Biology subjects

Barzegar Behrooz, A.

Publications and source records attributed to Barzegar Behrooz, A..

7 recordsLinked to original sources

bioRxiv2026

Exploratory Network Analysis of Oral Bacteria Taste Signaling Autophagy Crosstalk in Oral Squamous Cell Carcinoma and Multi-Target Ligand Design for the MAPK1 STAT3 mTOR Axis

G protein-coupled receptor (GPCR) signaling represents a critical interface between oral bacteria and host cellular regulation in oral squamous cell carcinoma (OSCC). Here, we integrated systems biology, exploratory machine learning, and structure-based drug design to characterize potential associations between bacteria-related signaling and autophagy and to identify candidate therapeutic targets. Taste-associated signaling genes belonging to the GPCR superfamily were curated from KEGG, while OSCC- and autophagy-associated proteins were obtained from STRING, Reactome, UniProt, KEGG, and HMDB. Ten bacteria-associated host-interaction datasets were integrated using NetworkAnalyst to construct protein- protein interaction networks, and key hub nodes were identified through degree and betweenness centrality. Feature matrices derived from network topology were analyzed using exploratory dimensionality reduction (PCA), hierarchical clustering, and supervised models (SVM and Gradient Boosting) to assess whether network-derived features showed separability according to literature-informed bacterial reference categories; a Dysbiosis Index was additionally calculated. Results suggested that bacterial sensing through taste-associated GPCR signaling may converge on a MAPK1-centered axis linking calcium signaling, autophagy, and oncogenic pathways. Pathobiont-associated networks showed greater representation of inflammatory and terminal-autophagy-related signaling through MAPK1-STAT3, whereas commensal-associated networks were more closely aligned with cytoprotective autophagy through balanced MAPK1-TP53/PTEN networks. Exploratory machine learning analyses highlighted MDM2 and AKT3 as high-contribution, network-associated candidate features linked to group separability within the current dataset. A dual-target MTDL (SG101) was designed to target downstream nodes (MDM2 and JAK2), showing favorable predicted docking interactions and computationally predicted ADMET properties. In conclusion, bacteria-associated host taste signaling may be linked to differing autophagy-related network states in OSCC, and targeting downstream regulatory hubs with multi-target ligands represents a hypothesis-generating strategy that warrants experimental validation for pathway-oriented therapy.

cancer biology↗

bioRxiv2026

A treatment-resilient lipid metabolic program drives temozolomide resistance in glioblastoma

Temozolomide (TMZ) resistance remains a major barrier to durable control of glioblastoma (GB). Our previous studies showed that simvastatin can enhance TMZ-induced cell death in non-resistant GB cells by disrupting autophagosome-lysosome fusion and engaging stress-response pathways, whereas established TMZ-resistant cells maintain impaired autophagy flux and remain refractory to TMZ, simvastatin, and their combination. Here, we asked whether this loss of therapeutic responsiveness is accompanied by a treatment-resilient lipid state. Targeted LC-MS quantified 304 lipid species across 25 analytical classes in non-resistant (NR) and TMZ-resistant (R) U251-mKate cells under control, simvastatin (ST), TMZ, and TMZ-ST conditions. Global heatmap, principal-component, volcano, and exploratory PLS-DA analyses demonstrated persistent NR/R lipidomic separation across all four treatment states. Resistant cells recurrently displayed enrichment of lysophospholipids, selected sphingolipids/glycosphingolipids, and cholesteryl esters, with depletion or redistribution of several glycerophospholipid and diacylglycerol pools. A family-resolved analysis across 19 lipid families showed that resistance status was most strongly associated with phosphatidylinositol (PI; PERMANOVA R^2=0.52), phosphatidylglycerol (PG; R^2=0.49), lysophosphatidylcholine (LPC; R^2=0.46), lysophosphatidylethanolamine (LPE; R^2=0.45), ether/plasmalogen phosphatidylcholine (R^2=0.45), and phosphatidylcholine (R^2=0.41). Structure-informed target prediction of discriminant lipids generated pathway hypotheses involving Rap1, PI3K-Akt, phospholipase D, calcium, PPAR, and lipid-metabolic signaling. Transmission electron microscopy showed persistent vesicle-rich, autophagosome-like architecture in resistant cells across treatment conditions, consistent with the previously established late-stage autophagy defect. These data extend the autophagy-cholesterol model of TMZ resistance to a broader membrane-remodeling program and indicate that failure of statin sensitization is associated with coordinated lipid-family remodeling rather than a single lipid species or pathway. The identified lipid families and cholesterol-storage phenotype provide testable vulnerabilities for future functional validation. An exploratory family-level linear SVM analysis provided an orthogonal proof-of-concept: several membrane and storage-lipid families retained complete NR/R separation when an entire treatment was withheld, but these internal results were interpreted as supplementary evidence rather than as a validated classifier.

