Biology subjects

Ferro, A.

Publications and source records attributed to Ferro, A..

9 recordsLinked to original sources

bioRxiv2024

The cytokine receptor Fn14 is a molecular brake on neuronal activity that mediates circadian function in vivo

To survive, organisms must adapt to a staggering diversity of environmental signals, ranging from sensory information to pathogenic infection, across the lifespan. At the same time, organisms intrinsically generate biological oscillations, such as circadian rhythms, without input from the environment. While the nervous system is well-suited to integrate extrinsic and intrinsic cues, how the brain balances these influences to shape biological function system-wide is not well understood at the molecular level. Here, we demonstrate that the cytokine receptor Fn14, previously identified as a mediator of sensory experience-dependent synaptic refinement during brain development, regulates neuronal activity and function in adult mice in a time-of-day-dependent manner. We show that a subset of excitatory pyramidal (PYR) neurons in the CA1 subregion of the hippocampus increase Fn14 expression when neuronal activity is heightened. Once expressed, Fn14 constrains the activity of these same PYR neurons, suggesting that Fn14 operates as a molecular brake on neuronal activity. Strikingly, differences in PYR neuron activity between mice lacking or expressing Fn14 were most robust at daily transitions between light and dark, and genetic ablation of Fn14 caused aberrations in circadian rhythms, sleep-wake states, and sensory-cued and spatial memory. At the cellular level, microglia contacted fewer, but larger, excitatory synapses in CA1 in the absence of Fn14, suggesting that these brain-resident immune cells may dampen neuronal activity by modifying synaptic inputs onto PYR neurons. Finally, mice lacking Fn14 exhibited heightened susceptibility to chemically induced seizures, implicating Fn14 in disorders characterized by hyperexcitation, such as epilepsy. Altogether, these findings reveal that cytokine receptors that mediates inflammation in the periphery, such as Fn14, can also play major roles in healthy neurological function in the adult brain downstream of both extrinsic and intrinsic cues. HighlightsO_LINeuronal activity induces Fn14 expression in pyramidal neurons of the hippocampus C_LIO_LIFn14 constrains neuronal activity near daily transitions between light and dark C_LIO_LILoss of Fn14 lengthens the endogenous circadian period and disrupts sleep-wake states and memory C_LIO_LIMicroglia contact excitatory synapses in an Fn14-dependent manner C_LI

neuroscience↗

bioRxiv2023

Integrated high-confidence and high-throughput approaches for quantifying synapse engulfment by oligodendrocyte precursor cells

Oligodendrocyte precursor cells (OPCs) sculpt neural circuits through the phagocytic engulfment of synapses during development and in adulthood. However, precise techniques for analyzing synapse engulfment by OPCs are limited. Here, we describe a two-pronged cell biological approach for quantifying synapse engulfment by OPCs which merges low-and high-throughput methodologies. In the first method, an adeno-associated virus encoding a pH-sensitive, fluorescently-tagged synaptic marker is expressed in neurons in vivo. This construct allows for the differential labeling of presynaptic inputs that are contained outside of and within acidic phagolysosomal compartments. When followed by immunostaining for markers of OPCs and synapses in lightly fixed tissue, this approach enables the quantification of synapses engulfed by around 30-50 OPCs within a given experiment. In the second method, OPCs isolated from dissociated brain tissue are fixed, incubated with fluorescent antibodies against presynaptic proteins, and then analyzed by flow cytometry. This approach enables the quantification of presynaptic material within tens of thousands of OPCs in less than one week. These methods extend beyond the current imaging-based engulfment assays designed to quantify synaptic phagocytosis by brain-resident immune cells, microglia. Through the integration of these methods, the engulfment of synapses by OPCs can be rigorously quantified at both the individual and populational levels. With minor modifications, these approaches can be adapted to study synaptic phagocytosis by numerous glial cell types in the brain.

neuroscience↗

bioRxiv2023

Integrating extracellular vesicle and circulating cell-free DNA analysis on a single plasma aliquot from breast cancer patients improves the detection of HER2 positivity

BackgroundMulti-analyte liquid biopsies represents an emerging opportunity for non-invasive cancer assessment. We developed ONCE (ONe Aliquot for Circulating Elements), a novel multi-analytes liquid biopsy approach for the isolation of extracellular vesicles (EVs) and cell-free DNA (cfDNA) from a single aliquot of blood. MethodsWe assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining RNA and DNA signals on n=64 healthy donors (HD) and non-metastatic BrCa patients. Specifically, we investigated EVs-derived RNA (EV-RNA) and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Additionally, we utilized imaging flow cytometry to evaluate EVs as potential carriers of the HER2 protein. ResultsWestern blot analysis and immunocapture assay revealed that EVs-enriched proteins were detected at similar levels among the HER2+ and HER2- subtypes. Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, we observed HER2 protein on the surface of EVs isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EVs as companion analyte to cfDNA. ConclusionsThis data confirms the relevance of combining cfDNA and EV-RNA analytes for cancer assessment and supports the ONCE approach as a valuable tool for multi-analytes liquid biopsies clinical implementation.

cancer biology↗

bioRxiv2022

Oligodendrocyte precursor cells engulf synaptic inputs in an experience- and microglia-dependent manner

Oligodendrocyte precursor cells (OPCs) are a highly proliferative class of non-neuronal progenitors that largely give rise to myelinating oligodendrocytes. Although OPCs persist across the lifespan, their functions beyond oligodendrogenesis remain to be fully characterized. Here, we show that OPCs contribute to neural circuit remodeling by internalizing presynaptic thalamocortical inputs in both the developing and adult mouse visual cortex. Inputs internalized by OPCs localize to lysosomal compartments, consistent with OPC engulfment of synapses occuring through phagocytosis. We further show that engulfment by OPCs is heightened during experience-dependent plasticity, and that this experience-dependent increase in engulfment requires microglia. These data identify a new function for OPCs beyond the generation of oligodendrocytes and reveal that distinct non-neuronal populations collaborate to modulate synaptic connectivity.

