Biology subjects

Arapidi, G. P.

Publications and source records attributed to Arapidi, G. P..

5 recordsLinked to original sources

bioRxiv2025

A trans-acting enhancer lncRNA modulates androgen-dependent gene expression via sequence-specific interaction with the Androgen Receptor

BackgroundEnhancer RNAs (eRNAs) have been shown to modulate the transcriptional landscape of prostate cancer (PCa). The Androgen Receptor (AR), a well-known modulator of eRNA expression, contains an RNA-binding region that interacts with RNA molecules in a sequence-specific manner. However, there is currently no evidence that AR forms complexes with eRNAs to regulate gene expression. MethodsTo explore the eRNA-AR interactome, we reanalyzed publicly available RNA-seq, ChIP-seq, and AR-RIP-seq data from prostate cancer cell lines to identify a single long non-coding eRNA that interacts with AR (ARA-elncRNA1). Using linear regression, we identified genomic regions where AR occupancy is associated with the expression level of ARA-elncRNA1. We further demonstrated that this eRNA recruits AR to YY1-mediated enhancer-promoter loops, stabilizing these interactions. A series of experiments, including RIP-qPCR, ChIP-qPCR, and EMSA, were conducted to validate the proposed model. Finally, we investigated the role of ARA-elncRNA1 in prostate cancer cells survival. ResultsWe confirmed the sequence-specific interaction between AR and ARA-elncRNA1. This eRNA not only regulates AR occupancy at the promoters of several AR-dependent genes but also protects AR from proteasomal degradation. The AR:ARA-elncRNA1 complex interacts with YY1 and influences enhancer-promoter looping. Additionally, ARA-elncRNA1 was found to inhibit the proliferation of prostate cancer (PCa) cells in vitro and expression level of lncRNA was associated with a lower Gleason score. ConclusionsOur findings revealed the existence of an eRNA that directly binds to AR and regulates, in trans, the expression of several AR-dependent genes. We demonstrated that eRNAs can not only interact with AR but also modulate chromatin structure. These insights shed new light on the functional roles of eRNAs and their contribution to cancer development.

cancer biology↗

bioRxiv2023

Unlocking DNA Damage Sensitivity of Cancer Cells: The Potential of Splicing Inhibitors

Despite the growing interest in pre-mRNA alternative splicing (AS) as a therapeutic anticancer target, the potential of splicing inhibitors in treating solid tumors remains largely unexplored. We conducted a meta-analysis of transcriptome data from six different tumor types and revealed that splicing inhibitors induced similar patterns of AS, resulting in widespread exon-skipping and intron retention events that often lead to nonsense-mediated decay of the transcripts. Interestingly, in many cases exon skipping is induced by a compensatory cellular response to splicing inhibitor treatment. It involves an upregulation of multiple splicing factors and incomplete recognition of branch points by U2 snRNP. These post transcriptional changes downregulate one-third of essential DNA repair genes, thereby creating a therapeutic vulnerability that can be exploited for cancer treatment. To harness this vulnerability, we proposed a new approach to cancer treatment consisting of sequential addition of a splicing inhibitors followed by a DNA-damaging agent. Our in vitro and in vivo experiments demonstrated that this strategy exhibits promising therapeutic potential for a wide range of tumors.

cancer biology↗

bioRxiv2023

Phase separation of Treacle is indispensable for ribosomal transcription and DNA repair.

We investigated the role of the nucleolar protein Treacle in organizing and regulating the nucleolus in human cells. Our results support Treacles ability to form liquid-like phase condensates through electrostatic interactions among molecules. The formation of these biomolecular condensates is crucial for segregating nucleolar fibrillar centers from the dense fibrillar component and ensuring high levels of rRNA gene transcription and accurate rRNA processing. Both the central and C-terminal domains of Treacle are required to form liquid-like condensates. The initiation of phase separation is attributed to the C-terminal domain. The central domain is characterized by repeated stretches of alternatively charged amino-acid residues and is vital for condensate stability. Overexpression of mutant forms of Treacle that cannot form liquid-like phase condensates compromises the assembly of fibrillar centers, suppressing rRNA gene transcription and disrupting rRNA processing. These mutant forms also fail to recruit DNA topoisomerase II binding protein 1 (TOPBP1), suppressing the DNA damage response in the nucleolus.

cell biology↗

bioRxiv2023

Non-Human Peptides Revealed in Blood Reflect the Composition of Small Intestine Microbiota

The previously underestimated effects of commensal gut microbiota on the human body are increasingly being investigated using omics. The discovery of active molecules of interaction between the microbiota and the host may be an important step towards elucidating the mechanisms of symbiosis. Here, we show that in the bloodstream of healthy people, there are over 900 peptides that are fragments of proteins from microorganisms which naturally inhabit human biotopes, including the intestinal microbiota. Absolute quantitation by multiple reaction monitoring has confirmed the presence of bacterial peptides in the blood plasma and serum in the range of approximately 0.1 nM to 1 M. The abundance of microbiota peptides reaches its maximum about 5h after a meal. Most of the peptides correlate with the bacterial composition of the small intestine and are likely obtained by hydrolysis of membrane proteins with trypsin, chymotrypsin and pepsin -- the main proteases of the gastrointestinal tract. The peptides have physicochemical properties allowing them selectively pass the intestinal mucosal barrier and resist fibrinolysis. Proposed approach to the identification of microbiota peptides in the blood may be useful for determining the microbiota composition of hard-to-reach intestinal areas and for monitoring the permeability of the intestinal mucosal barrier.

biochemistry↗

bioRxiv2022

Co-expression analysis reveals gene cluster associated with methylation of enhancers and chromosomal instability under TP63 and TRIM29 regulation

AO_SCPLOWBSTRACTC_SCPLOWProstate adenocarcinoma (PRAD) is the second most common cause of cancer-related deaths in men. PRAD is often characterized by DNA methylation variability and a high rate of large genomic rearrangements. To elucidate the reasons behind such high variance, we used weighted gene co-expression network analysis for integration RNA-seq, DNA methylation and copy number alterations data from The Cancer Genome Atlas PRAD. Our results show that only a single cluster of co-expressed genes is associated with genomic and epigenomic instability. Within this cluster, TP63 and TRIM29 are key transcription regulators. We revealed that TP63 regulates the level of enhancer methylation in prostate basal epithelium cells. TRIM29 forms a complex with TP63 and together regulate the expression of genes specific to the prostate basal epithelium. Moreover, TRIM29 binds DNA repair proteins and prevents formation of the TMPRSS2:ERG gene fusion typically observed in PRAD. Therefore, the study shows that TRIM29 and TP63 are important regulators maintaining the identity of the basal epithelium under physiological conditions. Finally, we uncover the role of TRIM29 in PRAD development.

systems biology↗