlightsO_LIAlignment and integrated analysis of spatial transcriptomic and metabolomic data C_LIO_LINuclei-only and cell-morphology segmentations are concordant for cell annotation C_LIO_LISpatially distinct regions are conserved in transcriptomic and metabolomic datasets C_LIO_LIMulti-omic exploration of glioma leading edge identifies novel biological features C_LI

bioinformatics↗

bioRxiv2024

A lipid signature of BAK-driven apoptotic pore formation

Apoptotic cell death is regulated by the BCL-2 protein family, with clusters of BAK or BAX homodimers driving pore formation in the mitochondrial outer membrane via a poorly understood process. There is growing evidence that, in addition to BAK and BAX, lipids play an important role in pore formation. Towards a better understanding of the lipidic drivers of apoptotic pore formation in isolated mitochondria, two complementary approaches were taken. Firstly, the lipids released during BAK-mediated pore formation were measured with targeted lipidomics, revealing enrichment of long chain polyunsaturated lysophospholipids (LPLs) in the released fraction. In contrast, the BAK protein was not released suggesting that BAK and LPLs locate to distinct microdomains. Secondly, added cholesterol not only prevented pore formation but prevented the clustering of BAK homodimers. Our data lead us to a model in which BAK clustering triggers formation of a separate microdomain rich in LPLs that can progress to lipid shedding and the opening of a lipid-lined pore. Pore stabilisation and growth may be due to BAK dimers then moving to the pore edge. Our BAK-lipid microdomain model supports the heterogeneity of BAK assemblies, and the observed lipid-release signature gives new insight into the genesis of the apoptotic pore.

cell biology↗

bioRxiv2023

Matrix selection for the visualization of small molecules and lipids in brain tumors using untargeted MALDI-TOF mass spectrometry imaging

Matrix-assisted laser desorption/ionization mass spectrometry imaging allows the study of metabolic activity in the tumor microenvironment of brain cancers. The detectable metabolites within these tumors are contingent upon the choice of matrix, deposition technique, and polarity setting. In this study, we compared the performance of three different matrices, two deposition techniques, and use of positive and negative polarity in two different brain cancer types and across two species. Optimal combinations were confirmed by comparative analysis of lipid and small molecule abundance using liquid chromatography-mass spectrometry and RNA-sequencing assessing differential metabolites between normal and tumor regions. Our findings indicate that the recrystallized cyano-4-hydroxycinnamic acid matrix in positive polarity offered superior performance for both detected metabolites and consistency with other techniques. Beyond these implications for brain cancer, our work establishes a workflow to identify optimal matrices for spatial metabolomics studies.

molecular biology↗

bioRxiv2023

Divergent roles for caspase-8 and MLKL in high-fat diet induced obesity and NAFLD in mice

Cell death frequently occurs in the pathogenesis of obesity and non-alcoholic fatty liver disease (NAFLD). However, the exact contribution of core cell death machinery to disease manifestations remains ill-defined. Here, we show via the direct comparison of mice genetically deficient in apoptotic caspase-8 in myeloid cells, or the essential necroptotic regulators, Receptor-interacting protein kinase-3 (RIPK3) and Mixed lineage kinase domain-like (MLKL), that RIPK3-caspase-8 signaling regulates macrophage inflammatory responses and drives adipose tissue inflammation and NAFLD upon high-fat diet feeding. In contrast, MLKL, divergent to RIPK3, contributes to both obesity and NAFLD in a manner largely independent of inflammation. We also uncover that MLKL regulates the expression of molecules involved in lipid uptake, transport and metabolism and, congruent with this, we discover a shift in the hepatic lipidome upon MLKL deletion. Collectively, these findings highlight MLKL as an attractive therapeutic target to combat the growing obesity pandemic and metabolic disease.

immunology↗

bioRxiv2019

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium

Vancomycin resistant Enterococcus faecium (VREfm) is an emerging antibiotic resistant pathogen. Strain-level investigations are beginning to reveal the molecular mechanisms used by VREfm to colonize regions of the human bowel. However, the role of commensal bacteria during VREfm colonization, in particular following antibiotic treatment, remains largely unknown. We employed amplicon 16S rRNA gene sequencing and metabolomics in a murine model system to try and investigate functional roles of the gut microbiome during VREfm colonization. First-order taxonomic shifts between Bacteroidetes and Tenerricutes within the gut microbial community composition were detected both in response to pretreatment using ceftriaxone, and to subsequent VREfm challenge. Using neural networking approaches to find co-occurrence profiles of bacteria and metabolites, we detected key metabolome features associated with butyric acid during and after VREfm colonization. These metabolite features were associated with Bacteroides, indicative of a transition towards a pre-antibiotic naive microbiome. This study shows the impacts of antibiotics on the gut ecosystem, and the progression of the microbiome in response to colonisation with VREfm. Our results offer insights towards identifying potential non-antibiotic alternatives to eliminate VREfm through metabolic re-engineering to preferentially select for Bacteroides. ImportanceThis study demonstrates the importance and power of linking bacterial composition profiling with metabolomics to find the interactions between commensal gut bacteria and a specific pathogen. Knowledge from this research will inform gut microbiome engineering strategies, with the aim of translating observations from animal models to human-relevant therapeutic applications.

microbiology↗