Biology subjects

Orlando, V.

Publications and source records attributed to Orlando, V..

8 recordsLinked to original sources

bioRxiv2025

Endogenous retrotransposon reverse transcriptase supports osteocyte function: implications for antiretroviral therapy-associated bone loss

Retrotansposable elements such as LINE-1 and HERV-K encode endogenous reverse transcriptases (RTs) with emerging roles in human biology. People living with HIV, particularly those receiving nucleoside reverse transcriptase inhibitor (NRTI)-based therapy, have increased risk of low bone mineral density (BMD), but the underlying mechanisms remain unclear. Here we show that endogenous RT activity, estimated by L1-Ta and HERV-K DNA content, is enriched in human bone and markedly reduced in osteoporosis, where it correlates with BMD and osteocyte gene expression. In vitro, nucleoside reverse transcriptase inhibitors (NRTIs), widely used as antiretroviral drugs, impair osteocyte endocrine function, disrupting vitamin D3-induced FGF23 production and parathyroid hormone- mediated regulation of SOST. These findings identify endogenous RT activity as a regulator of osteocyte function and bone homeostasis, and suggest that its pharmacological inhibition may contribute to antiretroviral therapy-associated bone loss.

molecular biology↗

bioRxiv2025

Thermo-Dynamic Flux Balance Analysis, a novel approach to simulate circadian metabolism

Circadian metabolism arises from complex, time-dependent interactions across organs, yet experimental characterization in humans remains limited. Current whole-body metabolic models are either too large for dynamic simulation or insufficiently detailed to capture temporal physiology. We developed a multi-tissue human metabolic reconstruction, HGEM1.19+, an extensively curated model for dynamic simulation. We introduced Thermo-Dynamic Flux Balance Analysis (tdFBA), a novel formulation that integrates thermodynamic constraints, organ-specific enzyme capacities, solubility limits, osmotic balance and pH buffering. Murine circadian transcriptomics and metabolomics were integrated with human datasets to parameterize temporal dynamics. A genetic algorithm optimized internal parameters under CHOW diet conditions and model performance was evaluated using circadian metabolomics and gene-sage patterns. The framework recapitulated key metabolic oscillations under CHOW diet and partially reconstructed perturbed states including HFD, BMAL1 knockout, and tissue-specific re-entrainment. tdFBA enables physiologically grounded, multi-organ dynamic simulations and provides a foundation for exploring human circadian metabolism and perturbation responses.

systems biology↗

bioRxiv2025

Histone Succinylation-Driven LINE-1 Reactivation Links High-Fat Diet Stress to Hepatic Inflammation and Liver Disease

Endogenous retroelements such as LINE-1 (L1) are stress-responsive genomic elements increasingly implicated in stress induced inflammation and associated pathogenic states. Here, we uncover a novel mechanism whereby high-fat diet-associated palmitic acid stress triggers chromatin remodeling that derepresses L1 elements and an IRF3-dependent interferon response, leading to innate immune activation in hepatocytes. Mechanistically, we show that that palmitic acid exposure promoted p300/CBP-mediated H3K122 succinylation at L1 promoters, coupled with reduced sirtuin desuccinylase cofactor availability, thereby enhancing chromatin accessibility and transcription. Antisense oligonucleotide-mediated L1 silencing abrogated this response by resetting chromatin homeostasis, demonstrating a causal role for L1 in palmitate-induced inflammation. In vivo, L1 knockdown in a fructose-palmitate-cholesterol (FPC) diet-induced mouse model of MASLD/MASH improved insulin sensitivity, reduced hepatic inflammation, and ameliorated fibrosis. These findings identify L1 derepression as a key epigenetic and inflammatory effector of dietary lipid stress and establish L1 inhibition as a potential therapeutic strategy for metabolic liver disease.

molecular biology↗

bioRxiv2025

AGO1 interacts with NEAT1 lncRNA and impacts nuclear compartments

Argonaute 1 (AGO1), a central component of the RNA interference (RNAi) pathway, has recently been implicated in nuclear functions, particularly in chromatin organization and gene regulation. However, the role of AGO1 in lncRNA-driven nuclear compartmentalization remains elusive. In this study, we uncover a novel function for AGO1 in the regulation of nuclear architecture through its interaction with the long non-coding RNA (lncRNA) NEAT1. NEAT1 lncRNA is required for the formation of paraspeckles, nuclear substructures involved in multiple cellular processes. We show that AGO1 physically interacts with NEAT1 and other key paraspeckle proteins (PSPs) and co-localizes with paraspeckles in the nucleus. AGO1 depletion disrupts expression of both NEAT1 isoforms, reduces the interaction of essential PSPs with NEAT1 lncRNA, and leads to impaired paraspeckle formation. Furthermore, depletion of NEAT1 results in the mis-localization of AGO1 from paraspeckles and alters active chromatin compartments. Together, our findings establish a new functional relationship between AGO1 and NEAT1 in nuclear compartmentalization and chromatin architecture.

