Biology subjects

Orlando, F.

Publications and source records attributed to Orlando, F..

4 recordsLinked to original sources

bioRxiv2026

The RNA cargo of plasma-derived extracellular vesicles in mCRPC patients captures cancer cells and tumor microenvironment signals

Circulating analytes in cancer patients capture tumor-related signals. We profiled matched extracellular vesicle (EV) total RNA and cell-free DNA (cfDNA) from the same plasma aliquots of chemo-naive metastatic castration-resistant prostate cancer (mCRPC) patients treated with Enzalutamide (n=54 patients, n=119 longitudinal samples; NCT06981377) at four Italian clinical centers and interrogated data from >10,000 cancer patients' and healthy individuals' samples. Transcript integrity analysis identified coding and non-coding species with fragmentation patterns varying across RNA biotypes. EV-RNA data deconvolution revealed signal from immune populations, including fractions classified as CD4+ T cells, whose abundance increased with disease progression in plasma EVs and mCRPC tissues. By leveraging tissue data-informed mining, we established a novel prostate cancer-related EV-RNA signature that resulted in an independent predictor of poor prognosis and captured tumor microenvironment-derived signals. Integrating EV-RNA and ctDNA information improved patient stratification for progression-free survival. These findings suggest a multifaceted role for plasma EVs as a source of cancer biomarkers.

cancer biology↗

bioRxiv2025

T2T-CHM13 reference genome reduces mapping bias and enhances alignment accuracy at disease-associated variants

1The T2T-CHM13v2.0 reference genome added previously uncharacterized genomic sequences and improved the accuracy of repetitive stretches compared to former human genome assemblies. By comprehensive allelic variation analysis and read mapping statistics from sequencing reads aligned to hg38 and T2T-CHM13 assemblies in samples encompassing different sequencing designs and ethnicity groups, we observed that T2T-CHM13v2.0 assembly significantly reduces the reference mapping bias (RMB) and increases read mapping precision at clinically relevant sites, including BRCA1 pathogenic variants. Further, we report the presence of sequence dissimilarities among reference genomes in the proximity of ClinVar annotated variants, suggesting the need for data re-analysis and potential redesign of probes targeting clinically relevant regions. Overall, these findings support the implementation of T2T-CHM13 reference for the improvement of sequencing data analyses in the clinical genomic setting.

genomics↗

bioRxiv2025

Precision RNAi in Tomato Using Synthetic Trans-Acting Small Interfering RNAs Derived From Minimal Precursors

RNA interference (RNAi) is a highly conserved gene silencing mechanism regulating gene expression at transcriptional and post-transcriptional levels in plants. Synthetic trans-acting small interfering RNAs (syn-tasiRNAs) have emerged as powerful tools for highly specific and efficient gene silencing. However, their application in crops has been constrained by the need for transgene integration and the relatively long length of TAS-derived precursors. Here, we developed a novel syn-tasiRNA platform for Solanum lycopersicum (tomato) based on minimal precursors targeted by endogenous SlmiR482b microRNA. These minimal precursors, comprising only a 22-nt miRNA target site, an 11-nt spacer and the syn-tasiRNA sequence(s), effectively produced functional syn-tasiRNAs in both transgenic and transient virus-induced gene silencing (syn-tasiR-VIGS) systems. To facilitate their broader application, we engineered a series of vectors for high-throughput cloning and efficient syn-tasiRNA expression from SlmiR482b-based minimal precursors in tomato. Our results show that minimal precursors induce robust gene silencing of endogenous tomato genes and confer antiviral resistance to the economically important tomato spotted wilt virus. Furthermore, we show that syn-tasiR-VIGS can be applied in a transgene-free manner through crude extract delivery, leading to efficient silencing of endogenous genes. This study establishes minimal syn-tasiRNA precursors as a versatile and efficient tool for precision RNAi in tomato, with applications in functional genomics and crop improvement.

plant biology↗

bioRxiv2019

Dalbavancin and wound healing: new evidences/insights in a mouse model of skin infection.

Dalbavancin is an effective antibiotic widely used to treat skin infection. Our aim was to determinate the effects of dalbavancin administration on wound healing compared to vancomycin, and to elucidate if EGFR, MMP-1, MMP-9 and VEGF could be involved in its therapeutic mechanism. A mouse model of MRSA skin infection was established. Mice were treated daily with vancomycin (10mg/kg) and weekly with dalbavancin, at day 1 (20 mg/kg) and day 8 (10 mg/kg). After 14 days wounds were excised and bacterial counts were perfomed. Wound healing was assessed by histological and immunohistochemical staining, followed by protein extraction and immunoblotting. Our microbiological results confirmed that both dalbanvancin and vancomycin are effective in reducing the bacterial load in wounds. Dalbavancin had a strong effect compared with infected untreated animals and vancomycin treated group. The wounds treated with dalbavancin showed robust epidermal coverage with a reconstitution of the regular and keratinized epidermal lining and a well-organized granulation tissue with numerous blood vessels, although slightly less than in the uninfected group, while in vancomycin treated group the epithelium appeared in general still hypertrophic, the granulation tissue appears even less organized. We observed elevated EGFR and VEGF expression in both treated groups, although it was higher in dalbavancin treated mice. MMP-1 and MMP-9 were decreased in uninfected and in both treated tissue when compared with untreatd infected wounds. This study showed faster healing with dalbavancin treatment that might be associated with a higher EGFR and VEGF levels.

pharmacology and toxicology↗