Biology subjects

Martinez-Nunez, R. T.

Publications and source records attributed to Martinez-Nunez, R. T..

8 recordsLinked to original sources

bioRxiv2025

Human airway epithelia clear rhinovirus-infected cells using two waves of cell extrusion

Epithelial barriers represent the first line of defence against pathogens, yet their role in innate immunity is typ-ically relegated to pathogen detection and immune cell recruitment. This perspective ignores a fundamental evolutionary principle: epithelia defended against pathogens long before complex immune systems evolved. Here, we demonstrate that human bronchial epithelial monolayers retain this ancestral capacity, autono-mously clearing rhinovirus (RV) within 24 hours by selectively extruding infected cells--a process we term virus-induced cell extrusion (VICE). VICE occurs in two waves: a rapid response occurring independently of virus entry, followed by a replication-dependent wave. Barrier-defective epithelia that cannot extrude fail to clear RV. While extrusion maintains barrier integrity and eliminates local infection, it also expels virus-laden cells, promoting transmission. Thus, VICE enables leukocyte-independent epithelial defence while inadver-tently promoting viral transmission, reflecting an evolutionary strategy that prioritizes barrier integrity over containment. These findings redefine epithelia as central players in viral pathogenesis and host protection.

cell biology↗

bioRxiv2025

Inhibiting epithelial cell extrusion and inflammation synergistically reverses asthmatic airway remodelling

Airway smooth muscle (ASM) hyperresponsiveness is the defining feature of asthma, yet neither its origins nor the processes that establish and maintain it are understood. Here, using a mouse model, we show that hyperresponsiveness arises from ASM realignment into dense, parallel bundles reinforced by excess extracellular matrix, a fundamental remodelling rather than mere amplification of existing contractile ASM. This remodelling is initiated and sustained by a mechanical feedforward cycle. Allergen treatment initiates a contraction-relaxation cycle that realigns ASM into a bronchoconstrictive state. As bronchoconstriction triggers crowding and excess airway epithelial cell extrusion 1, the wounding then locks ASM into a hypercontractile architecture that drives further constriction. Gadolinium, a mechanosensitive channel blocker that inhibits extrusion, prevents this remodelling and hyperresponsiveness--unlike the corticosteroid budesonide. Critically, in mice with fully established disease, gadolinium reverses all asthmatic features and restores normal airway function, while budesonide alone cannot. Budesonide, however, synergises with gadolinium to normalise protein and gene expression. These findings reframe asthma pathogenesis as a mechanically driven, pharmacologically reversible process -- suggesting that asthma may be curable rather than merely treatable.

cell biology↗

bioRxiv2025

The RNA binding protein Insulin Growth factor 2 binding Protein 3 (IGF2BP3) modulates IL-13/IL-4 signalling in human bronchial epithelial cells and is dysregulated in type 2 disease

Type 2 immunity encompasses the coordinated cellular responses mainly driven by IL-4 and IL-13 to target extracellular parasites. Uncontrolled, type 2 responses underpin asthma and allergy. At the cellular level, IL-13 and IL-4 bind to receptors IL-13R1 and IL-4R and trigger STAT6 phosphorylation leading to the transcription of type 2 mediators. Further regulators of this fundamental pathway remain poorly understood. We demonstrate that the RNA binding protein Insulin Growth Factor 2 Binding Protein 3 (IGF2BP3) inhibits IL-13/IL-4 effects in airway epithelium and is increased in type 2 pathology, where it correlates with an IL-13-driven signature. Mechanistically, IGF2BP3 directly binds IL4R and IL13RA1 mRNAs, which are also methylated. Depleting IGF2BP3 increased IL4R and IL13RA1 mRNAs half-life, IL-4R and IL-13R1 surface expression and IL-13/IL-4-dependent STAT6 phosphorylation. Reducing IGF2BP3 levels skewed primary airway epithelial cells towards a type 2 phenotype and enhanced IL-13-mediated transcriptional effects genome-wide. Lastly, we found IGF2BP3 levels upregulated in airway epithelium in several type 2 disease cohorts, and an IGF2BP3-dependent IL-13-driven signature predominant in type 2 high vs type 2 low asthma. Our data positions IGF2BP3 as a novel inhibitor of IL-13/IL-4 effects and type 2 disease biomarker.

