Biology subjects

Lopez, G.

Publications and source records attributed to Lopez, G..

At least 19 recordsLinked to original sources

bioRxiv2026

CONSTITUTIVE STIM1L DELETION ALTERS STORE-OPERATED CALCIUM ENTRY KINETICS BUT DOES NOT PERTURB THE DEVELOPMENT AND FUNCTION OF MOUSE SKELETAL MUSCLE

Store-operated calcium entry (SOCE) is a ubiquitous calcium (Ca2+) signalling mechanism that replenishes endoplasmic and sarcoplasmic reticulum Ca2+ stores. We previously identified STIM1L, a skeletal muscle-enriched STIM1 splice variant that enables rapid SOCE activation in human myotubes. To determine its physiological role in vivo, we generated a constitutive knockout mouse model that selectively abolishes STIM1L expression while preserving the canonical STIM1 isoform. Stim1l-KO mice developed normally and exhibited no overt abnormalities, but both sexes showed reduced voluntary wheel-running activity, suggesting neuromuscular perturbation. Skeletal muscle deprived of STIM1L did not show any histological alterations or changes in fibre- type and size. Likewise, force-frequency relationships and fatigue resistance measured ex vivo in isolated extensor digitorum longus and soleus muscles were indistinguishable from control muscles. This lack of difference may be explained by the increased expression of STIM1 in several skeletal muscles and suggests that changes in the voluntary running activity of Stim1l-KO mice may arise from STIM1L loss in non-muscular tissues, including the central nervous system. Notwithstanding, primary myotubes derived from Stim1l-KO mice displayed a marked delay in SOCE activation kinetics, whereas SOCE amplitude remained comparable to controls. This was consistent with a compensatory STIM1 upregulation maintaining overall Ca2+ entry capacity. Interestingly, electrically evoked Ca2+ transients in intact Stim1l-KO flexor digitorum brevis fibres exhibited significantly faster decay kinetics than controls. This revealed another role of STIM1L in Ca2+ handling in skeletal muscle that appears independent of its contribution to SOCE activation. Together, these findings establish STIM1L as a regulator of SOCE activation kinetics and indicate an additional role in myofibre Ca2+ clearance, while suggesting that compensatory upregulation of canonical STIM1 may preserve muscle structure and contractile function in its absence in mice.

physiology↗

bioRxiv2026

Development and characterization of a miniaturized focused ultrasound extraction (FUSE) system to enable rapid, point-of-care genetic testing

Point-of-care (POC) molecular detection has enabled rapid and accessible testing at or near the site of need, facilitating timely decision-making in clinical, field, and industrial settings. Despite these advancements, molecular detection platforms remain limited in their ability to prepare DNA from complex tissue matrices, restricting their applicability to a narrow range of sample types. To address sample preparation inefficiencies, focused ultrasound extraction (FUSE) has been developed for the rapid release of DNA from robust tissue matrices. FUSE disintegrates target tissue and releases DNA by delivering high pressure ultrasound pulses that generate a cavitation bubble cloud. In prior work, FUSE was performed using large, laboratory-based equipment. Here, a miniaturized FUSE device was designed and tested to enable POC DNA sample preparation. Design constraints were defined based on prior FUSE experiments, and based on these metrics, a 750 kHz cylindrical transducer was fabricated. The pressure output was measured, and high-speed optical imaging demonstrated that the transducer generated sustained cavitation within the defined focal region. The feasibility of DNA extraction from piscine and timber tissues was evaluated, and results show that the device can release DNA with quality suitable for PCR-based detection from both tissue types. These results demonstrate the potential of this device to rapidly extract DNA from complex samples and expand the applicability of molecular detection platforms.

bioengineering↗

bioRxiv2025

A Modular Toolkit For Theophylline-Dependent Synthetic Auxotrophs Via Riboswitch-Gated Essential Genes

