Biology subjects

Donnarumma, F.

Publications and source records attributed to Donnarumma, F..

11 recordsLinked to original sources

bioRxiv2026

A multilayered in silico analysis links UHRF1, DNA methylation and developmental chromatin memory to lineage-dependent prognosis in gastric, renal and adrenal cancers

Aberrant DNA methylation is a hallmark of cancer, but its clinical interpretation remains debated. UHRF1, a key epigenetic adaptor for DNA methylation maintenance and chromatin bivalency regulation in embryonic stem cells, is frequently overexpressed yet shows context-dependent prognostic behaviour. By integrating bulk and single-cell transcriptomics, CpG-resolution methylation, developmental chromatin states, immune profiling and clinical outcomes across gastric (STAD), clear-cell renal (KIRC) and adrenal (ACC) carcinomas, we identified a four-class UHRF1-embryonic morphogenesis (UHRF1-EM) framework resolving this paradox. This axis revealed an inverse prognostic pattern: whilst across all three tumours EM-low and EM-high states mark better or worse prognosis, respectively, UHRF1-high levels associate with favourable outcome in STAD (UH-EML), and unfavourable in KIRC and ACC (UH-EMH). The classification proved reproducible and independently prognostic after adjustment for stage and molecular subtypes, outperforming existing classifiers and exceeding pathological stage in KIRC and ACC. Multivariable models incorporating UHRF1-EM yielded uniformly positive {Delta}C-indices. Hypermethylation associated with the UHRF1-EM axis was enriched at ESC bivalent developmental loci (EM and oncofoetal genes), but not at housekeeping cell-cycle sites. In STAD, this pattern was related to oncofoetal gene downregulation and best prognosis, whereas in KIRC and ACC it matched with gene-body/enhancer methylation, higher EM expression, immunosuppressive microenvironments and worst prognosis. Together, these findings establish the UHRF1-EM axis as a clinically robust molecular classifier and support a mechanistic model in which tumour-specific epigenetic engagement of developmental loci may contribute to the prognostic inversion, providing a foundation for further mechanistic experimental validation.

cancer biology↗

bioRxiv2025

Cardiolipin Remodeling as a Regulatory Switch in Osteogenesis: Insights from Multimodal Metabolic Imaging and Molecular Profiling

Cardiolipin (CL), a mitochondria-specific phospholipid, plays a fundamental role in respiratory chain organization and bioenergetic efficiency, yet its contribution to osteogenic differentiation is poorly defined. Here, we used a multimodal approach integrating untargeted LC-MS lipidomics, Raman spectroscopy, fluorescence lifetime imaging microscopy (FLIM), and structural imaging to investigate CL remodeling during human adipose-derived stem cell differentiation. Lipidomics revealed a selective enrichment of highly unsaturated CL species, accompanied by transcriptional upregulation of the cardiolipin biosynthetic and remodeling enzymes CDS1/2, PGS1, CRLS1, TAZ, and HADHA. Lipidomics also revealed a time-dependent increase in membrane-associated lipids including phosphatidylcholine (PC), serine, and phosphatidylinositol (PI). These lipids were implicated in supporting mitochondrial membrane expansion, oxidative phosphorylation, and signaling processes critical for osteoblast maturation. Spatial imaging techniques confirmed cardiolipin accumulation and redistribution in differentiated cells, while Raman-based direct classical least squares (DCLS) analysis provided label-free mapping of lipid species. Gene Ontology (GO) enrichment and protein-protein interaction network analysis further identified biological pathways related to bone remodeling, cardiolipin metabolism, and osteoblast-specific signaling. Fluorescence Lifetime Imaging Microscopy (FLIM) data revealed a metabolic shift from glycolysis to oxidative phosphorylation during differentiation, supported by structural and gene expression evidence. These changes temporally coincided with matrix mineralization and collagen organization, linking CL metabolism to both cellular bioenergetics and extracellular matrix production. Our findings identify cardiolipin remodeling as a metabolic checkpoint in osteogenesis and suggest that targeted modulation of CL pathways may provide new therapeutic strategies for enhancing bone regeneration.