molecular biology↗

bioRxiv2023

Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay

Nucleotide sequences along a gene provide instructions to transcriptional and co-transcriptional machinery allowing genome expansion into the transcriptome. Interestingly, nucleotide sequence can often be shared between two genes and in some occurrences, a gene is located completely within a different gene, these are known as host/nested genes pairs. In these instances, if both genes are transcribed, overlap can result in a transcriptional crosstalk where genes regulate each other. Despite this, a comprehensive annotation of where such genes are located, and their expression patterns is lacking. To address this, we provide an up-to-date catalogue of host/nested gene pairs in mouse and human, showing that over a tenth of all genes contain a nested gene. We discovered that transcriptional co-occurrence is often tissue-specific. This co-expression was especially prevalent within the transcriptionally permissive tissue, testis. We used this developmental system and scRNA-seq analysis to demonstrate that co-expression of pairs can occur in single cells and transcription in the same place at the same time can enhance transcript diversity of the host gene. In agreement, host genes are more transcript diverse than the rest of the transcriptome and we propose that nested gene expression drives this observed diversity. Given that host/nested gene configurations were common in both human and mouse genomes, the interplay between pairs is therefore likely selected for, highlighting the relevance of transcriptional crosstalk between genes which share nucleic acid sequence. The results and analysis are available on an Rshiny application.

genomics↗

bioRxiv2022

The RNA binding proteins ZFP36L1 and ZFP36L2 modulate transcriptional and post-transcriptional genome-wide effects of glucocorticoids

Glucocorticoids (GCs) are one of the most used anti-inflammatory drugs worldwide. Despite their widespread use, our understanding of their post-transcriptional effects remains poorly understood. The tristetraprolin (TTP) RNA binding protein (RBP) family (ZFP36, ZFP36L1 and ZFP36L2) has been implicated in inflammation regulation via binding to AU-rich elements (ARE) in mRNAs, with TTP being implicated in GC modulation. We hypothesised that ZFP36L1 and ZFP36L2 are part of the GC pathway and tested this hypothesis in bronchial epithelium, which commonly encounters GC in vivo upon inhalation. Our data show that dexamethasone, a commonly used GC, modulated the levels, subcellular localisation and RNA binding of ZFP36L1/L2. Employing Frac-seq (subcellular fractionation and RNA-sequencing), we show that GC modulated distinct subsets of RNAs in a subcellular-dependent manner. In addition to their mostly known transcriptional effects (116 differentially expressed genes, DEGs), GCs modified the binding to monosomes of myriad mRNAs (83 differentially bound genes, DBGs). We also demonstrate that ZFP36L1/L2 modulated gene expression mainly at the total cytoplasmic and polyribosome binding levels. ZFP36L1/L2 down-regulation led to an increase in ARE-containing mRNAs and a pronounced modification of the effects of GC on gene expression. We observed a small overlap of genes modulated by GCs when comparing control and ZFP36L1/L2 knockdown cells, in a subcellular-dependent manner Our data also suggest a novel role for these RBPs and GCs in epithelial biology via regulation of mRNAs encoding proteins important for epithelial cell function including cellular structure. We believe that our data has further implications in how we investigate gene expression. We show the power of employing sub-cellular fractionation when analysing genome-wide effects for known transcriptional modulators such as GCs, as well as a tool to demonstrate the extent of the effect of RBPs on gene expression modulation beyond total RNA levels.

molecular biology↗

bioRxiv2021

Drug repurposing based on a Quantum-Inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2 including vitamin B12