Synthetic auxotrophs are a useful means for developing genetically encoded biocontainment systems. Current methods for developing synthetic auxotrophs are complicated or expensive, limiting access and adoption of biocontainment technologies. To address this gap, we developed a simple and modular platform for creating synthetic auxotrophs based on ligand-dependent translational gating of essential genes. By inserting a theophylline-responsive riboswitch upstream of essential genes in Escherichia coli, we created strains whose viability depends on the presence of theophylline. We systematically applied this approach to 29 essential genes, obtained ligand-dependent growth phenotypes for 19 targets, and found that 18 of these essential genes yielded stringent live-die synthetic auxotrophs. These strains exhibited robust theophylline dependence with escape frequencies ranging from 1 x 10-5 to 1 x 10-6 (most below limit of detection). Our modular design allows for the rapid (<1 week), low-cost, and reliable generation of synthetic auxotrophs. This work introduces ligand-dependent translational control as a new mechanism for engineering synthetic auxotrophy and provides an accessible platform that expands the biocontainment toolkit.

synthetic biology↗

bioRxiv2025

CtBP1 coordinates synaptic, metabolic and contractile changes induced by denervation in skeletal muscle

Nerve injury triggers dramatic atrophy of skeletal muscle, accompanied with synaptic and metabolic changes. Regulation of denervation-induced muscle fiber remodeling involves several factors governing genetic reprogramming and proteostasis changes. Here, we demonstrate that the transcriptional co-repressor CtBP1 coordinates synaptic and metabolic changes in muscle fibers upon denervation. CtBP1 was present both in sub- and non-synaptic myonuclei in innervated muscle. Although CtBP1 levels remained unchanged in denervated muscle, CtBP1 accumulated transiently in myonuclei after 2 days of denervation. Ctbp1 knockdown perturbed the expression of a large set of activity-independent and -dependent genes in innervated and denervated skeletal muscles. CtBP1 loss had limited effect on the expression of most synaptic genes, but increased transcript levels of Chrne, encoding the adult {varepsilon} sub-unit of acetylcholine receptors (AChR). However, it did not affect AChR turnover or maintenance of the post-synaptic compartment upon denervation. Importantly, we uncovered that Ctbp1 knockdown promotes denervation-induced changes in metabolic gene expression, including most genes encoding proteins of the respiratory chain complexes. Consistently, it enhanced the switch towards slower, oxidative fibers in fast muscle after 2 weeks of denervation. Moreover, CtBP1 loss precipitated the profound ultrastructural remodeling of mitochondria network induced after denervation. Hence, our study unveils the role of CtBP1 in the integrated muscle response to denervation, with important implications for CtBP1-related muscle diseases. One-sentence summaryLoss of CtBP1 perturbs synaptic, metabolic and contractile changes induced by denervation in skeletal muscle

physiology↗

bioRxiv2025

Unveiling Candidate Drivers in Cancer Progression Using Somatic-IV Analysis

MotivationIdentifying causal drivers of cancer progression is crucial for developing effective anti-cancer therapies. However, disentangling causality from correlation remains challenging due to confounding factors within the complex genetic and transcriptomic landscapes of cancer. ResultsTo address this challenge, we introduce the Somatic Instrumental Variable analysis (Somatic-IV), which integrates genetic, transcriptomic, and clinical outcome data to identify candidate driver genes likely playing a causal role in disease progression. Somatic-IV estimates genetic-exposure and genetic-outcome associations, utilizing MR-Egger regression to estimate bias-reduced causal effects. We assessed the statistical properties and performance of Somatic-IV through a simulation study and demonstrated its utility in pancreatic adenocarcinoma (PDAC) and colorectal cancer (CRC). Our analysis identified ZBED2 and CSNK2A2 as likely drivers of PDAC and CRC cancer progression, respectively. Somatic-IV is a novel approach for generating target hypotheses and guiding the development of effective therapies for cancer patients. Availability and implementationThe Somatic-IV package is available at: https://github.com/wzhang1984/Somatic_IV_package

bioinformatics↗

bioRxiv2024

Zymoseptoria tritici stealth infection is facilitated by stage-specific down-regulation of a β-glucanase

