Biology subjects

Guzman, C.

Publications and source records attributed to Guzman, C..

14 recordsLinked to original sources

bioRxiv2026

Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

Astrocytes are central regulators of neuroinflammation, yet the mechanisms by which they convert common inflammatory signals into cell type-specific transcriptional responses remain poorly understood. Here we mapped transcription initiation genome-wide in primary mouse astrocytes stimulated with interleukin-1B (IL-1B) and defined the active regulatory elements that drive astrocyte reactivity. We find that inducible enhancer transcription in astrocytes is encoded by a transcription-initiation grammar in which lineage-restricted transcription factors, particularly NFIA and TEAD4, cooperate with inflammatory transcription factors such as NF-{kappa}B, AP-1 and IRF to drive stimulus-dependent transcription activation. The motifs of these inflammatory transcription factors show a strong positional bias upstream of induced transcription start sites, supporting their direct role in controlling initiation upon stimulation. Moreover, NF-{kappa}B and TEAD4 motifs are preferentially associated with sites showing altered patterns of transcription initiation in response to inflammatory stimulus. Comparison with stimulated macrophages revealed that, despite substantial overlap in induced genes, astrocytes exhibit a largely distinct enhancer repertoire, indicating that shared inflammatory signals are interpreted through cell type-specific regulatory landscapes. Finally, transcribed astrocyte regulatory elements are functionally conserved in human astrocytes and are enriched for genetic risk variants associated with neurological disorders. Together, these findings define a cell type-specific regulatory logic for astrocyte inflammatory responses and link astrocyte enhancer regulation to human disease susceptibility.

genomics↗

bioRxiv2024

Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers

Leukocyte extravasation is a key component of the innate immune response, while circulating tumor cell extravasation is a critical step in metastasis formation. Despite their importance, the mechanisms underlying leukocyte and tumor cell extravasation remain incompletely understood. Here, we developed an imaging pipeline that integrates fast, label-free live-cell imaging with deep learning-based image analysis to quantitatively track and compare the initial steps of extravasation--cell landing and arrest on an endothelial monolayer--under physiological flow conditions. We find that pancreatic ductal adenocarcinoma (PDAC) cells exhibit variable adhesion strength and flow sensitivity. Remarkably, some PDAC cells demonstrate comparable endothelial engagement as leukocytes, preferentially arresting at endothelial junctions, potentially due to increased stiffness at these sites, which leads to exposure to the underlying basal extracellular matrix. PDAC cells also tend to cluster in regions with high, heterogeneous expression of the endothelial CD44 receptor. Simulations suggest that clustering results from the combination of CD44-mediated attachment and localized flow disturbances that facilitate subsequent cell attachment. Targeting CD44 using siRNA or function-blocking antibodies, or degrading its ligand hyaluronic acid (HA), almost completely abolishes PDAC cell attachment. Overall, we demonstrate that cancer and immune cells share both common and unique features in endothelial adhesion under flow, and identify CD44 and HA as key mediators of PDAC cell arrest.

cell biology↗

bioRxiv2024

Neuronal and non-neuronal functions of the synaptic cell adhesion molecule, neurexin, in Nematostella vectensis.

The transition from diffusion-mediated cell-cell communication to faster and more targeted synaptic signaling in animal nervous systems has long been of interest to evolutionary biologists. Although genome sequencing of early-diverging metazoans has revealed the broad distribution of synapse-related genes among them, synaptic structures have been observed only in Cnidaria, the sister group to Bilateria. How synaptic machinery evolved remains largely unknown. In this study, we investigated the function of neurexins (Nrxns), a core family of presynaptic cell adhesion molecules with critical roles in bilaterian chemical synapses, using the cnidarian model, Nematostella vectensis. Neural Nrxns, named delta-Nrxns, are expressed mainly in neuronal cell clusters that exhibit both peptidergic and classical neurotransmitter signaling. Knockdown of Nrxn{delta} genes reduced spontaneous peristalsis of N. vectensis polyps. Interestingly, gene knockdown and pharmacological studies suggested that Nrxn{delta} is involved in glutamate- and glycine-mediated signaling rather than peptidergic signaling. Knockdown of the epithelial Nrxn in N. vectensis revealed a major role in cell adhesion, particularly between ectodermal and endodermal epithelia. Overall, this study provides molecular, functional, and cellular insights into the ancestral, non-neural function of Nrxns, as well as key information for understanding how and why this family of cell adhesion molecules was recruited to synaptic machinery.

