Biology subjects

Nikolaidis, N.

Publications and source records attributed to Nikolaidis, N..

7 recordsLinked to original sources

bioRxiv2026

Population-associated molecular variation in histologically normal breast tissue is context-dependent and associated with distinct transcriptional states

Population-associated molecular variation in breast tissue may contribute to differences in tissue biology and disease susceptibility, yet the extent to which such variation is shaped by underlying tissue states remains unclear. Here, we performed RNA-seq and lipidomic profiling of histologically normal breast tissue samples from African American (AA) and Caucasian White (CW) individuals, followed by conceptual integration of the resulting transcriptomic and lipidomic patterns. Unsupervised analysis revealed two distinct baseline transcriptional states (G1 and G2) that defined the primary axis of molecular variation across the cohort and corresponded to epithelial-enriched (G1) and vascular-enriched (G2) tissue contexts as determined by cell-type deconvolution. Global comparisons between AA and CW samples showed minimal transcriptomic differences, with only a single gene reaching significance after multiple testing correction. However, when stratified by baseline tissue state, 191 genes were differentially expressed within G1, with coordinated upregulation of extracellular matrix organization and proliferative/cytoskeletal processes in AA samples. These patterns were consistently supported across multiple enrichment approaches. No comparable population-associated differences were observed within G2. Lipidomic analyses showed partial but non-significant trends consistent with transcriptomic structure, suggesting that lipid variation provides complementary but limited support for baseline molecular differences, likely reflecting constraints of bulk tissue composition. Together, these findings suggest that population-associated molecular differences in normal breast tissue are context-dependent and emerge within specific baseline transcriptional states, where distinct biological programs can coexist and be differentially modulated. These findings highlight the importance of tissue heterogeneity in shaping molecular variation and its potential relevance to disease-associated tissue states.

bioinformatics↗

bioRxiv2026

Lipid-Gated Vesicular Trafficking Directs HSPA1A to the Plasma Membrane Through the Endo-Lysosomal Network

HSPA1A is a stress-inducible molecular chaperone that localizes to the plasma membrane (PM) of heat-shocked and cancer cells, where its membrane-associated form contributes to therapeutic resistance, membrane stabilization, and immune modulation. Because HSPA1A lacks a signal peptide, it does not follow the classical secretory pathway; instead, it reaches the PM through unconventional routes whose vesicular intermediates and intracellular lipid requirements remain largely undefined. Here, we show that following heat shock, HSPA1A undergoes coordinated redistribution across the endo-lysosomal network. It transiently associates with PI(3)P-enriched early endosomes, progresses through Rab4A- and Rab4B-positive recycling endosomes, and accumulates in LAMP1-positive lysosomes, while avoiding degradative and slow-recycling routes. Pharmacological inhibition of the ER-Golgi pathway did not affect HSPA1As PM localization, while disruption of endosomal maturation and lysosomal function resulted in significant reductions. Heat shock drives a progressive increase in lysosomal BMP immunoreactivity, and pharmacological BMP accumulation increased PM-HSPA1A, whereas intracellular antibody-mediated BMP blockade reduced it, identifying BMP-enriched lysosomes as regulatory hubs that govern HSPA1A PM competence. Using a rapamycin-inducible compartment-specific phosphatase system, we further demonstrate that PI(4)P is required not only at the PM for final docking but within early endosomes, late endosomes, and lysosomes, establishing a distributed PI(4)P requirement across the endosomal network. Together, these findings define a lipid-gated vesicular trafficking mechanism for HSPA1A PM localization and identify lysosomal BMP and endosomal PI(4)P as additional regulatory layers relevant to cancer cells in which constitutive lipid remodeling may sustain membrane-associated HSPA1A and its pro-survival functions.

Cell Biology↗

bioRxiv2025

Dynamic Lipidome Reorganization in Response to Heat Shock Stress

The heat shock response (HSR) is a conserved cellular mechanism critical for adaptation to environmental and physiological stressors, with broad implications for cell survival, immune responses, and cancer biology. While the HSR has been extensively studied at the proteomic and transcriptomic levels, the role of lipid metabolism and membrane reorganization remains underexplored. Here, we integrate mass spectrometry-based lipidomics with RNA sequencing to characterize global lipidomic and transcriptomic changes in HeLa cells exposed to three conditions: control, heat shock (HS), and HS with eight hours of recovery. Heat shock-induced extensive lipid remodeling, including significant increases in fatty acids, glycerophospholipids, and sphingolipids, with partial normalization during recovery. Transcriptomic analysis identified over 2,700 upregulated and 2,300 downregulated genes under heat shock, with GO enrichment suggesting potential transcriptional contributions to lipid metabolism. However, transcriptional changes alone did not fully explain the observed lipidomic shifts, suggesting additional layers of regulation. Joint pathway analysis revealed enrichment in glycerophospholipid and sphingolipid metabolism, while network analysis identified lipid transport regulators (STAB2, APOB), stress-linked metabolic nodes (KNG1), and persistent sphingolipid enrichment during recovery. These findings provide a comprehensive framework for understanding lipid-mediated mechanisms of the HSR and highlight the importance of multi-omics integration in stress adaptation and disease biology.

bioinformatics↗

bioRxiv2025

Heat Shock-Induced PI(4)P Increase Drives HSPA1A Translocation to the Plasma Membrane in Cancer and Stressed Cells through PI4KIII Alpha Activation