Plant cell walls constitute a major defence barrier against pathogens, although it is unclear how specific cell wall components impact pathogen colonisation. Pathogens secrete cell wall degrading enzymes (CWDEs) to facilitate plant colonisation, but damaged, infected cells are often a source of cell wall-derived oligosaccharides that trigger host immunity. The mechanisms by which pathogens minimize the release of cell wall-derived oligosaccharides while colonizing the host remain to be elucidated. We combined biochemical, molecular genetics and transcriptomic analyses to functionally characterize a glycoside hydrolase (ZtGH45) from the wheat pathogen Zymoseptoria tritici. ZtGH45 gene is expressed during the necrotrophic phase of the fungus, coinciding with an accumulation of wheat {beta}-1,3/1,4-mixed-linked glucan (MLG)-derived oligosaccharides. We show that overexpression of ZtGH45 enhances {beta}-1,3/1,4-glucan hydrolysis and the derived oligosaccharides trigger an immune response in wheat, which hinders Z. tritici virulence. The results demonstrate that tight regulation of ZtGH45 is critical for the infection process to prevent early accumulation of MLG oligosaccharides that would prematurely induce host immunity counterbalancing fungal virulence. We suggest that the balance between plant cell wall degradation by fungal CWDE and the release of immunogenic wall-derived oligosaccharides governs the outcome of host invasion by pathogens.

plant biology↗

bioRxiv2024

Deletions Rate-Limit Breast and Ovarian Cancer Initiation

Optimizing prevention and early detection of cancer requires understanding the number, types and timing of driver mutations. To quantify this, we exploited the elevated cancer incidence and mutation rates in germline BRCA1 and BRCA2 (gBRCA1/2) carriers. Using novel statistical models, we identify genomic deletions as the likely rate-limiting mutational processes, with 1-3 deletions required to initiate breast and ovarian tumors. gBRCA1/2-driven hereditary and sporadic tumors undergo convergent evolution to develop a similar set of driver deletions, and deletions explain the elevated cancer risk of gBRCA1/2-carriers. Orthogonal mutation timing analysis identifies deletions of chromosome 17 and 13q as early, recurrent events. Single-cell analyses confirmed deletion rate differences in gBRCA1/2 vs. non-carrier tumors as well as cells engineered to harbor gBRCA1/2. The centrality of deletion-associated chromosomal instability to tumorigenesis shapes interpretation of the somatic evolution of non-malignant tissue and guides strategies for precision prevention and early detection.

cancer biology↗

bioRxiv2024

Comparative study of enriched dopaminergic neurons from siblings with Gaucher disease discordant for parkinsonism

Inducible pluripotent stem cells (iPSCs) derived from patient samples have significantly enhanced our ability to model neurological diseases. Comparative studies of dopaminergic (DA) neurons differentiated from iPSCs derived from siblings with Gaucher disease discordant for parkinsonism provides a valuable avenue to explore genetic modifiers contributing to GBA1-associated parkinsonism in disease-relevant cells. However, such studies are often complicated by the inherent heterogeneity in differentiation efficiency among iPSC lines derived from different individuals. To address this technical challenge, we devised a selection strategy to enrich dopaminergic (DA) neurons expressing tyrosine hydroxylase (TH). A neomycin resistance gene (neo) was inserted at the C-terminus of the TH gene following a T2A self-cleavage peptide, placing its expression under the control of the TH promoter. This allows for TH+ DA neuron enrichment through geneticin selection. This method enabled us to generate comparable, high-purity DA neuron cultures from iPSC lines derived from three sisters that we followed for over a decade: one sibling is a healthy individual, and the other two have Gaucher disease (GD) with GBA1 genotype N370S/c.203delC+R257X (p.N409S/c.203delC+p.R296X). Notably, the younger sister with GD later developed Parkinson disease (PD). A comprehensive analysis of these high-purity DA neurons revealed that although GD DA neurons exhibited decreased levels of glucocerebrosidase (GCase), there was no substantial difference in GCase protein levels or lipid substrate accumulation between DA neurons from the GD and GD/PD sisters, suggesting that the PD discordance is related to of other genetic modifiers.