evolutionary biology↗

bioRxiv2022

Trait-specific indirect effects underlie variation in the response of spiders to cannibalistic social partners

Organisms may respond in different ways to the risk posed by conspecifics, but the cause of such variation remains elusive. Here, we use a half-sib/full-sib design to evaluate the contribution of (indirect) genetic or environmental effects to the behavioral response of the cannibalistic wolf spider Lycosa fasciiventris (Dufour, 1835) towards conspecific cues. Spiders showed variation in relative occupancy time, activity, and velocity on patches with or without conspecific cues, but direct genetic variance was only found for occupancy time. These three traits were correlated and could be lumped in a principal component: spiders spending more time in patches with conspecific cues moved less and at a lower rate in those areas. Genetic and/or environmental components of carapace width and weight loss in the social partner were significantly correlated with the principal component of focal individuals. Variation in these traits may reflect the quality and/or quantity of cues produced by social partners, hence focal individuals were likely behaving along a continuum of strategies in response to the risk posed by social partners. Therefore, environmental and genetic trait variation in the social partners may be key to maintain trait diversity in focal individuals, even in the absence of direct genetic variation.

evolutionary biology↗

bioRxiv2022

Systematic analysis of transcriptional and epigenetic effects of genetic variation in Kupffer cells enables discrimination of cell intrinsic and environment-dependent mechanisms

Noncoding genetic variation is a major driver of phenotypic diversity but determining the underlying mechanisms and the cell types in which it acts remain challenging problems. Here, we investigate the impact of natural genetic variation provided by phenotypically diverse inbred strains of mice on gene expression and epigenetic landscapes of Kupffer cells. Analysis of gene expression in Kupffer cells and other liver cell types derived from C57BL/6J, BALB/cJ and A/J mice provided evidence for strain-specific differences in environmental factors influencing Kupffer cell phenotypes, including preferential Leptin signaling in BALB/cJ Kupffer cells. Systematic analysis of transcriptomic and epigenetic data from F1 hybrids of these mice, and transcriptomic data from strain-specific Kupffer cells engrafted into a common host enabled quantitative assessment of cis versus trans effects of genetic variation on gene expression and an estimate of cell autonomous versus non cell autonomous effects. Under homeostatic conditions, trans effects of genetic variation were dominant, with the majority of trans regulation being non cell autonomous. In contrast, strain specific responses to acutely administered LPS were primarily associated with genetic variation acting in cis to modify response elements for lineage determining and signal dependent transcription factors. Collectively, these findings reveal cell intrinsic and environmental effects of natural genetic variation on gene expression, demonstrate the use of enhancers as detectors of trans effects of genetic variation, and provide a new resource for understanding the impact of genetic variation on gene expression in Kupffer cells.

genomics↗

bioRxiv2021

Myosin-X-dependent assembly of the extracellular matrix limits breast cancer invasion

Ductal carcinoma in situ (DCIS) is a pre-invasive stage of breast cancer, where the tumor is encapsulated by a basement membrane (BM). At the invasive phase, the BM barrier is compromised enabling tumor cells to escape into the surrounding stroma. The molecular mechanisms that establish and maintain an epithelial BM barrier in vivo are poorly understood. Myosin-X (MYO10) is a filopodia-inducing motor protein implicated in metastasis and poor clinical outcome in patients with invasive breast cancer (IBC). We compared MYO10 expression in patient-matched normal breast tissue and DCIS lesions and found elevated MYO10 expression in DCIS samples, suggesting that MYO10 might facilitate the transition from DCIS to IBC. Indeed, MYO10 promoted the formation of filopodia and cell invasion in vitro and positively regulated the dissemination of individual cancer cells from IBC lesions in vivo. However, MYO10-depleted DCIS xenografts were, unexpectedly, more invasive. In these xenografts, MYO10 depletion compromised BM formation around the lesions resulting in poorly defined tumor borders and increased cancer cell dispersal into the surrounding stroma. Moreover, MYO10-depleted tumors showed increased EMT-marker-positive cells, specifically at the tumor periphery. We also observed cancer spheroids undergoing rotational motion and recruiting BM components in a filopodia-dependent manner to generate a near-continuous extracellular matrix boundary. Taken together, our data identify a protective role for MYO10 in early-stage breast cancer, where MYO10-dependent tumor cell protrusions support BM assembly at the tumor-stroma interface to limit cancer progression, and a pro-invasive role that facilitates cancer cell dissemination at later stages. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/464987v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@d90a4eorg.highwire.dtl.DTLVardef@133ba9borg.highwire.dtl.DTLVardef@1204a05org.highwire.dtl.DTLVardef@dba254_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Filopodia sculpt the tumor-proximal stroma in pre-invasive ductal carcinoma in situ (DCIS). - Filopodia-dependent basement membrane (BM) assembly limits invasive transition of DCIS-like tumors in vivo. - Loss of MYO10-dependent filopodia impairs BM assembly and induces an EMT-like phenotype at the tumor-stroma interface in vivo. - MYO10 filopodia are anti-invasive in DCIS but facilitate dissemination in invasive breast cancer.

