Biology subjects

Russo, C.

Publications and source records attributed to Russo, C..

10 recordsLinked to original sources

bioRxiv2026

An in vitro platform with self-sustaining trans-epithelial oxygen gradient to model intestinal barrier function modulation

In vitro models of the small intestine frequently neglect the role of physiological oxygen tension in drug absorption studies. To meet the throughput demands of preclinical drug development while maintaining compatibility with standard permeability assays, we engineered a new technology, termed Gradient-on-Platform. This system enables the establishment of physiologically relevant oxygen gradients across intestinal epithelium in vitro models by leveraging Caco-2 cells metabolic oxygen consumption. In this work, we demonstrated that exposure to physiomimetic oxygen conditions modulates epithelial barrier function, mitigating the excessively tight Caco-2 phenotype typically observed under conventional aerobic cultures, which leads to underestimation of drug bioavailability in vitro. Indeed, while complete hypoxia disrupts epithelial barriers, oxygen gradients drive Caco-2 TEER toward values more consistent with ex vivo measurements and result in a 3-fold increase in paracellular permeability compared to fully aerobic controls. The incorporation of physiologically relevant oxygen gradients into a scalable, assay-compatible platform could represent a pivotal step toward improving the predictive accuracy of in vitro preclinical drug absorption assays.

bioengineering↗

bioRxiv2026

p63 and p73 regulate convergent and factor-specific transcriptional programs in cutaneous squamous cell carcinoma

Aberrant transcriptional regulation is a defining feature of squamous cell carcinoma (SCC), yet how lineage transcription factors coordinate shared and factor-specific oncogenic programs remains poorly understood. Although TP63 (p63) is frequently amplified in SCC, the contribution of its paralog TP73 (p73) has remained unclear. Here we show that p73, together with p63, is upregulated in skin SCC and is required for tumorigenesis. Mechanistically, p63 and p73 form heteromeric complexes and co-occupy distal enhancer elements, establishing a shared chromatin regulatory framework. Integration of chromatin and transcriptomic profiling reveals that this common enhancer landscape supports both convergent and divergent transcriptional outputs. Both factors cooperatively sustain core proliferation but also exert regulatory biases, with p63 preferentially reinforcing epithelial lineage circuits and p73 contributing to DNA replication and stress-associated pathways. Among shared downstream targets, p63/p73 co-regulation of multiple epidermal growth factor receptor (EGFR) ligands establishes a feed-forward signaling module that amplifies mitogenic signaling. Amphiregulin emerges as a dominant functional mediator, and its depletion phenocopies key aspects of p63/p73 loss, including impaired proliferation and tumor formation. Together, these findings support a model in which shared enhancer occupancy by p63 and p73 drives cooperative and factor-specific transcriptional programs, linking chromatin regulation to signaling and tumor maintenance.

molecular biology↗

bioRxiv2025

The globally dispersed sun-coral species is _Tubastraea coccinea_ (Cnidaria: Anthozoa)

Species of the genus Tubastraea (sun corals) have dispersed globally over recent decades, but morphological trait identification has led to taxonomic confusion, with multiple authors proposing conflicting species identifications due to high morphological plasticity and overlapping diagnostic traits. We combined global-scale molecular phylogenetics with chromosome-level genome assemblies to resolve this taxonomic issue. Using mitochondrial and nuclear markers from 287 specimens across five ocean regions, including type localities in Bora Bora (T. coccinea) and Galapagos (T. tagusensis), we reconstructed phylogenetic relationships and inferred demographic history through approximate Bayesian computation. We also generated high-quality, chromosome-level genome assemblies for three morphologically distinct morphotypes from the Brazilian coastline. Phylogenetic and species delimitation analyses revealed two well-supported clades: a small, geographically restricted T. tagusensis clade confined to the Galapagos Islands, and a large cosmopolitan clade containing all worldwide samples, including T. coccinea from its type locality. Chromosome-level genomic analyses confirmed that the three morpho-types represent a single species, sharing a triploid karyotype of 14 chromosomes with extensive synteny and gene-tree discordance consistent with incomplete lineage sorting. Dispersed-route analyses identified the Centralwestern Pacific as the ancestral source, with at least three independent, humanmediated colonization events establishing populations in the Southwestern Atlantic, Gulf of Mexico, and Western Pacific. However, preliminary analysis suggests a Galapagos (Southeastern Pacific) origin rather than Centralwestern Pacific for the T. tagusensis and T. coccinea cluster. Our results definitively establish Tubastraea coccinea as the cosmopolitan species responsible for global dissemination, while T. tagusensis is endemic to the Galapagos and not involved in the worldwide dis-persion.