neuroscience↗

bioRxiv2024

Blockade of Interleukin-6 (IL-6) Signaling in Dedifferentiated Liposarcoma (DDLPS) Decreases Mouse Double Minute 2 (MDM2) Oncogenicity via Alternative Splicing

Effective therapies for retroperitoneal (RP) dedifferentiated liposarcoma (DDLPS) remain unavailable. Loco-regional recurrence occurs in >80% of cases; 5-year disease-specific survival is only 20%. DDLPS is especially prevalent in the retroperitoneum and abdomen; evaluation of the DDLPS microenvironment in these high-fat compartments appears pertinent. Adipose is a main supplier of interleukin-6 (IL6); excessive activation of IL6 signal transducer glycoprotein 130 (GP130) underlies the development of some diseases. The role of GP130 pathway activation remains unstudied in DDLPS, so we examined the role of microenvironment fat cell activation of the IL6/GP130 signaling cascade in DDLPS. All DDLPS tumors and cell lines studied expressed elevated levels of the GP130-encoding gene IL6ST and GP130 protein compared to normal tissue and cell line controls. IL6 increased DDLPS cell growth and migration, possibly through increased signal transducer and activator of transcription 1 (STAT1) and 3 (STAT3) activation, and upregulated mouse double minute 2 (MDM2). GP130 loss conveyed opposite effects; pharmacological blockade of GP130 by SC144 produced the MDM2 splice variant MDM2-ALT1, known to inhibit full length MDM2 (MDM2-FL). Although genomic MDM2 amplification is pathognomonic for DDLPS, mechanisms driving MDM2 expression, regulation, and function beyond the MDM2:p53 negative feedback loop are poorly understood. Our findings suggest a novel preadipocyte DDLPS-promoting role due to IL6 release, via upregulation of DDLPS MDM2 expression. Pharmacological GP130 blockade reduced the IL6-induced increase in DDLPS MDM2 mRNA and protein levels, possibly through enhanced expression of MDM2-ALT1, a possibly targetable pathway with potential as future DDLPS patient therapy.

molecular biology↗

bioRxiv2022

Tumor infiltrating iNKT cells sustain neutrophil pro-tumorigenic functions influencing disease progression in human colorectal cancer

iNKT cells account for a relevant fraction of effector T-cells in the intestine. Although iNKT cells are cytotoxic lymphocytes, their role in colorectal cancer (CRC) remains controversial. From the analysis of colonic LPMCs of human and murine CRC specimens we report that tumor-infiltrating iNKT cells are characterized by an IL17/GM-CSF pro-tumorigenic phenotype, while maintaining cytotoxic properties in the adjacent non-tumoral tissue. Exposure of iNKT cells to the tumor-associated pathobiont Fusobacterium nucleatum blunted their cytotoxic capability and enhanced iNKT cell-mediated neutrophils chemotaxis, which upregulated PMN-MDSC gene signatures and functions. Importantly, in vivo stimulation of iNKT cells with GalCer restored their anti-tumorigenic functions. Survival analyses demonstrated that human CRC co-infiltration by iNKT cells and tumor-associated neutrophils correlates with negative outcomes. Our results reveal a functional plasticity of human intestinal iNKT cells with pro- and anti-tumorigenic activities in CRC, suggesting an iNKT pivotal role in shaping the cancer developmental trajectory.

immunology↗

bioRxiv2022

A group of Arabidopsis thaliana Leucine Rich Repeat-Malectin Receptor Kinases are required for the activation of immune responses triggered by cellulose and mixed-linked glucan oligosaccharides

