Sergi, B. | Search bioRxiv

bioRxiv2026

GLproxScape reconstructs spatial chromatin occupancy landscapes from tiled genomic locus proteomics

Genomic locus proteomics combines proximity labeling with mass spectrometry to identify the proteins associated with user-defined genomic loci. However, per-region enrichment values from tiled guide designs are typically pooled before hit calling, collapsing the latent spatial structure encoded by overlapping measurements. Here, we describe GLproxScape, an R package that treats per-region enrichments as indirect spatial measurements and reconstructs latent chromatin occupancy landscapes through a Gaussian labeling-kernel forward model. Sequence-specific transcription factors are resolved by motif-anchored non-negative least-squares deconvolution against JASPAR or HOCOMOCO position weight matrices, while chromatin regulators which lack defined DNA-binding motifs are inferred as broad occupancy zones, enabling recovery of overlapping members of multi-subunit complexes. Applied to published genomic locus proteomics datasets at the human TERT, MYC, FOXP2, and FOXQ1 loci and the mouse Ripk3 locus, GLproxScape recovered known regulators with predicted positions independently supported by ChIP-Atlas peaks, reconstructed candidate co-binding relationships, and identified chromatin complexes inaccessible to pooled analyses. Systematic sgRNA-ablation experiments further showed that densely tiled designs improve event recovery and positional stability, providing concrete experimental guidance for future genomic locus proteomics studies.

bioinformatics↗

bioRxiv2024

Epidrug Screening Identifies Type I PRMT Inhibitors as Modulators of Lysosomal Exocytosis and Drug Sensitivity in Cancers

Epigenetic changes drive differential gene expression, contributing to oncogenic transformation and drug resistance. Lysosomes are crucial in cell signaling and the sequestration of toxins and chemotherapeutic agents. This sequestration followed by expulsion through lysosomal exocytosis is a factor in drug resistance. The epigenetic regulation of lysosomal exocytosis remains poorly understood. Our research focuses on this regulation, hypothesizing that epigenetic modifier drugs (epidrugs) capable of inhibiting lysosomal exocytosis and could serve as potential therapeutics. Additionally, we investigate their potential synergy with drugs known to be sequestered in lysosomes. To examine this concept, we screened approximately 150 epigenetic drugs targeting various reader, writer, or eraser proteins. These drugs were assessed for their combined cytotoxic effects with cisplatin, their impact on lysosomal exocytosis, and on lysosomal biogenesis. Our findings reveal that among the epidrugs showing synergy with cisplatin and further reducing cell viability in combination, two type I PRMT inhibitors, MS023 and GSK3368715, inhibited lysosomal exocytosis. Notably, neither of these drugs altered the expression of the CLEAR lysosomal biogenesis network of genes, suggesting the involvement of novel regulators in lysosomal functions. To explore the specific components of the trafficking machinery affected by PRMT inhibitors, we conducted an RNA-seq analysis, uncovering several differentially expressed genes (DEGs). In addition to previously described functions such as methylation activity, or DNA repair; these DEGs included those involved in vesicular trafficking, lysosomal enzyme activity and lysosome dynamics, offering potential insights into the mechanism of reduced exocytosis and identifying a novel mode for its regulation. Additionally, both inhibitors exhibited synergy with other drugs known to be sequestered in lysosomes, such as carboplatin, oxaliplatin, sunitinib, and doxorubicin, indicating that inhibition of lysosomal exocytosis may be a common phenomenon for such drugs. These findings underscore the potential of Type I PRMT inhibitors as therapeutic agents in cancer treatment. Consistently, analysis on the publicly available patient data revealed that lower levels of type I PRMTs (PRMT1 and 6) were associated with better patient response to these drugs, further suggesting their potential as drug candidates for combination therapy to enhance chemotherapy efficacy and improve cancer patient survival rates.

cancer biology↗