Biology subjects

Shojaei, S.

Publications and source records attributed to Shojaei, S..

8 recordsLinked to original sources

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

A conserved cytoplasmic glutamic acid mediates pH-dependent gating in bacterial urea channel UreI

The bacterial UreI channel family enables rapid urea uptake, essential for urease activity and acid resistance. While pH-dependent gating in Helicobacter pylori UreI (HpUreI) is attributed to periplasmic histidines, the role of cytoplasmic residues remains unexplored. The UreI homolog from Streptococcus salivarius (SsUreI), lacking periplasmic histidines, serves as a simplified model to identify gating determinants. Here, we combine yeast complementation assays, in vitro studies, and MD simulations to show that cytoplasmic glutamic acid E136 mediates pH-dependent gating in SsUreI. Mutagenesis in H. pylori/H. hepaticus homologs confirm E136 as a conserved pH sensor across UreI channels. Protonation of E136 disrupts its salt bridge with R20, increasing cytoplasmic-loop flexibility and urea-permeable filter conformations. These findings challenge the paradigm of exclusive periplasmic pH sensing, supporting a Gram-negative-specific dual-sensor model (E136 + histidines). By elucidating this molecular mechanism, we identify E136 as a therapeutic target to disrupt UreI-mediated acid resistance in pathogenic bacteria.

biophysics↗

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

Assessing Autophagy Flux in Glioblastoma Temozolomide Resistant Cells

Autophagy is a critical cellular process involved in the degradation and recycling of cytoplasmic components, playing a dual role in cancer by either promoting cell survival or facilitating cell death. In glioblastoma (GB), autophagy has been implicated in resistance to the chemotherapeutic agent Temozolomide (TMZ). This study presents a novel method to accurately measure autophagy flux in TMZ-resistant glioblastoma cells, combining advanced imaging techniques with biochemical assays. By quantifying key autophagy markers such as LC3-II and SQSTM1, our approach provides detailed insights into the dynamic processes of autophagosome formation and clearance under therapeutic stress. This method not only advances our understanding of autophagy in GB chemoresistance but also has significant implications for the development of autophagy-targeted therapies. The ability to monitor and manipulate autophagy flux in real-time offers a promising avenue for monitoring and understnading TMZ resistance and improving patient outcomes in glioblastoma treatment.

molecular 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

Metabolic Vulnerabilities of Temozolomide-Resistant Glioblastoma Cells: Implications for Targeted Therapies and Overcoming Chemoresistance

Chemoresistance is a major clinical challenge in the management of glioblastoma (GB), making it difficult to achieve long-term success with traditional treatments. Therefore, there is a need for the development of novel drugs. We explored the metabolic vulnerabilities of temozolomide (TMZ)-resistant GB and their potential implications for targeted therapies. In monolayer and tumoroid cultures, we found elevated reliance on oxidative phosphorylation in TMZ-resistant cells. Notably, iron reduction in TMZ-resistant cells reduced viability and proliferation, upregulated hypoxia-inducible factor 1- (Hif1-) expression, induced autophagy, inhibited autophagic flux, and increased reactive oxygen species (ROS) generation, indicating the significance of iron in metabolic vulnerabilities of these cells. Hypoxic cells showed acquired resistance to iron chelation compared to their normoxic state, suggesting an adaptive mechanism associated to hypoxia. Viability, size, and invasion were reduced in TMZ-resistant tumoroids. Additionally, we reported IC50 for the combination of TMZ with a range of DFO and DFP, making the combination therapy a promising drug candidate to improve therapeutic treatments. TeaserCombining iron reduction and chemotherapy in drug-resistant glioblastoma cells enhances therapeutic outcomes.

cancer biology↗

bioRxiv2022

A multi-omics analysis of glioma chemoresistance using a hybrid microphysiological model of glioblastoma

Chemoresistance is a major clinical challenge in the management of glioblastoma (GBM) Temozolomide (TMZ) is the chemotherapeutic drug of choice for GBM; however, the therapeutic effect of TMZ is limited due to the development of resistance. Recapitulating GBM chemoresistance in a controlled environment is thus essential in understanding the mechanism of chemoresistance. Herein, we present a hybrid microphysiological model of chemoresistant GBM-on-a-chip (HGoC) by directly co-culturing TMZ-resistant GBM spheroids with healthy neurons to mimic the microenvironment of both the tumor and the surrounding healthy tissue. We characterized the model with proteomics, lipidomics, and secretome assays. The results showed that our artificial model recapitulated the molecular signatures of recurrent GBM in humans. Both showed alterations in vesicular transport and cholesterol pathways, mitotic quiescence, and a switch in metabolism to oxidative phosphorylation associated with a transition from mesenchymal to amoeboid. This is the first report to unravel the interplay of all these molecular changes as a mechanism of chemoresistance in glioblastoma. Moreover, we have shown that the acquisition of resistance increases invasiveness and the presence of neurons decreases this property.

bioengineering↗