Biology subjects

Palacios, J.

Publications and source records attributed to Palacios, J..

5 recordsLinked to original sources

bioRxiv2024

Single-cell RNA sequencing on formalin-fixed and paraffin-embedded (FFPE) tissue identified multi-ciliary cells in breast cancer

The purpose of this study was to evaluate the suitability of paraffin-embedded (FFPE) samples and fixed fresh (FF) samples for single-cell RNA sequencing (scRNAseq). To this end, we compared whether single-cell profiles from FFPE and matched FF tissue samples from one invasive carcinoma of no especial type carcinoma (invasive ductal carcinoma -IDC) and one invasive lobular carcinoma (ILC) were similar when captured using the common immunohistochemical (IHC) and immune features of the tumors. FF and FFPE tissue derived libraries showed high-quality parameters. The cell heterogeneity obtained was similar, although, there were some differences in the number of cells captured, but there were no specific cell populations captured exclusively by one of the two different approaches. The combined analysis of the four samples identified six types of epithelial cells (normal basal cells, four subpopulations of neoplastic cells in the IDC and one in the ILC), and different tumoral microenvironment populations. scRNAseq results from epithelial neoplastic cells were concordant with common IHC markers. In addition, after quantitative assessment of the whole slide images using QuPath, the proportion of immune cells identified by IHQ in FFPE sections were similar to those obtained by scRNAseq. Confirming the suitability of scRNAseq using FFPE tissue, this technique identified one subpopulation of neoplastic cells present only in the IDC, characterized by the expression of genes related with multi-ciliated cell (MCC) differentiation (FOXJ1, ROPN1L, TPPP3, CFAP45). IHC analysis of FOXJ1 expression confirmed the presence of positive cells only in the IDC in a similar proportion to that obtained by scRNAseq. Analysis of FOXJ1 in a cohort of 214 ER-positive invasive carcinomas demonstrated protein expression in at least 1% of cells in 33% of tumors, suggesting frequent focal MCC differentiation. Our results support the suitability of scRNAseq analysis using FFPE tissue and identified a subpopulation of neoplastic MCC in breast cancer.

cancer biology↗

bioRxiv2024

Spatial transcriptomics unveils the in situ cellular and molecular hallmarks of the lung in fatal COVID-19

Severe Coronavirus disease 2019 (COVID-19) induces heterogeneous and progressive diffuse alveolar damage (DAD) highly disrupting lung tissue architecture and homeostasis, hampering disease management leading to fatal outcomes. Characterizing DAD pathophysiology across disease progression is of ultimate importance to better understand the molecular and cellular features driving different DAD patterns and to optimize treatment strategies. To contextualize the interplay between cell types and assess their distribution, spatial transcriptomics (ST) techniques have emerged, allowing unprecedented resolution to investigate spatial architecture of tissues. To this end, post-mortem lung tissue provides valuable insights into cellular composition and their spatial relationships at the time of death. Here, we have leveraged VisumST technology in post-mortem COVID-19 induced acute and proliferative DAD lungs including control samples with normal morphological appearance, to unravel the immunopathological mechanisms underlying DAD, providing novel insights into cellular and molecular communication events driving DAD progression in fatal COVID-19. We report a progressive loss of endothelial cell types, pneumocytes type I and natural killer cells coupled with a continuous increase of myeloid and stromal cells, mostly peribronchial fibroblasts, over disease progression. Spatial organization analysis identified variable cellular compartments, ranging from major compartments defined by cell type lineages in control lungs to increased and more specific compartmentalization including immune-specific clusters across DAD spectrum. Importantly, spatially informed ligand-receptor interaction (LRI) analysis revealed an intercellular communication signature defining COVID-19 induced DAD lungs. Transcription factor (TF) activity enrichment analysis identified TGF-B pathway as DAD driver, highlighting SMAD3 and SMAD7 TFs activity role during lung fibrosis. Integration of deregulated LRIs and TFs activity allowed us to propose a downstream intracellular signaling pathway in peribronchial fibroblasts, suggesting potential novel therapeutic targets. Finally, spatio-temporal trajectories analysis provided insights into the alveolar epithelium regeneration program, characterizing markers of pneumocytes type II differentiation towards pneumocytes type I. In conclusion, we provide a spatial characterization of lung tissue architecture upon COVID-19 induced DAD progression, identifying molecular and cellular hallmarks that may help optimize treatment and patient management.

