Biology subjects

Fernandez, P.

Publications and source records attributed to Fernandez, P..

10 recordsLinked to original sources

bioRxiv2026

Podoplanin shapes epidermal morphogenesis and coordinates stem cell and epidermal-dermal responses during inflammatory remodelling

Skin development and adaptation to inflammatory stress require keratinocytes to coordinate changes in cell behaviour with tissue organisation. Cell adhesion and the cortical cytoskeleton support the structural plasticity underlying these responses. Here, using complementary mouse models of global podoplanin deletion and conditional deletion in basal keratinocytes driven by keratin 5-Cre (K5Cre), we identify a role for the small transmembrane glycoprotein podoplanin in maintaining basal layer organisation and coordinating differentiation with barrier acquisition during development, as well as in inflammatory skin remodelling. Podoplanin expression was dynamically regulated during epidermal morphogenesis, becoming enriched in basal epithelial compartments before declining postnatally in the interfollicular epidermis. Both deletion models exhibited basal layer disorganisation, altered division orientation and increased epidermal thickness. Premature or expanded expression of differentiation markers was accompanied by delayed barrier acquisition, indicating that podoplanin loss uncouples differentiation marker expression from functional maturation. Barrier function subsequently recovered despite persistent histological abnormalities. In primary keratinocytes, podoplanin deficiency disrupted junctional actin organisation, reduced ERM phosphorylation and impaired junctional enrichment of pERM and doubly phosphorylated myosin light chain 2 (ppMLC2), despite largely preserved recruitment of adhesion proteins. In adult skin, K5Cre-mediated deletion altered differentiation marker dynamics following topical application of the proinflammatory agent 12-O-tetradecanoylphorbol-13-acetate (TPA), while the epidermal thickening response remained largely comparable to controls. These epidermal changes were accompanied by altered dermal thickness dynamics and an absence of TPA-induced podoplanin expression in dermal fibroblasts. Furthermore, TPA reduced the number of BrdU-retaining cells in the interfollicular epidermis of controls but not K5Cre-mediated conditional podoplanin knockout mice. This difference is consistent with impaired activation or mobilisation of slow-cycling cells, suggesting altered responsiveness within the epidermal stem and progenitor compartment. Together, these findings establish keratinocyte-expressed podoplanin as a regulator of epidermal organisation and functional maturation, with effects extending beyond the epithelium to shape the dermal response to inflammatory challenge.

cell biology↗

bioRxiv2026

Refinement and maintenance of receptive field size in primary visual cortex occurs without visual experience in mice

A critical step in visual cortical maturation is refinement of receptive field (RF) size, producing higher acuity vision. This was previously studied using species with well-developed vision (e.g., carnivores, primates), in which visual experience was necessary for refinement but not maintenance of RFs in visual cortex. In contrast, in Syrian hamsters, a crepuscular species with low visual acuity, dark rearing had no effect on RF refinement in juveniles, but RFs re-enlarged in adulthood, resulting in reduced acuity. These inter-species differences raise the question of whether the need for visual experience is primarily related to the phylogenetic position of the species or to its ecological niche. Here we report that dark rearing had no effect on development or maintenance of RF properties of visual cortical neurons in nocturnal mice. Mice with lifelong visual deprivation refined and maintained their RF size over time. Furthermore, the development of stimulus direction tuning was unaffected by dark rearing. In contrast, surround suppression, orientation tuning and the sharpness of direction tuning were abnormal in dark reared mice. These and our previous results from hamsters show that species living in an ecological niche with minimal daylight exposure require little to no visual experience to develop and maintain refined RFs. This study is an important step in developing a better understanding of the role of visual experience in the development of visual processing circuitry and suggests that diurnal mammals may be a better model for human visual cortical development than mice. SIGNIFICANCE STATEMENTThe role of visual experience in development and plasticity of receptive fields in visual cortex was initially studied using animals with well-developed visual systems (carnivores, primates). Mice have been used more recently, primarily because of genetic manipulations. Now that gene alteration is possible in other species, whether mice are the best choice for visual development and plasticity studies needs reevaluation. We assayed the role of visual experience in mouse visual cortical development, focusing on receptive field refinement. We report that visual experience is unnecessary for the refinement of receptive fields in visual cortex, suggesting that mice (Mus musculus) may not be the best animal model to demonstrate how visual experience influences the development of visual cortical circuitry in humans.

