Biology subjects

Simm, S.

Publications and source records attributed to Simm, S..

5 recordsLinked to original sources

bioRxiv2026

Species-specific iNOS expression distinguishes epithelial and myeloid IFNγ responses in tuberculosis

RationaleTuberculosis vaccines aim to elicit protective immunity, with IFN{gamma}-producing CD4 T cells considered central mediators of host defense. In murine models, IFN{gamma} activates macrophages to induce inducible nitric oxide synthase (iNOS), resulting in nitric oxide-dependent control of Mycobacterium tuberculosis (Mtb). ObjectiveTo define the relevance of IFN{gamma}-induced iNOS activity in humans and other natural host of virulent mycobacterial species. MethodsWe systematically compared IFN{gamma}-induced effector responses in Mtb-infected myeloid cells across species. Using bulk RNA sequencing, functional infection assays, and nitric oxide measurements, we assessed IFN{gamma} responsiveness in human and mouse macrophages. These analyses were extended to monocytes from seven mammalian species and complemented by reanalysis of publicly available single-cell RNA-sequencing datasets and spatial proteomic imaging of tuberculous granulomas. Measurements and Main ResultsSingle-cell transcriptomic reanalysis revealed minimal NOS2 expression in myeloid cells from human and non-human primate granulomas. In vitro, IFN{gamma} pretreatment failed to induce NOS2 transcription, iNOS activity, or Mtb growth restriction in human macrophages, in stark contrast to murine cells. Across species, iNOS activity was largely restricted to mice, with limited induction in cattle monocytes. Instead, human respiratory epithelial cells consistently expressed NOS2, and multiplexed ion beam imaging localized iNOS protein to epithelial compartments adjacent to granulomatous lesions. ConclusionIFN{gamma} signaling is uncoupled from iNOS induction in primate myeloid cells and epithelial compartments represent dominant sources of iNOS in human tuberculosis. These findings, challenge murine macrophage-centric paradigms and IFN{gamma}-based correlates used in TB vaccine development and central to pathophysiology of tuberculosis and other pneumonias.

immunology↗

bioRxiv2025

Diversity of stomatal and cuticular structures affect microbial colonization in temperate forest tree species

Throughout their life cycle, tree leaves are subject to colonization and degradation by microorganisms, including fungi, bacteria, and algae. These relationships co-evolved with chemical properties, leaf shape, and surface structures. Here we quantified leaf abaxial surface texture features based on variables extracted from scanning electron microscopic images, resulting in an abstract quantitative texture complexity score. This complexity score was used to test functional hypotheses such as growth habitat preferences and microbial colonization patterns. Here we show that the evolution of leaf surface texture complexity traits correlated with anatomical features such as stomatal density and leaf orientation and correlated with Ellenberg temperature habitat indicator. Furthermore, increasing leaf surface texture complexity was found to be negatively correlated with plant pathogen richness (broad-leaved species) or lichenization (conifers), suggesting protection effects. Moreover, we found a negative correlation of leaf surface texture complexity with fungal and bacterial specialists. Our results highlight leaf surface texture complexity as a key, previously underappreciated trait shaping microbial diversity and leaf-microbe interaction patterns. This opens promising avenues for future research on plant-microbe co-evolution, trait-based ecosystem modeling, and the potential use of surface traits in forest management and disease resistance strategies.

plant biology↗

bioRxiv2025

Regulation of the transcriptome, miRNAs, and alternative splicing in a FSGS zebrafish injury model