cell biology↗

bioRxiv2025

Inferential planning in the frontal cortex

How the brain plans and maintains sequences of future actions remains a central question in systems neuroscience. Recent studies in the frontal cortex have revealed that multiple elements of a sequence are represented simultaneously in separable neural subspaces, challenging classical serial models of sequential planning. Here, we show that these representations emerge naturally under inferential planning in which sequential actions are inferred from sensory evidence and goals. Using a hierarchical generative model, we reproduce key neural phenomena observed in primate frontal cortex, including the simultaneous activation of multiple plan elements, the emergence of (almost) orthogonal memory subspaces, and their reuse across forward and backward sequence tasks. Our approach provides a mechanistic account of how probabilistic inference over control states gives rise to distributed and dynamic neural representations of plans. This framework not only unifies previously disparate findings on planning, working memory, and motor preparation, but also generates novel, testable predictions about the dynamics of active inference, the role of sensory subspaces, and the impact of uncertainty on sequence processing.

neuroscience↗

bioRxiv2025

Establishment and functional characterization of bovine endometrial epithelial organoids

Pre-implantation embryonic loss constitutes a major barrier to reproductive efficiency in livestock, yet the extrinsic determinants of embryonic survival remain poorly defined. Intra-organoid fluid (IOF) faithfully recapitulates native tissue secretions across multiple organ systems. We hypothesized that bovine endometrial epithelial organoids (BEEO) would produce IOF that mirrored in vivo uterine luminal fluid composition and extend embryo culture duration in vitro. We pursued three objectives: (a) establish and morphologically characterize BEEO, (b) define BEEO transcriptomic and secretory responses to estradiol (E2), medroxyprogesterone acetate (MPA), and interferon-tau (IFN{tau}), and (c) determine whether BEEO-derived IOF can support in vitro embryonic development beyond Day 8 (hatched blastocyst stage) under conventional culture conditions. BEEO were established from primary endometrial tissue (n=4) and maintained a stable epithelial phenotype through multiple passages. Transcriptomic profiling revealed robust responses to stimulation, with E2, MPA, and IFN{tau} inducing distinct gene expression programs consistent with in vivo effects. IOF metabolomic analysis confirmed hormone-dependent regulation of IOF secretory output, with E2+MPA (diestrus mimic) enhancing the production of metabolites implicated in conceptus development. Remarkably, IOF from diestrus mimic-stimulated BEEO, despite being diluted approximately seven-fold in PBS, maintained embryo survival rates comparable to optimized commercial medium, and exceeded PBS-only controls. These findings position BEEO as a physiologically relevant model for dissecting maternal-embryo interactions in vitro and identifying targets to improve fertility in cattle and other livestock.

cell biology↗

bioRxiv2025

Oviduct fluid metabolic regulation of embryonic genome methylation

Adverse maternal health and lifestyle during pregnancy can program offspring susceptibility to noncommunicable diseases in adulthood. Oviduct fluid facilitates key preimplantation milestones, including embryonic genome activation. However, the regulatory mechanisms governing oviduct fluid composition, and the developmental consequences of its disruption, remain unclear. Capitalizing on conserved dynamics between human and bovine embryonic genome activation, we first established and characterized bovine oviduct epithelial organoids as a model system. Organoids were then exposed to {Delta}-tetrahydrocannabinol (THC) and cannabidiol (CBD) to test the hypothesis that exocannabinoids alter intra-organoid fluid composition. Treatment altered the organoid transcriptome and intra-organoid fluid metabolome, notably elevating 5'-deoxyadenosine levels. Subsequent embryo culture with 5'-deoxyadenosine during embryonic genome activation resulted in aberrant DNA methylation patterning - independently of direct THC and CBD exposure. These findings identify a novel, indirect, mechanism by which maternal exposures disrupt embryonic development through changes in oviductal metabolite secretions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/659599v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@19ac750org.highwire.dtl.DTLVardef@935709org.highwire.dtl.DTLVardef@13723a8org.highwire.dtl.DTLVardef@105f473_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

cell biology↗

bioRxiv2025

Transcriptome-proteome profiling in Burkholderia thailandensis during the transition from exponential to stationary phase

