Biology subjects

Ashktorab, H.

Publications and source records attributed to Ashktorab, H..

4 recordsLinked to original sources

bioRxiv2025

Single-Cell Pharmacogenomic Landscapes of Epigenetic Therapy in Gastric Cancer

Gene expression signatures ("molecular phenotypes") are extensively utilized in cancer research. To study how gastric cancer (GC) molecular phenotypes are shaped by cell-intrinsic genetic alterations interacting with cell-extrinsic therapeutic pressures, we performed direct capture Perturb-seq (dcPerturb-seq) to interrogate >200 GC-related genes across 4 distinct epigenetic drug classes in multiple gastric lines. We captured 17.7 million pharmocogenomic expression interactions in 625,866 cells representing baseline and post-therapeutic molecular phenotypes. This single-cell pharmacogenomic compendium confirmed previously known gene-driven molecular phenotypes, elucidated poorly characterized genes, and uncovered novel gene dosage-molecular phenotype relationships. Molecular phenotypes in post-therapeutic surviving cells revealed diverse gene perturbation-associated pathways causing convergent drug resistance (EMT plasticity, cell cycle alterations, metabolic reprogramming), highlighting combinatorial strategies for restoring sensitivity. Mapping of in vitro molecular phenotypes to primary human GCs imparted prognostic information and insights into spatial heterogeneity. Comparative analysis of gene perturbations across therapies and lines revealed both conserved and context-specific molecular alterations. Our results illustrate how Perturb-seq approaches can systematically map diverse cancer-associated molecular phenotypes across multiple gene/drug/cell line interactions, yielding translational insights.

cancer biology↗

bioRxiv2024

Discovering cancer stem-like cells using Spatial transcriptomic analysis: Nuclear factor I X as a novel therapeutic target for gastric cancer

BackgroundGastric cancer (GC) is characterized by significant intratumoral heterogeneity and stem cells presenting as promising therapeutic targets. Despite advancements in spatial transcriptome analysis, unexplored targets for addressing cancer stemness remain unknown. This study aims to identify Nuclear Factor IX (NFIX) as a critical regulator of cancer stemness in GC and evaluate its clinicopathological significance and function. MethodsSpatial transcriptome analysis was conducted on GC. NFIX expressions correlation with clinicopathological factors and prognosis was assessed through immunostaining in 127 GC cases. Functional analyses in cancer cell lines validated these findings. ResultsSpatial transcriptome analysis stratified GC tissues based on genetic profiles, pinpointing CSC-like cells and further refined the classification to identify and highlight the NFIXs significance, validated by Monocle 3 and CytoTRACE analyses. Knockdown experiments in cancer cell lines demonstrated the involvement of NFIX in cancer cell proliferation and kinase activity. ConclusionsThis study underscores spatial transcriptome analysiss role in refining GC tissue classification and identifying therapeutic targets, highlighting NFIX as pivotal. NFIX expression correlates with poor prognosis and drives GC progression, suggesting its potential as a novel therapeutic target for personalized GC therapies.

pathology↗

bioRxiv2022

Communication between the nucleus and the mitochondria via NDUFS4 alternative splicing in gastric cancer cells

A constant communication between the nucleus and the mitochondria allows both organelles to ensure cellular homeostasis and adaptation to mitochondrial stress. Mitochondrial biogenesis and function are controlled by anterograde regulatory pathways involving a large number of nuclear-encoded proteins. Transcriptional networks controlling the nuclear-encoded mitochondrial genes are known, however alternative splicing (AS) regulation has not been implicated in this communication. Here, we show that IQGAP1, a scaffold protein that regulates AS of distinct subsets of genes in gastric cancer cells, participates in AS regulation that strongly affects mitochondrial respiration. Combined proteomic analyses and RNA-seq profiles of IQGAP1KO and parental cells show that IQGAP1KO alters a specific AS event of the mitochondrial respiratory chain complex I subunit NDUFS4 and downregulates a subset of complex I subunits. In IQGAP1KO cells, respiratory complex I intermediates accumulate resembling assembly deficiencies observed in patients with Leigh syndrome bearing NDUFS4 mutations. Mitochondrial complex I activity is significantly lower in KO compared to parental cells, while exogenous expression of IQGAP1 partially restores NDUFS4 AS pattern and expression and reverses mitochondrial defects of IQGAP1KO cells. Our work sheds light to a novel facet of IQGAP1 in mitochondrial quality control that involves fine-tuning of complex I activity through AS regulation.

molecular biology↗

bioRxiv2022

The scaffolding protein Flot2 regulates cytoneme-based transport of Wnt3 in gastric cancer

The Wnt/{beta}-catenin signalling pathway regulates multiple cellular processes during development and many diseases, including cell proliferation, migration, and differentiation. Despite their hydrophobic nature, Wnt proteins exert their function over long distances to induce paracrine signalling. Recent studies have identified several factors involved in Wnt secretion, however, our understanding of how Wnt ligands are transported between cells to interact with their cognate receptors is still debated. Here, we demonstrate that gastric cancer cells utilise cytonemes to transport Wnt3 intercellularly to promote proliferation. Furthermore, we identify the membrane-bound scaffolding protein Flotillin-2 (Flot2), frequently overexpressed in gastric cancer, as a regulator of these cytonemes. Together with the Wnt co-receptor and cytoneme initiator Ror2, Flot2 determines the number and length of Wnt3 cytonemes in gastric cancer. Finally, we show that Flot2 is necessary for Wnt8a cytonemes during zebrafish embryogenesis, suggesting a conserved mechanism for Flot2-mediated Wnt transport on cytonemes in development and disease.

cancer biology↗