cancer biology↗

bioRxiv2026

Autophagy Cholesterol Axis Remodeling Supports Malignant Progression and Chemoresistance in Glioma

Glioma progression and resistance to temozolomide (TMZ) remain major clinical challenges. Here, we investigated whether dysregulated autophagy and cholesterol metabolism are coordinately remodeled during glioma progression and TMZ resistance. Tissue microarray analysis of astrocytoma and glioblastoma specimens revealed progressive autophagosome accumulation, reflected by increased LC3{beta} puncta, coupled with impaired autophagic flux compared with adjacent normal brain tissue. These alterations intensified with tumor grade and were associated with upregulation of farnesyl diphosphate synthase (FDPS), linking malignant progression to cholesterol pathway remodeling. TMZ-resistant (R) glioblastoma cells exhibited epithelial-to-mesenchymal transition, mitotic quiescence, and mitochondrial remodeling consistent with a therapy-tolerant phenotype. Bioenergetic profiling demonstrated reduced respiratory reserve, diminished ATP-linked respiration, and elevated proton leak, indicating constrained metabolic flexibility. In parallel, impaired autophagy flux was associated with suppression of de novo cholesterol synthesis and transcriptional downregulation of SREBP-2 and LDL-R. Comprehensive lipidomic profiling revealed marked cholesterol metabolic reprogramming in R cells, characterized by accumulation of specific cholesteryl esters, including CE 22:5, CE 22:6, CE 22:4, and CE 20:4, despite reduced cholesterol biosynthesis. Pharmacologic inhibition of the mevalonate pathway with simvastatin significantly altered cholesteryl ester profiles but failed to restore autophagy flux or sensitize R cells to TMZ-induced apoptosis, even under combined TMZ-simvastatin treatment. Lay AbstractAs gliomas progress from astrocytoma to glioblastoma, autophagy becomes dysregulated and cholesterol metabolism is rewired. This coordinated remodeling supports tumor survival, metabolic plasticity, and resistance to temozolomide therapy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/697885v2_ufig1.gif" ALT="Figure 1000"> View larger version (79K): org.highwire.dtl.DTLVardef@1183dd2org.highwire.dtl.DTLVardef@82e20dorg.highwire.dtl.DTLVardef@c6c8dforg.highwire.dtl.DTLVardef@adb427_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsAutophagy flux blockade intensifies during progression from astrocytoma to glioblastoma Dysregulated autophagy is coupled to altered cholesterol metabolism in malignant gliomas TMZ-resistant glioblastoma cells undergo epithelial-to-mesenchymal transition and mitotic quiescence Resistant cells exhibit constrained bioenergetic capacity and mitochondrial remodeling Impaired autophagy suppresses de novo cholesterol synthesis and lipid recycling Lipidomics reveals accumulation of long-chain cholesteryl esters in TMZ-resistant cells Statin-based cholesterol inhibition fails to resensitize glioblastoma cells to temozolomide

cancer biology↗

bioRxiv2025

Hierarchical Machine Learning Uncovers Topological Signatures of Autophagy Regulation by Oral Bacteria in Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) progression has been increasingly linked to dysbiosis of the oral microbiome. We hypothesized that pathogenic versus commensal bacteria differentially rewire host autophagy networks to either promote or inhibit OSCC progression. To test this, we constructed host-bacterium autophagy interactomes from KEGG, STRING, and curated databases, identifying key network hubs (e.g., MAPK1, STAT3) via graph-theoretic metrics. We then applied a hierarchical unsupervised machine learning pipeline, combining two-stage principal component analysis with permutation testing and linear discriminant analysis (LDA), to interrogate differences in network topology. This multi-layer approach revealed a clear separation between pro-cancer (pathogenic) and anti-cancer (commensal) bacterial network signatures, with Fusobacterium nucleatum and Streptococcus mitis emerging as dominant global outliers. Pathogenic taxa activated inflammatory-metabolic autophagy signatures (e.g., NFKB1, MYC, ACACA), whereas commensals stabilized kinase-homeostasis signaling (EGFR, PTEN, HSP90AA1). Permutation testing confirmed that these network differences were highly significant and non-random (p < 0.001). We also derived a Dysbiosis Index that robustly distinguished the pro- versus anti-cancer bacterial cohorts with high predictive power. Collectively, our findings highlight oral microbiota-autophagy network topologies as potential biomarkers of OSCC dysbiosis and as novel therapeutic targets. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/696881v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@13eb27forg.highwire.dtl.DTLVardef@138bccborg.highwire.dtl.DTLVardef@1f2e651org.highwire.dtl.DTLVardef@1eee140_HPS_FORMAT_FIGEXP M_FIG C_FIG Lay summaryHealthy mouth bacteria help cells stay balanced and protected. When harmful bacteria take over, they disrupt cell recycling (autophagy), increase inflammation, and causing cells to become more aggressive, which can promote oral cancer development.