Plant immune system perceives through the extracellular ectodomains (ECDs) of Pattern Recognition Receptors (PRRs) a diversity of carbohydrate ligands from plant and microbial cell walls, which activate Pattern-Triggered Immunity (PTI). Among these ligands are oligosaccharides derived from mixed-linked {beta}-1,3/{beta}-1,4-glucans (MLGs, e.g., {beta}-1,4-D-(Glc)2-{beta}-1,3-D-Glc, MLG43) and cellulose (e.g., {beta}-1,4-D-(Glc)3, CEL3). The mechanisms of perception of carbohydrates by plants are poorly characterized, with the exception of that determining recognition of fungal chitin oligosaccharides (e.g., {beta}-1,4-D(GlcNAc)6, CHI6) that involves several PRRs with LysM-ECDs that function as receptor or co-receptors. Here, we describe the isolation and characterization of Arabidopsis thaliana mutants impaired in glycan perception (igp), which are defective in PTI activation mediated by MLG43 and CEL3, but not CHI6. igp1-igp4 are altered in receptor-like kinases [RLKs: AT1G56145 (IGP1), AT1G56130 (IGP2/3), and AT1G56140 (IGP4)] with Leucine-Rich-Repeat (LRR) and Malectin (MAL) domains in their ECDs. igp4 is a T-DNA insertional, loss of function mutant whereas igp1 and the allelic igp2/igp3 harbour point mutations (E906K and G773E, respectively) in their kinase domains, which impact their structure and surface electrostatic potential as revealed by in silico structural analyses. Notably, Isothermal Titration Calorimetry assays with purified ECD-RLKs showed that AT1G56145 binds with high affinity CEL3 (Kd = 1.19 {+/-} 0.03 M) and cellopentaose (Kd = 1.40 {+/-} 0.01 M), but not MLG43, supporting AT1G56145 function as a plant PRR for cellulose oligosaccharides. Our data suggest that these LRR-MAL RLKs are receptor/co-receptors of a novel mechanism of perception of cellulose and MLG-derived oligosaccharides and PTI activation in Arabidopsis thaliana. Significance StatementNew oligosaccharides that trigger plant immunity have been described recently, but the mechanisms of perception of these glycans are unknown. We describe here three Arabidopsis thaliana receptor kinases (AT1G56130, AT1G56140, and AT1G56145) with Leucine Rich Repeat (LRR) and Malectin (MAL) domains in their extracellular ectodomains (ECDs), which function as Pattern Recognition Receptors (PRRs) triggering immune response mediated by oligosaccharides from cellulose ({beta}-1,4-glucan) and mixed-linked {beta}-1,3/1,4-glucans (MLGs) of plant and microbial cell walls. The ECD-AT1G56145 binds cellulose oligosaccharides, but not MLGs, supporting its function as a novel receptor of carbohydrate ligands in plants. Our data indicate that these LRR-MAL-PRRs control a complex mechanism of oligosaccharides perception and immune activation that differs from that of fungal chitin oligosaccharides recognition which involves LysM-PRRs.

plant biology↗

bioRxiv2022

ALT in Pediatric Brain Tumors Can Occur without ATRX Mutation and is Enriched in Patients with Pathogenic Germline MMR Variants

BackgroundTo achieve replicative immortality, most cancers develop a telomere maintenance mechanism, such as reactivation of telomerase or alternative lengthening of telomeres (ALT). There are limited data on the prevalence and clinical significance of ALT in pediatric brain tumors, and ALT-directed therapy is not available. MethodsWe performed C-circle analysis (CCA) on 579 pediatric brain tumors that had corresponding tumor/normal whole genome sequencing through the Open Pediatric Brain Tumor Atlas (OpenPBTA). We detected ALT in 6.9% (n=40/579) of these tumors and completed additional validation by ultrabright telomeric foci in situ on a subset of these tumors. We used CCA to validate TelomereHunter for computational prediction of ALT status and focus subsequent analyses on pediatric high-grade glioma (pHGG) Finally, we examined whether ALT is associated with recurrent somatic or germline alterations. ResultsALT is common in pHGG (n=24/63, 38.1%), but occurs infrequently in other pediatric brain tumors (<3%). Somatic ATRX mutations occur in 50% of ALT+ pHGG and in 30% of ALT-pHGG. Rare pathogenic germline variants in mismatch repair (MMR) genes are significantly associated with an increased occurrence of ALT. Conclusions: We demonstrate that ATRX is mutated in only a subset of ALT+ pHGG, suggesting other mechanisms of ATRX loss of function or alterations in other genes may be associated with the development of ALT in these patients. We show that germline variants in MMR are associated with development of ALT in patients with pHGG. Key PointsATRX alterations are frequent, but not required, for an ALT phenotype in pHGGs pHGG patients with germline mismatch repair variants have higher rate of ALT + tumors TelomereHunter is validated to predict ALT in pHGGs Importance of the StudyWe performed orthogonal molecular and computational analyses to detect the presence of alternative lengthening of telomeres in a highly characterized cohort of pediatric brain tumors. We demonstrate that many pHGG utilize ALT without a mutation in ATRX, suggesting either loss of function of ATRX via an alternative mechanism or an alternate means of development of ALT. We show that germline variants in MMR genes are significantly associated with ALT in pHGG. Our work adds to the biological understanding of the development of ALT and provides an approach to stratify patients who may benefit from future ALT-directed therapies in this patient population.

