Biology subjects

Turchi, L.

Publications and source records attributed to Turchi, L..

10 recordsLinked to original sources

bioRxiv2026

ULTRAPETALA1 remodels PRC2 recruitment to nucleosomes

Polycomb Repressive Complex 2 (PRC2) establishes transcriptional repression through trimethylation of histone H3 lysine 27 (H3K27me3), a modification essential for developmental patterning. Here, we describe a novel plant-specific PRC2 variant (PRC2.3) that employs a distinct nucleosome-targeting mechanism mediated by accessory factor ULTRAPETALA1 (ULT1), which promotes H3K27me3 deposition at over 1,300 developmental genes. The cryo-EM structure of the PRC2SWN-ULT1-nucleosome complex reveals that ULT1 antagonizes the canonical PRC2 binding mode and instead bridges PRC2 to the nucleosome using its own interaction surfaces. ULT1 binds consecutive purines in the nucleosomal DNA and the histone H2A/H2B acidic patch, while enabling PRC2 to accommodate H3K36 modifications. We further show that in planta ULT1 enhances H3K27me3 at purine-rich loci and at genes associated with H3K36 marks, and identify the ULT1-H2A/H2B interface as required for reproductive transition and flower organogenesis. Our findings demonstrate that PRC2 can deploy mechanistically distinct recruitment strategies to control key developmental switches.

Molecular Biology↗

bioRxiv2025

Human cortico-vascular assembloids reveal a CELF2-AHNAK-dependent switch from neuronal to endothelial tropism in glioblastoma cells

Glioblastoma (GB) remains one of the most aggressive human cancers, driven by profound cellular plasticity and dynamic interactions with the neurovascular niche. Yet, existing preclinical models fail to reproduce the human brain-vascular interface, limiting studies of tumor-host crosstalk and invasion. To overcome this gap, we developed a human induced pluripotent stem cell (hiPSC)-derived cortico-endothelial (CO+EO) assembloid model by fusing cortical and endothelial organoids from the same genetic background. These assembloids spontaneously form branched vascular networks enriched in tight junction proteins (CLDN5, OCLN, ZO-1), thereby recapitulating a key blood-brain barrier (BBB)-like property and providing a physiologically relevant human platform for exploring glioblastoma-neurovascular interactions. Using this system, we uncover a previously unrecognized CELF2-dependent glioblastoma stem cell (GSC) tropism. CELF2-expressing GSCs preferentially infiltrate neural regions, where they trigger neuronal apoptosis and disrupt endothelial tight junction integrity, supporting an aggressive phenotype. Conversely, CELF2-deficient GSCs lose neurotropism, acquire mesenchymal features, and are redirected toward vascular compartments. This endothelial affinity requires the scaffold protein AHNAK, strongly expressed at the plasma membrane of CELF2-deficient cells and enriched at tumor-endothelial interfaces. AHNAK knockdown abolished endothelial infiltration, demonstrating its critical role in vascular tropism. Analysis of patient GB samples confirmed that CELF2-positive tumor cells are enriched in poorly vascularized, mitotically active areas and excluded from vessel-rich zones, closely paralleling assembloid findings. Transcriptomic profiling further revealed that CELF2 promotes a neuronal progenitor-like program while repressing mesenchymal and vascular-associated gene expression, thereby shaping tumor identity, invasive behavior, and tissue preference. Collectively, our study introduces CO+EO assembloids as an original human model of glioblastoma plasticity at the neurovascular interface. We identify CELF2 as a master regulator of GSC tropism and AHNAK as a mediator of vascular affinity, unveiling a novel molecular axis that governs glioblastoma invasion and highlighting new therapeutic opportunities. Key points- Developed cortico-endothelial assembloids mimicking the brain microenvironment. - Identified CELF2 level as a determinant of glioblastoma cell tropism toward neuronal or endothelial niches. - Showed CELF2-positive GB cells disrupt endothelial tight junctions, unlike CELF2-negative cells. Importance of the studyThis study presents a novel, physiologically relevant in vitro model of glioblastoma (GB) that faithfully recapitulates the complex human brain microenvironment, including both vascular and neuronal components. By combining cortical and endothelial organoids derived from human iPSCs into cortico-endothelial assembloids (CO+EOs), the model enables detailed analysis of GB cell behavior, including migration, tissue tropism, and impact on the neurovascular interface. The work identifies CELF2 as a key molecular determinant of GB cell tropism and neurovascular interaction. The discovery that CELF2-expressing GB cells preferentially infiltrate neuronal tissue and disrupt endothelial tight junctions, whereas CELF2-deficient cells favor endothelial regions without compromising tight junction integrity, offers critical insights into tumor heterogeneity and mechanisms of invasiveness. These findings not only enhance our understanding of how GB cells interact with distinct microenvironmental niches but also provide a powerful platform for testing therapeutic strategies targeting tumor-microenvironment interactions. Graphical AbstractSchematic representation of CO+EO assembloids comprising an endothelial (yellow) and a cortical (red) domain. On the left, control CELF2-expressing GB cells preferentialy infiltrate the neuronal compartment, where they trigger neuronal apoptosis and disrupt BBB-like tight junctions upon contact with endothelial cells. On the right, CELF2-deprived GB cells exhibit reduced neural invasion and increased tropism for endothelial cells, consistent with a mesenchymal signature shift partially driven by elevated AHNAK expression. These cells exert limited impact on neuronal viability and BBB integrity, and display partial loss of GSC identity, as indicated by reduced OLIG2 expression. The CO+EO assembloid model thus recapitulates key features of cortico-endothelial human tissue heterogeneity and provides a reliable platform to dissect the molecular mechanisms underlying GSC tropism and their tissue-specific interactions O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/683634v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@26440org.highwire.dtl.DTLVardef@103b93eorg.highwire.dtl.DTLVardef@176ca48org.highwire.dtl.DTLVardef@1da502f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Beyond binding motif: genomic context predicts transcription factor dependent regulation in Arabidopsis

