Biology subjects

Tschopp, P.

Publications and source records attributed to Tschopp, P..

11 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

Developmental genetic basis of dorsal spine reduction in acidic-adapted threespine stickleback fish

The repeated emergence of similar phenotypes in independent populations is a widespread feature of evolution, yet the extent to which repeated evolution reflects shared molecular mechanisms, and the factors that determine this similarity, remain unclear. Here, we investigate the genetic basis of dorsal spine reduction in threespine stickleback fish, an adaptive trait that has evolved repeatedly in freshwater populations. Phenotypic analyses of crosses between a spine-reduced population from Scotland and the ancestral marine form reveal a major-effect locus, with the spine-reducing allele acting dominantly and influencing body patterning. Bulk segregant analysis maps this effect to a single region on chromosome VI that overlaps the hoxdb gene cluster. Transcriptomic analyses of larval stages show a gain of hoxdb expression in the developing spine region of spine-reduced fish, consistent with the dominance of the derived allele. Together, these results indicate dorsal spine reduction in threespine stickleback through cis-regulatory changes at hoxdb, a mechanism found to mediate dorsal spine evolution in a different species of stickleback fish too. These findings highlight the role of hox genes in adaptive divergence between natural populations within a species and provide a clear example of parallel evolution at the molecular level between species.

evolutionary 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

Adaptive cellular evolution in the intestinal tracts of hyperdiverse African cichlid fishes

Adaptations related to how nutrients are acquired and processed play a central role in the colonization of novel ecological niches and, therefore, in organismal diversification. While the evolution of feeding structures has been studied extensively in this context, the nature of dietary adaptations in the digestive tract remains largely unexplored. Here, we investigate the cellular and molecular basis of dietary adaptations in the massive radiation of cichlid fishes in Lake Tanganyika using comprehensive single-cell transcriptomic data derived from the intestines of 24 endemic cichlid species with distinct habitats and diets. We show that, at the cellular level, dietary adaptations are primarily driven by anterior enterocytes, and that both the relative abundance and gene expression profiles of these cells have evolved in response to rapid dietary specializations. These dietary adaptations are driven by rapidly evolving cell population-specific genes, suggesting that alterations in epithelial cell specification programs and molecular makeup promote ecological diversification.

evolutionary biology↗

bioRxiv2024

Distinct Gene Regulatory Dynamics Drive Skeletogenic Cell Fate Convergence During Vertebrate Embryogenesis

Cell type repertoires have expanded extensively in metazoan animals, with some clade-specific cells being paramount to their evolutionary success. A prime example are the skeletogenic cells of vertebrates that form the basis of their developing endoskeletons. Depending on anatomical location, these cells originate from three different embryonic precursor lineages - the neural crest, the somites, and the lateral plate mesoderm - yet they converge developmentally towards similar cellular phenotypes. Furthermore, these lineages have gained skeletogenic competency at distinct timepoints during vertebrate evolution, thus questioning to what extent different parts of the vertebrate skeleton rely on truly homologous cell types. Here, we investigate how lineage-specific molecular properties of the three precursor pools are integrated at the gene regulatory level, to allow for phenotypic convergence towards a skeletogenic cell fate. Using single-cell transcriptomics and chromatin accessibility profiling along the precursor-to-skeletogenic cell continuum, we examine the gene regulatory dynamics associated with this cell fate convergence. We find that distinct transcription factor profiles are inherited from the three precursor states, and that lineage-specific enhancer elements integrate these different inputs at the cis-regulatory level, to execute a core skeletogenic program. We propose a lineage-specific gene regulatory logic for skeletogenic convergence from three embryonic precursor pools. Early skeletal cells in different body parts thus share only a partial deep homology. This regulatory uncoupling may render them amenable to individualized selection, to help to define distinct morphologies and biomaterial properties in the different parts of the vertebrate skeleton.

developmental biology↗

bioRxiv2023

Self-organized BMP signaling dynamics underlie the development and evolution of tetrapod digit patterns

