Life Science Zurich

Recent advances in sequencing technologies have increasingly enabled the identification of genetic causes for human monogenic diseases. However, systematic understanding remains limited due to the rarity, genetic heterogeneity, and complex genotype–phenotype relationships of these diseases. Primary ciliopathies are a diverse group of rare disorders caused by variants in genes associated with the cilium, a cellular organelle involved in signaling during development and cell homeostasis. These genetic variants result in a wide spectrum of clinical phenotypes involving the brain, eye, kidney, and skeleton. It remains unclear to what extent this phenotypic diversity can be attributed to the disease-causing genes and their specific roles in ciliary function. Here, we systematically compared human primary ciliopathies with each other and with mouse phenotypes by propagating known disease genes through a network of protein interactions. Network propagation improved the clustering of primary ciliopathies with shared clinical phenotypes and facilitated the identification of mouse phenotypes closely related to primary ciliopathies, due to shared groups of proteins in the interaction network. By leveraging this phenotype-specific approach, we prioritized candidate genes for specific ciliopathies and identified likely pathogenic variants in CEP43, a previously unrecognized ciliopathy gene, in three previously unsolved cases. This study demonstrates that network propagation enhances the genetic and phenotypic understanding of primary ciliopathies, aiding in the prioritization of candidate genes and providing a framework for unraveling shared underlying mechanisms for other rare genetic diseases.

Current single-cell RNA sequencing (scRNA-seq) methods suffer from biases that restrict the detection of cellular transcripts to 10-40% of total RNAs. This hinders the identification of transcripts of interest. Additionally, information retrieved from most high-throughput scRNA-seq methods is confined to untranslated regions toward transcript ends, resulting in loss of detail in internal regions. In this review, we outline biases in scRNA-seq protocol steps that limit transcript and region detection. We then discuss the advantages and disadvantages of targeted sequencing solutions, grouped into five categories according to the protocol step they target. Finally, we present a decision tree that guides researchers in selecting the most suitable targeted method for their experiment.

Agricultural grassland management intensity strongly influences soil microbial community structure in Europe, though the influence of individual practices, such as fertilization and cutting frequency, requires further investigation. Using a 46 year old field experiment in the Swiss Jura region, we examined how both fertilizer input and cutting frequency influence both soil microbial community structure and functional potential. For community structures of soil bacteria and fungi (determined via genetic metabarcoding) and plants (determined via plant species relevés) the effect of fertilization had a stronger effect than that of cutting frequency. The fatty acid biomarker for arbuscular mycorrhizal fungi (AMF, 16:1ω5), however, responded more to cutting frequency (relative effect size = 87.71 %) than fertilization (relative effect size = −7.90 %). Among bacteria with genes linked to soil phosphorous (P) and nitrogen (N) mobilization, only the abundance of the gcd gene (inorganic P solubilisation) displayed a significant fertilization effect. These findings suggest that long-term mineral fertilizer application is a key driver of differences in microbial community structure in grasslands of contrasting management type, and may influence bacterial P solubilisation capacity. Some microbial groups, such as AMF, appear more sensitive to cutting frequency, possibly due to additional plant re-growth. This study highlights the importance of disentangling agricultural management practices to better predict grassland plant and soil microbial responses to intensification.

Abstract Description Emerging single-cell spatial-omics techniques, such as Imaging Mass Cytometry (IMC), provide high-resolution cellular phenotyping in heterogeneous tissues. However, these methods are limited in detecting molecular features like lipids, glycans, and metabolites. In contrast, mass spectrometry imaging (MSI) excels at analyzing these features but lacks the cellular resolution needed for precise single cell spatial context. To bridge this gap, we developed an integrative framework combining IMC and MSI through a specialized wet lab workflow and refined image alignment software. This approach enabled us to investigate glycosylation changes in human liver inflammation. While individual technologies detected only minor, previously documented changes, integrating their data revealed distinct single-cell molecular signatures, including unique N-glycan profiles in inflammatory immune cells. These profiles correlated with macrophage markers such as CD206, CD163, and HLA-DR. Spatial transcriptomics further validated these findings. Ongoing studies extend this work to animal models, leveraging mass spectrometry to further characterize immune cell glycosylation at the single-cell level. By integrating spatial-omics technologies, we uncover intricate molecular glycosylation patterns of individual cells in complex tissues, opening new frontiers for understanding biology and advancing therapy. Funding Sources RSG-24-1255025-01-IBCD and R01CA258882 to S.G.. Topic Categories Technological Innovations in Immunology (TECH)

Multicellular self-organization relies on complex interactions across multiple length scales, shaping the transcriptional activity and molecular phenotype of individual cells. Despite advances in spatial omics technologies, mapping protein state composition at high spatial resolution to capture the molecular phenotype across whole-mount structures has remained challenging. Here, we introduce high-throughput 3D iterative indirect immunofluorescence imaging (3D-4i) for the simultaneous detection of multiple proteins and protein states across the entire embryo, and a 3D-dedicated computer vision pipeline for quantifying morphological and molecular properties across subcellular, single-cell, and whole-embryo scales in hundreds of samples. Applying this pipeline to early zebrafish embryos undergoing mid-blastula transition, we determine the cell cycle phase for each cell across the embryo, allowing us to uncover the spatiotemporal dynamics by which global meta-synchronous mitotic waves transition to cell cycle desynchronization. Using statistical analysis, we find that cell cycle phase is the major source of variability in transcription within a division cycle, and combining this with analysis of key transcription factors and chromatin modifier state enables accurate prediction of transcriptional output during zygotic genome activation in individual cells. Collectively, our results demonstrate the strength of 3D-4i in quantifying multimodal effects across spatiotemporal scales and show how it can be utilized to unravel the complex contribution of causal factors that collectively drive multicellular self-organization.

