Biology subjects

Pagella, P.

Publications and source records attributed to Pagella, P..

15 recordsLinked to original sources

bioRxiv2026

Enhancer pioneering activity of Wnt/β-catenin signaling

Wnt/{beta}-catenin signaling is widely understood as a molecular switch that activates preprogrammed regulatory states. Whether it also actively reshapes chromatin to establish those states has remained unclear. To address this, we performed time-resolved ATAC-seq and CUT&RUN analyses in HEK293T cells and monitored {beta}-catenin-dependent changes in chromatin accessibility and complex assembly following pathway activation. In addition to conventional Wnt-responsive elements (WREs), which are constitutively accessible and pre-bound by TCF/LEF transcription factors (TFs), we identified a second class of WREs, that are initially inaccessible but become activated upon stimulus. At these latent enhancers, {beta}-catenin functions as a pioneer-like factor together with HDAC1 and CBP, mediating chromatin remodeling and TCF/LEF occupancy. Together, these results extend the current view of Wnt/{beta}-catenin signaling by showing that it can establish regulatory elements de novo. Here, {beta}-catenin emerges as the central regulator of transcriptional control and remodeling, providing a framework for the dynamic and context-dependent nature of Wnt-driven gene regulation in development and disease.

genomics↗

bioRxiv2026

An Innervated and Vascularized HNSCC-on-a-Chip Model Built on Defined and Tunable Engineered Extracellular Matrices

Understanding the tumor microenvironment (TME) requires experimental platforms that faithfully recapitulate its key components. Here, we present an innervated and vascularized head and neck squamous cell carcinoma (HNSCC)-on-a-chip platform built with fully defined and tunable engineered extracellular matrices (eECMs). In a stepwise increase of complexity, we first co-cultured patient-derived HNSCC cells, cancer-associated fibroblasts, and endothelial cells within tailored eECMs, revealing matrix-dependent differences in self-organization and chemotherapeutic sensitivity. We then integrated these 3D constructs into a cancer-vasculature-interface, which enabled analysis of eECM-dependent directional collective migration and metastatization. Finally, we incorporated HNSCC-specific innervation through injectable 3D human bioengineered trigeminal ganglia, establishing a chip-based innervation-tumor-vasculature tri-interface. Together, this all-human platform captures fundamental determinants of HNSCC progression, including a fully defined ECM, vasculature, and innervation, within a single modular system that is broadly adaptable for interrogating how the tumor microenvironment shapes solid tumor behavior and therapeutic responses. TeaserHNSCC-on-a-chip integrates defined ECM, vasculature, and innervation to investigate tumor behavior and therapeutic responses.

bioengineering↗

bioRxiv2024

The Transcription Factor Binding Landscape of Mouse Development

Gene regulators physically associate to the genome, in a combinatorial fashion, to drive tissue-specific gene expression programs. Uncovering the genome-wide activity of all gene regulators across tissues is therefore needed to understand how the genome is regulated during development. Here, we take a first step forward towards achieving this goal. Using CUT&RUN, we systematically measured the genome-wide binding profiles of key transcription factors and cofactors that mediate the activity of ontogenetically relevant signaling pathways in select mouse tissues at two developmental stages. Computation of the numerous genome-wide binding datasets unveiled a large degree of tissue and time-specific activity for each gene regulator, and several factor-specific idiosyncrasies. Moreover, we identified "popular" regulatory regions that are bound by a multitude of pathway regulators. Popular regions tend to be more evolutionarily conserved, implying their essentiality. Consistently, they lie in the proximity of genes whose dysregulation causes early embryonic lethality in the mouse. Moreover, the human homologs of these regions are also bound by many gene regulators and are highly conserved in human populations, indicating that they retain functional relevance for human development. This work constitutes a decisive step towards understanding how the genome is simultaneously read and used by gene regulators in a holistic fashion and unveils multiple genomic mechanisms that drive embryonic development.

genomics↗

bioRxiv2024

Trigeminal ganglion and tooth innervation modifications following genetic and pharmacological Nogo-A inhibition

Nogo-A is a major regulator of neural development and regeneration, but its role in tooth innervation remains largely unknown. Neurons from trigeminal ganglia support teeth homeostasis and regeneration, and disorders of their function could have significant pathophysiological consequences. In this study, we show that Nogo-A is expressed in the trigeminal ganglia and in the neurons innervating the teeth, and that its deletion affects both the number and patterning of neurons in teeth. In organotypic cultures, Nogo-A blocking antibodies affect the trigeminal ganglia-derived neuronal outgrowths and allow premature innervation of tooth germs. RNA sequencing analysis revealed that Nogo-A deletion induces alterations linked to functions at synapses and interference with neurotrophin signalling during the differentiation and maturation of trigeminal neurons. Taken together, these results reveal for the first time the importance of Nogo-A as a major regulator of tooth innervation and point to its potential as a clinical therapeutic target.