Bacterial cells commonly exist in stationary phase, for instance within a host cell. Burkholderia thailandensis is closely related to, and a surrogate for highly pathogenic Burkholderia species. Understanding the molecular mechanisms that characterize the transition of B. thailandensis from exponential to stationary phases is critical to understanding responses to stress or nutrient limitation. We present here an integrated transcriptomic and proteomic analysis of gene and protein expression changes during entry into stationary phase. We identified 928 differentially expressed genes and 832 differentially expressed proteins. Genes encoding proteins involved in benzoate degradation and O-antigen nucleotide sugar biosynthesis were among the most highly upregulated in stationary phase, whereas processes such as translation and flagellar biosynthesis were downregulated. Proteins related to fatty acid degradation and butanoate metabolism accumulated along with proteins involved in synthesis of secondary metabolites. Markedly downregulated proteins included ribosomal proteins as well as the house-keeping iron-sulfur biogenesis proteins. An only modest correlation between transcriptome and proteome changes was seen, and the RpoS sigma factor was not significantly increased during early stationary phase; RpoS is typically abundant during stationary phase and critical for expression of stress-response genes. Our data therefore point to distinct adaptive mechanisms in B. thailandensis, including post-translational regulation.

microbiology↗

bioRxiv2021

Spatially resolved analysis of Pseudomonas aeruginosa biofilm proteomes measured by laser ablation sample transfer

Heterogeneity in the distribution of nutrients and O2 gradients during biofilm growth gives rise to changes in phenotype. There has been long term interest in identifying spatial differences during biofilm development including clues that identify chemical heterogeneity. Laser ablation sample transfer (LAST) allows site-specific sampling combined with label free proteomics to distinguish radially and axially resolved proteomes for Pseudomonas aeruginosa biofilms. Specifically, differential protein abundances on oxic vs. anoxic regions of a biofilm was observed by combining LAST with bottom up proteomics. This study reveals active metabolism in the anoxic region of the biofilm with respect to the oxic region in P. aeruginosa, an aerobe by nature. Protein abundance data related to cellular acclimations to chemical gradients include identification of glucose catabolizing proteins, high abundance of proteins from arginine and polyamine metabolism, and proteins that could also support virulence and environmental stress mediation on the anoxic region. Finally, this methodology requires only a few mm2 of biofilm area to identify hundreds of proteins.

microbiology↗

bioRxiv2020

Shared population-level dynamics in monkey premotor cortex during solo action, joint action and action observation

Studies of neural population dynamics of cell activity from monkey motor areas during reaching show that it mostly represents the generation and timing of motor behavior. We compared neural dynamics in dorsal premotor cortex (PMd) during the performance of a visuomotor task executed individually or cooperatively and during an observation task. In the visuomotor conditions, monkeys applied isometric forces on a joystick to guide a visual cursor in different directions, either alone or jointly with a conspecific. In the observation condition, they observed the cursors motion guided by the partner. We found that in PMd neural dynamics were widely shared across action execution and observation, with cursor motion directions more accurately discriminated than task types. This suggests that PMd encodes spatial aspects irrespective of specific behavioral demands. Furthermore, our results suggest that largest components of premotor population dynamics, which have previously been suggested to reflect a transformation from planning to movement execution, may rather reflect higher cognitive-motor processes, such as the covert representation of actions and goals shared across tasks that require movement and those that do not. HIGHLIGHTSO_LIIn PMd neural dynamics is shared across action execution and mere observation C_LIO_LITask directional features are more accurately discriminated than action types C_LIO_LISpatial aspects are encoded in PMd independently from specific behavioral demands C_LIO_LIPMd dynamics largely reflect higher cognitive-motor processes rather than strictly motor-related functions C_LI

neuroscience↗

bioRxiv2020

Hippocampal place cells encode global location but not changes in environmental connectivity in a 4-room navigation task