neuroscience↗

bioRxiv2026

A Novel Secretome Rewrites the Immune Response in Viral Acute Respiratory Distress Syndrome

BackgroundHyperinflammatory syndromes such as viral acute respiratory distress syndrome (ARDS) demand immunotherapies that are safe and effective at suppressing cytokine storm. As a novel treatment for ARDS, PRS CK STORM is proposed as a next-generation cell-free secretome derived from co-cultures of M2 macrophages and mesenchymal stromal cells. MethodsWe performed a double-blind, randomized controlled trial to test the effects of PRS CK STORM in K18-hACE2 transgenic mice infected intranasally with 105 PFU of SARS-CoV-2 BE.1.1. This was complemented by a mechanistic analysis of this secretome using transcriptomic and COX2 enzymatic activity studies, as well as a compositional analysis of its proteomic and miRNA profile. ResultsIn a lethal SARS-CoV-2 ARDS mouse model, PRS CK STORM significantly improved lung histopathology to a degree on par with corticosteroids, while stimulating angiogenesis in damaged lung tissue. Early and late cytokine profiling showed marked reductions in IFN-{gamma}. In response to PRS CK STORM treatment, transcriptomic analyses in inflamed macrophages revealed robust downregulation of key proinflammatory drivers (MyD88, TRAF6, IKK2, NF-{kappa}B, COX2). In vitro enzymatic assays confirmed potent, dose-dependent inhibition of COX2, with high inter-batch reproducibility. A compositional analysis revealed this secretome to be rich in anti-inflammatory miRNAs, immune-modulating proteins, and regenerative factors. ConclusionsPRS CK STORM operates as a multi-target immune recalibrator, enabling broad downregulation of pathological inflammation while promoting tissue repair. Its off-the-shelf, GMP-manufactured format ensures reproducibility and scalability, offering a novel resolution pharmacology approach for cytokine storm syndromes originated from ARDS and beyond.

immunology↗

bioRxiv2024

Transcriptional control of C. elegans male tail tip morphogenesis by DMD-3

Sexual dimorphic morphogenesis is governed by DM-domain transcription factors (TFs) in many animals, but how these transcriptional control links to the morphogenetic mechanisms is insufficiently known. The DM-domain TF DMD-3 in C. elegans is the master regulator of a male-specific development that changes the shape of the tail tip from long and pointed in larvae to short and round in adults. This tail tip morphogenesis (TTM) requires cell-shape changes, cell migration and fusion. To understand how transcriptional regulation by DMD-3 governs TTM, we used male-specific ChIP-seq to identify its direct targets. We found 1,755 DMD-3 bound sites. We identify a DMD-3 associated binding motif and validate its function in TTM. This motif is similar to the binding motif of EOR-1, and we suggest that DMD-3 acts cooperatively with EOR-1 and possibly other TFs. DMD-3 targets 270 genes that play a role in TTM. These genes include other TFs but also effectors and components of morphogenetic mechanisms. By deleting the DMD-3 bound region endogenously and observing changes in reporter expression and tail tip phenotypes, we identify tissue specific enhancers in the cis-regulatory region of fos-1, pan-1, nmy-2 and hmr-1 that play a role in TTM. For fos-1, we propose that a feed-forward loop is responsible for tail-tip specific increase of gene-expression. This study provides insights into the architecture of the genetic regulatory network controlling a morphogenetic process. Article SummaryDM domain transcription factors are often responsible for sexually dimorphic morphogenesis, but how they connect to morphogenetic mechanisms is insufficiently known. Here, we use ChIP-seq to determine the direct targets of DMD-3, which is the master regulator of male-specific tail tip morphogenesis (TTM) in C. elegans. We find that DMD-3 targets 270 TTM genes which include other transcription factors but also effectors and components of morphogenetic mechanisms. This study provides insights into the architecture of the genetic regulatory network controlling a morphogenetic process.

developmental biology↗

bioRxiv2024

Inbreeding and gallbladder cancer risk: Homozygosity associations adjusted for indigenous American ancestry, BMI and genetic risk of gallstone disease

