Biology subjects

Turner, D. L.

Publications and source records attributed to Turner, D. L..

6 recordsLinked to original sources

bioRxiv2026

Attenuated interferon signalling in alveolar epithelium limits resistance to Streptococcus pyogenes

The upper respiratory tract is a primary niche for Streptococcus pyogenes colonisation and disease. Lower respiratory tract infection (pneumonia) is the most common invasive S. pyogenes syndrome. Studies have not previously examined how epithelial cells, from the airway to the alveolus, respond to S. pyogenes infection. Here, we established a scalable human in vitro model by differentiating induced pluripotent stem cells (iPSCs) into mature pseudostratified airway epithelium or alveolar type 2 epithelial cells, cultured at air-liquid interface and infected with S. pyogenes (M1UK and M75 strains). Both strains attached to iPSC-derived lung epithelial cells, with significantly greater adherence to the airway epithelium by M75 compared to M1UK. Moreover, invasion by both S. pyogenes strains of alveolar epithelial cells was greater than for the airway epithelium. Dynamic S. pyogenes gene expression changes were evident between 6 and 24 hours after infection, which was influenced by the infected cell type; however, virulence genes were not significantly altered. While infection of the airway epithelium induced rapid and dynamic inflammatory signalling, the alveolar epithelium demonstrated augmented cell death and mounted a transcriptional pro-inflammatory and proliferative response that was uncoupled from cytokine secretion. The airway epithelium model exhibited consistently higher baseline type I interferon (IFN) signalling than the alveolar epithelium. Invasion by S. pyogenes and inflammation was significantly reduced in IFN-{beta}-treated alveolar epithelial cells. In summary, we have established the first model of S. pyogenes infection in physiologically relevant airway and alveolar epithelial cells. Our findings suggest that host responses to infection are influenced by lung compartment, the S. pyogenes strain type, and infection timepoint, highlighting context-specific pathways that could be leveraged therapeutically.

microbiology↗

bioRxiv2026

Significantly Improved Mouse and Rat Genome Annotation Using Sequence Read Archive RNA-seq Data

To detect currently unannotated genes with low expression levels with high sensitivity and accuracy, we developed a new exon->gene->transcript annotation pipeline that can identify previously undetected multi-exon transcripts using large volumes of RNA-Seq data. Our pipeline incorporates three new algorithms: 1) model-based spliced exon detection, 2) exon-to-gene assignment across multiple tissue/datasets through exon community discovery, and 3) ranking top transcripts by a stepwise minimum flow procedure. The design of our pipeline allowed us to leverage hundreds of Tbases of public RNA-seq data as input to improve mouse and rat genome annotation. Using this data, our pipeline identified close to 15K and 21K unannotated genes in GENCODE M37 and ENSEMBL 114 for mouse and rat, respectively. Each species also gained over 200K predicted transcripts containing at least one new exon, although most were transcripts from GENCODE/ENSEMBL annotated genes with newly assigned exons. To make our genome annotation available for common use, we have packaged this new annotation in standard file formats for the analysis of bulk and single cell RNA-seq data (GTF, 10X genome files). We have also provided two use examples which demonstrate the utility of our newly annotated genes in functional analyses, showing that their expression can be differentially regulated in relationship to cell type and selective breeding. Due to the efficiency provided by our pipeline, we expect that as new RNA-seq data become available in the coming years it will significantly benefit rat gene/transcript annotation, eventually enabling us to approach the target of complete gene and transcript annotation.

genomics↗

bioRxiv2025

Macrophages Mediate Antiviral Immunity and Repair of Type 2 Alveolar Epithelial Cells in a Human Stem Cell Model

