Biology subjects

Karakyriakou, B.

Publications and source records attributed to Karakyriakou, B..

4 recordsLinked to original sources

bioRxiv2026

A Dimeric Rocaglate Promotes Multivalent eIF4A-RNA Assembly

Ligand dimerization represents a powerful strategy to enhance avidity, potency, and selectivity. Leveraging the natural-product molecular glue Rocaglamide (RocA), we identified BisRoc, a dimeric rocaglate ligand that potently and durably suppresses translation and exhibits greater specificity across a cancer cell line panel than the monomeric RocA. CRISPRi screening revealed that BisRoc activity is influenced by cellular context, including IFITM-mediated uptake, ABC-type efflux transporters, and the translation initiation factor eIF4A2. Mechanistic studies showed that the paralogs eIF4A1 and eIF4A2 are differentially sensitive to BisRoc-induced dimerization. Owing to the presence of multiple binding sites on RNAs, BisRoc-bridged eIF4A-RNA motifs assemble into higher-order complexes that promote stress-granule formation more efficiently than monomeric RocA. Given the widespread multivalency of RNA-RBP interactions, this ligand dimerization strategy may be extended to modulate the higher-order assembly of other RNA-binding proteins. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/710667v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1f0ce69org.highwire.dtl.DTLVardef@7f7fadorg.highwire.dtl.DTLVardef@976e81org.highwire.dtl.DTLVardef@1d7eaf2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Endothelial cell-specific DNA methylation alterations identified in breast cancer with epigenetic deconvolution

DNA methylation alterations are epigenetic modifications that regulate gene expression and contribute to carcinogenesis. Technical challenges and high costs limit the use of single-cell sequencing approaches to measure and understand cell-specific DNA methylation alterations in the tumor microenvironment (TME). Using cell type deconvolution (HiTIMED) and an interaction testing framework (CellDMC), we identified DNA methylation alterations in tumor endothelial cells (TECs) from measures in bulk biospecimens. Alterations in TECs contribute to abnormal angiogenesis, resulting in disorganized, leaky blood vessels that can hinder drug delivery and immune access. We hypothesize that TECs in the TME exhibit distinct DNA methylation patterns compared to normal endothelial cells, driving phenotypic changes that support tumor growth and vascular dysfunction. We used genome-scale DNA methylation data and a testing and validation set design (tumor, n=1,080; nontumor, n=415) to identify TEC-specific DNA methylation alterations in breast cancer. Between cohorts, we validated 4,562 TEC-specific CpGs (4,163 hypermethylated and 399 hypomethylated), and found that many map to genes regulating angiogenesis and endothelial function. Integration with mRNA data from tumor samples in both discovery and validation sets revealed genes whose expression correlates with TEC-specific DNA methylation patterns and endothelial cell proportions, highlighting potentially novel therapeutic targets. This study demonstrates the utility of cellular deconvolution to uncover cell lineage-specific epigenetic changes in cancer using bulk specimen, and identifies TEC-specific methylation alterations as novel potential targets for therapeutic intervention.

cancer biology↗

bioRxiv2023

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability

Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors of a wide-range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed DrugMap, an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NF{kappa}B1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NF{kappa}B1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription factor activity.

systems biology↗

bioRxiv2022

Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities

Histone deacetylases (HDACs) have been widely pursued as targets for anti-cancer therapeutics. However, many of these targets are universally essential for cell survival, which may limit the therapeutic window that can be achieved by drug candidates. By examining large collections of CRISPR/Cas9-based essentiality screens, we discovered a genetic interaction between HDAC1 and HDAC2 wherein each paralog is synthetically lethal with hemizygous deletion of the other. This collateral synthetic lethality is caused by recurrent chromosomal translocations that occur in diverse solid and hematological malignancies, including neuroblastoma and multiple myeloma. Using genetic deletion or dTAG-mediated degradation, we show that HDAC2 disruption suppresses the growth of HDAC1-deficient neuroblastoma in vitro and in vivo. Mechanistically, we find that targeted degradation of HDAC2 in these cells prompts the degradation of several members of the nucleosome remodeling and deacetylase (NuRD) complex, leading to diminished chromatin accessibility at HDAC2/NuRD-bound sites of the genome and impaired control of enhancer-associated transcription. Furthermore, we reveal that several of the degraded NuRD complex subunits are dependencies in neuroblastoma and multiple myeloma, providing motivation to develop paralog-selective HDAC1 or HDAC2 degraders. Altogether, we identify HDAC1/2 collateral synthetic lethality as a new therapeutic target and reveal a novel mechanism for exploiting NuRD-associated cancer dependencies.

cancer biology↗