neuroscience↗

bioRxiv2024

Wnt signaling alters CTCF binding patterns and global chromatin structure

Wnt signaling plays a pivotal role during development, stem cell maintenance, and tissue homeostasis. Upon Wnt pathway activation, {beta}-catenin translocates to the nucleus where it binds the TCF/LEF transcription factors to drive the context-specific expression of Wnt target genes. Coordinating gene expression programs in vertebrates requires a complex interplay between the regulatory and the 3D organization of the genome. However, the impact of Wnt signaling on genome structure has been poorly explored. Here we investigated how Wnt signaling activation influences the binding patterns of CTCF, one of the core architectural proteins that helps establish the 3D genome organization be demarcating topologically associated domains (TAD). This study uncovered a series of CTCF rearrangements under Wnt, that we termed RUW. Notably, RUW sites that were gained upon Wnt activation were typically dependent on {beta}-catenin and were characterized by both CTCF and TCF/LEF binding. Accordingly, many CTCF RUWs aligned with {beta}-catenin binding patterns, and {beta}-catenin and CTCF co-localized in vivo in discreet nuclear puncta only upon pathway activation. Genome-wide investigation of CTCF-mediated 3D genomic interactions upon Wnt pathway stimulation supported the role of the identified RUWs in mediating Wnt-dependent chromatin loops. Lastly, targeted disruption of selected CTCF binding sites demonstrated their functional contribution to Wnt target gene regulation, implicating regulation of the 3D genomic structure in the execution of transcriptional programs orchestrated by developmental pathways.

developmental biology↗

bioRxiv2023

The Developmental Transcription Factor TBX3 Physically Engages with the Wnt/β-catenin Transcriptional Complex in Human Colorectal Cancer Cells to Regulate Metastasis Genes

Wnt signaling orchestrates gene expression in a plethora of processes during development and adult cell homeostasis via the action of nuclear {beta}-catenin. Furthermore, neoplasia of the colorectal epithelium begins with aberrant Wnt/{beta}-catenin signaling. Yet, little is known about how {beta}-catenin generates context-specific transcriptional outcomes. We have previously identified the developmental transcription factor TBX3 as a tissue-specific component of the Wnt/{beta}-catenin nuclear complex during mouse forelimb development. In this study, we show that TBX3 is present and functionally active in human colorectal cancers. TBX3s genomic binding pattern suggests a regulatory role that broadly coincides with that of Wnt/{beta}-catenin. Moreover, proteomics proximity labelling indicated that, during Wnt pathway activation, TBX3 is vicinal to several protein partners, including the transcription factors TCF/LEF and chromatin remodeling complexes which are usually found at Wnt responsive elements. Sequence and structure analysis revealed that TBX3 possesses an exposed Asp-Pro-Phe (NPF) motif predicted by AlphaFold2 Multimer to mediate direct interactions with several Wnt-activated TBX3 partners. Deletion of NPF abrogates TBX3 proximity to these partners and its ability to modulate Wnt-dependent transcription. TBX3 emerges as a key modulator of the oncogenic activity of Wnt/{beta}-catenin in colorectal cancer, and its mechanism of action exposes a novel druggable protein-interaction surface.

developmental biology↗

bioRxiv2023

Exhaustive identification of genome-wide binding events of transcriptional regulators with ICEBERG

Genome-wide protein interaction assays aspire to map the complete binding pattern of gene regulators. How-ever, common practice relies on replication and high stringency statistics which favor false negatives over false positives, thereby excluding portions of signal which may represent biologically relevant events. Here, we present ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), an experimental and analytical pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regulatory regions and {beta}-catenin targets in human colorectal cancer cells. The ICE-BERG datasets allow benchmarking of individual replicates, comparison of the performance of peak calling and replication approaches and expose the arbitrary nature of other strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG established a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that might underlie novel mechanisms of colorectal cancer progression.

genomics↗

bioRxiv2023

Single-cell transcriptomics analysis reveals extracellular matrix remodelling in carious human dental pulp

The carious lesion is a bacteria caused destruction of tooth mineralized matrices marked by concurrent tissue reparative and immune responses in the dental pulp. While major molecular players in tooth pulp decay have been uncovered, a detailed map of the molecular and cellular landscape of the diseased pulp is still missing. Here we used single-cell RNA sequencing analysis, to generate a comprehensive single-cell atlas of the carious human dental pulp tissue. Our data demonstrated modifications in various cell clusters of the carious pulp, such as immune cells, mesenchymal stem cells (MSC) and fibroblasts, when compared to the healthy dental pulp. These changes include upregulation of genes encoding extracellular matrix (ECM) components and the enrichment of the fibroblast cluster with myofibroblasts. Assessment of the Fibronectin fibres mechanical strain showed a significant tension reduction in the carious human pulp, compared to the healthy one. Collectively, the present data demonstrate molecular, cellular and biomechanical alterations in the carious pulp tissue, indicative of extensive ECM remodelling and reminiscent of fibrosis observed in other organs.