Transcription Factors (TFs) play a crucial role in the spatiotemporal control of gene expression. Despite the presence of many potential TF binding sites (TFBS) across the genome, TFs do not interact with all of them, and, among those, only a subset leads to actual regulation. In this work, we investigate how the genomic context of a putative TFBS, including the occurrence of binding motifs for other TFs, can be used to predict effective transcriptional regulation by a TF of interest. We focus on LEAFY (LFY), a plant-specific TF and master regulator of flower development. Using available transcriptomes and TF-DNA binding experiments, we identify 1164 LFY binding sites associated with a regulatory response in Arabidopsis thaliana. We then apply a machine learning approach based on properties of the surrounding genomic region, to discriminate these regulatory LFY binding sites from non-regulatory ones. Detailed analysis of the models components reveals that, for LFY, the density and quality of binding sites constitute the most important features but were not sufficient on their own to predict regulatory activity. The presence of binding sites for other transcription factors and the overall richness in TFBS were also essential. These results clarify the nature of the regulatory code by which LFY operates and could serve as a basis for the study of the regulatory elements of other transcription factors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/655699v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1a1a80org.highwire.dtl.DTLVardef@1c1fee5org.highwire.dtl.DTLVardef@1457164org.highwire.dtl.DTLVardef@176c46_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2024

The dual trxG/PcG protein ULTRAPETALA1 modulates H3K27me3 and directly enhances POLYCOMB REPRESSIVE COMPLEX 2 activity for fine-tuned reproductive transitions

AbstractThe antagonistic POLYCOMB (PcG) REPRESSIVE COMPLEX 2 (PRC2) and trithorax (trxG) chromatin machineries play a major role in orchestrating gene expression during the development of multicellular eukaryotes. These complexes are well known for depositing and maintaining the repressive H3K27me3 and activating H3K4me3 marks, respectively. However, the mechanisms that govern the switch between these functions remains elusive, especially in plants, whose lifelong, flexible development relies heavily on this process. Here we demonstrate that the plant specific ULTRAPETALA1 (ULT1) protein, previously reported as a trxG factor that antagonizes the PRC2 enzymatic subunit CURLY LEAF (CLF), also exhibits a repressive function, increasing H3K27me3 levels at over a thousand genes. We discovered a physical interaction between ULT1 and PRC2 components, particularly the SWINGER (SWN) enzymatic subunit. We further show that in vitro ULT1 significantly enhances the enzymatic activity of PRC2SWN, and to a lesser extent also that of PRC2CLF, corroborating our epigenomic and developmental genetic data that reveal different ULT1 activity depending on the catalytic subunit of the PRC2 complex. This study provides new insights into the relative activities of CLF and SWN and introduces a novel mechanistic framework for a chromatin switch mediated by a bivalent trxG/PcG factor. Key messageULTRAPETALA1 counteracts or promotes PRC2 activity at hundreds of developmental genes in Arabidopsis thaliana, and activates the deposition of the repressive H3K27me3 chromatin mark via direct interaction with PRC2. This is the first instance of a bivalent factor which functions as a cofactor of PRC2 HMTs.