Budding yeast undergoes replicative aging through asymmetric cell divisions. Yeast mother cells progressively age as they generate successive daughter cells, until they ultimately die. However, their daughters are born rejuvenated, that is, most of them recover a full lifespan potential, with little impact of their mothers' age at their birth. In this review, we will discuss recent findings regarding the mechanisms of replicative aging and rejuvenation. Based on these insights, we will also discuss which evolutionary forces may havepresided over the emergence of aging in yeast. We suggest that aging and rejuvenation represent two adaptive strategies that each bring their own benefits.

The establishment of the body plan during gastrulation represents a hallmark of animal life. It emerges from the interplay of gene-regulatory programs and positional cues, yet how these signals are integrated post-transcriptionally remains largely unexplored. Here, we combine the scalability of mouse gastruloids with a single-cell CRISPR screening platform to functionally dissect germ layer specification at single-cell transcriptomic resolution. Focusing on post-transcriptional regulation, we systematically map drivers of mesodermal and endodermal fate and identify the deadenylase Cnot8. Loss of Cnot8 leads to widespread poly(A) tail elongation and transcript stabilization, shifting mesoderm differentiation toward ectopic notochord fate, thereby profoundly impacting axial patterning. Collectively, our findings identify mRNA deadenylation as a fundamental mechanism linking cellular identity with morphogenetic signaling during mammalian body plan formation.

Aberrant aggregates of the 42-residue form of the amyloid-β peptide (Aβ42) are cytotoxic in Alzheimer's disease (AD). Cost-effective and chronically safe disease-modifying therapeutics are needed to address the AD medical emergency worldwide. To increase our understanding of the mechanisms of Aβ42-induced cytotoxicity and to investigate clinically relevant aminosterols, we study the impact of claramine on the aggregation kinetics and properties of Aβ42 aggregates, as well as the ability of these proteotoxic species to bind and disrupt cell membranes. Whereas previously studied aminosterols accelerated Aβ42 aggregation, we show that claramine potently inhibits Aβ42 amyloid fibril formation. We find that claramine stabilizes soluble Aβ42, speeding up primary and secondary nucleation into species with antiparallel β-sheet structure that are elongation incompetent, thereby depleting Aβ42 monomers from the aggregation reaction. This steroid-polyamine also dissociates Aβ42 fibrillar aggregates, resulting in the abrogation of the autocatalytic capacity of Aβ42 fibrils, and it also inhibits the aggregation of a tau fragment relevant to AD. Upon exposure of human neuroblastoma cells to stabilized Aβ42 oligomers, claramine effectively neutralized Aβ42 oligomer-induced cytotoxicity by preventing their binding to cell membranes. Owing to the unique mechanism of action of aminosterols to reduce the toxicity of soluble Aβ42 aggregates by protecting cell membranes, and the newly characterized ability of claramine to inhibit Aβ42 fibril formation and dissociate fibrillar Aβ42 resulting in the interruption of the positive feedback loop in Aβ42 aggregation, our findings further emphasize the relevance of this family of natural products as potential treatments for AD and other protein misfolding diseases.

Repressive chromatin domains often localize to the nuclear lamina or nucleolus. Although nucleolar-associated domains (NADs) have recently been mapped, their mechanisms of nucleolar association and functional significance remain unclear. Here, we show that nucleophosmin (NPM1), a factor located in the granular component of the nucleolus, mediates NAD association in mouse embryonic stem cells. NPM1 binds NADs, interacts with the histone methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of a DNA-binding-deficient mutant disrupts NAD-nucleolus association and reduces H3K9me2 specifically at NADs. G9a is dispensable for NAD-nucleolus contacts, indicating that H3K9me2 is acquired after NADs associate with NPM1 at nucleoli. These findings reveal mechanistic insights into how genomic domains associate with nucleoli and form repressive chromatin and indicate that the nucleolus not only serves as a scaffold for positioning repressive domains but also plays a direct role in establishing their repressive chromatin states.

The renal thick ascending limb (TAL) plays a key role in water and ion homeostasis. Apical potassium secretion via the renal outer medullary potassium channel (ROMK) is essential for transepithelial sodium reabsorption via the furosemide-sensitive Na-K-2Cl-cotransporter and creates the electrochemical gradient for paracellular ion transport through Claudin tight junction proteins. Interestingly, the TAL exhibits transcriptomic heterogeneity and variable apical ROMK abundance. Single-cell RNA sequencing suggests that the cortical TAL consists of at least three distinct cell types, but whether ROMK distribution aligns with these types remains unclear. We analyzed perfusion-fixed mouse kidneys using RNAscope in situ hybridization (ISH), iterative indirect immunofluorescence imaging (4i multiplexing), and machine learning. ROMK mRNA expression was seen in all TAL cells. In contrast, apical ROMK protein abundance was found on almost all macula densa (MD) cells but was heterogeneous along the rest of the TAL. In the remaining TAL, only about 60% of the TAL cells had strong apical ROMK staining, while 40% lacked apical ROMK but showed weak perinuclear signals. ISH revealed that apical ROMK-positive cells express Ptger3 mRNA, whereas apical ROMK-negative cells express Foxq1 mRNA. Multiplexing analysis showed that ROMK-positive cells form Claudin-10b-positive tight junctions, while ROMK-negative cells form Claudin-16/19-positive junctions and express basolateral Kir4.1. Despite universal ROMK mRNA expression, apical ROMK distribution aligns with molecularly distinct TAL cell types. This unique ROMK expression pattern suggests functional heterogeneity for ROMK along the TAL.