Flexible navigation relies on a cognitive map of space, thought to be implemented by hippocampal place cells: neurons that exhibit location-specific firing. In connected environments, optimal navigation requires keeping track of ones location and of the available connections between subspaces. We examined whether the dorsal CA1 place cells of rats encode environmental connectivity in four geometrically-identical boxes arranged in a square. Rats moved between boxes by pushing saloon-type doors that could be locked in one or both directions. While rats demonstrated knowledge of environmental connectivity, their place cells did not respond to connectivity changes, nor did they represent doorways differently from other locations. Importantly, place cells coded the space in a global frame, expressing minimal repetitive fields despite the repetitive geometry (global coding). These results suggest that CA1 place cells provide a spatial map that does not explicitly include connectivity.

neuroscience↗

bioRxiv2020

Multimodal Label-free Monitoring of Adipogenic Stem Cell Differentiation using Endogenous Optical Biomarkers

Stem cell-based therapies carry significant promise for treating human diseases. However, clinical translation of stem cell transplants for effective therapy requires precise non-destructive evaluation of the purity of stem cells with high sensitivity (< 0.001% of the number of cells). Here, we report a novel methodology using hyperspectral imaging (HSI) combined with spectral angle mapping (SAM)-based machine learning analysis to distinguish differentiating human adipose derived stem cells (hASCs) from control stem cells. The spectral signature of adipogenesis generated by the HSI method enabled identification of differentiated cells at single cell resolution. The label-free HSI method was compared with the standard methods such as Oil Red O staining, fluorescence microscopy, and qPCR that are routinely used to evaluate adipogenic differentiation of hASCs. Further, we performed Raman microscopy and multiphoton-based metabolic imaging to provide complimentary information for the functional imaging of the hASCs. Finally, the HSI method was validated using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) imaging of the stem cells. The study presented here demonstrates that multimodal imaging methods enable label-free identification of stem cell differentiation with high spatial and chemical resolution. This could provide a powerful tool to assess the safety and efficacy of stem cell-based regenerative therapies.

biophysics↗

bioRxiv2020

A framework to identify structured behavioral patterns within rodent spatial trajectories

Animal behavior is highly structured. Yet, structured behavioral patterns - or "statistical ethograms" - are not immediately apparent from the full spatiotemporal data that behavioral scientists usually collect. Here, we introduce a framework to quantitatively characterize rodent behavior during spatial (e.g., maze) navigation, in terms of movement building blocks or motor primitives. The hypothesis that we pursue is that rodent behavior is characterized by a small number of motor primitives, which are combined over time to produce open-ended movements. We assume motor primitives to be organized in terms of two sparsity principles: each movement is controlled using a limited subset of motor primitives (sparse superposition) and each primitive is active only for time-limited, time-contiguous portions of movements (sparse activity). We formalize this hypothesis using a sparse dictionary learning method, which we use to extract motor primitives from rodent position and velocity data collected during spatial navigation, and successively to reconstruct past trajectories and predict novel ones. Three main results validate our approach. First, rodent behavioral trajectories are robustly reconstructed from incomplete data, performing better than approaches based on standard dimensionality reduction methods, such as principal component analysis, or single sparsity. Second, the motor primitives extracted during one experimental session generalize and afford the accurate reconstruction of rodent behavior across successive experimental sessions in the same or in modified mazes. Third, in our approach the number of motor primitives associated with each maze correlates with independent measures of maze complexity, hence showing that our formalism is sensitive to essential aspects of task structure. The framework introduced here can be used by behavioral scientists and neuroscientists as an aid for behavioral and neural data analysis. Indeed, the extracted motor primitives enable the quantitative characterization of the complexity and similarity between different mazes and behavioral patterns across multiple trials (i.e., habit formation). We provide example uses of this computational framework, showing how it can be used to identify behavioural effects of maze complexity, analyze stereotyped behavior, classify behavioral choices and predict place and grid cell displacement in novel environments.

animal behavior and cognition↗