The lung alveoli are constantly exposed to inhaled pathogens and inorganic hazards, relying on robust defence mechanisms to maintain homeostasis. Alveolar macrophages and type 2 alveolar epithelial cells (AT2s) collaborate to orchestrate protection. Compromised defence can dysregulate immunity and repair, leading to acute and chronic respiratory diseases. To better understand these processes and drive therapeutic discovery, human model systems that capture key cell interactions are essential. Here, we develop the first induced pluripotent stem cell (iPSC)-derived platform that integrates AT2 cells and macrophages in an air-liquid interface culture. Coculture enhanced AT2-specific gene expression and lipid synthesis, while macrophages actively phagocytosed AT2-derived surfactant. iPSC-derived AT2s supported macrophage survival by producing M-CSF and coculture promoted an alveolar macrophage-like phenotype. Additionally, during respiratory infection macrophages played a crucial role in modulating proinflammatory signalling, enhancing antiviral immunity, and restricting viral replication. Furthermore, we identify a role for iPSC-derived macrophages in epithelial repair, with VEGF signalling to macrophages increasing epithelial permeability. We present an iPSC-derived air-interface platform to study AT2-macrophage interactions in homeostasis, infection, and repair, providing insights into their potential roles in the initiation and progression of respiratory diseases.

cell biology↗

bioRxiv2024

Foxn3 is part of a transcriptional network that regulates cilia genes in the developing mouse retina

Analysis of retinas from mice with a targeted disruption of the gene encoding the forkhead transcription factor Foxn3 revealed additional displaced amacrine interneurons and retinal astrocytes in the inner plexiform and ganglion cell layers, as well as ectopic primary cilia on bipolar and amacrine interneurons. Foxn3 is a transcriptional repressor and numerous genes linked to cilia structure or assembly were upregulated in embryonic retinas without Foxn3, including Foxj1, a forkhead transcription factor required for motile cilia. CUTCRUN analysis revealed that many of the upregulated retinal genes were bound by the Foxn3 and Rfx3 proteins. A short hydrophobic motif (LXXLXWL) shared by the Foxj1, Foxn4, and Foxn3 proteins was found to be required for association with the Rfx3 protein and for transcriptional repression by Foxn3, as well as for full transcriptional activation by Foxn4 with Rfx3. AlphaFold 3 predicts an interaction between the shared hydrophobic motif and the Rfx3 dimerization domain. Mutations in Rfx3 at the predicted interaction site disrupted association of Rfx3 with Foxn3 or Foxn4. These results reveal a new layer of transcriptional regulation of genes required for cilia, with Foxn3 functioning as a repressor of cilia genes and limiting primary cilia formation in the developing retina.

developmental biology↗

bioRxiv2021

Brain I3 Binding Protein regulates K-Ras4B membrane localization and signaling

Membrane localization of Ras proteins is necessary for their biological functions and oncogenic activity. We report here on the identification of Brain I3 Binding Protein (BRI3BP) as a novel binding partner for Ras. We show that K-Ras4B plasma membrane localization and biological function are reduced in the absence of BRI3BP. BRI3BP interacts with K-Ras4B and K-Ras4A and our data suggest that BRI3BP operates within the recycling endosomal compartment to regulate K-Ras localization to the plasma membrane. This study uncovers a new regulatory protein for Ras membrane localization.

cell biology↗

bioRxiv2020

Regulation of retinal amacrine cell generation by miR-216b and Foxn3

The mammalian retina contains a complex mixture of different types of neurons. We find that the microRNA miR-216b is preferentially expressed in postmitotic retinal amacrine cells in the mouse retina, and expression of miR-216a/b and miR-217 in the retina depend in part on Ptf1a, a transcription factor required for amacrine cell differentiation. Surprisingly, ectopic expression of miR-216b, or the related miR-216a, can direct the formation of additional amacrine cells in the developing retina. In addition, we observe the loss of bipolar neurons in the retina after miR-216b expression. We identify the mRNA for the transcriptional regulator Foxn3 as a retinal target of miR-216b by Argonaute PAR-CLIP and reporter analysis. Inhibition of Foxn3 in the postnatal developing retina by RNAi also increases the formation of amacrine cells and reduces bipolar cell formation, while overexpression of Foxn3 inhibits amacrine cell formation prior to the expression of Ptf1a. Disruption of Foxn3 by CRISPR in embryonic retinal explants also reduces amacrine cell formation. Co-expression of Foxn3 can partially reverse the effects of ectopic miR-216b on retinal cell type formation. Our results identify Foxn3 as a novel regulator of interneuron formation in the developing retina and suggest that miR-216b likely regulates expression of Foxn3 and other genes in amacrine cells.

neuroscience↗