HSPA1A, a major heat shock protein, is known to translocate to the plasma membrane (PM) in response to cellular stress and cancer, where it plays protective roles in membrane integrity and stress resistance. Although phosphatidylinositol 4-phosphate [PI(4)P] is essential in this translocation, the signals that trigger and facilitate HSPA1As movement remain undefined.Given that membrane lipid composition dynamically shifts during stress, we hypothesized that heat shock-induced PI(4)P changes are crucial for HSPA1As PM localization. To test this hypothesis, we investigated the mechanisms driving PI(4)P changes and HSPA1A PM localization under heat shock. Lipidomic analysis, enzyme-linked immunosorbent assay (ELISA), and confocal imaging revealed a rapid PI(4)P increase at the PM post-heat shock, with levels peaking at 0 hours and declining by 8 hours. RNA sequencing and protein quantification indicated no transcriptional increase in PI4KIII alpha, the kinase responsible for PI(4)P synthesis, suggesting an alternative regulatory mechanism. Hypothesizing that heat shock enhances PI4KIII alpha activity, we performed ELISA coupled with immunoprecipitation, confirming a significant rise in PI4KIII alpha activity following heat shock. Functional analyses further demonstrated that RNAi-mediated PI4KIII alpha depletion or pharmacological PI(4)P reduction, using GSK-A1, impairs HSPA1As localization to the PM, confirming that HSPA1A translocation is PI(4)P-dependent. Our findings identify PI4KIII alpha activity as a key regulator of PI(4)P accumulation and subsequent HSPA1A recruitment to the PM in stressed and cancer cells. This lipid-mediated response offers new insights into stress adaptation and potentially modifiable pathways for therapeutic interventions to control HSPA1A function in cancer.

biochemistry↗

bioRxiv2024

Transcriptomics Unveil Canonical and Non-Canonical Heat Shock-Induced Pathways in Human Cell Lines

The cellular stress response (CSR) is a conserved mechanism that protects cells from environmental and physiological stressors. The heat shock response (HSR), a critical component of the CSR, utilizes molecular chaperones to mitigate proteotoxic stress caused by elevated temperatures. We hypothesized that while the canonical HSR pathways are conserved across cell types, specific cell lines may exhibit unique transcriptional responses to heat shock. To test this, we compared the transcriptomic responses of HEK293, HepG2, and HeLa cells under control conditions immediately following heat shock and after an 8-hour recovery period. RNA sequencing revealed conserved activation of canonical HSR pathways, including the unfolded protein response, alongside enrichment of the non-canonical "Receptor Ligand Activity" pathway across all cell lines. Cell line-specific variations were also observed, with HepG2 cells displaying more uniquely expressed genes and elevated expression levels (fold changes) of shared genes under stress conditions. Validation by qPCR confirmed the activation of key genes within the "Receptor Ligand Activity" pathway across time points. These findings provide insights into conserved and context-specific aspects of the HSR, contributing to a more comprehensive understanding of stress response mechanisms across mammalian cells.

bioinformatics↗

bioRxiv2024

Heat-Induced Phosphatidylserine Changes Drive HSPA1A's Plasma Membrane Localization

Heat shock protein A1A (HSPA1A) is a molecular chaperone crucial in cell survival. In addition to its cytosolic functions, HSPA1A translocates to heat-shocked and cancer cells plasma membrane (PM). In cancer, PM-localized HSPA1A (mHSPA1A) is associated with increased tumor aggressiveness and therapeutic resistance, suggesting that preventing its membrane localization could have therapeutic value. This translocation depends on HSPA1As interaction with PM phospholipids, including phosphatidylserine (PS). Although PS binding regulates HSPA1As membrane localization, the exact trigger for this movement remains unclear. Given that lipid modifications are a cancer hallmark, we hypothesized that PS is a crucial lipid driving HSPA1A translocation and that heat-induced changes in PS levels trigger HSPA1As PM localization in response to heat stress. We tested this hypothesis using pharmacological inhibition and RNA interference (RNAi) targeting PS synthesis, combined with confocal microscopy, lipidomics, and western blotting. Lipidomic analysis and PS-specific biosensors confirmed a heat shock-induced PS increase, peaking immediately post-stress. Inhibition of PS synthesis with fendiline and RNAi significantly reduced HSPA1As PM localization, while depletion of cholesterol or fatty acids had minimal effects, confirming specificity for PS. Further experiments showed that PS saturation and elongation changes did not significantly impact HSPA1As PM localization, indicating that the total PS increase, rather than specific PS species, is the critical factor. These findings reshape current models of HSPA1A trafficking, demonstrating that PS is a crucial regulator of HSPA1As membrane translocation during the heat shock response. This work offers new insights into lipid-regulated protein trafficking and highlights the importance of PS in controlling cellular responses to stress.

cell biology↗

bioRxiv2024

PRRGO: A Tool for Visualizing and Mapping Globally Expressed Genes in Public Gene Expression Omnibus RNA-Sequencing Studies to PageRank-scored Gene Ontology Terms

We herein report PageRankeR Gene Ontology (PRRGO), a downloadable web application that can integrate differentially expressed gene (DEG) data from the gene expression omnibus (GEO) GEO2R web tool with the gene ontology (GO) database [1]. Unlike existing tools, PRRGO computes the PageRank for the entire GO network and can generate both interactive GO networks on the web interface and comma-separated values (CSV) files containing the DEG statistics categorized by GO term. These hierarchical and tabular GO-DEG data are especially conducive to hypothesis generation and overlap studies with the use of PageRank data, which can provide a metric of GO term centrality. We verified the tool for accuracy and reliability across nine independent heat shock (HS) studies for which the RNA-seq data was publicly available on GEO and found that the tool produced increasing concordance between study DEGs, GO terms, and select HS-specific GO terms.

bioinformatics↗