Biology subjects

Zambelli, F.

Publications and source records attributed to Zambelli, F..

9 recordsLinked to original sources

bioRxiv2026

Critical Fragility Emerges from Chromosomal Instability in Cancer

Genomic instability is a major driver of tumor evolution, promoting diversification and adaptation while simultaneously increasing the accumulation of deleterious alterations. How tumor populations balance these opposing effects remains poorly understood. Here, we introduce a computational framework that explicitly represents diploid genomes, functional gene classes, point mutations, and chromosome-segregation errors in spatially constrained and well-mixed tumor populations. We identify a viability boundary separating sustained tumor expansion from instability-induced population collapse. Within the viable regime, mutation and selection generate a stable distribution of genomic-instability classes that is accurately captured by an analytical replicator--mutator description. Near the viability boundary, tumor dynamics exhibit prolonged extinction transients and strong sensitivity to stochastic fluctuations, with important differences between solid and liquid architectures. Chromosomal alterations further modify growth by creating transient benefits through increased gene dosage and genetic redundancy, while ultimately increasing genomic fragility. Finally, simulated interventions show that eliminating low-instability subpopulations or increasing the global mutational burden can displace tumors beyond their viability boundary and trigger irreversible collapse. These results identify genome instability as both an evolutionary advantage and an intrinsic vulnerability, providing a quantitative framework for developing therapies that exploit the limits of tumor evolution.

cancer biology↗

bioRxiv2026

Transcription controls chromatin-nuclear lamina contacts through distinct Lamin A and LBR tethering mechanisms

Lamina-associated domains (LADs) are large genomic regions that interact with the nuclear lamina (NL). Much of the underlying "grammar" governing their positioning at the nuclear periphery remains unclear. LADs are composed of heterochromatin and typically harbor repressed genes, and their association with the NL is generally incompatible with strong transcriptional activity. The extent to which transcription globally shapes chromatin-NL interactions is not fully understood. Here, we combined acute transcription inhibition using Flavopiridol or Triptolide with genome-wide mapping of chromatin-NL contacts. We found that chromatin-NL interactions are rapidly rewired upon transcription inhibition. Changes in chromatin-NL contacts upon transcription shutdown are predictable based on transcriptional activity and the presence of H3K9me3-marked heterochromatin. This rewiring is reversible, as genome-NL interactions quickly return to baseline levels following drug wash-off. Notably, gain and loss of chromatin-NL interactions upon transcription shutdown reflect two distinct tethering mechanisms. Inter-LADs genomic regions (iLADs) enriched in highly active genes and located near stable LADs, which are tethered by Lamin A (LMNA/C), become re-attached to the NL following transcription inhibition. In parallel, H3K9-methylated regions tethered to the nuclear envelope by the Lamin B receptor (LBR) undergo extensive detachment from the NL. Strikingly, LMNA/C and LBR oppositely regulate transcription-sensitive LADs and are required for transcriptional control of chromatin-NL contacts. Together, our findings highlight the plasticity and dynamic nature of chromatin-NL interactions and provide the first evidence that LMNA/C- and LBR-mediated tethering mechanisms exhibit distinct sensitivities to transcription inhibition. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/738400v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@16781a2org.highwire.dtl.DTLVardef@6febd1org.highwire.dtl.DTLVardef@1e3220forg.highwire.dtl.DTLVardef@d137f7_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LITranscription inhibition alters chromatin-NL contacts rapidly and reversibly C_LIO_LIActive transcription prevents inter-LADs located near LMNA/C-tethered LADs from associating with the nuclear lamina. C_LIO_LILBR-tethered heterochromatin is repositioned away from the NL C_LIO_LITranscription-dependent modulation of chromatin-NL contacts is dependent on LMNA/C and partially on LBR C_LI

genomics↗

bioRxiv2025

Unraveling the network signatures of oncogenicity in virus-human protein-protein interactions