genetics↗

bioRxiv2025

SUZ12-Nucleic Acid Interactions Constrain PRC2 Activity to Maintain Targeted Gene Silencing Essential to Diffuse Midline Glioma

Polycomb Repressive Complex 2 (PRC2) mediates transcriptional silencing through trimethylation of histone H3 at lysine 27 (H3K27me3), an epigenetic modification critical for development and frequently altered in cancer. Pediatric diffuse midline gliomas (DMGs) bearing the histone H3 K27M mutation exhibit global loss of H3K27me3 due to dominant inhibition of PRC2 by the mutant histone. Despite widespread hypomethylation, focal retention of H3K27me3 persists, and tumor cells maintain dependency on residual PRC2 activity for proliferation. The molecular basis underlying this residual enzymatic function and its regulation remain poorly defined. To address this mechanism, we investigated the role of SUZ12, the architectural core of PRC2 that facilitates interactions with accessory subunits. We identified the SUZ12 N-terminal region as a regulatory domain that constrains PRC2 catalytic activity through transient interactions with nucleic acids, thereby limiting non-specific chromatin engagement. Expression of a truncated SUZ12 variant retaining the catalytic VEFS domain, but lacking the nucleic acid-binding regulatory elements, led to widespread H3K27 hypermethylation, displacement of canonical PRC1 complexes, disruption of chromatin architecture, and impaired H3 K27M glioma cell growth in vitro and in vivo. Biochemical analyses revealed a SUZ12 N-terminal domain that modulates PRC2 activity by promoting non-productive binding to nucleic acids, thus establishing a kinetic equilibrium essential for precise chromatin targeting. These findings redefine Polycomb specificity as a dynamic equilibrium between productive nucleosomal engagement and non-productive nucleic acid interactions, providing critical insights into PRC2 regulation and highlighting potential therapeutic vulnerabilities in PRC2-dependent cancers.

molecular biology↗

bioRxiv2025

Efficacy of DNA Methyltransferase Inhibitor Immune Priming Therapy in Combination with PD-1 Inhibitors to Treat High-Risk Pediatric Brain Tumors

BackgroundDespite intensive therapies, outcomes for high-risk pediatric brain tumors (PBTs) remain dismal, prompting the search for novel treatments. DNA methyltransferase inhibitors (DNMTi) have been shown to prime tumors to improve response to checkpoint inhibition. The aim of this study was to investigate the potential of decitabine (DAC), in combination with a PD-1 inhibitor, to improve survival in pediatric high-risk brain tumor models. MethodsAnalysis of human PBT datasets was performed to determine gene expression levels of immune cell associated markers. Tumor response to DAC, with or without a PD-1 inhibitor, was tested in murine models representing H3-wildtype diffuse intrinsic pontine glioma (DIPG), H3K27-mutant diffuse midline glioma (DMG), atypical teratoid rhabdoid tumor (ATRT), and medulloblastoma (MB). CyTOF analysis of allograft tumors was performed to characterize changes within the tumor microenvironment. ResultsAnalysis of PBT subtypes revealed heterogeneous expression of immune cell markers, checkpoint receptors, and MHC molecules. DAC treatment decreased DNA methylation and increased neoantigen expression in human and mouse tumor cells. DAC alone or in combination with a PD-1 inhibitor resulted in prolonged survival in syngeneic mouse models of DIPG and ATRT but not DMG and MB models. CyTOF analysis of mouse tumors revealed changes in local immune cell infiltration upon combination treatment. ConclusionsDAC in combination with a PD-1 inhibitor can alter the immune microenvironment in mouse tumor models. Changes were observed in H3-wildtype DIPG and ATRT models, suggesting that certain tumor subtypes may respond to checkpoint blockade after immune augmentation with DNMTi. Key PointsO_LIPBTs show heterogenous expression of immune cell infiltrates C_LIO_LIDAC or DAC plus a PD-1 inhibitor shows extension of survival in H3-wildtype DIPG and ATRT mouse models C_LIO_LIMyeloid-derived suppressor cell abundance could be a major contributing factor to treatment response C_LI Importance of the StudyChildren with high-risk PBTs face dismal outcomes. Immune checkpoint inhibitor (ICI) successes have been demonstrated in a variety of adult malignancies; however, such beneficial outcomes have not been realized in PBTs. Here we investigate single and combination treatment of DNMTi and PD-1 checkpoint inhibition in syngeneic mouse models of high-risk PBTs. Our results suggest that some H3-wildtype DIPG and ATRT tumor types may be responsive to checkpoint therapy post immunomodulation and warrant further investigation.