cancer biology↗

bioRxiv2024

BCL2L13 Influences Autophagy and Ceramide Metabolism without Affecting Temozolomide Resistance in Glioblastoma

Temozolomide (TMZ) resistance in glioblastoma (GBM) arises through metabolic rewiring that links mitochondrial function, autophagy balance, and sphingolipid metabolism. TMZ resistant (R) U251 cells exhibited suppressed apoptosis and complete blockade of autophagy flux, evidenced by LC3II and p62 accumulation and insensitivity to Bafilomycin A1. BCL2L13, strongly upregulated in R cells, emerged as a dual regulator of mitophagy and ceramide metabolism. BCL2L13 knockdown (KD) produced opposite effects in TMZ sensitive (NR) and resistant cells: in NR cells, KD elevated LC3II, reduced respiratory reserve, and triggered compensatory lipid synthesis; in R cells, KD decreased LC3II without restoring flux or TMZ sensitivity. Lipidomic profiling revealed that BCL2L13 loss reactivated CerS6 in NR cells, increasing C16:0 and mid-chain ceramides, while relieving CerS2 inhibition in R cells, elevating very long chain (C22 to C24) and glycosylated ceramides. These distinct sphingolipid signatures were confirmed by PLS-DA and KEGG enrichment, which highlighted steroid hormone, arachidonic, and linoleic acid metabolism in NR KD cells versus neuroactive ligand-receptor and signaling pathways in R KD cells. Together, these findings position BCL2L13 as a molecular integrator of mitochondrial respiration, autophagy flux, and CerS-dependent lipid remodeling, unveiling a context-specific metabolic mechanism that supports GBM cell survival under chemotherapeutic stress.

cancer biology↗

bioRxiv2024

Unlocking a New Path: An Autophagometer that Measures Flux Using a Non-Fluorescent Immunohistochemistry Method

Macroautophagy/autophagy, a crucial cellular process, is typically measured using fluorescence-based techniques, which can be costly, complex, and impractical for clinical settings. In this paper, we introduce a novel, cost-effective, non-fluorescent immunohistochemistry (IHC) method for evaluating autophagy flux. This technique, based on antigen-antibody reactions and chromogenic detection, provides clear, quantifiable results under standard light microscopy, eliminating the need for expensive equipment and specialized reagents. Our method simplifies technical requirements, making it accessible to routine clinical laboratories and research settings with limited resources. By comparing our approach with traditional fluorescence methods, we demonstrate its superior effectiveness, cost-efficiency, and applicability to patient samples. This innovative technique has the potential to significantly advance autophagy research and improve clinical diagnostics, offering a practical and robust tool for studying autophagy mechanisms in diseases such as cancer and neurodegenerative disorders. Our non-fluorescent IHC method represents a significant step forward in evaluating autophagy flux, making it more accessible and reliable, with the promise of enhancing our understanding and treatment of autophagy-related diseases.

molecular biology↗

bioRxiv2024

The 40 Hz flickering light restores synaptic plasticity and mitochondrial phenotype in experimental model of Alzheimer's disease

Alzheimers disease (AD) is the most prevalent form of dementia and a public health priority. The causes of AD are not completely understood. Pathogenetic factors including mitochondrial dysfunction, oxidative stress, reduced energy status, and compromised ion channels contribute to the onset and progression of the disease. Flickering light therapy in experimental and clinical AD has shown promising outcomes. However, the mechanisms behind the effect of flickering light at the molecular and cellular level has not yet been fully investigated. In this study, we established streptozotocin (STZ)-induced AD models by intracerebroventricular (ICV) injection of STZ in Wistar rats and monitored their memory decline. Sham and AD rats were either exposed or not exposed to 40 Hz flickering light for 7 consecutive days after 7 days of STZ injection. Memory and cognition-related behavioral analysis, pathological, electrophysiological, and biochemical assessment of the brain tissue, and mitochondrial function assays were conducted after the treatment. Cognitive and memory impairment, examined by Morris water maze (MWM), novel object recognition (NOR), and passive avoidance (PA) test, was observed in the STZ-induced AD rats and light treatment improved these behaviors. STZ injection led to significant accumulation of reactive oxygen species (ROS) and amyloid beta (A{beta}), decreased serotonin and dopamine levels, and mitochondrial respiration. The 40 Hz flickering light reversed all these parameters in the light treatment group. The synaptic plasticity of STZ-induced AD rats was severely affected, but flickering light prevented the loss of synaptic plasticity and activity in the light-treated AD rats. Additionally, flickering 40 Hz white light elevated the levels of mitochondrial metabolites and the current and possible opening of the mitochondrial calcium-sensitive potassium (mitoBKCa) channel which were significantly downregulated in AD rat neurons. The 40 Hz flickering light restored mitochondrial function and synaptic plasticity of neurons in AD rats and improved the cognition of animals; therefore, it can be a promising strategy to reduce AD progression.

cell biology↗