cell biology↗

bioRxiv2022

Interrogating Metabolic Interactions Between Skeletal Muscle and Liver Circadian Clocks In Vivo

Expressed throughout the body, the circadian clock system achieves daily metabolic homeostasis at every level of physiology, with clock disruption associated with metabolic disease (1, 2). Molecular clocks present in the brain, liver, adipose, pancreas and skeletal muscle each contribute to glucose homeostasis (3). However, it is unclear; 1) which organ clocks provide the most essential contributions, and 2) if these contributions depend on inter-organ communication. We recently showed that the liver clock alone is insufficient for most aspects of daily liver glucose handling and requires connections with other clocks (4). Considering the pathways that link glucose metabolism between liver and skeletal muscle, we sought to test whether a clock connection along this axis is important. Using our previous published methodology for tissue-specific rescue of Bmal1 in vivo (4, 5), we now show that in the absence of feeding-fasting cycles, liver and muscle clocks are not sufficient for systemic glucose metabolism, nor do they form a functional connection influencing local glucose handling or daily transcriptional rhythms in each tissue. However, the introduction of a daily feeding-fasting rhythm enables a synergistic state between liver and muscle clocks that leads to restoration of systemic glucose tolerance. These findings reveal limited autonomous capabilities of liver and muscle clocks and highlight the need for inter-organ clock communication for glucose homeostasis which involves at least two peripheral metabolic organs.

cell biology↗

bioRxiv2020

Development and validation of a clinical risk score to predict the risk of SARS-CoV-2 infection from administrative data: a population-based cohort study from Italy

BackgroundThe novel coronavirus (SARS-CoV-2) pandemic spread rapidly worldwide increasing exponentially in Italy. To date, there is lack of studies describing clinical characteristics of the population most at risk of infection. Hence, we aimed to identify clinical predictors of SARS-CoV-2 infection risk and to develop and validate a score predicting SARS-CoV-2 infection risk comparing it with unspecific surrogates. MethodsRetrospective case/control study using administrative health-related database was carried out in Southern Italy (Campania region) among beneficiaries of Regional Health Service aged over than 30 years. For each subject with Covid-19 confirmed diagnosis (case), up to five controls were randomly matched for gender, age and municipality of residence. Odds ratios and 90% confidence intervals for associations between candidate predictors and risk of infection were estimated by means of conditional logistic regression. SARS-CoV-2 Infection Score (SIS), was developed by generating a total aggregate score obtained from assignment of a weight at each selected covariate using coefficients estimated from the model. Finally, the score was categorized by assigning increasing values from 1 to 4. SIS was validated by comparison with specific and unspecific predictors of SARS-CoV-2 infection. ResultsSubjects suffering from diabetes, anaemias, Parkinsons disease, mental disorders, cardiovascular and inflammatory bowel and kidney diseases showed increased risk of SARS-CoV-2 infection. Similar estimates were recorded for men and women and younger and older than 65 years. Fifteen conditions significantly contributed to the SIS. As SIS value increases, risk progressively increases, being odds of SARS-CoV-2 infection among people with the highest SIS value (SIS=4), 1.74 times higher than those unaffected by any SIS contributing conditions (SIS=1). ConclusionThis study identified conditions and diseases making individuals more vulnerable to SARS-CoV-2 infection. Our results are a decision-maker support tool for identifying population most at risk allowing adoption of preventive measures to minimize a potential new relapse damage.

scientific communication and education↗

bioRxiv2019

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodelling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However, they still present some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.

genomics↗

bioRxiv2019

AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells

Aside from their roles in the cytoplasm, RNA-interference components have been reported to localize also in the nucleus of human cells. In particular, AGO1 associates with active chromatin and appears to influence global gene expression. However, the mechanistic aspects remain elusive. Here, we identify AGO1 as a paraspeckle component that in combination with the NEAT1 lncRNA maintains 3D genome architecture. We demonstrate that AGO1 interacts with NEAT1 lncRNA and its depletion affects NEAT1 expression and the formation of paraspeckles. By Hi-C analysis in AGO1 knockdown cells, we observed global changes in chromatin organization, including TADs configuration, and A/B compartment mixing. Consistently, distinct groups of genes located within the differential interacting loci showed altered expression upon AGO1 depletion. NEAT1 knockout cells displayed similar changes in TADs and higher-order A/B compartmentalization. We propose that AGO1 in association with NEAT1 lncRNA can act as a scaffold that bridges chromatin and nuclear bodies to regulate genome organization and gene expression in human cells.

genomics↗