Biology subjects

De Simone, M.

Publications and source records attributed to De Simone, M..

6 recordsLinked to original sources

bioRxiv2025

MagPiezo: a Magnetogenetic Platform for Remote Activation of Endogenous Piezo1 Channels in Endothelial Cells

This work introduces MagPiezo, a novel magnetogenetic platform designed to enable remote and targeted manipulation of endogenous Piezo1 channels without genetic modification. MagPiezo integrates a custom-built magnetic applicator and 19 nm octahedral mixed ferrite nanoparticles (MFs) with enhanced magnetocrystalline anisotropy, engineered to selectively target Piezo1 channels. The application of a low intensity (< 40 mT), low frequency (1 Hz) magnetic field is sufficient to generate wireless torque forces in the piconewton range capable of gating Piezo1 channels in vitro. Remarkably, applying MagPiezo for short times (< 1 h) induces robust responses in endothelial cells, including calcium influx, cytoskeletal reorganization and transcriptional activation. Unlike other magnetogenetic tools, MagPiezo avoids the need to assemble the magnetic nanoparticles (MNPs) into bigger beads to reach the opening threshold and does not need to genetically engineer Piezo1 channels. Moreover, it uses low magnetic field intensities and frequencies, enhancing its potential for in vivo translation. Therefore, MagPiezo is a powerful platform for manipulating Piezo1 channels and dissecting mechanotransduction events in vascular biology, paving the way for new strategies to modulate mechanoreceptors both in vitro and in vivo.

bioengineering↗

bioRxiv2025

Promoter-centric gene regulation in drug-resistant cancer

In eukaryotic cells, gene-distal regulatory elements (REs) facilitate long-range gene regulation, ensuring cell type-specific transcriptional programs. This mechanism is frequently disrupted in cancer, often driven by transcription factors (TFs) that serve as targets for cancer therapy. However, targeting these TFs can lead to acquired resistance mechanisms that are not fully understood. We demonstrate that mesothelioma cancer cells, dependent on the oncogenic driver TF family TEAD, develop resistance to a pan-TEAD inhibitor and revert to an evolutionarily ancient, promoter-centric gene regulatory mechanism to recover gene expression following TEAD inhibition. Base-pair-resolution 3D chromatin conformation mapping reveals that RE-promoter interactions are disrupted in resistant cells, despite epigenetic and transcriptomic recovery. Mechanistically, in resistant cells, TF complexes, including resistance-specific FOSL1 and KLF4, preferentially bind and enhance promoter activity to recover gene expression, rendering distal REs dispensable. Our findings highlight promoter elements and promoter-specific TFs as potential therapeutic targets using a model of drug-resistant cancer.

cancer biology↗

bioRxiv2024

G-CSF and IL-6 drive myeloid dysregulation during severe viral infection

Dysregulated myeloid states are associated with disease severity in both sepsis and COVID-19. However, their relevance in non-COVID-19 viral infection, the factors driving their induction, and their role in tissue injury remain poorly understood. We performed a meta-analysis of 1,622,180 myeloid cells from 890 COVID-19 or sepsis patients and controls across 19 published blood scRNA-seq datasets, which revealed severity-associated gene programs in both neutrophils and monocytes pointing to emergency myelopoiesis (EM). Using published bulk transcriptional data from 562 individuals with non-COVID-19 viral disease, we show that these signatures are similarly upregulated during severe influenza and RSV infection. Analysis of transcriptional and proteomic responses in tocilizumab-treated COVID-19 patients show that IL-6 signaling blockade results in a partial reduction of EM signatures and a compensatory increase in the growth factor G-CSF. Using a cellular model of human myelopoiesis, we show that both IL-6 and G-CSF stimulate the production of myeloid cells that express EM signatures in vitro. Using a mouse model of severe influenza infection, we demonstrate the effect of IL-6 and G-CSF signaling blockade on EM-associated myeloid cells, and highlight the opposing effects of EM-induced neutrophils and monocytes on tissue injury. Our study demonstrates the link between systemic cytokines and myeloid dysregulation during severe infection in humans, and highlights the cooperative role of IL-6 and G-CSF signaling in driving infection-induced myelopoiesis.

immunology↗

bioRxiv2024

Comparative Analysis of Commercial Single-Cell RNA Sequencing Technologies

This study evaluates ten commercially available single-cell RNA sequencing (scRNA-seq) approaches across four technology groups: Emulsion-based kits from 10x Genomics and Fluent Biosciences; Microwell-based kits from Becton Dickinson, Honeycomb Technologies and Singerlon Technologies; Combinatorial-indexing kits from Parse Biosciences and Scale Biosciences; and a Matrigel-based kit from Scipio Biosciences. Peripheral blood mononuclear cells (PBMCs) from a single donor were used to assess analytical performance. Key features such as sample compatibility, cost, and experimental duration were also compared. Notably, superior analytical performance was demonstrated by the Chromium Fixed RNA Profiling kit from 10x Genomics, which uniquely features probe hybridization for transcript detection. Additionally, the Rhapsody WTA kit from Becton Dickinson provided a cost-effective balance of performance and expense per cell. With a rich dataset of 218,154 cells, this work provides a basis for differentiating commercial scRNA-seq technologies, which is intended to facilitate the effective application and further methodological development of single cell transcriptomics.

molecular biology↗

bioRxiv2020

The enhancement of activity rescues the establishment of Mecp2 null neuronal phenotypes

Mecp2 deficiency, the gene responsible for Rett syndrome (RTT), affects brain maturation by impairing neuronal activity, transcription and morphology. These three elements are physiologically linked in a feed-forward cycle where neuronal activity modulates transcription and morphology to further increase network maturity. We hypothesized that the reduced activity displayed by maturing Mecp2 null neurons during development could perturb such cycle, sustaining an improper transcriptional program that, ultimately, impairs neuronal maturation. Accordingly, we show that by enhancing activity within an early time window, Ampakine redirects, in vitro, the development of null neuronal networks towards more physiological routes. Similarly, the administration of the drug to newborn null offspring delays the progression of symptoms, significantly prolonging life span. Our data highlights the role of altered neuronal activity during the establishment of Mecp2 null networks and the importance of such early defects to the typically poor maturity of RTT brain functions in adulthood. We propose the existence of an "early molecular phase" of Rett syndrome, a detailed description of which might disclose relevant targets for new rescue treatments.

neuroscience↗

bioRxiv2018

Single cell derived organoids capture the self-renewing subpopulations of metastatic ovarian cancer

High Grade Serous Ovarian cancer (HGSOC) is a major unmet need in oncology, due to its precocious dissemination and the lack of meaningful human models for the investigation of disease pathogenesis in a patient-specific manner. To overcome this roadblock, we present a new method to isolate and grow single cells directly from patients ascites, establishing the conditions for propagating them as single-cell derived ovarian cancer organoids (scOCOs). By single cell RNA sequencing (scRNAseq) we define the cellular composition of metastatic ascites and trace its propagation in 2D and 3D culture paradigms, finding that scOCOs retain and amplify key subpopulations from the original patients samples and recapitulate features of the original metastasis that do not emerge from classical 2D culture, including retention of individual patients specificities. By enabling the enrichment of uniquely informative cell subpopulations from HGSOC metastasis and the clonal interrogation of their diversity at the functional and molecular level, this method transforms the prospects of precision oncology for ovarian cancer.

cancer biology↗