genetics↗

bioRxiv2024

Nicotinamide Metabolism Reprogramming Drives Reversible Senescence of Glioblastoma Cells

Recent studies show that metabolites, beyond their metabolic roles, can induce significant changes in cell behavior. Herein, we investigate the non-canonical role of nicotinamide (vitamin B3) on glioblastoma (GB) cell behavior. Nicotinamide induced senescence in GB cells, characterized by reduced proliferation, chromatin reorganization, increased DNA damage, enhanced beta-galactosidase activity, and decreased Lamin B1 expression. Nicotinamide-induced senescence was accompanied by an unexpected reprogramming of its metabolism, marked by simultaneous downregulated transcription of NNMT (nicotinamide N-methyltransferase) and NAMPT (nicotinamide phosphoribosyl-transferase). Nicotinamide effects on GB cells were mediated by decreased levels of SOX2. Consistently, analyses of patients single cell transcriptome datasets showed that GB cells with low NNMT and NAMPT expression levels were enriched in gene modules related to senescence. Remarkably, senescent GB cells retained tumor-forming ability in vivo, albeit to a lesser extent compared to control cells. Further experiments at the single-cell level and transcriptomic analyses demonstrated that nicotinamide-induced senescence in GB cells is fully reversible. Overall, our findings identify a novel reversible senescent state in GB tumors and highlight the non-canonical role of NAM as a key driver of cancer cell plasticity.

cancer biology↗

bioRxiv2024

Investigating the effects of transcutaneous Vagus Nerve Stimulation on motor cortex excitability and inhibition through paired-pulse Transcranial Magnetic Stimulation

Transcutaneous Vagus Nerve stimulation (tVNS) has been proposed as a prospective treatment for clinical conditions with altered GABAergic transmission. While possible effects of tVNS on behavioral performance in inhibitory control tasks have been previously reported, neurophysiological evidence showing its effects on GABA-mediated inhibition in the motor cortex is limited. Concurrently, the possible influence of participants gender and state conditions remains unexplored. Here, we applied, single- and paired-pulse TMS to the right or the left primary motor in two different groups of participants. We measured corticospinal excitability (CSE), short and long intracortical inhibition (SICI and LICI), cortical silent period (cSP) and intracortical facilitation (ICF) indexes. The measures were taken, in separated sessions of a within-subject design, at baseline prior to tVNS and after delivering active and sham tVNS in the Cymba conchae of the left ear. To exploit state dependent effects and assess the role of tVNS in motor learning, tVNS was applied, during the execution of a computerized visuomotor task. In the left TMS group, we observed better visuomotor performance during active than sham tVNS, regardless of participants gender. Interestingly, in both groups, we found a specific increase of SICI, which is mediated by GABAa activity, after active compared to sham-tVNS and baseline evaluations, which was specifically limited to female participants. No effects on CSE, ICF or GABAb-mediated intracortical inhibition indexes were observed. The results show specific effects of tVNS on motor learning and GABAa-mediated motor inhibition, providing supportive evidence for the application of tVNS as an alternative and coadjuvant treatment for disorders featured by altered inhibition mechanisms.

neuroscience↗

bioRxiv2023

HD-Zip II transcription factors control distal stem cell fate in Arabidopsis roots by linking auxin signaling to the FEZ/SOMBRERO pathway