Climate change, increasing urbanization and global human mobility have increased the risk of emergent infectious diseases and the risk for their pandemic potential. Consequently, there is a pressing need for methods that can provide rapid insights about the potential enduring effects on the human hosts. In-silico methods can be more suitable than in-vitro and in-vivo methods to identify effects potentially manifesting after a long time, under the hypothesis that the underlying causes can be ascribed to perturbed biomolecular processes. Here we focus on oncogenicity, i.e., the risk of developing cancer subsequent to a viral infection, a phenomenon estimated to account for approximately 15% of global cancer prevalence. We characterize viruses in terms of their oncogenic potential by analyzing a multilayer representation of protein-protein interaction networks reconstructed from the human interactome. Our frame-work facilitates classification and allows us to identify sub-sets of proteins in-volved in oncogenesis, highlighting the mechanisms underpinning viral oncogenicity, including factors like chromatin structure. Our framework serves as a foundational resource for medical research, paving the way for the study of other potential long-term effects associated with emerging viruses.

systems biology↗

bioRxiv2024

Pathological PNPase variants with altered RNA binding and degradation activity affect the phenotype of bacterial and human cell models

Human PNPase (hPNPase) is an essential RNA exonuclease located in mitochondria, where it contributes to RNA import from the cytoplasm, degradation of mitochondrial RNA, and R-loop homeostasis. Biallelic mutations in the hPNPase PNPT1 gene cause different genetic diseases, ranging from hereditary hearing loss to Leigh syndrome. In this work, we used an Escherichia coli model we recently developed to test the effects of four pathological PNPT1 mutations associated with diseases of different severity. Moreover, we generated a new human cell model by introducing PNPT1 mutations into 293T cells via CRISPR-Cas editing. Notably, the bacterial cells expressing the different mutant alleles exhibited similar phenotypes consistent with hPNPase loss of function. In contrast, the human cell model responded differently to the two mutations tested, with responses correlating with the severity of the respective pathologies. We interpreted the data derived from both models in the light of the in vitro RNA binding and degradation activity of the purified wild-type and mutated hPNPase variants. We found that all pathogenic mutations tested caused defects in protein assembly and affected the degradation and RNA binding efficiency to varying degrees. However, the severity of the conditions caused by different mutations did not correlate with the catalytic activity of the mutant proteins. Also, we demonstrated that human PNPase, like its bacterial orthologue, is capable of trimming ssDNA and some mutations inhibit such activity.

genetics↗

bioRxiv2023

SOX2 and NR2F1 coordinate the gene expression program of the early postnatal visual thalamus

The thalamic dorsolateral geniculate nucleus, (dLGN) receives visual input from the retina via the optic nerve, and projects to the cortical visual area, where eye-derived signals are elaborated. The transcription factors SOX2 and NR2F1 are directly involved in the differentiation of dLGN neurons, based on mouse work and patient mutations leading to vision defects. However, whether they regulate each other, or control common targets is still unclear. By RNA-seq analysis of neonatal dLGN from thalamo-specific Sox2 and Nr2f1 mouse mutants, we found a striking overlap of deregulated genes. Among them, VGF, a cytokine transported along thalamic-cortical axons is strongly downregulated in both mutants. CUT&RUN analysis of SOX2 binding in dLGN chromatin identified a binding pattern characteristic of the dLGN. Collectively, the SOX2 and NR2F1- coregulated genes, and cognate SOX2 binding sites, contribute as a basis to understand the gene regulatory network driving the differentiation and connectivity of thalamic neurons.

developmental biology↗

bioRxiv2022

Perturbation of protein homeostasis brings plastids at the crossroad between repair and dismantling

