Biology subjects

de Pretis, S.

Publications and source records attributed to de Pretis, S..

6 recordsLinked to original sources

bioRxiv2026

PatHoST: weakly supervised reconstruction of pathogen spatial distributions from host transcriptomes

Dual host-pathogen spatial transcriptomics enables spatially resolved investigation of infection, yet the completeness of pathogen detection remains poorly characterized. Here, we generated pathogen-only spatial transcriptomic sections from a chronic Mycobacterium abscessus lung infection model to experimentally benchmark pathogen detection, revealing substantially increased pathogen transcript recovery compared with conventional dual profiling. Building on these data, we developed PatHoST, a weakly supervised computational framework that uses pathogen-derived information to generate silver-standard labels and learns host transcriptional programs predictive of pathogen presence. PatHoST reconstructed pathogen spatial distributions across independent tissue sections and enabled the identification of localized host regulatory programs beyond conventional cluster-based analyses. Application to human SARS-CoV-2 lung spatial transcriptomics supported generalization across host species and pathogen classes. Together, PatHoST combines purpose-built experimental benchmarking with weakly supervised inference to recover latent pathogen information and extend the analytical capabilities of dual host-pathogen spatial transcriptomics.

bioinformatics↗

bioRxiv2025

Early endothelial activation at the blood-nerve barrier defines a hallmark of ALS

Vascular defects are common in Amyotrophic Lateral Sclerosis (ALS). The prevailing view is that breakdown of the blood-brain and blood-spinal cord barriers contributes to neurodegeneration. Here, we reveal that selective and early vulnerability of peripheral nerve endothelium --manifested as endothelial cell activation and interlinked blood-nerve barrier dysfunction-- constitutes a core feature of ALS pathogenesis, arising before vascular alterations in the central nervous system (CNS) and motor neuron pathology. Vascular changes in ALS patients have been largely studied in postmortem samples, limiting insight into their onset, causes, and pathogenic role. Surveying diagnostic motor nerve samples from ALS patients across clinical stages, we observed endothelial damage that preceded axonal loss and demyelination, marking vascular dysfunction as an early disease event. Similar ultrastructural abnormalities were detected in pre-symptomatic ALS mouse models (SOD1 and TARDBP mutants). Notably, endothelial cells became dysfunctional even when not carrying mutant TDP-43, indicating they respond to non-cell autonomous disease signals. Transcriptional, histological, and functional analyses revealed that these alterations were largely confined to peripheral nerves, while spinal cord vessels exhibited delayed and more focal changes. Single-cell sequencing identified ALS-susceptible endothelial cell subsets prone to a pro-inflammatory phenotype and impaired blood-nerve barrier function, increasing permeability via the transcellular route. These changes coincided with reactivity of nerve-resident macrophages and neutrophil infiltration. Neutrophil depletion attenuated endothelial activation and barrier leakiness, mitigating axonopathy in ALS mice. Our work unmasks the greater susceptibility of the peripheral nerve vasculature in ALS relative to the CNS. The early activation of peripheral nerve endothelium, combined with its potential reversibility, identifies a therapeutic window and suggests strategies for targeting the vascular-immune axis to protect the motor system.

neuroscience↗

bioRxiv2024

Dual host-bacterial gene expression to study pathogenesis and the regulation of virulence factors in tissue during respiratory infections

Co-localization of spatial transcriptome information of host and pathogen can revolutionize our understanding of microbial pathogenesis. Here, we aimed to demonstrate that customized bacterial probes can be successfully used to identify host-pathogen interactions in formalin-fixed-paraffin-embedded (FFPE) tissues by probe-based spatial transcriptomics technology. We analyzed the spatial gene expression of bacterial transcripts with the host transcriptomic profile in murine lung tissue chronically infected with Mycobacterium abscessus embedded in agar beads. Customized mycobacterial probes were designed for the constitutively expressed rpoB gene (an RNA polymerase {beta} subunit) and the virulence factor precursor lsr2, modulated by oxidative stress. We found a correlation between the rpoB expression, bacterial abundance in the airways, and an increased expression of lsr2 virulence factor in lung tissue with high oxidative stress. Overall, we demonstrate the potential of dual bacterial and host gene expression assay in FFPE tissues, paving the way for the simultaneous detection of host and bacterial transcriptomes in pathological tissues.

microbiology↗

bioRxiv2022

Dimensionality reduction and statistical modeling of scGET-seq data

Single cell multiomics approaches are innovative techniques with the ability to profile orthogonal features in the same single cell, giving the opportunity to dig more deeply into the stochastic nature of individual cells. We recently developed scGET-seq, a technique that exploits a Hybrid Transposase (tnH) along with the canonical enzyme (tn5), which is able to profile altogether closed and open chromatin in a single experiment. This technique adds an important feature to the classic scATAC-seq assays. In fact, the lack of a closed chromatin signal in scATAC: (i) restricts sampling of DNA sequence to a very small portion of the chromosomal landscapes, substantially reducing the ability to investigate copy number alteration and sequence variations, and (ii) hampers the opportunity to identify regions of closed chromatin, that cannot be distinguished between non-sampled open regions and truly closed. scGET-seq overcomes these issues in the context of single cells. In this work, we describe the latest advances in the statistical analysis and modeling of scGET-seq data, touching several aspects of the computational framework: from dimensionality reduction, to statistical modeling, and trajectory analysis.

bioinformatics↗

bioRxiv2020

Translation is required for miRNA-dependent decay of endogenous transcripts.

Posttranscriptional repression by microRNA (miRNA) occurs through transcript destabilization or translation inhibition. Whereas RNA degradation explains most miRNA-dependent repression, transcript decay occurs co-translationally, raising questions regarding the requirement of target translation to miRNA-dependent transcript destabilization. To assess the contribution of translation to miRNA-mediated RNA destabilization, we decoupled these two molecular processes by dissecting the impact of miRNA loss of function on cytosolic long noncoding RNAs (lncRNAs). We show, that despite interacting with miRNA loaded RNA-induced silencing complex (miRISC), the steady state abundance and degradation rates of these endogenously expressed non-translated transcripts are minimally impacted by miRNA loss. To validate the requirement of translation for miRNA-dependent decay, we fused a miRISC bound lncRNA, whose levels are unaffected by miRNAs, to the 3end of a protein-coding gene reporter and show that this results in its miRNA-dependent transcript destabilization. Furthermore, analysis of the few lncRNAs whose levels are regulated by miRNAs revealed these tend to associate with translating ribosomes and are likely misannotated micropeptides, further substantiating the necessity of target translation for miRNA-dependent transcript decay. Our analyses reveal the strict requirement of translation for miRNA-dependent transcript destabilization and demonstrate that the levels of coding and noncoding transcripts are differently affected by miRNAs.

genomics↗

bioRxiv2019

Dynamics of transcriptional regulation from total RNA-seq experiments

The kinetic rates of RNA synthesis, processing and degradation determine the dynamics of transcriptional regulation by governing both the abundance and the responsiveness to modulations of premature and mature RNA species. The study of RNA dynamics is largely based on the integrative analysis of total and nascent transcription, with the latter being quantified through RNA metabolic labeling. We describe here INSPEcT-, a computational method based on mathematical modeling of intronic and exonic expression, able to derive the dynamics of transcription from steady state or time course profiling of just total RNA, without requiring any information on nascent transcripts. Our approach closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcripts half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions where nascent transcription cannot be readily profiled. Finally, we applied INSPEcT- to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady state or time course data, with or without the profiling of nascent RNA.

systems biology↗