Biology subjects

Oliviero, S.

Publications and source records attributed to Oliviero, S..

12 recordsLinked to original sources

bioRxiv2026

Post-Weaning Gut Microbiota Colonization Reveals Divergent Recovery of Skeletal Muscle and Peripheral Nerves

We previously demonstrated that the absence of a complex gut microbiota (CGM) impairs the postnatal development of peripheral nerves and motor targets in germ-free (GF) mice. In this study, we investigated whether establishing a complex gut microbiota after weaning could reverse these developmental alterations. To address this question, GF mice were colonized with a complex gut microbiota by co-housing with conventionally raised mice. Microbiota composition, peripheral nerve morphology and transcriptional profiles, skeletal muscle proteome, neuromuscular junction architecture and circulating metabolites were comprehensively analyzed and compared with those of GF, gnotobiotic OMM12 and CGM mice. Post-weaning colonization partially restored microbial diversity and resulted in a compositionally distinct microbial community with reduced alpha diversity and enrichment of Duncaniella muris strain B8. Despite successful microbial colonization, peripheral nerve abnormalities persisted, including axon hypermyelination, transcriptional alterations in sciatic nerves, elongated nodes of Ranvier, and dysregulated axon-glia interactions. In contrast, skeletal muscle defects were largely rescued, with restoration of muscle mass, normalization of proteomic profiles, recovery of metabolic and structural pathways, and reduced fragmentation of the postsynaptic neuromuscular junction, although presynaptic abnormalities persisted. These findings demonstrate that microbiota-dependent developmental alterations differ markedly in their reversibility across the neuromuscular system. Specifically, post-weaning colonization with a complex gut microbiota resulted in broad recovery of skeletal muscle but failed to rescue peripheral nerve abnormalities. Our findings provide a framework for future studies investigating how the timing of microbial colonization, microbiota composition, and microbiota-derived signals influence the reversibility of microbiota-dependent neuromuscular alterations.

neuroscience↗

bioRxiv2026

Geroprotective interventions preserve trabecular bone during ageing in female mice

Geroprotectors extend lifespan and improve several aspects of healthspan, yet their effects on skeletal ageing remain poorly understood. They hold potential advantages over current bone-targeted osteoporosis therapies, as they may simultaneously improve bone, neuromuscular function, and vision, thereby reducing the risk of falls, the major cause of fractures. Here we examined, for the first time, the long-term effects of rapamycin, acarbose, and 17-estradiol, administered at lifespan-extending doses on trabecular and cortical bone architecture in male and female UM-HET3 mice measured with micro-computed tomography at 12 and 22 months of age. Bayesian modelling analysis reveals that all interventions produced responses in trabecular bone in females at 22 months. These effects were driven mainly by increases in trabecular number, with little evidence for changes in trabecular thickness. In contrast, treatment effects in males were generally negligible. Cortical responses were modest. Moderate increases in cortical area fraction were observed in females treated with rapamycin or 17-estradiol at 22 months, whereas cortical thickness remained largely unchanged, suggesting a geometrical rather than anabolic effect. Interestingly, geroprotectors strongest skeletal responses in females contrasts with the predominantly male-biased lifespan extension reported for acarbose and 17-estradiol, suggesting differential mechanisms mediating lifespan extension and bone structure preservation.

pharmacology and toxicology↗

bioRxiv2025

Brain injury reactivates a developmental program driving genesis and integration of transient LGE-class interneurons

Brain lesions can unlock a latent neurogenic potential in parenchymal astrocytes. However, the identity of their neuronal progeny has remained unclear. Here, we show that neurons generated by striatal astrocytes following excitotoxic lesions are transient, yet they reach advanced stages of morphological and functional maturation and integrate into cortico-striatal-thalamic circuits. Single-cell RNA-seq mapping onto an embryonic reference revealed that these cells are not related to adult striatal neuron types but instead belong to the LGE-MEIS2/PAX6 interneuron class. Notch abrogation, which mimics neurogenic activation, drives both cortical and striatal astrocytes toward this same interneuron class, revealing a shared intrinsic commitment. In primates, LGE-MEIS2/PAX6 cells transiently populate the embryonic striatum and cortex, and through spatial transcriptomics, we reveal that in mice these cells are also present and widely distributed throughout the telencephalon during embryonic and postnatal development. Thus, unlike other vertebrates in which adult telencephalic astroglia preserve the potential to generate constitutive region-specific neurons, the homologous cells in mammals converge on the generation of a specific transient neuron class, possibly representing a reservoir for circuit plasticity in adult life.

