Biology subjects

Rusconi, F.

Publications and source records attributed to Rusconi, F..

7 recordsLinked to original sources

bioRxiv2026

Epigenetic evolution of colorectal cancer and its microenvironment reveals new vulnerabilities

Epigenetics is central to tumorigenesis, but the co-evolution of the cancer epigenome and its microenvironment is severely understudied. Here, we measure chromatin accessibility and transcriptome, at single cell resolution, of a set of normal colon, primary colorectal cancers and metastases, and identify recurrent epigenetic alterations in tumour cells. We also found that the normal epithelium adjacent to the cancer had recurrent epigenetic alterations associated with inflammatory programs that were partially shared with tumour cells. Distinct tumour-intrinsic transcription factor binding programs were associated with differential abundance of malignant stroma cell identities. We then leveraged matched patient-derived organoids, to assess the functional impact of the most recurrent epigenetic alterations on cancer cell viability, using CRISPR interference. We found a set of epigenetic-driven cancer dependencies, related to developmental reprogramming and cellular stress resilience, representing new potential therapeutic targets.

cancer biology↗

bioRxiv2025

Cell-autonomous mitochondrial calcium flux governs oligodendrocyte regeneration

Oligodendrocyte (OL) lineage cells drive central nervous system remyelination, yet the intrinsic mechanisms that define their regenerative potential remain unclear. We identify spontaneous, cell-autonomous intracellular Ca2+ signaling as a critical mechanism regulating OL regeneration following demyelination. Longitudinal in vivo imaging and ex vivo recordings reveal that Ca2+ signaling arises intrinsically within OL lineage cells after demyelination, and occurs independently from neuronal or behavioral activity. Mechanistically, mitochondrial Ca2+ flux sustains intracellular Ca2+ signals in oligodendroglia, and its in vivo disruption impairs oligodendrocyte precursor cell (OPC) proliferation, differentiation, and repopulation at the lesion site. Conversely, enhancing oligodendroglial Ca2+ signaling in vivo using chemogenetics stimulates lineage expansion and differentiation. In primary human OPC cultures, modulation of mitochondrial Ca2+ flux similarly reduces proliferation, indicating a conserved role for this pathway across species. These findings identify mitochondrial Ca2+ flux as a central driver of the oligodendroglial regeneration and a potential therapeutic target in demyelinating diseases.

neuroscience↗

bioRxiv2024

Inner membrane protein OutB is covalently attached to peptidoglycan in the γ-proteobacterium Dickeya dadantii

Gram-negative bacteria possess a multilayered envelope comprising an inner membrane (IM), a thin peptidoglycan (PG) layer, and an outer membrane (OM). In Escherichia coli and certain other {gamma}-proteobacteria, Braun lipoprotein (Lpp) covalently tethers the OM to PG. Only a few other OM proteins have been found to be covalently linked to PG in Gram-negative bacteria. Here, we showed that in the phytopathogenic {gamma}-proteobacterium Dickeya dadantii, an IM protein, OutB, is covalently attached to PG, thereby tethering itself and the associated type 2 secretion system to the cell wall. In contrast to Lpp, OutB reaches the PG layer from the IM side. By modifying the length of Lpp, which would displace the PG layer in the periplasm, we found that the elongated Lpp+21 improved OutB attachment to PG, whereas the shortened Lpp{Delta}21 reduced it. We showed that two L,D-transpeptidases, Ldt03 and Ldt84, tether Lpp and OutB to PG by the same catalytic mechanism involving the formation of an amide bond between their C-terminal lysine and the stem peptide. Ldt03 and Ldt84, each display substrate specificity for the type of peptide stem and preferentially cross-link Lpp to monomeric and dimeric muropeptide, respectively. The C-terminal Lpp-like box of OutB is almost identical to that of Lpp; it tolerates substantial amino acid substitutions and allows PG-tethering of a bona fide periplasmic protein. Thus, it seems possible that the repertoire of periplasmic and membrane proteins tethered to PG may be more extensive than currently assumed.

microbiology↗

bioRxiv2023

Peptidoglycan-tethered and free forms of the Braun lipoprotein are in dynamic equilibrium in Escherichia coli

Peptidoglycan (PG) is a giant macromolecule that completely surrounds bacterial cells and prevents lysis in hypo-osmotic environments. This net-like macromolecule is made of glycan strands linked to each other by two types of transpeptidases that form either 4[->]3 (PBPs) or 3[->]3 (LDTs) cross-links. Previously, we devised a heavy isotope-based PG full labeling method coupled to mass spectrometry to determine the mode of insertion of new-subunits into the expanding PG network (Atze et al., 2022). We showed that PG polymerization operates according to different modes for the formation of the septum and of the lateral cell walls, as well as for bacterial growth in the presence or absence of {beta}-lactams in engineered strains that can exclusively rely on LDTs for PG cross-linking when drugs are present. Here, we apply our method to the resolution of the kinetics of the reactions leading to the covalent tethering of the Braun lipoprotein (Lpp) to PG and the subsequent hydrolysis of that same covalent link. We find that Lpp and disaccharide-peptide subunits are independently incorporated into the expanding lateral cell walls. Newly synthesized septum PG appears to contain small amounts of tethered Lpp. LDTs did mediate intense shuffling of Lpp between PG stems leading to a dynamic equilibrium between the PG-tethered and free forms of Lpp.