cell biology↗

bioRxiv2020

An integrated genomics approach towards deciphering human genome codes shaping HIV-1 proviral transcription and fate

A large body of work has revealed fundamental principles of HIV-1 integration into the human genome. However, the effect of the integration site to proviral transcription activity has so far remained elusive. Here we combine open-source, large-scale datasets including epigenetics, transcriptome, and 3D genome architecture to interrogate the chromatin states, transcription activity landscape, and nuclear sub-compartments around HIV-1 integration sites in CD4+ T cells to decipher human genome codes shaping the transcription of proviral classes defined based on their position and orientation in the genome. Using a Hidden Markov Model, we describe the importance of specific chromatin states and genome architecture in the control of HIV-1 transcription activity. Additionally, implementation of a machine-learning logistic regression model reveals upstream chromatin accessibility, transcription activity, and categorical nuclear sub-compartments as optimal features predicting HIV-1 transcriptional outcomes. We finally demonstrate clinical relevance by interrogating the positions of intact proviruses persisting in patients under suppressive therapy and provide a compass compatible with clinical decision-making.

genomics↗

bioRxiv2019

Mechano-responsiveness of fibrillar adhesions on stiffness-gradient gels

Fibrillar adhesions are important structural and adhesive components in fibroblasts that are critical for fibronectin fibrillogenesis. While nascent and focal adhesions are known to respond to mechanical cues, the mechanoresponsive nature of fibrillar adhesions remains unclear. Here, we used ratiometric analysis of paired adhesion components to determine an appropriate fibrillar adhesion marker. We found that active 5{beta}1-integrin exhibits the most definitive fibrillar adhesion localisation compared to other proteins, such as tensin-1, reported to be in fibrillar adhesions. To elucidate the mechanoresponsiveness of fibrillar adhesions, we designed and fabricated thin polyacrylamide (PA) hydrogels, embedded with fluorescently labelled beads, with physiologically relevant stiffness gradients using a cost-effective and reproducible technique. We generated a correlation curve between bead density and hydrogel stiffness, thus allowing the use of bead density as a readout of stiffness, eliminating the need for specialised knowhow including atomic force microscopy (AFM). We find that stiffness promotes the growth of fibrillar adhesions in a tensin-dependent manner. Thus, the formation of these extracellular matrix-depositing structures is coupled to the mechanical parameters of the cell environment and may enable cells to fine-tune their matrix environment in response to alternating physical conditions.

cell biology↗

bioRxiv2019

Fluctuation-based Super-Resolution Traction Force Microscopy

Cellular mechanics play a crucial role in tissue morphogenesis and homeostasis and are often misregulated in disease. Traction force microscopy (TFM) is one of the key methods that has enabled researchers to study fundamental aspects of mechanobiology; however, the power of TFM is limited by poor resolution and low throughput. Here, we propose a simplified protocol and imaging strategy, relying on super-resolution microscopy enabled by fluorophore fluctuation analysis, to enhance the output of TFM, by increasing both bead density as well as the accuracy of bead tracking in TFM gels. Our analysis pipeline can be used on either camera-based confocal or widefield microscopes and is fully compatible with available TFM analysis software. In addition, we demonstrate that our workflow can be used to gain biologically relevant information and is suitable for long-term live measurement of traction forces even in light-sensitive cells. Finally, we propose that our strategy could be used to considerably simplify the implementation of TFM screens. Our streamlined protocol can be performed with minimal hardware and software investment, and has the potential to standardize high-resolution TFM.

