Rafi, Ibnul et al. (2019) International Worm Meeting "The neuropeptidergic connectome of Caenorhabditis elegans."

Temmerman, Liesbet, Vertes, Petra, Hobert, Oliver, YANG, Xinyi, Vandewyer, Elke, Schafer, William, Beets, Isabel, Sanchez, Lidia, Chen, Chi, Rafi, Ibnul, Bael, Sven

[International Worm Meeting, 2019]

A "connectome" describes the complete synaptic wiring diagram of a brain. Past and current connectomic efforts are focused on determining the anatomical, i.e. chemical and electrical synaptic connections between neurons in a brain, thereby completely ignoring aspects of neuronal communication that are likely of equal importance but are not captured by anatomical connections: Neuromodulatory communication by neuropeptides and their cognate receptors. Neuropeptidergic communication is usually non-synaptic, i.e. neuropeptides are often released from non-synaptic sites and cognate neuropeptide receptors are often located distal from the source of the cognate neuropeptide. While the importance of a number of neuropeptides and their receptors in controlling behavior are well appreciated, the extent of usage of neuropeptidergic signaling is only beginning to be fully appreciated. Every neuron in an animal nervous system is now thought to express at least one neuropeptide, but the pathways of communication of these neuropeptidergic signals have not been comprehensibly mapped and, hence, our understanding of information flow in the nervous system remains incomplete. A consortium of four laboratories (Hobert, Schafer, Beets, Temmerman Labs) has received NIH funds to establish the first comprehensive neuropeptidergic connectome. We build such a connectome through (1) comprehensively defining ligand/receptor pairs through in vitro receptor activation assays, (2) defining the expression patterns of all neuropeptide and neuropeptide receptor encoding genes, (3) synthesizing these data into a neuropeptidergic network and computationally comparing the topology of this network to the synaptic connectivity network and (4) undertaking a preliminary functional validation of specific nodes and edges of this network. Comparing a neuropeptidergic connectome to that of the completely established synaptic connectome, we expect to describe a "multilayer connectome" with substantially distinct pathways of information flow, as well as distinct and similar topological features.

Taylor, Seth R et al. (2021) International Worm Meeting "Molecular topology of an entire nervous system"

Xu, Chuan, Barrett, Alec, Varol, Erdem, Cook, Steven J, Basavaraju, Manasa, Yemini, Eviatar, Hammarlund, Marc, Miller III, David M, Weinreb, Alexis, Abrams, Alexander, Rafi, Ibnul, Santpere, Gabriel, Vidal, Berta, Sestan, Nenad, Oikonomou, Panos, McWhirter, Rebecca, Cros, Cyril, Glenwinkel, Lori, Tavazoie, Saeed, Taylor, Seth R, Hobert, Oliver, Reilly, Molly B, Poff, Abigail

[International Worm Meeting, 2021]

Neurons are the fundamental structural and functional units of the nervous system. Although all neurons share many common features, they also display remarkably diverse morphological and functional characteristics. To uncover the underlying genetic programs that specify individual neuron identities, the CeNGEN consortium produced scRNA-Seq profiles of > 100,000 cells from the L4 stage C. elegans hermaphrodite, including all neuron classes and several non-neuronal cells (e.g., glia, muscle, hypodermis, reproductive tissues). In addition, we identified distinct subclasses for 10 of the 118 anatomically-defined classes. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses unique codes of ~23 neuropeptide genes and ~36 neuropeptide receptors thus pointing to an expansive "wireless" signaling network. To demonstrate the utility of this uniquely comprehensive gene expression catalog, we used computational approaches to identify cis-regulatory elements for neuron-specific gene expression. Because our scRNA-Seq data match the single cell resolution of the wiring diagram, we also sought to correlate expression of cell adhesion proteins with neuron-specific fasciculation and connectivity in the nerve ring. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity and function throughout the C. elegans nervous system. These data are available at cengen.org and can be interrogated with the web application CengenApp at cengen.shinyapps.io/CengenApp.

Varol, Erdem et al. (2021) International Worm Meeting "A computational approach linking neuron-specific gene expression with connectivity"

Barrett, Alec, McWhirter, Rebecca, Vidal, Berta, Tavazoie, Saeed, Hobert, Oliver, Weinreb, Alexis, Miller, David, Xu, Chuan, Taylor, Seth, Paninski, Liam, Yemini, Eviatar, Sestan, Nenad, Basavaraju, Manasa, Litwin-Kumar, Ashok, Cros, Cyril, Reilly, Molly, Santpere, Gabriel, Poff, Abigail, Glenwinkel, Lori, Abrams, Alexander, Hammarlund, Marc, Rafi, Ibnul, Varol, Erdem, Oikonomou, Panos, Cook, Steven

[International Worm Meeting, 2021]

There is strong prior evidence for genetic encoding of synaptogenesis, axon guidance, and synaptic pruning in neural circuits. Despite these foundational observations, the transcriptional codes that drive neural connectivity have not been elucidated. The C. elegans nervous system is a particularly useful model for studying the interplay between genetics and connectivity since its wiring diagram is highly stereotyped and uniquely well-defined by electron microscopy. Furthermore, recent evidence in C. elegans has suggested that a unique combination of transcription factors specifies each of the 118 neuron classes[1]. Motivated by evidence for the stereotypy of neural circuits and for the genetic encoding of neural identity, we introduce a novel statistical technique, termed Network Differential Gene expression analysis (nDGE), to test the hypotheses that neuron-specific gene expression dictates connectivity. Specifically, we test the hypothesis that pre-synaptic neural identity is defined by a "key" gene combination whose post-synaptic targets are determined by a "lock" gene combination. For our approach, we utilize neuron-specific gene expression profiles from the CeNGEN project[2] to investigate transcriptional codes for connectivity in the nerve ring[3]. We hypothesize that the expression of specific cell adhesion molecules (CAM) among synaptically-connected neurons drives synaptic maintenance in the mature nervous system. We posit that CAMs mediating synaptic stability would be more highly expressed in synaptically-connected neurons than in adjacent neurons with membrane contacts but no synapses. Thus, for each neuron, we compare the expression of all possible combinations of pairs of CAMs in the neuron and its synaptic partners relative to the neuron and its non-synaptic adjacent neurons. Two independent comparisons are generated, one for presynaptic neurons and a second result for postsynaptic neurons. Our nDGE analysis reveals that specific combinations of CAMs are correlated with connectivity in different subsets of neurons and thus provides a uniquely comprehensive road map for investigating the genetic blueprint for the nerve ring wiring diagram. Open source software of Network Differential Gene Expression (nDGE) is publicly available at https://github.com/cengenproject/connectivity_analysis along with a vignette showcasing the CAM results. 1. Reilly, M. B., Cros, C., Varol, E., Yemini, E., & Hobert, O. (2020). Unique homeobox codes delineate all the neuron classes of C. elegans. Nature, 584(7822), 595-601. 2. Taylor, S. R., Santpere, G., Weinreb, A., Barrett, A., Reilly, M. B., Xu, C. Varol, E., ... & Miller, D. M. (2020). Molecular topography of an entire nervous system. bioRxiv. 3. Cook, S. J.,... & Emmons, S. W. (2019). Whole-animal connectomes of both Caenorhabditis elegans sexes. Nature, 571(7763), 63-71.