pathology↗

bioRxiv2024

The G-Protein Couple Receptor Kinase 2 (GRK2) Orchestrates Hair Follicle Homeostasis

Tightly regulated cell-cell and cell-niche intercommunications via intertwined signaling networks are involved in maintaining normal hair follicle (HF) homeostasis, cycling and cell fate determination. However, knowledge of specific mechanisms by which hair loss takes place under pathological situations is needed. Using a keratinocyte-specific knockout mouse model, we uncover that the G-protein-coupled receptor kinase 2 (GRK2) signaling node plays a key role in HF homeostasis. Epidermal GRK2 ablation causes alterations during anagen induction, giving rise to abnormal cyst-like structures. HF-linked cysts display aberrant growth and differentiation patterns as well as lineage infidelity, displaying features of abortive HFs unable to fully acquire canonical hallmarks. Cysts triggered by GRK2 deletion displace the dermal papilla away from the bulge and promote irreversible changes in HF stem cell architecture, leading to bulge destruction and hair loss. Our data provide unforeseen roles of GRK2 in epidermal physiology and uncover mechanisms linking dystrophic follicular cysts formation with hair loss, with potential connections to pathogenic processes operating in immune-mediated alopecias.

cell biology↗

bioRxiv2024

Evaluating treatments for the protection of grapevine pruning wounds from natural infection by trunk disease fungi

Infection of grapevines by fungal pathogens causing grapevine trunk diseases (GTDs) primarily arises from annual pruning wounds made during the dormant season. While various studies have showcased the efficacy of products in shielding pruning wounds against GTDs infections, most of these investigations hinge on artificial pathogen inoculations, which may not faithfully mirror real field conditions. This study aimed to evaluate and compare the efficacy of various liquid formulation fungicides (pyraclostrobin + boscalid) and paste treatments, as well as biological control agents (BCA: Trichoderma atroviride SC1, T. atroviride I-1237, and T. asperellum ICC012 + T. gamsii ICC080), for their potential to prevent natural infection of grapevine pruning wounds by trunk disease fungi in two field trials located in Samaniego (Northern Spain) and Madiran (Southern France) over three growing seasons. Wound treatments were applied immediately after pruning in February. One year after pruning, canes were harvested from vines and brought to the laboratory for assessment of Trichoderma spp. and fungal trunk pathogens. More than 1,200 fungal isolates associated with five GTDs (esca, Botryophaeria, Diaporthe and Eutypa diebacks, and Cytospora canker) were collected from the two vineyards each growing season. Our findings reveal that none of the products under investigation exhibited complete effectiveness against all the GTDs. The efficacy of these products was particularly influenced by the specific year of study. A notable exception was observed with the biocontrol agent T. atroviride I-1237, which consistently demonstrated effectiveness against Botryosphaeria dieback infections throughout each year of the study, irrespective of the location. The remaining products exhibited efficacy in specific years or locations against particular diseases, with the physical barrier (paste) showing the least overall effectiveness. The recovery rates of Trichoderma spp. in treated plants were highly variable, ranging from 17% to 100%, with both strains of T. atroviride yielding the highest isolation rates. This study underscores the importance of customizing treatments for specific diseases, taking into account the influence of environmental factors for BCA applications.

microbiology↗

bioRxiv2021

Hidden conformations differentiate day and night in a circadian pacemaker

The AAA+ protein KaiC is the central pacemaker for cyanobacterial circadian rhythms. Composed of two hexameric rings with tightly coupled activities, KaiC undergoes changes in autophosphorylation on its C-terminal (CII) domain that restrict binding of of clock proteins on its N-terminal (CI) domain to the evening. Here, we use cryo-electron microscopy to investigate how daytime and nighttime states of CII regulate KaiB binding to CI. We find that the CII hexamer is destabilized during the day but takes on a rigidified C2-symmetric state at night,concomitant with ring-ring compression. Residues at the CI-CII interface are required for phospho-dependent KaiB association, coupling ATPase activity on CI to cooperative KaiB recruitment. Together these studies reveal how daily changes in KaiC phosphorylation regulate cyanobacterial circadian rhythms. One-Sentence SummaryCryo-EM structures of KaiC in its day and night states reveal the structural basis for assembly of clock regulatory complexes.

biochemistry↗