BackgroundFocal Segmental Glomerulosclerosis (FSGS) is a severe kidney disorder with complex and not yet fully understood pathogenesis. Alternative splicing (AS) - the generation of distinct protein isoforms from the same gene - might play a critical role by the regulation of gene functions and disease development. MethodsTo investigate the role of AS in FSGS, we used a zebrafish model, which mimics key human FSGS features, including foot process effacement, matrix accumulation, podocyte detachment and parietal epithelial cell activation. We performed total RNA sequencing of isolated zebrafish glomeruli and whole larvae, followed by integrative bioinformatic analysis to identify AS events and regulatory miRNAs. ResultsOur data revealed a downregulation of essential podocyte genes (nphs1, nphs2, podxl, wt1) and an inhibition of pathways associated with nephron development and cytoskeletal organization. We also observed increased expression of the transcription factor stat3 and disease-associated miRNAs such as miR-21 and miR-193. AS analysis identified approximately [~]7,000 splicing events, primarily exon skipping ([~]80%), affecting genes such as nphs1, magi2, and ptpro. A total of 136 and 612 alternatively spliced genes were found at 5 and 6 days post-fertilization (dpf), respectively. Isoform switch analysis uncovered 70 genes affected by AS in FSGS, including epb41l5 (linked to podocyte adhesion), fgfr1a (fibroblast growth signaling), and members of the SRSF splicing factor family (e.g., srsf3a). ConclusionsThese findings emphasize the importance of transcriptional and post-transcriptional regulation, including AS, in FSGS pathogenesis. Furthermore, they support the zebrafish model as a valuable system for identifying novel mechanisms and potential therapeutic targets for kidney diseases.

cell biology↗

bioRxiv2025

Regulation of early-stage tomato fruit growth by the splicing factor RS2Z36

Fruit growth is mediated by cell division and expansion. In tomato, the model for fleshy fruit development, both processes are tightly linked to changes in gene expression, including transcriptional regulation and RNA processing. While several transcription factors are implicated in fruit developmental programs, the role of splicing regulators remains largely unexplored. Expression profiling of splicing-related genes revealed expression patterns. The serine/arginine-rich splicing factor RS2Z36 is expressed in ovaries and during early fruit development. Loss-of-function mutations in RS2Z36 result in ovaries with altered patterning and in smaller, ellipsoid fruits. rs2z36 mutants display elongated pericarp cells along the longitudinal axis of pre-anthesis ovaries, indicating that RS2Z36-dependent expansion patterns are established before anthesis. RNA-seq uncovered widespread alternative splicing of genes across diverse biological processes, while proteome analysis revealed altered protein abundance and peptides derived from novel splice variants. In addition, rs2z36-1 pericarps show increased deposition of LM6-recognized arabinan and AGP epitopes. Together, these findings identify RS2Z36 as a regulator of ovary and fruit development and highlight a previously underappreciated role for splicing control in shaping early fruit morphology.

developmental biology↗

bioRxiv2024

Alternative splicing in mechanically stretched podocytes as a model of glomerular hypertension

BackgroundAlterations in pre-mRNA splicing play an important role in disease pathophysiology. However, the role of alternative splicing (AS) for podocytes in hypertensive nephropathy (HN) has not been investigated. The purpose of the Sys_CARE project was to identify AS events that play a role in the development and progression of HN. MethodsMurine podocytes were exposed to mechanical stretch, after which proteins and mRNA were analyzed by proteomics, RNA-Seq and several bioinformatic AS tools. ResultsBased on transcriptomics and proteomics analysis we could observe significant changes in gene expression and abundance of proteins under mechanical stretch compared to unstretched conditions. By RNA-Seq, we identified over 3,000 alternative spliced genes after mechanical stretch, including all types of AS events. We found 17 genes that showed an AS event in four different splicing analysis tools. From these, we focused on Myl6, a component of the myosin protein complex, and Shroom3, an actin-binding protein crucial for podocyte function. We found two Shroom3 isoforms that showed significant changes in expression upon mechanical stretch, which was verified by qRT-PCR and in situ hybridization. Furthermore, we observed an expression switch of two Myl6 isoforms after mechanical stretch. This switch is accompanied by a change in a C-terminally located amino acid sequence. ConclusionsIn summary, mechanical stretch of cultured podocytes is an excellent model to simulate hypertensive nephropathy. In depth RNA-Seq analysis disclosed alternative splicing events, such as in Shroom3 and Myl6, which may play a crucial role in the pathophysiology of hypertension-induced nephropathy.

cell biology↗