cancer biology↗

bioRxiv2021

Regulation of neurogenesis and gliogenesis by the matricellular protein CCN2 in the mouse retina

Cellular communication network (CCN) 2 is an extracellular matrix protein with cell type- and context-dependent functions. Using a combination of mouse genetics and omic approaches, we show that CCN2 is expressed in early embryonic retinal progenitor cells (RPCs) and becomes restricted to fully differentiated Muller glial cells (MGCs) thereafter. Germline deletion of CCN2 in mice decreases BrdU labeling, reduces RPC pool, and impairs the competency of remaining RPCs to generate early and late born retinal cell types. Retinal hypocellularity and microphthalmia ensue. The transcriptomic changes associated with CCN2 inactivation include reduced marker and transcriptional regulator genes of retinal ganglion cells, photoreceptors and MGCs. Yap (Yes-associated protein), a singular node for transcriptional regulation of growth and differentiation genes, is also a target of CCN2 signals. In an organotypic model of ex vivo cultured embryonic retinas, CCN2 and YAP immunoreactivity signals overlap. Lentivirus-mediated YAP expression in CCN2-deficient retinal explants increases the number of differentiating Sox9-positive MGCs. Taken together, our data indicate that CCN2 controls the proliferative and differentiation potentials of RPCs ultimately endowing, a subpopulation thereof, with Muller glial cell fate. Summary statementA CCN2-YAP regulatory axis controls retinal progenitor cell growth and lineage commitment to neuronal and glial cell fates.

developmental biology↗

bioRxiv2021

Defining the Yeast Resistome through in vitro Evolution and Whole Genome Sequencing

In vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in the model microbe, Saccharomyces cerevisiae. Analysis of 355 curated, laboratory-evolved clones, resistant to 80 different compounds, demonstrates differences in the types of mutations that are identified in selected versus neutral evolution and reveals numerous new, compound-target interactions. Through enrichment analysis we further identify a set of 137 genes strongly associated with or conferring drug resistance as indicated by CRISPR-Cas9 engineering. The set of 25 most frequently mutated genes was enriched for transcription factors and for almost 25 percent of the compounds, resistance was mediated by one of 100 independently derived, gain-of-function, single nucleotide variants found in 170-amino-acid domains in two Zn2C6 transcription factors, YRR1 and YRM1 (p < 1x 10 -100). This remarkable enrichment for transcription factors as drug resistance genes may explain why it is challenging to develop effective antifungal killing agents and highlights their important role in evolution.

genetics↗

bioRxiv2020

Integrative genomics identifies lncRNA regulatory networks across 1,044 pediatric leukemias and solid tumors

Long non-coding RNAs (lncRNAs) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curate RNA sequencing data for 1,044 pediatric leukemia and solid tumors and integrate paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. We report a total of 2,657 robustly expressed lncRNAs across six pediatric cancers, including 1,142 exhibiting histotype-specific expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multi-dimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell-type specific transcription factors further implicated distinct histotype-specific and developmental lncRNAs. We integrated our analyses to prioritize lncRNAs for experimental validation and showed that silencing of TBX2-AS1, our top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming our computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies.