neuroscience↗

bioRxiv2025

Bedaquiline Amplifies Proteasome Inhibitor Efficacy and Overcomes Resistance in Multiple Myeloma

Proteasome inhibitors (PIs) are cornerstone therapies for multiple myeloma (MM), yet resistance remains a major barrier to durable responses. To identify druggable vulnerabilities that enhance PIs efficacy, we performed a small-molecule chemical screen in the presence of carfilzomib (CFZ). We identified bedaquiline (BDQ), an FDA-approved antimycobacterial agent, as a potent synergistic partner. BDQ and its fumarate salt (BDQ-F) significantly amplified CFZ-induced cytotoxicity in PI-sensitive and PI-resistant MM cells, in AL amyloidosis and other B-cell malignancies, with minimal toxicity toward normal cells. Mechanistic studies confirmed that BDQ specifically targets the ATP5F1C subunit of mitochondrial ATP synthase. BDQ-CFZ combination triggered extensive apoptosis, exacerbating proteotoxic stress and proteasome-associated pathways. BDQ specifically enhanced CFZs inhibition of the proteasomes chymotrypsin-like activity. Importantly, BDQ synergized with multiple proteasome and ubiquitin-activating enzyme inhibitors, but not with other standard MM agents, underscoring its selective interaction with the UPS pathway. BDQ-CFZ co-treatment markedly reduced MM cell viability and tumor burden in patient-derived cells and zebrafish xenograft models. These findings support the therapeutic repurposing of BDQ to potentiate PIs efficacy and overcome resistance in MM and related B-cell malignancies. KEY POINTSO_LIBedaquiline synergizes with proteasome inhibitors in MM and other hematologic malignancies, sparing normal cells C_LIO_LIBedaquiline targets ATP synthase {gamma} and boosts carfilzomib by enhancing chymotrypsin-like proteasome inhibition C_LI NOVELTYWe identify the antimicrobial bedaquiline and its fumarate salt as potent enhancers of proteasome inhibitor efficacy in multiple myeloma and other B-cell malignancies. By inhibiting ATP synthase {gamma}, bedaquiline amplifies chymotrypsin-like proteasome inhibition and overcomes drug resistance. This study reveals a mitochondria- proteasome vulnerability and proposes a clinically actionable strategy to restore sensitivity and reduce toxicity of proteasome-based therapies. VISUAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/661768v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@339391org.highwire.dtl.DTLVardef@1d3271org.highwire.dtl.DTLVardef@daa0faorg.highwire.dtl.DTLVardef@17eb4eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

TGF-beta dynamically controls epithelial identity in a 3D model of human epiblast

Pluripotency is the ability to give rise to all cell types of the body and is first observed in a mass of disorganised cells of the embryo. Upon implantation, pluripotent cells form a columnar epithelium and undergo lumenogenesis. At gastrulation, a portion of the pluripotent epiblast will undergo epithelial to mesenchymal transition (EMT), forming the primitive streak (PS). It still remains unclear what molecular mechanism supports the epithelial identity of the pluripotent epiblast before gastrulation. Here we developed an optimised, chemically defined 3D model of human pluripotent epiblast formation in which conventional pluripotent stem cells (PSCs) self-organise into a columnar epithelium with a lumen in 48 hours. From 72 hours we observed spontaneous symmetry breaking and specification of PS-like cells, as confirmed by single-cell RNA sequencing. We found that Insulin and FGF signalling are both required for the proliferation and survival of the pluripotent epiblast model. Conversely, TGF-beta signalling maintains epithelial identity. Epithelial identity appears uncoupled from the expression of canonical pluripotency markers OCT4, NANOG and PRDM14, but under the control of ZNF398. Once the pluripotent epithelium is established, TGF-beta inhibition is inconsequential, and stimulation with Activin A leads to highly efficient PS induction. We conclude that TGF-beta dynamically orchestrates epithelial identity of human pluripotent cells.

