Biology subjects

Sacher, F.

Publications and source records attributed to Sacher, F..

5 recordsLinked to original sources

bioRxiv2026

Molecular address codes delineate circuit-specific motor neuron-muscle matchmaking in the developing tetrapod limb

An essential part of nervous systems development is the establishment and refinement of correct circuit architectures. In vertebrate neuromuscular circuits, this requires connecting the axons of motor neurons in the central nervous system to their corresponding muscle groups in the periphery. This process can roughly be sub-divided into two distinct phases: axon guidance towards their innervation territories, followed by the establishment of correct nerve-muscle connections. While the role of attractive and repulsive cues in axon guidance has been studied extensively, relatively little is known about the molecular interactions shaping motor neuron to muscle matchmaking that contribute to circuit specificity and refinement. Here, using the tetrapod limb as a model system, we focus on the maturation of three distinct neuromuscular circuits, targeting different proximal-distal and anterior-posterior territories of the developing chick forelimb, and sequence the transcriptomes of individually backfilled motor neurons as well as of the muscles they connect to. Comparative analyses across circuits suggest the presence of distinct molecular "address codes", based on individual signatures of matching profiles of secreted signaling factors and cell surface receptors. Furthermore, we probe for inherent transcriptional plasticity in this system, using an experimentally altered limb periphery that results in nerve miswiring, and sequence the corresponding motor neuron-muscle pairs. Lastly, to facilitate data exploration, we present an R Shiny app, to investigate circuit-specific ligand-receptor interaction profiles in both neuron-muscle and muscle-neuron directions, in control and experimentally altered limb configurations. Collectively, we present a resource to investigate the cellular and molecular basis for muscle-nerve matching during neuromuscular circuit refinement in the tetrapod limb, with implications for our understanding of vertebrate neuromuscular development and evolution, as well as regenerative approaches targeting re-innervation after injury or nerve damage.

developmental biology↗

bioRxiv2025

Transcriptional and cellular maturation of the chick spinal cord in the context of distinct neuromuscular circuits

The chicken spinal cord is a classic model system to study the early specification of neuronal cell types along its anterior-posterior axis. Here, we follow the ensuing maturation dynamics at limb levels with single cell resolution and contrast neuronal populations innervating appendages of distinct form and function. We use gene co-expression modules to identify rare cell populations with specific biological functions, and show that appendages with different motor outputs - wings and legs - rely on largely similar spinal cord cell type repertoires. Challenging the system with experimental alterations to the peripheral limb musculature reveals limited transcriptional changes, but spatially restricted plasticity in spinal cord motor neuron numbers. Collectively, our results provide a resource to investigate the molecular and cellular basis of neuronal maturation in the avian spinal cord and highlight the plastic nature of embryonic cells to adapt to changes in the limb periphery at both developmental and evolutionary timescales. HighlightsO_LICellular and transcriptional maturation of the developing chicken spinal cord at single-cell resolution C_LIO_LISingle-cell weighted gene co-expression network analysis isolates transcriptional maturation dynamics in different neuronal populations C_LIO_LIIn silico identification and in situ verification of novel markers for cerebrospinal fluid-contacting neurons C_LIO_LIMolecular characterization of the avian glycogen body C_LIO_LITranscriptional and compositional changes of spinal cord cell types in the context of different neuromuscular circuits C_LI

developmental biology↗

bioRxiv2024

A systems-based approach to uterine fibroids identifies differential splicing associated with abnormal uterine bleeding