immunology↗

bioRxiv2025

Foam film vitrification for cryo-EM

Electron cryomicroscopy (cryo-EM) has revolutionised structural biology, enhancing applicability, size limits and speed. Despite these successes, cryo-EM sample preparation remains a major bottleneck for routinely achieving high-resolution structures through single particle analysis. Challenges such as inconsistent ice thicknesses, air-water interface interactions and preferred particle orientation persist. Here, we introduce a blot-free vitrification method that uses free-standing surfactant-stabilised foam films to address some of these issues. The method achieves uniform ice thicknesses, enables thickness control of the foam film prior to vitrification, and for some specimens enhances orientation distribution efficiency. Furthermore, it reduces particle adsorption to carbon foil on the specimen support. The method simplifies cryo-EM specimen preparation, offering improved control over ice thickness and particle orientation, to help streamline and accelerate structure determination.

biophysics↗

bioRxiv2025

Fractal and Machine Learning analyses of MALDI-TOF Mass Spectrometry data in glioblastoma

Data pre-processing is a critical step in the analysis of MALDI-TOF MS spectra for machine learning applications, typically involving steps such as spectra trimming, baseline correction, smoothing, transformation, and peak picking or spectral binning. While traditional approaches focus on protein/peptide peaks as features, this study explores a novel method of feature extraction by treating MALDI-TOF spectra as time-series data. This study investigates the use of computational fractal-based analysis to assess the complexity of MALDI-TOF spectra. Fractal analysis, previously successful in glioblastoma diagnosis using MRI, was applied here to proteomics data for the first time. By treating each MALDI spectrum as a time series and calculating its fractal dimension using various algorithms, machine learning models were trained to differentiate between glioblastoma patients and healthy controls. We demonstrate that fractals are sufficient to obtain accurate models for glioblastoma diagnosis, despite still underperforming when compared to the traditional feature extraction method. We also show that fractals can be used as support features to increase model performance. This work highlights the potential and limitations of fractal analysis in proteomics, offering a new perspective for disease diagnosis and broadening the applicability of time-series data analysis in mass spectrometry.

bioinformatics↗

bioRxiv2023

H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs

Polycomb Repressive Complex 2 (PRC2)-mediated histone H3K27 tri-methylation (H3K27me3) recruits canonical PRC1 (cPRC1) to maintain heterochromatin. In early development, polycomb-regulated genes are connected through long-range 3D interactions which resolve upon differentiation. Here, we report that polycomb looping is controlled by H3K27me3 spreading and regulates target gene silencing and cell fate specification. Using glioma-derived H3 Lys-27-Met (H3K27M) mutations as tools to restrict H3K27me3 deposition, we show that H3K27me3 confinement concentrates the chromatin pool of cPRC1, resulting in heightened 3D interactions mirroring chromatin architecture of pluripotency, and stringent gene repression that maintains cells in progenitor states to facilitate tumor development. Conversely, H3K27me3 spread in pluripotent stem cells, following neural differentiation or loss of the H3K36 methyltransferase NSD1, dilutes cPRC1 concentration and dissolves polycomb loops. These results identify the regulatory principles and disease implications of polycomb looping and nominate histone modification-guided distribution of reader complexes as an important mechanism for nuclear compartment organization. Highlights{square} The confinement of H3K27me3 at PRC2 nucleation sites without its spreading correlates with increased 3D chromatin interactions. {square}The H3K27M oncohistone concentrates canonical PRC1 that anchors chromatin loop interactions in gliomas, silencing developmental programs. {square}Stem and progenitor cells require factors promoting H3K27me3 confinement, including H3K36me2, to maintain cPRC1 loop architecture. {square}The cPRC1-H3K27me3 interaction is a targetable driver of aberrant self-renewal in tumor cells.