microbiology↗

bioRxiv2022

Versatile and automated workflow for the analysis of oligodendroglial calcium signals in preclinical mouse models of myelin repair

Intracellular Ca2+ signals of oligodendroglia, the myelin-forming cells of the central nervous system, regulate vital cellular processes including myelination. However, studies on oligodendroglia Ca2+ signal dynamics are still scarce, especially during myelin repair, and there are no software solutions to properly analyze the unique Ca2+ signal characteristics in these cells. Here, we provide a comprehensive experimental and analytical workflow to acquire and analyze Ca2+ imaging data of oligodendroglia at the population and single-cell levels in preclinical mouse models of myelin repair. We report diverse ex vivo and in vivo experimental protocols to obtain reproducible Ca2+ imaging data from oligodendroglia in demyelinated lesions. Importantly, we provide an analytical pipeline containing two free, open source and cross-platform software programs, Occam and post-prOccam, that enable the fully automated analysis of one- and two-photon Ca2+ imaging datasets from oligodendroglia obtained by either ex vivo or in vivo Ca2+ imaging techniques. This versatile and accessible experimental and analytical framework, which revealed significant but uncorrelated spontaneous Ca2+ activity in oligodendroglia inside demyelinated lesions, should facilitate the elucidation of Ca2+-mediated mechanisms underlying remyelination and therefore help to accelerate the development of therapeutic strategies for the many myelin-related disorders, such as multiple sclerosis.

neuroscience↗

bioRxiv2021

Heavy isotope labeling and mass spectrometry reveal unexpected remodeling of bacterial cell wall expansion in response to drugs

Antibiotics of the {beta}-lactam (penicillin) family inactivate target enzymes called D,D-transpeptidases or penicillin-binding proteins (PBPs) that catalyze the last cross-linking step of peptidoglycan synthesis. The resulting net-like macromolecule is the essential component of bacterial cell walls that sustains the osmotic pressure of the cytoplasm. In Escherichia coli, bypass of PBPs by the YcbB L,D-transpeptidase leads to resistance to these drugs. We developed a new method based on heavy isotope labeling and mass spectrometry to elucidate PBP- and YcbB-mediated peptidoglycan polymerization. PBPs and YcbB similarly participated in single-strand insertion of glycan chains into the expanding bacterial side wall. This absence of any transpeptidase-specific signature suggests that the peptidoglycan expansion mode is determined by other components of polymerization complexes. YcbB did mediate {beta}-lactam resistance by insertion of multiple strands that were exclusively cross-linked to existing tripeptide-containing acceptors. We propose that this unprecedented mode of polymerization depends upon accumulation of linear glycan chains due to PBP inactivation, formation of tripeptides due to cleavage of existing cross-links by a {beta}-lactam-insensitive endopeptidase, and concerted cross-linking by YcbB.

biochemistry↗

bioRxiv2021

Lung organoids and microplastic fibers: a new exposure model for emerging contaminants

BackgroundThree-dimensional (3D) structured organoids are the most advanced in vitro models for studying human health effects, but they have been applied only once to evaluate the biological effects associated with microplastic exposure. Fibers from synthetic clothes and fabrics are a major source of airborne microplastics, and their release from dryer machines is still poorly understood. ObjectivesIn this study, we aimed to establish an in vitro organoid model of human lung epithelial cells to evaluate its suitability for studying the effects of airborne microplastic contamination on humans. Furthermore, we aimed to characterize the microplastic fibers (MPFs) released in the exhaust filter of a household dryer and to test their interactions and inflammatory effects on the established lung organoids. MethodsThe polyester fibers emitted from the drying of synthetic fabrics were collected. Morphological characterization of the fibers released into the air filter was performed by optical microscopy and scanning electron microscopy (SEM)/energy dispersive x-ray spectroscopy (EDS). The organoids were exposed to various MPF concentrations (1, 10, and 50 mg L-1) and analyzed by optical microscopy, SEM, and confocal microscopy. Gene expression analysis of lung-specific genes, inflammatory cytokines, and oxidative stress-related genes was achieved by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). ResultsWe successfully cultured organoids with lung-specific genes. The presence of MPFs did not inhibit organoid growth, but polarized cell growth was observed along the fibers. Moreover, the MPFs did not cause inflammation or oxidative stress. Interestingly, the MPFs were coated with a cellular layer, resulting in the inclusion of fibers in the organoid. DiscussionThis work could have potential long-term implications regarding lung epithelial cells undergoing repair. This preliminary exposure study using human lung organoids could form the basis for further research regarding the toxicological assessment of emerging contaminants such as micro- or nanoplastics.

molecular biology↗