cell biology↗

bioRxiv2023

Single-cell response to Wnt activation in human embryonic stem cells reveals uncoupling of Wnt target gene expression

Wnt signaling drives nuclear translocation of {beta}-catenin and its subsequent association with the DNA-bound TCF/LEF transcription factors, which dictate target gene specificity by recognizing Wnt responsive elements across the genome. {beta}-catenin target genes are therefore thought to be collectively activated upon Wnt pathway stimulation. However, this appears in contrast with the non-overlapping patterns of Wnt target gene expression in several contexts, including early mammalian embryogenesis. Here we followed Wnt target gene expression in human embryonic stem cells after Wnt pathway stimulation at a single-cell resolution. Cells changed gene expression program over time consistent with three key developmental events: i) loss of pluripotency, ii) induction of Wnt target genes, and iii) mesoderm specification. Contrary to our expectation, not all cells displayed equal amplitude of Wnt target gene activation; rather, they distributed in a continuum from strong to weak responders when ranked based on the expression of the target AXIN2. Moreover, high AXIN2 did not always correspond to elevated expression of other Wnt targets, which were activated in different proportions in individual cells. This uncoupling of Wnt target gene expression, which was also identified in single colorectal cancer cells with hyper-activated Wnt signaling, underlines the necessity to identify additional mechanisms that explain the heterogeneity of the Wnt/{beta}-catenin-mediated transcriptional outputs in single cells.

developmental biology↗

bioRxiv2022

The CUT&RUN Blacklist of Problematic Regions of the Genome

Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors and co-factors. The ENCODE project and others have compiled blacklists for ChIP-seq which have been widely adopted: these lists contain regions of high and unstructured signal, regardless of cell type or protein target. While CUT&RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different. We found that this results in a CUT&RUN-specific set of undesired high-signal regions. For this reason, we have compiled blacklists based on CUT&RUN data for the human and mouse genomes, identifying regions consistently called as peaks in negative controls by the CUT&RUN peak caller SEACR. Using published CUT&RUN data from our and other labs, we show that the CUT&RUN blacklist regions can persist even when peak calling is performed with SEACR against a negative control, and after ENCODE blacklist removal. Moreover, we experimentally validated the CUT&RUN Blacklists by performing reiterative negative control experiments in which no specific protein is targeted, showing that they capture >80% of the peaks identified. We propose that removing these problematic regions prior to peak calling can substantially improve the performance of SEACR-based peak calling in CUT&RUN experiments, resulting in more reliable peak datasets.

genomics↗

bioRxiv2022

Notch signaling pathway in tooth shape variations

Evolutionary changes in vertebrates are linked to genetic alterations that often affect tooth-crown shape, which is a criterion of speciation events. The Notch pathway is highly conserved between species and controls morphogenetic processes in most developing organs, including teeth. Epithelial loss of the Notch-ligand Jagged1 in developing mouse molars affects the location, size and interconnections of their cusps that lead to minor tooth-crown shape modifications convergent to those observed along Muridae evolution. These alterations are due to the modulation of numerous genes, where Notch signaling is a hub for essential morphogenetic networks. A three-dimensional metamorphosis approach allowed tooth morphology prediction in individuals carrying Jagged1 mutations. These results shed new light on Notch/Jagged1-mediated signaling as one of the crucial components for dental variations in evolution. Significance statementDental microevolution changes in vertebrates are regulated by the Notch signaling pathway.

developmental biology↗

bioRxiv2022

Nogo-A regulates the fate of human dental pulp stem cells towards osteogenic, adipogenic, and neurogenic differentiation