cell biology↗

bioRxiv2019

Integrin binding dynamics modulate ligand-specific mechanosensing in mammary gland fibroblasts

The link between the modulation of integrin activity and cellular mechanosensing of tissue rigidity, especially on different extracellular matrix ligands, remains poorly understood. Here, we find that primary mouse mammary gland stromal fibroblasts (MSFs) are able to spread efficiently on soft collagen-coated substrates, resembling the soft mammary gland tissue. In addition, MSFs generate high forces and display nuclear YAP at a low matrix stiffness, supported by mature focal adhesions, prominent actin stress fibers, and myosin phosphorylation. We describe that loss of the cytosolic integrin inhibitor, SHARPIN, impedes MSF spreading specifically on soft type I collagen but not on fibronectin. Through quantitative experiments and computational modelling, we find that SHARPIN-deficient MSFs display faster force-induced unbinding of adhesions from collagen-coated beads. Faster unbinding, in turn, impairs force transmission in these cells, particularly, at the stiffness optimum observed for wild-type cells, and increases actin retrograde flow. Mechanistically, we link the impaired mechanotransduction of SHARPIN-deficient cells on collagen to reduced levels of the collagen-binding integrin 11{beta}1. Our results unveil a collagen-specific mechanosensing mechanism and suggest a key function for integrin activity regulation and integrin 11{beta}1 in MSF mechanotransduction.

cell biology↗

bioRxiv2018

Mucosal CD8+ T cell responses induced by an MCMV based vaccine vector confer protection against influenza challenge

Cytomegalovirus (CMV) is a ubiquitous {beta}-herpesvirus that establishes life-long latent infection in a high percentage of the population worldwide. CMV induces the strongest and most durable CD8+ T cell response known in human clinical medicine. Due to its unique properties, the virus represents a promising candidate vaccine vector for the induction of persistent cellular immunity. To take advantage of this, we constructed a recombinant murine CMV (MCMV) expressing an MHC-I restricted epitope from influenza A virus (IAV) H1N1 within the immediate early 2 (ie2) gene. Only mice that were immunized intranasally (i.n.) were capable of controlling IAV infection, despite the greater potency of the intraperitoneally (i.p.) vaccination in inducing a systemic IAV-specific CD8+ T cell response. The protective capacity of the i.n. immunization was associated with its ability to induce IAV-specific tissue-resident memory CD8+ T (CD8TRM) cells in the lungs. Our data demonstrate that the protective effect exerted by the i.n. immunization was critically mediated by antigen-specific CD8+ T cells. CD8TRM cells promoted the induction of IFN{gamma} and chemokines that facilitate the recruitment of antigen-specific CD8+ T cells to the lungs. Overall, our results showed that locally applied MCMV vectors could induce mucosal immunity at sites of entry, providing superior immune protection against respiratory infections.\n\nAuthor summaryVaccines against influenza typically induce immune responses based on antibodies, small molecules that recognize the virus particles outside of cells and neutralize them before they infects a cell. However, influenza rapidly evolves, escaping immune recognition, and the fastest evolution is seen in the part of the virus that is recognized by antibodies. Therefore, every year we are confronted with new flu strains that are not recognized by our antibodies against the strains from previous years. The other branch of the immune system is made of killer T cells, which recognize infected cells and target them for killing. Influenza does not rapidly evolve to escape T cell killing; thus, vaccines inducing T-cell responses to influenza might provide long-term protection. We introduced antigen from influenza into the murine cytomegalovirus (MCMV) and used it as a vaccine vector inducing Killer T-cell responses of unparalleled strength. Our vector controlled flu replication and provided relief to infected mice, but only if we administered it through the nose, to activate killer T cells that will persist in the lungs close to the airways. Therefore, our data show that the subset of lung-resident killer T cells is sufficient to protect against influenza.