Uterine fibroids (UFs), benign tumours prevalent in up to 80% of women of reproductive age, are associated with significant morbidity, including abnormal uterine bleeding, pain and infertility. Despite identification of key genomic alterations in MED12 and HMGA2, the pathogenic mechanisms underlying UFs and heavy menstrual bleeding (HMB) remain poorly understood. To correlate systematically genetic, transcriptional and proteomic phenotypes, our study involved an integrative analysis of fibroid, myometrium and endometrium tissues from 137 patients, utilising genome-wide SNP arrays, targeted sequencing, RNA sequencing and proteomics. Our findings reveal 39.7% of UFs possess MED12 mutations, alongside novel variants in genes such as COL4A5 and COL4A6. Multi-omics factor analysis of integrated protein and mRNA highlighted differential regulation related to extracellular matrix remodelling, proteolysis and homeostasis in fibroid versus myometrium tissues, and distinct gene sets associated with RNA splicing in the endometrium of patients with HMB, particularly in MED12-mutated fibroids. Our study proposes a model, which is supported by in vivo evidence, where altered signalling of MED12-mutated fibroids influences RNA transcript isoform expression in endometrium, potentially leading to abnormal uterine bleeding. This integrative approach unravels complex molecular pathways in UF pathogenesis and HMB, offering novel insights for targeted therapeutic development.

systems biology↗

bioRxiv2021

Extracellular matrix gene expression signatures as cell type and cell state identifiers

Transcriptomic signatures based on cellular mRNA expression profiles can be used to categorize cell types and states. Yet whether different functional groups of genes perform better or worse in this process remains largely unexplored. Here we test the core matrisome - that is, all genes coding for structural proteins of the extracellular matrix - for its ability to delineate distinct cell types in embryonic single-cell RNA-sequencing (scRNA-seq) data. We show that even though expressed core matrisome genes correspond to less than 2% of an entire cellular transcriptome, their RNA expression levels suffice to recapitulate important aspects of cell type-specific clustering. Notably, using scRNA-seq data from the embryonic limb, we demonstrate that core matrisome gene expression outperforms random gene subsets of similar sizes and can match and exceed the predictive power of transcription factors. While transcription factor signatures generally perform better in predicting cell types at early stages of chicken and mouse limb development, i.e., when cells are less differentiated, the information content of the core matrisome signature increases in more differentiated cells. Our findings suggest that each cell type produces its own unique extracellular matrix, or matreotype, which becomes progressively more refined and cell type-specific as embryonic tissues mature. HighlightsO_LICell types produce unique extracellular matrix compositions C_LIO_LIDynamic extracellular matrix gene expression profiles hold predictive power for cell type and cell state identification C_LI

systems biology↗

bioRxiv2019

A Single-cell Transcriptomic Atlas of the Developing Chicken Limb

BackgroundThrough precise implementation of distinct cell type specification programs, differentially regulated in both space and time, complex patterns emerge during organogenesis. Thanks to its easy experimental accessibility, the developing chicken limb has long served as a paradigm to study vertebrate pattern formation. Through decades worth of research, we now have a firm grasp on the molecular mechanisms driving limb formation at the tissue-level. However, to elucidate the dynamic interplay between transcriptional cell type specification programs and pattern formation at its relevant cellular scale, we lack appropriately resolved molecular data at the genome-wide level. Here, making use of droplet-based single-cell RNA-sequencing, we catalogue the developmental emergence of distinct tissue types and their transcriptome dynamics in the distal chicken limb, the so-called autopod, at cellular resolution.\n\nResultsUsing single-cell RNA-sequencing technology, we sequenced a total of 17,628 cells coming from three key developmental stages of chicken autopod patterning. Overall, we identified 23 cell populations with distinct transcriptional profiles. Amongst them were small, albeit essential populations like the apical ectodermal ridge, demonstrating the ability to detect even rare cell types. Moreover, we uncovered the existence of molecularly distinct sub-populations within previously defined compartments of the developing limb, some of which have important signaling functions during autopod pattern formation. Finally, we inferred gene co-expression modules that coincide with distinct tissue types across developmental time, and used them to track patterning-relevant cell populations of the forming digits.\n\nConclusionsWe provide a comprehensive functional genomics resource to study the molecular effectors of chicken limb patterning at cellular resolution. Our single-cell transcriptomic atlas captures all major cell populations of the developing autopod, and highlights the transcriptional complexity in many of its components. Finally, integrating our data-set with other single-cell transcriptomics resources will enable researchers to assess molecular similarities in orthologous cell types across the major tetrapod clades, and provide an extensive candidate gene list to functionally test cell-type-specific drivers of limb morphological diversification.

developmental biology↗