Human teeth are highly innervated organs that contain a variety of mesenchymal stem cell populations that could be used for cell-based regenerative therapies. Specific molecules are often used in these treatments to favorably modulate stem cells function and fate. Nogo-A, a key regulator of neuronal growth and differentiation, is already used in clinical tissue regeneration trials. While the functions of Nogo-A in neuronal tissues are extensively explored, its role in teeth still remains unknown. In this work, we first immunohistochemically analyzed the distribution of Nogo-A protein in the dental pulp of human teeth. Nogo-A is localized in a variety of cellular and structural components of the dental pulp, including odontoblasts, fibroblasts, neurons and vessels. We also cross-examined Nogo expression in the various pulp cell clusters in a single cell RNA sequencing dataset of human dental pulp, which showed high levels of expression in all cell clusters, including that of stem cells. We then assessed the role of Nogo-A on the fate of human dental pulp stem cells and their differentiation capacity in vitro. Using immunostaining, Alizarin Red S and Oil Red O staining we showed that Nogo-A delayed the differentiation of cultured dental pulp stem cells towards the osteogenic, adipogenic and neurogenic lineages, while addition of the blocking anti-Nogo-A antibody had opposite effects. These results were further confirmed by qRT-PCR, which demonstrated overexpression of genes involved in osteogenic (RUNX2, ALP, SP7/OSX), adipogenic (PPAR-{gamma}2, LPL) and neurogenic (DCX, TUBB3, NEFL) differentiation in presence of the anti-Nogo-A antibody. Conversely, the osteogenic and adipogenic genes were downregulated by Nogo-A. Taken together, our results show that the functions of Nogo-A are not restricted to neuronal cells, but are extended to other cell populations, including dental pulp stem cells. We show that Nogo-A regulates their fates towards osteogenic, adipogenic and neurogenic differentiation, thus indicating its potential use in the clinics.

cell biology↗

bioRxiv2022

Time-resolved analysis of Wnt-signaling reveals β-catenin temporal genomic repositioning and cell type-specific plastic or elastic chromatin responses

Wnt signaling orchestrates gene expression via its effector {beta}-catenin. Whether {beta}-catenin targets genomic regions simultaneously or in a temporal fashion, and how this impacts the chromatin dynamics to modulate cell behavior, is currently unknown. Here we find that {beta}-catenin binds different loci at each time-point after stimulation, implying that the definition of Wnt-targets is fundamentally temporal. This process is intrinsically cell-type specific. In fact, Wnt/{beta}-catenin progressively shapes the chromatin of human embryonic stem cells consistent with their mesodermal differentiation: we call this genomic response plastic. In embryonic kidney cells, on the other hand, Wnt/{beta}-catenin drives a transient chromatin opening, followed by a re-establishment of the pre-stimulation state: a response that we define elastic. Finally, the Wnt-induced transient chromatin opening requires {beta}-catenin, suggesting a previously unappreciated pioneering role for this molecule. We submit that the plastic-vs-elastic behavior constitutes part of the mechanism explaining how Wnt/{beta}-catenin drives divergent cell-fate decisions during development and homeostasis.

genomics↗

bioRxiv2022

A New CUT&RUN Low Volume-Urea (LoV-U) protocol uncovers Wnt/β-catenin tissue-specific genomic targets

Upon WNT/{beta}-catenin pathway activation, stabilized {beta}-catenin travels to the nucleus where it associates with the TCF/LEF family of transcription factors, which constitutively bind to genomic Wnt Responsive Elements (WREs), to activate transcription of target genes. Discovering the binding profile of {beta}-catenin is therefore required to unambiguously assign direct targets of WNT signaling. Cleavage Under Target and Release Using Nuclease (CUT&RUN) has recently emerged as a prime technique for mapping the binding profile of chromatin interacting proteins. In our attempts to profile different regulators of the WNT/{beta}-catenin transcriptional complex, CUT&RUN performed reliably when targeting transcription factors such as TCF/LEF, but it failed to produce consistent binding patterns of the non-DNA-binding {beta}-catenin. Here, we present a biochemical modification of the CUT&RUN protocol, which we refer to as LoV-U (Low Volume and Urea), that enables the generation of robust and reproducible {beta}-catenin binding profiles. CUT&RUN-LoV-U uncovers direct WNT/{beta}-catenin target genes in human cells, as well as in ex vivo cells isolated from developing mouse tissue. CUT&RUN-LoV-U can profile all classes of chromatin regulators tested and is well suited for simultaneous processing of several samples. We submit that the application of our protocol will allow the detection of the complex system of tissue-specific WNT/{beta}-catenin target genes, together with other non-DNA-binding transcriptional regulators that act downstream of ontogenetically fundamental signaling cascades.

developmental biology↗

bioRxiv2021

A single cell atlas of human teeth

Teeth exert fundamental functions related to mastication and speech. Despite their great biomedical importance, an overall picture of their cellular and molecular composition is still missing. In this study, we have mapped the transcriptional landscape of the various cell populations that compose human teeth at single-cell resolution, and we analyzed in deeper detail their stem cell populations and their microenvironment. Our study identified great cellular heterogeneity in the dental pulp and the periodontium. Unexpectedly, we found that the molecular signatures of the stem cell populations were very similar, and that their distinctive behavior could be due to substantial differences between their microenvironments. Our findings suggest that the microenvironmental specificity is the potential source for the major functional differences of the stem cells located in the various tooth compartments and open new perspectives towards cell-based dental therapeutic approaches.

cell biology↗