Roberto Feuda

The mechanisms underlying how the brain can switch from a plastic to a degenerative state are unknown. Tolls and Toll-Like receptors (TLRs) could be involved since they underlie both neuroinflammation and structural brain plasticity. Here, we show that the Toll signalling adaptor Weckle (Wek) - a ZAD-Zinc-finger transcription factor - can switch the response from promoting innate immunity or cell death, to inducing growth instead. Myristoylated Wek binds Tolls at the membrane, and concerted PI3K and Toll signalling drive its nuclear translocation. Wek interacts with Yorkie (Yki) – the key regulator of growth restrained by Hippo - enabling its nuclear shuttling. Remarkably, Wek blocks innate immunity. Instead, Wek and Yki together drive glial cell proliferation and growth. Through this mechanism, Toll signalling could promote structural brain plasticity via Wek and Yki downstream. As Tolls and Yki are widespread, these findings could have important implications for understanding also regeneration and cancer.

Endoderm, one of three primary germ layers of vertebrate embryos, makes major contributions to the respiratory and gastrointestinal tracts and associated organs, including the liver and pancreas. In mammals, transcription factor (TF) SOX17 is vital for endoderm organ formation and can induce endoderm progenitor identity. Duplication of ancestral sox17 before or during the early evolution of ray-finned fishes produced paralogs sox32 and sox17 in zebrafish. Sox32 is required for specification of endoderm and progenitors of the left–right (LR) organizer (Kupffer's Vesicle, KV), with Sox17 a downstream target of Sox32 implicated in further KV development. Phenotypic evidence, therefore, suggests functional similarities between zebrafish Sox32 and Sox17 and mammalian SOX17. Here, we directly compare these orthologs and paralogs, using the early zebrafish embryo as a biological platform for functional testing. Our results indicate that, unlike Sox32, human SOX17 cannot induce endoderm specification in zebrafish. Furthermore, using hybrid protein functional analyses, we show that Sox32 specificity for the endoderm gene regulatory network is linked to evolutionary divergence in its DNA-binding High Mobility Group domain from its paralog Sox17. Additionally, changes in the C-terminal regions of Sox32 and Sox17 underpin their differing target specificities. Finally, we establish that specific conserved peptides in the Sox17 C-terminal domain are essential for its role in establishing correct organ asymmetry. Overall, our results illuminate the molecular basis for functional divergence of Sox32 and Sox17 in vertebrate endoderm development and LR patterning, and reveal that alterations in specific domains of both TFs at different points during the evolution of fish are critical to their distinct and essential functions.

To what extent conserved developmental programs specify homologous cell types is a central question in biology. Here, we address this by focusing on reconstructing monoaminergic neuron development in Drosophila melanogaster embryo using time- resolved single-cell genomics, spatial transcript mapping with hybridisation chain reaction, and targeted metabolomics. We uncover a regulatory landscape in which specific transcription factors are activated before biosynthetic enzymes, establishing a prospective temporal architecture for monoaminergic fate specification. Comparative analyses of developmental single-cell atlases from zebrafish and sea urchin indicate that components of this machinery are conserved across ∼550 million years of bilaterian evolution with orthologous transcription factors showing similar temporal dynamics. Together, these findings point to a putatively conserved regulatory core that interfaces with other context-dependent transcription factors; this interplay accommodates monoaminergic multifunction and subtype diversity across distinct neuroanatomies.

In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.

The evolutionary conservation of cell types over deep time has long been theorised but remains difficult to demonstrate. Monoaminergic neurons, which produce molecules such as serotonin and dopamine, are central to animal behaviour and cognition, yet their evolutionary origins remain unresolved. Here, we analysed single-cell transcriptomes from 16 metazoan species spanning eight phyla. Using a novel integration method, Orthogroup Recoding, together with experimental validation, we show that monoaminergic neurons form consistent transcriptional clusters across Bilateria. These clusters share a regulatory signature involving conserved transcription factors, including homologues of Fev , Lmx1b , Fer2 , Insm , and Isl , suggesting a common regulatory program. This signature extends beyond the brain including other monoaminergic cells, such as the gut enterochromaffin cells and larval sensory neurons. By contrast, non-bilaterian lineages lack the coordinated expression of the transcription factors and the biosynthetic machinery that regulate monoamine production. Our observations support the existence of a shared set of TFs that define ‘monoaminergic identity’ across in bilaterians.