molecular biology↗

bioRxiv2020

Advanced computational and statistical multiparametric analysis of Susceptibility-Weighted Imaging to characterize gliomas and brain metastases.

Susceptibility-weighted imaging (SWI) is a technique useful for evaluation of the internal structures of brain tumors, including microvasculature and microbleeds. Intratumoral patterns of magnetic susceptibility can be quantified by means of fractal analysis. Here, we propose a radiomics methodological pipeline to merge advanced fractal-based computational modelling with statistical analysis to objectively characterize the fingerprint of gliomas and brain metastases. Forty-seven patients with glioma (grades II-IV, according to the WHO 2016 classification system) and fourteen with brain metastases underwent 3 Tesla MRI using a SWI protocol. All images underwent computational analysis aimed to quantify three Euclidean parameters (related to tumor and SWI volume) and five fractal-based parameters (related to the pixel distribution and geometrical complexity of the SWI patterns). Principal components analysis, linear and quadratic discriminant analysis, K-nearest neighbor and support vector machine methods were used to discriminate between tumor types. The combination of parameters offered an objective evaluation of the SWI pattern in gliomas and brain metastases. The model accurately predicted 88% of glioblastoma, according to the quantification of intratumoral SWI features, failing to discriminate the other types. SWI is not normally used to classify brain tumors, however fractal-based multi-parametric computational analysis can be used to characterize intratumoral SWI patterns to objectively quantify tumors-related features. Specific parameters still have to be identified to provide completely automatic computerized differential diagnosis.

neuroscience↗

bioRxiv2020

Effects of C-peptide replacement therapy on bone microarchitecture parameters in streptozotocin-diabetic rats.

Pathological pathways involved in the development of diabetic complications are still unclear. Several studies suggested a pathogenic role of C-peptide deficiency in vascular and neuropathic complications. However, to date, the role of C-peptide on diabetes-related bone loss has not been investigated. The objective of this study was to test the effects of a 6-week regimen of rat C-peptide infusion on bone by combining micro-CT imaging with histological testing. Twenty-three, four-month-old male Wistar rats were randomly divided into three groups: Normal control group; Sham diabetic control group; Diabetic plus C-peptide group. Diabetes was induced by injection of streptozotocin. Rat C-peptide was delivered via subcutaneously osmopumps. We assessed several trabecular microarchitectural parameters and cellular and matrix proteins in bone tissue sections. At the end of the study, both the normal control and diabetic plus C-peptide groups had a higher tibia weight than the diabetic control group (p = 0.05 and p = 0.02, respectively). C-peptide levels significantly and positively correlated with the trabecular thickness (r= 0.45, p=0.08) and negatively with structure model index (r= -0.40, p=0.09). Furthermore, it positively correlated with one of the histological assessments (i.e. PLIN1 score; p=0.02). Micro-CT evaluation showed significant inter-group differences in trabecular thickness (p=0.02), trabecular space (p = 0.05) and cross-sectional thickness (p=0.05). Diabetic plus C-peptide group showed a higher trabecular thickness (p<0.001), cross-sectional thickness (p=0.03) and a lower trabecular space (p=0.05) than the normal control group. Both the normal control and diabetic plus C-peptide groups had more Runx-2 and PLIN1 positive cells in comparison to the diabetic control group (p = 0.045 and p = 0.034). For the first time we demonstrated that the diabetic rats receiving rat C-peptide had higher quality of trabecular bone, than diabetic rats not receiving it. C-peptide could have a role in the prevention of diabetes-related bone loss.

systems biology↗