Latin Americans have a rich genetic make-up that translates into heterogeneous fractions of the autosomal genome in runs of homozygosity (FROH), and heterogeneous types and proportions of indigenous American ancestry. While autozygosity has been linked to several human diseases, very little is known about the relationship between inbreeding, genetic ancestry and cancer risk in Latin Americans. Chile has one of the highest incidences of gallbladder cancer (GBC) in the world, and here we investigated the association between inbreeding, GBC, gallstone disease (GSD) and body mass index (BMI) in 4029 genetically admixed Chileans. We calculated individual FROH above 1.5 Mb and weighted polygenic risk scores for GSD, and applied multiple logistic regression to assess the association between homozygosity and GBC risk. We found that homozygosity was due to a heterogeneous mixture of genetic drift and consanguinity in the study population. Although we found no association between homozygosity and overall GBC risk, we detected interactions between FROH and sex, age, and genetic risk of GSD on GBC risk. Specifically, the increase in GBC risk per 1% FROH was 19% in men (P-value = 0.002), 30% in those under 60 years of age (P-value = 0.001), and 12% in those with a genetic risk of GSD above the median (P-value = 0.01). The present study highlights the complex interplay between inbreeding, genetic ancestry and genetic risk of GSD in the development of GBC. The applied methodology and our findings underscore the importance of considering the population-specific genetic architecture, along with sex- and age specific-effects, when investigating the genetic basis of complex traits in Latin Americans.

genetics↗

bioRxiv2023

Ensembling Unets, sparse representation and low dimensional visualization for rare chromosomal aberration detection in light microscopy images

AO_SCPLOWBSTRACTC_SCPLOWIn biological dosimetry, a radiation dose is estimated using the average number of chromosomal aberration per peripheral blood lymphocytes. To achieve an adequate precision in the estimation of this average, hundreds of cells must be analyzed in 2D microscopy images. Currently, this analysis is performed manually, as conventional computer vision techniques struggle with the wide variety of shapes showcased by chromosomes. The false discovery rate of current automated detection systems is high and variable, depending on small variations in data quality (chromosome spread, illumination variations ...), which makes using it in a fully automated fashion impossible. Automating chromosomal aberration is needed to reduce diagnosis time. Furthermore, an automated system can process more images, which improves confidence intervals around the estimated radiation dose. We build an object detection model to automate chromosomal aberration detection using recent advances in deep convolutional neural networks and statistical learning. We formulated the problem of rare aberration detection as a heatmap regression problem requiring the minimization of a sparsity-promoting loss to reduce the false alarm rate. Our Unet-based approach is analoguous to a one-stage object detector, and keeps the number of hyperparameters to a minimum. Finally, we demonstrate large performance improvements using an ensemble of checkpoints collected during a single run of training. A PCA-based strategy is used to provide cues for interpretation of our deep neural network-based model. The methodology is demonstrated on real, large, and challenging datasets depicting rare chromosomal aberrations and is favorably compared to a reference dosimetry technique.

bioinformatics↗

bioRxiv2023

Functional diversity reduces the risk of hydraulic failure in tree mixtures through hydraulic disconnection

Forest ecosystems are increasingly threatened by anthropogenic pressures, especially by the increase in drought frequency and intensity. Tree species mixtures could improve resilience to diverse global anthropogenic pressures. However, there is still little consensus on how tree diversity affects water stress. Although some studies suggest that mixing species with different drought response strategies could be beneficial, the underlying mechanisms have seldom been identified. By combining a greenhouse experiment and a soil-plant-atmosphere hydraulic model, we explored whether mixing a drought avoidant (Pinus halepensis) and a drought tolerant (Quercus ilex) tree species could reduce plant water stress (defined as the risk of hydraulic failure) during extreme drought, compared to their respective monocultures. Our experiment showed that mixing species with divergent drought response strategies had a neutral effect on the drought-avoidant species and a positive effect on the drought-tolerant species. The model simulations further suggested that the beneficial effect of mixture on plant water stress during extreme drought was related to changes in the hydraulic connection of the plant from both the soil and the atmosphere. The ability of the drought-avoidant species to disconnect from the soil and the atmosphere limits its exposure to water stress, whereas the ability of the drought-tolerant species to increase its hydraulic connection to the soil lowers its hydraulic risk. This study brings a new insight on the mechanisms and traits combinations improving drought resistance in diversified forests and plantations, with important implications for forest management under climate change.