Single-cell RNA-sequencing revolutionized our approach of transcriptomic studies, enabling to analyze gene expression across cell type in a tissue. Here we introduce an optimized cell dissociation and a Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq) protocol to perform single-cell RNA-seq in insects. Up to 400,000 cells can be used as starting material within a single experiment.

The evolution of the nervous system has been shrouded in controversy since the onset of the genomics era. A large part of this controversy stems from the lack of phylogenetic consensus for the main branches of the animal tree, where often animals with nervous systems do not form a monophyletic group. However, this question can be informed from other non-phylogenetic perspectives, such as comparative genomics. Here we ask how similar are genes differentially expressed in neurons across a representative set of eight animals with a nervous system and tally the presence or absence of their homologs in 10 other animals and two choanoflagellates. We show that proteins from 39 families are differentially expressed in all neurons, regardless of the phylogenetic placement of their lineage, and that the majority of these gene families are present in the (unicellular) closest relatives of animals, choanoflagellates. We found that the members of these 39 gene families are enriched in domains for ion transport and juxtacrine signalling, and that there is one gene family of zinc-dependent extracellular matrix-remodelling proteins which is only found in animals bearing a nervous system. Our results show that common genetic toolkits are in place for the function of nervous systems. We identify a large number of potential new genomic markers linked to the nervous system and hope they can complement ongoing research efforts to better understand this quintessentially animal system.

Blood feeding (hematophagy) is widespread across Diptera (true flies), yet the underlying genetic basis remains poorly understood. Using phylogenomics, we show that four gene families associated with neuromodulation, immune responses, embryonic development, and iron metabolism have undergone independent expansions within mosquitoes and sandflies. Our findings illuminate the underlying genetic basis for blood-feeding adaptations in these important disease vectors.

The evolution of vision is a major novelty in animals, playing a fundamental role in developing complex behaviours. Vision initiates with a light-triggered phototransduction cascade occurring in photoreceptor cells (PRCs). The two main PRC types, ciliary and rhabdomeric, employ both specific and common genes for phototransduction. Despite being crucial for vision, the origin and evolution of photoreceptor cells and phototransduction pathways remain unclear. Using phylogenetic methods, we studied the evolution of all phototransduction genes, elucidating their gene duplication patterns in over 80 species, including non-bilaterian metazoans and other eukaryotes. Then, we investigated the expression of phototransduction genes in available single-cell RNA-sequencing data from various animals, including non-bilaterians. By using phototransduction genes as markers, we identified putative photoreceptor-like cells across animals and compared their regulatory toolkits. Gene families encoding phototransduction components are generally ancient, predating the origin of vision. However, many phototransduction genes originated in the metazoan stem group. Moreover, putative photoreceptor cells identified in non-bilaterians appeared to express some but not all components of the two well-characterised phototransduction pathways, suggesting potential lineage-specific components involved in phototransduction. Finally, we identified conserved expression of certain transcription factors in putative PRCs in non-bilaterians, suggesting the homology of PRCs.

In this study, we explored the diversity and evolution of opsins using meta-omic data from the TARA Oceans and TARA Polar Circle expeditions, one of the largest marine datasets available. By using molecular clustering and phylogenetic analyses, we identified and characterized opsins across various taxonomic groups and gene subfamilies. Our results indicate that the majority of opsin sequences belong to arthropods and vertebrates. However, we also detected sequences from all major opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no novel opsin gene families were discovered, suggesting a comprehensive understanding of opsin diversity in marine ecosystems. Additionally, we present novel opsin sequences from less-studied taxa, which may serve as a valuable resource for future research into opsin function and diversity.