Repeating patterns of synovial joints are a highly conserved feature of articulated digits, with variations in joint number and location giving rise to a diverse range of digit morphologies and limb functions across the tetrapod clade. During development, joints form iteratively within the growing digit ray, as a population of distal progenitors alternately specifies joint and phalanx cell fates to segment the digit into distinct elements. Whilst numerous molecular pathways have been implicated in this fate choice, it remains unclear how they give rise to a repeating pattern. Here, using single cell RNA-sequencing and spatial gene expression profiling, we investigate the transcriptional dynamics of interphalangeal joint specification in vivo. Combined with mathematical modelling, we predict that interactions within the BMP signaling pathway - between the ligand GDF5, the inhibitor NOG, and the intracellular effector pSMAD - result in a self-organizing Turing system that forms periodic joint patterns. Our model is able to recapitulate the spatiotemporal gene expression dynamics observed in vivo, as well as phenocopy digit malformations caused by BMP pathway perturbations. By contrasting in silico simulations with in vivo morphometrics of two morphologically distinct digits, we show how changes in signaling parameters and growth dynamics can result in variations in the size and number of phalanges. Together, our results reveal a self-organizing mechanism that underpins tetrapod digit patterning and its evolvability, and, more broadly, illustrate how Turing systems based on a single molecular pathway may generate complex repetitive patterns in a wide variety of organisms.

developmental biology↗

bioRxiv2021

Direct Reprogramming of Non-limb Fibroblasts toCells with Properties of Limb Progenitors

The early limb bud consists of mesenchymal progenitors (limb progenitors) derived from the lateral plate mesoderm (LPM) that produce most of the tissues of the mature limb bud. The LPM also gives rise to the mesodermal components of the trunk, flank and neck. However, the mesenchymal cells generated at these other axial levels cannot produce the variety of cell types found in the limb bud, nor can they be directed to form a patterned appendage-like structure, even when placed in the context of the signals responsible for organizing the limb bud. Here, by taking advantage of a direct reprogramming approach, we find a set of factors (Prdm16, Zbtb16, and Lin28) normally expressed in the early limb bud, that are capable of imparting limb progenitor-like properties to non-limb fibroblasts. Cells reprogrammed by these factors show similar gene expression profiles, and can differentiate into similar cell types, as endogenous limb progenitors. The further addition of Lin41 potentiates proliferation of the reprogrammed cells while suppressing differentiation. These results suggest that these same four key factors may play pivotal roles in the specification of endogenous limb progenitors.

developmental 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↗

bioRxiv2021

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types

BackgroundDuring development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built - largely - by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear. ResultsHere, using a paradigm of morphological diversification, the tetrapod limb, and singlecell RNA-sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. We developed a user-friendly bioinformatics workflow to detect gene co-expression modules and test for their conservation across developmental stages and species boundaries. Using mouse limb data as reference, we identified 19 gene co-expression modules with varying tissue or cell type-restricted activities. Testing for co-expression conservation revealed modules with high evolutionary turnover, while others seemed maintained - to different degrees, in module make-up, density or connectivity - over developmental and evolutionary timescales. ConclusionsWe present an approach to identify evolutionary and developmental dynamics in gene co-expression modules during patterning-relevant stages of homologous cell type specification.

developmental 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↗

bioRxiv2019

Constrained Transcriptional Polarity In The Organization Of Mammalian Hox Gene Clusters

In many animal species with a bilateral symmetry, Hox genes are clustered either at one or at several genomic loci. This organization has a functional relevance, as the transcriptional control applied to each gene depends upon its relative position within the gene cluster. It was previously noted that vertebrate Hox clusters display a much higher level of genomic organization than their invertebrate counterparts. The former are always more compact than the latter, they are generally devoid of repeats and of interspersed genes, and all genes are transcribed by the same DNA strand, suggesting that particular factors constrained these clusters towards a tighter structure during the evolution of the vertebrate lineage. Here we investigate the importance of uniform transcriptional orientation by engineering several alleles within the HoxD cluster such as to invert one or several transcription unit(s), with or without a neighboring CTCF site. We observe that the association between the tight structure of mammalian Hox clusters and their regulation makes inversions likely detrimental to the proper implementation of this complex genetic system. We propose that the consolidation of Hox clusters in vertebrates, including transcriptional polarity, evolved in conjunction with the emergence of global gene regulation via the flanking regulatory landscapes, to optimize a coordinated response of selected subsets of target genes in cis.

developmental biology↗