cancer biology↗

bioRxiv2020

Neutrophil extracellular traps induce the epithelial-mesenchymal transition: implications in post-COVID-19 fibrosis

The release of neutrophil extracellular traps (NETs), a process termed NETosis, avoids pathogen spread but may cause tissue injury. NETs have been found in severe COVID-19 patients, but their role in disease development is still unknown. The aim of this study is to assess the capacity of NETs to drive epithelial-mesenchymal transition (EMT) of lung epithelial cells and to analyze the involvement of NETs in COVID-19. Neutrophils activated with PMA (PMA-Neu), a stimulus known to induce NETs formation, induce both EMT and cell death in the lung epithelial cell line, A549. Notably, NETs isolated from PMA-Neu induce EMT without cell damage. Bronchoalveolar lavage fluid of severe COVID-19 patients showed high concentration of NETs. Thus, we tested in an in vitro alveolar model the hypothesis that virus-induced NET may drive EMT. Co-culturing A549 at air-liquid interface with alveolar macrophages, neutrophils and SARS-CoV2, we demonstrated a significant induction of the EMT in A549 together with high concentration of NETs, IL8 and IL1{beta}, best-known inducers of NETosis. Lung tissues of COVID-19 deceased patients showed that epithelial cells are characterized by increased mesenchymal markers. These results show for the first time that NETosis plays a major role in triggering lung fibrosis in COVID-19 patients.

immunology↗

bioRxiv2020

Cell-to-cell Mathematical Modeling of Arrhythmia Phenomena in the Heart

With an aperiodic, self-similar distribution of two-dimensional arrangement of atrial cells, it is possible to simulate such phenomena as Fibrillation, Fluttering, and a sequence of Fibrillation-Fluttering. The topology of a network of cells may facilitate the initiation and development of arrhythmias such as Fluttering and Fibrillation. Using a GPU parallel architecture, two basic cell topologies were considered in this simulation, an aperiodic, fractal distribution of connections among 462 cells, and a chessboard-like geometry of 60x60 and 600x600 cells. With a complex set of initial conditions, it is possible to produce tissue behavior that may be identified with arrhythmias. Finally, we found several sets of initial conditions that show how a mesh of cells may exhibit Fibrillation that evolves into Fluttering.

biophysics↗

bioRxiv2020

Arabidopsis cell wall composition determines disease resistance specificity and fitness

Plant cell walls are complex structures subject to dynamic remodeling in response to developmental and environmental cues, and play essential functions in disease resistance responses. We tested the specific contribution of plant cell walls to immunity by determining the susceptibility of a set of Arabidopsis cell wall mutants (cwm) to pathogens with different parasitic styles: a vascular bacterium, a necrotrophic fungus and a biotrophic oomycete. Remarkably, most cwm mutants tested (31/38; 81.6%) showed alterations in their resistance responses to at least one of these pathogens, in comparison to wild-type plants, illustrating the relevance of wall composition in determining disease resistance phenotypes. We found that the enhanced resistance of cwm plants to the necrotrophic and vascular pathogens negatively impacted on cwm fitness traits, like biomass and seed yield. Enhanced resistance of cwm plants is not only mediated by canonical immune pathways, like those modulated by phytohormones or Microbe-Associated Molecular Patterns, which are not de-regulated in all cwm tested. Pectin-enriched wall fractions isolated from cwm plants triggered immune responses in other plants, suggesting that wall-mediated defensive pathways might contribute to cwm resistance. Cell walls of cwm plants show a high diversity of composition alterations as revealed by glycome profiling that detect specific wall carbohydrate moieties. Mathematical analysis of glycome profiling data identified correlations between the amounts of specific wall carbohydrate moieties and disease resistance phenotypes of cwm plants. These data support the relevant and specific function of plant wall composition in plant immune response modulation and in balancing disease resistance/development trade-offs.

plant biology↗