immunology↗

bioRxiv2018

Superresolution architecture of pluripotency guarding adhesions

Human pluripotent stem cells (hPSC) can generate almost all adult cell lineages. While it is clear that key transcriptional programmes are important elements for maintaining pluripotency, the equally essential requirement for cell adhesion to specific extracellular matrix components remains poorly defined. Our recent observation that hPSC colonies form unusually large \"cornerstone\" focal adhesions (FA), distinct from parental somatic cells, that are lost following differentiation, emphasises the potential of these atypical FA as gatekeepers of pluripotency. Here, using nanopatterns, we further demonstrate that physical restriction of adhesion size, in hPSC colonies, is sufficient to trigger differentiation. Using superresolution two-colour interfero-metric photo-activated localization microscopy (iPALM), we examined the three-dimensional architecture of these cornerstone adhesions and report vertical lamination of FA proteins with three main structural peculiarities: 1) integrin {beta}5 and talin are present at high density, at the edges of cornerstone FA, adjacent to a vertical kank-rich protein wall. 2) Vinculin localises higher than expected with respect to the substrata and displays a head-above-tail orientation, and 3) surprisingly, actin and -actinin are present in two discrete layers, a previously undescribed localisation for these proteins. Finally, we report that depletion of kanks diminishes FA patterning, and actin organisation within the colony, indicating a key role for kanks in hPSC colony architecture.

cell biology↗

bioRxiv2017

Direct in vivo mapping of functional suppressors in glioblastoma genome

Glioblastoma (GBM) is one of the deadliest cancers, with limited effective treatments and single-digit five-year survival 1-7. A causative understanding of genetic factors that regulate GBM formation is of central importance 8-19. However, a global, quantitative and functional understanding of gliomagenesis in the native brain environment has been lacking due to multiple challenges. Here, we developed an adeno-associated virus (AAV) mediated autochthonous CRISPR screen and directly mapped functional suppressors in the GBM genome. Stereotaxic delivery of an AAV library targeting significantly mutated genes into fully immunocompetent conditional Cas9 mice robustly led to gliomagenesis, resulting in tumors that recapitulate features of human GBM. Targeted capture sequencing revealed deep mutational profiles with diverse patterns across mice, uncovering in vivo roles of previously uncharacterized factors in GBM such as immune regulator B2m, zinc finger protein Zc3h13, transcription repressor Cic, epigenetic regulators Mll2/3 and Arid1b, alongside canonical tumor suppressors Nf1 and Pten. Comparative cancer genomics showed that the mutation frequencies across all genes tested in mice significantly correlate with those in human from two independent patient cohorts. Co-mutation analysis identified frequently co-occurring driver combinations, which were validated using AAV minipools, such as Mll2, B2m-Nf1, Mll3-Nf1 and Zc3h13-Rb1. Distinct from Nf1-oncotype tumors, Rb1-oncotype tumors exhibit undifferentiated histopathology phenotype and aberrant activation of developmental reprogramming signatures such as Homeobox gene clusters. The secondary addition of Zc3h13 or Pten mutations drastically altered the gene expression profiles of Rb1 mutants and rendered them more resistant to the GBM chemotherapeutic temozolomide. Our study provides a systematic functional landscape of GBM suppressors directly in vivo, opening new paths for high-throughput molecular mapping and cancer phenotyping.

systems biology↗

bioRxiv2017

Pooled AAV-CRISPR Screen with Targeted Amplicon Sequencing

High-resolution, high-throughput direct in vivo screening of functional genetic factors in native tissues has long been challenging. Adeno-associated viruses (AAV) are powerful carriers of transgenes and have been shown to mediate efficient genome editing in various organs in mice. Here, we developed a new technological approach, Pooled AAV-CRISPR Screen with Targeted Amplicon Sequencing (PASTAS), and demonstrated its application for directly mapping functional cancer driver variants in the mouse liver in an autochthonous manner. Intravenous delivery of an AAV-CRISPR library targeting a set of the most frequently mutated tumor suppressor genes into fully immunocompetent conditional Cas9 knock-in mice consistently generated highly complex autochthonous liver tumors. The molecular landscapes of these genetically diverse tumors were mapped out by deep direct readout of Cas9-generated variants at predicted sgRNA cut sites using molecular inversion probe sequencing. Co-occurrence and correlation analyses as well as validation with lower complexity minipools further confirmed the potency of various co-mutated drivers. The PASTAS method can be applied to virtually any gene sets, any cancer types, or any type of in vivo genetic studies other than cancer.

systems biology↗