In multicellular organisms, specialized tissues are generated by specific populations of stem cells through cycles of asymmetric cell divisions, where one daughter undergoes differentiation and the other maintains proliferative properties. In Arabidopsis thaliana roots, the columella - a gravity-sensing tissue which protects and defines the position of the stem cell niche - represents a typical example of a tissue whose organization is exclusively determined by the balance between proliferation and differentiation. The columella derives from a single layer of stem cells through a binary cell fate switch that is precisely controlled by multiple, independent regulatory inputs. Here, we show that the HD-Zip II transcription factors HAT3, ATHB4, and AHTB2, redundantly regulate columella stem cell fate and patterning in the Arabidopsis root. The HD-Zip II transcription factors promote columella stem cell proliferation by acting as effectors of the FEZ/SMB circuit and, at the same time, by interfering with auxin signaling to counteract hormone-induced differentiation. Overall, our work shows that HD-Zip II connect two opposing parallel inputs to fine tune the balance between proliferation and differentiation in columella stem cells. Summary statementHD-Zip II transcription factors redundantly regulate columella stem cells activity by counteracting auxin-mediated differentiation downstream of the FEZ/SMB proliferative input

plant biology↗

bioRxiv2022

Plant-TFClass: a structural classification for plant transcription factors

Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved thanks to the DNA-binding domain (DBD) present in each TF. DBDs show a vast diversity of protein folds within and across organisms, ranging from simple long basic alpha helices to complex structural combinations of alpha, beta and loop folds. In mammals, the structural conformation of the DBDs and the way it establishes contact with DNA has been used to organize TFs in a hierarchical classification named TFClass. However, such classification is missing from plants that possess many DBD types absent from mammals. Here, we reviewed the numerous TF DBD 3D-structures and models available for plants to organize all plant TFs types following the TFClass hierarchy (Superclass/Class/Family/Subfamily). We classified most of the 55 recognized plant TF types within the existing TFClass framework. This extended classification led us to add six new classes and 34 new families corresponding to TF DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF and TF binding sites comparison across TF families and across organisms.

plant biology↗

bioRxiv2022

The F-box cofactor UFO redirects the LEAFY floral regulator to novel cis-elements

In angiosperms, flower patterning requires the localized expression of the APETALA3 (AP3) floral homeotic gene involved in petal and stamen development. AP3 is synergistically induced by the master transcription factor (TF) LEAFY (LFY) and the F-box protein UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show that the connection to ubiquitination pathways suggested by the F-box domain of UFO is mostly dispensable for its function and that UFO instead acts by forming a transcriptional complex with LFY and binds to newly discovered regulatory elements. Cryo-electron microscopy explains how a LFY-UFO complex forms on these novel DNA sites due to direct interaction of UFO with LFY and DNA. Finally, we show that this complex has a deep evolutionary origin, largely predating flowering plants. This work reveals a novel mechanism of an F-box protein in directly modulating the DNA-binding specificity of a master TF.

plant biology↗

bioRxiv2022

Human glioblastoma cell motility depends on the activity of the cysteine metabolism enzyme 3-Mercaptopyruvate sulfurtransferase

Cancer cells in similar functional states are found in all glioblastoma, despite the genomic heterogeneity observed between and within these brain tumors. Metabolism being downstream of all signaling pathways regulating cell behaviors, we looked for metabolic weaknesses in link with motility, a key functional state for glioblastoma aggressiveness. A signature-driven data reduction approach highlighted motile cells present in thirty tumors from four independent single-cell transcriptomic datasets. Analyses integrating trajectory modeling disclosed, as characteristic of motile cells, enhanced oxidative stress coupled with mobilization of the cysteine metabolism enzyme 3-Mercaptopyruvate sulfurtransferase (MPST). The soundness of this prediction was verified using migration and invasion assays with patient-derived cells and tissue organoids. Pharmacological and genetic manipulations showed that enhanced ROS production and MPST activity are required for the cells motility. Biochemical assays indicated that MPST acts by protecting protein cysteine residues from dismal hyperoxidation. In vivo, MPST knockdown translated in reduced tumor burden, and a robust increase in mice survival. These results show that enhanced oxidative stress coupled with MPST mobilization plays a key role in glioblastoma cell motility.

cancer biology↗