neuroscience↗

bioRxiv2021

Harnessing gene-gene interactions via an RNA-Sequencing network analysis framework improves precision medicine prediction in rheumatoid arthritis

The study of gene-gene interactions in RNA-Sequencing (RNA-Seq) data has traditionally been hard owing the large number of genes detectable by Next-Generation Sequencing (NGS). However, differential gene-gene pairs can inform our understanding of biological processes and yield improved prediction models. Here, we utilised four well curated pathway repositories obtaining 10,537 experimentally evaluated gene-gene interactions. We then extracted specific gene-gene interaction networks in synovial RNA-Seq to characterise histologically-defined pathotypes in early rheumatoid arthritis patients. Specific gene-gene networks were also leveraged to predict response to methotrexate-based disease-modifying anti-rheumatic drug (DMARD) therapy in the Pathobiology of Early Arthritis Cohort (PEAC). We statistically evaluated the differential interactions identified within each network using robust linear regression models, and the ability to predict response was evaluated by receiver operating characteristic (ROC) curve analysis. The analysis comparing different histological pathotypes showed a coherent molecular signature matching the histological changes and highlighting novel pathotype-specific gene interactions and mechanisms. Analysis of responders vs non-responders revealed higher expression of apoptosis regulating gene-gene interactions in patients with good response to conventional synthetic DMARD. Detailed analysis of interactions between pairs of network-linked genes identified the SOCS2/STAT2 ratio as predictive of treatment success, improving ROC area under curve (AUC) from 0.62 to 0.78. In conclusions, we demonstrate a novel, powerful method which harnesses gene interaction networks for leveraging biologically relevant gene-gene interactions leading to improved models for predicting treatment response.

genomics↗

bioRxiv2021

The cytokine receptor Fn14 regulates neuronal transcription during development and brain function in the adult

Cytokine signaling pathways that promote inflammation in peripheral tissues are repurposed to coordinate the refinement of synaptic connections in the developing brain. However, the downstream mechanisms through which these pathways mediate neural circuit maturation remain to be fully defined. Here, we demonstrate that Fn14, a cytokine receptor that promotes inflammation outside of the central nervous system, shapes the transcriptional profiles and chromatin landscapes of neurons in the developing brain. Single-nucleus RNA-sequencing revealed hundreds of misregulated genes in the thalamocortical neurons of the visual thalami of mice lacking either Fn14 or its microglial derived cytokine ligand TWEAK, including genes encoding proteins with critical roles in synaptic function, histone modification, and chromatin remodeling. Whole-genome analysis uncovered significant alterations in chromatin accessibility in the brains of mice lacking Fn14 or in wild-type mice following microglial depletion, and chromatin changes due to both manipulations were enriched near genes encoding regulators of synaptic function. Loss of microglia also led to the retention of excess synapses, suggesting that microglia may link modifications in neuronal chromatin to the functional refinement of neural circuits. Consistent with Fn14 shaping brain function beyond the visual system, Fn14 knockout mice displayed impairments in memory task proficiency as well as heightened sensitivity to pharmacologically induced seizures. Taken together, these results define a previously undescribed interaction between microglia, cytokine signaling, and the neuronal epigenome that is likely to contribute to neural circuit refinement and function in the brain.

neuroscience↗

bioRxiv2020

MiREDiBase: a manually curated database of editing events in microRNAs

MicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase.

bioinformatics↗

bioRxiv2020

Divergent use of metabolic fluxes in breast cancer metastasis

Breast cancers can metastasize to many organs. But how do disseminated cells from a primary tumor adapt to distal tissues? Here we combined metabolomics, flux measurements, and mathematical modeling to study metabolic fluxes in breast cancer cells adapted to home to different organs. We found that lung-homing cells maintain high glycolytic flux despite low levels of glycolytic intermediates, by constitutively activating a pathway sink into lactate. Their distinct behavior--a strong Warburg effect--has a gene expression signature: a high ratio of lactate dehydrogenase to pyruvate dehydrogenase gene expression, which also correlates with lung metastases in patients with breast cancer. Surprisingly, this strong Warburg effect does not necessarily increase cellular growth rate, suggesting that lactate secretion may be a trait under selection in lung metastasis. Our results stress that metabolic fluxes may not correlate with metabolic intermediates, a finding relevant for metastatic tropism.

cancer biology↗

bioRxiv2020

PHENSIM: Phenotype Simulator

Despite the unprecedented growth in our understanding of cell biology, it still remains challenging to connect it to experimental data obtained with cells and tissues physiopathological status under precise circumstances. This knowledge gap often results in difficulties in designing validation experiments, which are usually labor-intensive, expensive to perform, and hard to interpret. Here we propose PHENSIM, a computational tool using a systems biology approach in order to simulate how cell phenotypes are affected by the activation/inhibition of one or multiple biomolecules and does so by exploiting signaling pathways. Our tools applications include predicting the outcome of drug administration, knockdown experiments, gene transduction, and exposure to exosomal cargo. Importantly, PHENSIM enables the user to make inferences on well-defined cell lines and includes pathway maps from three different model organisms. To assess our approachs reliability, we built a benchmark from transcriptomics data gathered from NCBI GEO and performed four case studies on known biological experiments. Our results show high prediction accuracy, thus highlighting the capabilities of this methodology. PHENSIM standalone Java application is available at https://github.com/alaimos/phensim, along with all data and source codes for benchmarking. A web-based user interface is accessible at https://phensim.atlas.dmi.unict.it/.

bioinformatics↗