ecology↗

bioRxiv2021

Effect of ozone exposure on Amyotrophic Lateral Sclerosis (ALS) pathology using a mice model of TDP-43 proteinopathy

BackgroundOzone (O3), one of the main photochemical pollutants in the atmosphere today, is a serious health risk factor. Although the effects of O3 exposure have been documented on many diseases, they have not yet been examined on Amyotrophic Lateral Sclerosis (ALS)- a fatal progressive and neurodegenerative disease. ObjectivesTo investigate the effect of the O3 exposure in a mice model of TDP-43 proteinopathy, exploring a possible association between the O3 exposure and the ALS pathogenesis. MethodsTDP-43A315T and wild-type (WT) mice were exposed to O3 (0.25 ppm) or filtered air (FA) for 15 days (4 hours/day). We assessed (1) weight loss (2) motor performance (3) plasma glucose content and (4) metabolic markers from plasma samples of the animals. ResultsThroughout the experiment, we observed a progressive decline in body weight and the motor coordination in TDP-43A315T mice compared to WT controls. Although there was a trend, there were no significant differences in the decline of body weight of TDP-43A315T mice when exposed to either FA or O3. In O3-TDP-43A315T mice, the disease duration lasted longer. In addition, O3-TDP-43A315T mice showed improvements in motor performance as well TDP-43A315T mice were hypoglycemic compared to WT mice. However, FA-TDP-43A315T mice showed lower plasma glucose levels at the disease end-stage. We found altered levels of adipokines and metabolic proteins in TDP-43A315T mice compared to WT controls. A positive correlation was found among GIP and glucagon compared to insulin concentrations in control mice. Interestingly, resistin, Gastric Inhibitory Peptide (GIP), Glucagon Like Peptide 1 (GIP-1) and insulin levels were higher in O3-TDP-43A315T mice. DiscussionWe provide new evidence about a mechanistic link between O3 exposure and the improvement of the metabolic disturbances present in TDP-43A315T mice. Further studies are needed to corroborate the obtained results as they warrant to understanding the underlying mechanisms.

neuroscience↗

bioRxiv2019

Mechanical plasticity of the ECM directs invasive branching morphogenesis in human mammary gland organoids

Although branching morphogenesis is central for organogenesis in diverse organs, the underlying self-organizing principles have yet to be identified. Here, we show that invasive branching morphogenesis in human mammary organoids relies on an intricate tension-driven feedback mechanism, which is based on the nonlinear and plastic mechanical response of the surrounding collagen network. Specifically, we demonstrate that collective motion of cells within organoid branches generates tension that is strong enough to induce a plastic reorganization of the surrounding collagen network which results in the formation of mechanically stable collagen cages. Such matrix encasing in turn directs further tension generation, branch outgrowth and plastic deformation of the matrix. The identified mechanical feedback-loop sets a framework to understand how mechanical cues direct organogenesis.

developmental biology↗

bioRxiv2019

A custom genotyping array reveals population-level heterogeneity for the genetic risks of prostate cancer and other cancers in Africa

Although prostate cancer is the leading cause of cancer mortality for African men, the vast majority of known disease associations have been detected in European study cohorts. Furthermore, most genome-wide association studies have used genotyping arrays that are hindered by SNP ascertainment bias. To overcome these disparities in genomic medicine, the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network has developed a genotyping array that is optimized for African populations. The MADCaP Array contains more than 1.5 million markers and an imputation backbone that successfully tags over 94% of common genetic variants in African populations. This array also has a high density of markers in genomic regions associated with cancer susceptibility, including 8q24. We assessed the effectiveness of the MADCaP Array by genotyping 399 prostate cancer cases and 403 controls from seven urban study sites in sub-Saharan Africa. We find that samples from Ghana and Nigeria cluster together, while samples from Senegal and South Africa yield distinct ancestry clusters. Using the MADCaP array, we identified cancer-associated loci that have large allele frequency differences across African populations. Polygenic risk scores were also generated for each genome in the MADCaP pilot dataset, and we found that predicted risks of CaP are lower in Senegal and higher in Nigeria.\n\nSignificanceWe have developed an Africa-specific genotyping array which enables investigators to identify novel disease associations and to fine-map genetic loci that are associated with prostate and other cancers.

genomics↗