The COVID-19 pandemic has accelerated the need to identify new therapeutics at pace, including through drug repurposing. We employed a Quadratic Unbounded Binary Optimization (QUBO) model, to search for compounds similar to Remdesivir (RDV), the only antiviral against SARS-CoV-2 currently approved for human use, using a quantum-inspired device. We modelled RDV and compounds present in the DrugBank database as graphs, established the optimal parameters in our algorithm and resolved the Maximum Weighted Independent Set problem within the conflict graph generated. We also employed a traditional Tanimoto fingerprint model. The two methods yielded different lists of compounds, with some overlap. While GS-6620 was the top compound predicted by both models, the QUBO model predicted BMS-986094 as second best. The Tanimoto model predicted different forms of cobalamin, also known as vitamin B12. We then determined the half maximal inhibitory concentration (IC50) values in cell culture models of SARS-CoV-2 infection and assessed cytotoxicity. Lastly, we demonstrated efficacy against several variants including SARS-CoV-2 Strain England 2 (England 02/2020/407073), B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). Our data reveal that BMS-986094 and different forms of vitamin B12 are effective at inhibiting replication of all these variants of SARS-CoV-2. While BMS-986094 can cause secondary effects in humans as established by phase II trials, these findings suggest that vitamin B12 deserves consideration as a SARS-CoV-2 antiviral, particularly given its extended use and lack of toxicity in humans, and its availability and affordability. Our screening method can be employed in future searches for novel pharmacologic inhibitors, thus providing an approach for accelerating drug deployment.

microbiology↗

bioRxiv2019

Alzheimers disease-related dysregulation of protein synthesis causes key pathological features with ageing

Alzheimers disease (AD) is characterised by A{beta} and tau pathology as well as synaptic degeneration. Recently, it was suggested that the development of these key disease features may at least in part be due to increased protein synthesis that is regulated by fragile X mental retardation protein (FMRP) and its binding partner CYFIP2. Using an unbiased screen, we show that exposure of primary neurons to A{beta} increases FMRP-regulated protein synthesis and involves a reduction of CYFIP2 levels. Modelling this CYFIP2 reduction in mice, we find A{beta} accumulation, development of pre-tangle tau pathology, gliosis, loss of synapses, and deficits in memory formation with ageing. We conclude that reducing endogenous CYFIP2 expression is sufficient to cause some key features of AD in mice. We therefore propose a central role for CYFIP2 in AD as a modulator of protein synthesis, highlighting a novel direction for therapeutic targeting.

neuroscience↗

bioRxiv2017

Genome-wide post-transcriptional dysregulation by microRNAs in human asthma as revealed by Frac-seq

MicroRNAs are small non-coding RNAs that inhibit gene expression post-transcriptionally, implicated in virtually all biological processes. Although the effect of individual microRNAs is generally studied, the genome-wide role of multiple microRNAs is less investigated. We assessed paired genome-wide expression of microRNAs with total (cytoplasmic) and translational (polyribosome-bound) mRNA levels employing Frac-seq in human primary bronchoepithelium from healthy controls and severe asthmatics. Severe asthma is a chronic inflammatory disease of the airways characterized by poor response to therapy. We found genes (=all isoforms of a gene) and mRNA isoforms differentially expressed in asthma, with novel inflammatory and structural mechanisms disclosed solely by polyribosome-bound mRNAs. Gene expression (=all isoforms of a gene) and mRNA expression analysis revealed different molecular candidates and biological pathways, with differentially expressed polyribosome-bound and total mRNAs also showing little overlap. We reveal a hub of six dysregulated microRNAs accounting for [~]90% of all microRNA targeting, displaying preference for polyribosome-bound mRNAs. Transfection of this hub in healthy cells mimicked asthma characteristics. Our work demonstrates extensive post-transcriptional gene dysregulation in asthma, where microRNAs play a central role, illustrating the feasibility and importance of assessing post-transcriptional gene expression when investigating human disease.

systems biology↗