developmental biology↗

bioRxiv2023

FVIII interacts with cell surface to regulate endothelial cell functionality

Haemophilia A (HA) is a rare bleeding disorder caused by factor 8 (F8) mutations. Clinical manifestations are spontaneous bleedings that primarily consist of hemarthrosis and intracranial haemorrhages. To date, the impairment of vessel stability in HA patients and the correlation between FVIII and endothelial functionality is poorly understood. Here we show that FVIII plays a role in endothelial cell functionality. Blood Outgrowth endothelial cells (BOECs) knockout generated by CRISPR/Cas9, HA BOECs and HA iPSCs-derived ECs showed alteration of vessel-formation, endothelial cell migration, and vessel permeability. Importantly, the impaired EC phenotype was rescued by treatment with recombinant human FVIII or by lentiviral vector (LV) expressing FVIII. The FVIII function on endothelium was confirmed in vivo in a mouse model of severe HA which showed that an altered angiogenesis and vesselpermeability could be treated by exogenous FVIII. BOECstranscriptomic profiles revealed that FVIIIregulates the expression of endothelial basement membrane and extracellular matrix genes. Furthermore, exogenous expression of Nidogen2, identified as a FVIII regulated gene, restored the extracellular matrix integrity and EC functionality of HA ECs. In conclusion, FVIII is not only a coagulation factor but also an endothelial cell autocrine factor which promotes vessel stability.

molecular biology↗

bioRxiv2023

Lifelong tissue memory relies on spatially organised dedicated progenitors located distally from the injury

It is believed epithelial cells that have participated in a wound repair elicit a more efficient but locally restricted response to future injuries. However here we show that the cell adaptation resulting from a localised tissue damage has a wide spatial impact at a scale not previously noticed. We demonstrate that away from injured site, after a first injury a specific epithelial stem cell population gives rise to long term wound-memory progenitors residing in their own niche of origin. Notably these progenitors have not taken part in the first wound healing but become pre-activated through priming. This adaptation differs from classical features of trained immunity previously shown to be adopted by other epithelial stem cells. Our newly identified wound-distal memory cells display a cell-autonomous transcriptional pre-activated state leading to an enhanced wound repair ability that can be partially recapitulated through epigenetic perturbation even in absence of an injury. Importantly, the harmful consequences of wound repair, such as exacerbated tumorigenesis, occur within these primed cells and follow their spatial distribution. Overall, we show that sub-organ scale adaptation of an injury relies on spatially organised and memory-dedicated progenitors, characterised by an epigenetic actionable cell state, that predisposes to tumour onset.

cell biology↗

bioRxiv2022

RNABSdb and 3plex enable deep computational investigation of triplex forming lncRNAs

1.Long non-coding RNAs (lncRNAs) regulate gene expression through different molecular mechanisms, including DNA binding. We curated the first database of RNA Binding Sites (RNABSdb) by harmonising publicly available raw-data of RNA-DNA binding experiments. This resource is crucial to enable systematic studies on transcriptional regulation driven by lncRNAs. Focusing on high quality experiments, we find that the number of binding sites for each lncRNAs varies from hundreds to tens of thousands. Despite being poorly characterised, the formation of RNA:DNA:DNA triple helices (TPXs) is one of the molecular mechanisms that allows lncRNAs to bind the genome and regulate gene expression. We developed 3plex, a software able to predict TPXs in silico. We show that 3plex outperforms previous existing approaches leveraging the data collected in RNABSdb for lncRNAs known to form functional TPXs. Moreover this analysis shows that TPXs tend to be shorter and more degenerated than previously expected. Finally, we applied 3plex to all the lncRNAs collected in RNABSdb and we show that the majority of them could directly bind the genome by TPXs formation. Data and software are available at https://molinerislab.github.io/RNABSdb/ and https://github.com/molinerisLab/3plex.

bioinformatics↗

bioRxiv2022

Nr2f1-dependent shaping of mitochondrial architecture in newborn mouse hippocampal neurons unravels novel insights into the neurodevelopmental disorder BBSOAS

The nuclear receptor Nr2f1 plays a key role during cortical development by acting as a strong transcriptional regulator in embryonic and postnatal neural cells. In humans, its mutations cause the Bosch-Boonstra-Schaaf optic atrophy-intellectual syndrome (BBSOAS), a rare neurodevelopmental disorder characterized by multiple clinical features including optic nerve atrophy, intellectual disability, and autistic traits. In this study by genome-wide and in silico analyses we found that key factors for mitochondrial function and dynamics represent potential genomic targets under direct Nr2f1 transcriptional control in neurons. Although mitochondrial dysfunction is increasingly implicated in neurodevelopmental disorders, whether and how Nr2f1 can regulate mitochondria function in neural cells is still completely unknown. To address these questions, we have combined mouse genetics, neuroanatomical and imaging approaches. To genetically manipulate Nr2f1 function in newborn neurons we focused on the adult mouse hippocampal dentate gyrus, a site of persistent neurogenesis where Nr2f1 is highly expressed. We showed that conditional Nr2f1 loss-of-function within the hippocampal neurogenic niche lead to a reduced mitochondrial mass associated to mitochondrial fragmentation in newborn neurons, likely reflecting alteration in mitochondrial dynamics. Accordingly, we showed that the fusion factor Mfn2, which is as a putative Nr2f1 target, is downregulated following both Nr2f1 adult depletion and embryonic haploinsufficiency in mice. Overall, our study provides the first evidence of a crucial role of Nr2f1 in shaping mitochondria in neurons and opens a promising avenue for the identification of new mechanisms implicated in BBSOAS pathogenesis involving mitochondrial dysfunction.