The chloroplast proteome is a dynamic mosaic of plastid- and nuclear-encoded proteins. Plastid protein homeostasis is maintained through the balance between de novo synthesis and proteolysis. Intracellular communication pathways, including the plastid-to-nucleus signalling and the protein homeostasis machinery, made of stromal chaperones and proteases, shape chloroplast proteome based on developmental and physiological needs. However, the maintenance of fully functional chloroplasts is costly and under specific stress conditions the degradation of damaged chloroplasts is essential to the maintenance of a healthy population of photosynthesising organelles while promoting nutrient redistribution to sink tissues. In this work, we have addressed this complex regulatory chloroplast- quality-control pathway by modulating the expression of two nuclear genes encoding plastid ribosomal proteins PRPS1 and PRPL4. By transcriptomics, proteomics and transmission electron microscopy analyses, we show that the increased expression of PRPS1 gene leads to chloroplast degradation and early flowering, as an escape strategy from stress. On the contrary, the overaccumulation of PRPL4 protein is kept under control by increasing the amount of plastid chaperones and components of the unfolded protein response (cpUPR) regulatory mechanism. This study advances our understanding of molecular mechanisms underlying chloroplast retrograde communication and provides new insight into cellular responses to impaired plastid protein homeostasis.

plant biology↗

bioRxiv2020

Single cell analysis reveals the impact of age and maturation stage on the human oocyte transcriptome

Study questionTo which degree does maternal age affect the transcriptome of human oocytes at the germinal vesicle (GV) stage or at metaphase II after maturation in vitro (IVM-MII)? Summary answerWhile the oocytes transcriptome is predominantly determined by maturation stage, transcript levels of genes related to chromosome segregation, mitochondria and RNA processing are affected by age after in vitro maturation of denuded oocytes. What is known alreadyFemale fertility is inversely correlated with maternal age due to both a depletion of the oocyte pool and a reduction in oocyte developmental competence. Few studies have addressed the effect of maternal age on the human mature oocyte (MII) transcriptome, which is established during oocyte growth and maturation, and the pathways involved remain unclear. Here, we characterize and compare the transcriptomes of a large cohort of fully grown GV and IVM-MII oocytes from women of varying reproductive age. Study design, size, durationIn this prospective molecular study, 37 women were recruited from May 2018 to June 2019. The mean age was 28.8 years (SD=7.7, range 18-43). A total of 72 oocytes were included in the study at GV stage after ovarian stimulation, and analyzed as GV (n=40) and in vitro matured oocytes (IVM-MII; n=32). Participants/materials, setting, methodsDenuded oocytes were included either as GV at the time of ovum pick-up or as IVM-MII after in vitro maturation for 30 hours in G2 medium, and processed for transcriptomic analysis by single-cell RNA-seq using the Smart-seq2 technology. Cluster and maturation stage marker analysis were performed using the Seurat R package. Genes with an average fold change greater than 2 and a p-value < 0.01 were considered maturation stage markers. A Pearson correlation test was used to identify genes whose expression levels changed progressively with age. Those genes presenting a correlation value (R) >= |0.3| and a p-value < 0.05 were considered significant. Main results and the role of chanceFirst, by exploration of the RNA-seq data using tSNE dimensionality reduction, we identified two clusters of cells reflecting the oocyte maturation stage (GV and IVM-MII) with 4,445 and 324 putative marker genes, respectively. Next we identified genes, for which RNA levels either progressively increased or decreased with age. This analysis was performed independently for GV and IVM-MII oocytes. Our results indicate that the transcriptome is more affected by age in IVM-MII oocytes (1,219 genes) than in GV oocytes (596 genes). In particular, we found that genes involved in chromosome segregation and RNA splicing significantly increase in transcript levels with age, while genes related to mitochondrial activity present lower transcript levels with age. Gene regulatory network analysis revealed potential upstream master regulator functions for genes whose transcript levels present positive (GPBP1, RLF, SON, TTF1) or negative (BNC1, THRB) correlation with age. Limitations, reasons for cautionIVM-MII oocytes used in this study were obtained after in vitro maturation of denuded GV oocytes, therefore, their transcriptome might not be fully representative of in vivo matured MII oocytes. The Smart-seq2 methodology used in this study detects polyadenylated transcripts only and we could therefore not assess non-polyadenylated transcripts. Wider implications of the findingsOur analysis suggests that advanced maternal age does not globally affect the oocyte transcriptome at GV or IVM-MII stages. Nonetheless, hundreds of genes displayed altered transcript levels with age, particularly in IVM-MII oocytes. Especially affected by age were genes related to chromosome segregation and mitochondrial function, pathways known to be involved in oocyte ageing. Our study thereby suggests that misregulation of chromosome segregation and mitochondrial pathways also at the RNA-level might contribute to the age-related quality decline in human oocytes. Study funding/competing interest(s)This study was funded by the AXA research fund, the European commission, intramural funding of Clinica EUGIN, the Spanish Ministry of Science, Innovation and Universities, the Catalan Agencia de Gestio dAjuts Universitaris i de Recerca (AGAUR) and by contributions of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership and to the "Centro de Excelencia Severo Ochoa". The authors have no conflict of interest to declare.