neuroscience↗

bioRxiv2020

HNRNPM controls circRNA biogenesis and splicing fidelity to sustain prostate cancer cell fitness

Cancer cells are differentially dependent on the splicing machinery compared to normal untransformed cells. The splicing machinery thus represents a potential therapeutic target in cancer. To identify splicing factors important for prostate cancer cell (PCa) cell growth, we performed a parallel pooled shRNA screen on in vitro passaged cells and in vivo xenografted PCa tumor lines. Our screen revealed HNRNPM as a potential regulator of PCa cell growth. RNA- and eCLIP-sequencing data suggest that HNRNPM is bound to transcripts of key homeostatic genes and that loss of HNRNPM binding in a subset of these genes results in aberrant exon inclusion and exon back-splicing events in target transcripts. In both linear and circular mis-spliced transcripts, HNRNPM appears to preferentially bind to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM dependent linear splicing events using splice-switching antisense oligonucleotides (SSOs) was sufficient to inhibit cell growth in HNRNPM expressing cells. This suggests that prostate cancer cell dependence on HNRNPM is likely a result of mis-splicing of key homeostatic coding and non-coding genes. Taken together, our data reveal a role for HNRNPM in supporting prostate cancer cell fitness, and also as a potential therapeutic target in PCa.

genomics↗

bioRxiv2020

Subepidermal blisters are healed by wedge-shaped keratinocytes of hair follicle origin

Injury in adult tissue generally reactivates developmental programs to foster regeneration, but it is not known whether this paradigm applies to growing tissue. Here, by employing blisters, we show that epidermal wounds heal at the expense of skin development. The regenerated epidermis suppresses the expression of tissue morphogenesis genes accompanied by delayed hair follicle (HF) growth. Lineage tracing experiments, cell proliferation dynamics, and mathematical modeling reveal that the progeny of HF junctional zone stem cells, which undergo a morphological transformation, repair the blisters while not promoting HF development. In contrast, the contribution of interfollicular stem cell progeny to blister healing is small. These findings demonstrate that tissue development can be sacrificed for the sake of wound regeneration and suggest that tissue repair does not coincide with the reactivation of developmental programs in all regenerative contexts. Our study elucidates the key cellular mechanism of wound healing in skin blistering diseases.

cell biology↗

bioRxiv2018

Dysregulation of splicing-related proteins in prostate cancer is controlled by FOXA1

Prostate cancer (PCa) is genomically driven by dysregulation of transcriptional networks involving the transcriptional factors (TFs) FOXA1, ERG, AR, and HOXB13. However, the role of these specific TFs in the regulation of alternative pre-mRNA splicing (AS), which is a proven therapeutic vulnerability for cancers driven by the TF MYC, is not described. Using transcriptomic datasets from PCa patients, we tested for an association between expression of FOXA1, ERG, AR, HOXB13, and MYC, and genes involved in AS - termed splicing-related proteins (SRPs), which have pleiotropic roles in RNA metabolism. We identified FOXA1 as the strongest predictor of dysregulated SRP gene expression, which was associated with PCa disease relapse after treatment. Subsequently, we selected a subset of FOXA1-binding and actively-transcribed SRP genes that phenocopy the FOXA1 dependency of PCa cells, and confirmed in vitro via knockdown and over-expression that FOXA1 regulates SRP gene expression. Finally, we demonstrated the persistence of a FOXA1-SRP gene association in treatment-relapsed castration-resistant PCa (CRPCa) patients. Our data demonstrate, for the first time, that FOXA1 controls dysregulated SRP gene expression, which is associated with poor PCa patient outcomes. Analogous to MYC-driven cancers, our findings implicate the therapeutic targeting of SRPs and AS in FOXA1-overexpressing PCa.

cancer biology↗