developmental biology↗

bioRxiv2020

VINYL: Variant prIoritizatioN bY survivaL analysis

MotivationClinical applications of genome re-sequencing technologies typically generate large amounts of data that need to be carefully annotated and interpreted to identify genetic variants associated with pathological conditions. In this context, accurate and reproducible methods for the functional annotation and prioritization of genetic variants are of fundamental importance, especially when large volumes of data - like those produced by modern sequencing technologies - are involved. ResultsIn this paper, we present VINYL, a highly accurate and fully automated system for the functional annotation and prioritization of genetic variants in large scale clinical studies. Extensive analyses of both real and simulated datasets suggest that VINYL show higher accuracy and sensitivity when compared to equivalent state of the art methods, allowing the rapid and systematic identification of potentially pathogenic variants in different experimental settings.

bioinformatics↗

bioRxiv2018

Laniakea: an open solution to provide Galaxy \"on-demand\" instances over heterogeneous cloud infrastructures.

BackgroundGalaxy is rapidly becoming the de facto standard among workflow managers for bioinformatics. A rich feature set, its overall flexibility, and a thriving community of enthusiastic users are among the main factors contributing to the popularity of Galaxy and Galaxy based applications. One of the main advantages of Galaxy consists in providing access to sophisticated analysis pipelines, e.g., involving numerous steps and large data sets, even to users lacking computer proficiency, while at the same time improving reproducibility and facilitating teamwork and data sharing among researchers. Although several Galaxy public services are currently available, these resources are often overloaded with a large number of jobs and offer little or no customization options to end users. Moreover, there are scenarios where a private Galaxy instance still constitutes a more viable alternative, including, but not limited to, heavy workloads, data privacy concerns or particular needs of customization. In such cases, a cloud-based virtual Galaxy instance can represent a solution that overcomes the typical burdens of managing the local hardware and software infrastructure needed to run and maintain a production-grade Galaxy service.\n\nResultsHere we present Laniakea, a robust and feature-rich software suite which can be deployed on any scientific or commercial Cloud infrastructure in order to provide a \"Galaxy on demand\" Platform as a Service (PaaS). Laying its foundations on the INDIGO-DataCloud middleware, which has been developed to accommodate the needs of a large number of scientific communities, Laniakea can be deployed and provisioned over multiple architectures by private or public e-infrastructures. The end user interacts with Laniakea through a front-end that allows a general setup of the Galaxy instance, then Laniakea takes charge of the deployment both of the virtual hardware and all the software components. At the end of the process the user has access to a private, production-grade, yet fully customizable, Galaxy virtual instance. Laniakeas supports the deployment of plain or cluster backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours, that is Galaxy configurations tailored for specific tasks. As a proof of concept, we provide a demo Laniakea instance hosted at an ELIXIR-IT Cloud facility.\n\nConclusionsThe migration of scientific computational services towards virtualization and e-infrastructures is one of the most visible trends of our times. Laniakea provides Cloud administrators with a ready-to-use software suite that enables them to offer Galaxy, a popular workflow manager for bioinformatics, as an on-demand PaaS to their users. We believe that Laniakea can concur in making the many advantages of using Galaxy more accessible to a broader user base by removing most of the burdens involved in running a private instance. Finally, Laniakeas design is sufficiently general and modular that could be easily adapted to support different services and platforms beyond Galaxy.

bioinformatics↗