Synthetic ablations in the C. elegans nervous system

Abstract Synthetic lethality, the finding that the simultaneous knockout of two or more individually nonessential genes leads to cell or organism death, has offered a systematic framework to explore cellular function, and also offered therapeutic applications. Yet the concept lacks its parallel in neuroscience—a systematic knowledge base on the role of double or higher order ablations in the functioning of a neural system. Here, we use the framework of network control to systematically predict the effects of ablating neuron pairs and triplets on the gentle touch response. We find that surprisingly small sets of 58 pairs and 46 triplets can reduce muscle controllability in this context, and that these sets are localized in the nervous system in distinct groups. Further, they lead to highly specific experimentally testable predictions about mechanisms of loss of control, and which muscle cells are expected to experience this loss.

[1]  Cori Bargmann,et al.  Control of larval development by chemosensory neurons in Caenorhabditis elegans. , 1991, Science.

[2]  Danielle S Bassett,et al.  The importance of the whole: Topological data analysis for the network neuroscientist , 2018, Network Neuroscience.

[3]  Aravinthan D. T. Samuel,et al.  Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans , 2011, Nature Methods.

[4]  Emma K. Towlson,et al.  The Rich Club of the C. elegans Neuronal Connectome , 2013, The Journal of Neuroscience.

[5]  Randall D. Beer,et al.  Connecting a Connectome to Behavior: An Ensemble of Neuroanatomical Models of C. elegans Klinotaxis , 2013, PLoS Comput. Biol..

[6]  Attila Balint,et al.  Systematic analysis of complex genetic interactions , 2018, Science.

[7]  L. Avery,et al.  Pharyngeal pumping continues after laser killing of the pharyngeal nervous system of C. elegans , 1989, Neuron.

[8]  S. Lockery,et al.  Evolution and Analysis of Minimal Neural Circuits for Klinotaxis in Caenorhabditis elegans , 2010, The Journal of Neuroscience.

[9]  Gal Haspel,et al.  A connectivity model for the locomotor network of Caenorhabditis elegans , 2012, Worm.

[10]  Aravinthan D. T. Samuel,et al.  Laser microsurgery in Caenorhabditis elegans. , 2012, Methods in cell biology.

[11]  Wim Fias,et al.  Brain networks under attack: robustness properties and the impact of lesions. , 2016, Brain : a journal of neurology.

[12]  T. Killingback,et al.  Attack Robustness and Centrality of Complex Networks , 2013, PloS one.

[13]  Kerry Bloom,et al.  Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation. , 2013, Cell reports.

[14]  Eli Shlizerman,et al.  Low-dimensional functionality of complex network dynamics: neurosensory integration in the Caenorhabditis Elegans connectome. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[15]  Albert-László Barabási,et al.  Target control of complex networks , 2014, Nature Communications.

[16]  Yi Wang,et al.  Computer Assisted Assembly of Connectomes from Electron Micrographs: Application to Caenorhabditis elegans , 2013, PloS one.

[17]  S. Nijman Synthetic lethality: General principles, utility and detection using genetic screens in human cells , 2011, FEBS letters.

[18]  C. Markert,et al.  Developmental genetics , 2005, Experientia.

[19]  Peter Andras,et al.  Simulation of robustness against lesions of cortical networks , 2007, The European journal of neuroscience.

[20]  Zhaoyang Feng,et al.  The Neural Circuits and Synaptic Mechanisms Underlying Motor Initiation in C. elegans , 2011, Cell.

[21]  Danielle S. Bassett,et al.  Two’s company, three (or more) is a simplex , 2016, Journal of Computational Neuroscience.

[22]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[23]  Eli Shlizerman,et al.  Neural Interactome: Interactive Simulation of a Neuronal System , 2017, bioRxiv.

[24]  Aravinthan D. T. Samuel,et al.  C. elegans locomotion: small circuits, complex functions , 2015, Current Opinion in Neurobiology.

[25]  Tao Jia,et al.  Control Capacity and A Random Sampling Method in Exploring Controllability of Complex Networks , 2013, Scientific Reports.

[26]  Lav R. Varshney,et al.  Structural Properties of the Caenorhabditis elegans Neuronal Network , 2009, PLoS Comput. Biol..

[27]  M. V. D. Heuvel,et al.  Simulated rich club lesioning in brain networks: a scaffold for communication and integration? , 2014, Front. Hum. Neurosci..

[28]  Paul W. Sternberg,et al.  Synaptic polarity of the interneuron circuit controlling C. elegans locomotion , 2013, Front. Comput. Neurosci..

[29]  H. Horvitz,et al.  The GABAergic nervous system of Caenorhabditis elegans , 1993, Nature.

[30]  R. Kálmán Mathematical description of linear dynamical systems , 1963 .

[31]  Yee Lian Chew,et al.  Network control principles predict neuron function in the Caenorhabditis elegans connectome , 2017, Nature.

[32]  Adam P. Rosebrock,et al.  A global genetic interaction network maps a wiring diagram of cellular function , 2016, Science.

[33]  Albert-László Barabási,et al.  Caenorhabditis elegans and the network control framework—FAQs , 2018, Philosophical Transactions of the Royal Society B: Biological Sciences.

[34]  Caenorhabditis Elegans Martinchalfieandjohnsulston Developmental Genetics of the Mechanosensory Neurons of Caenorhabditis elegans , 2003 .

[35]  Mauricio Barahona,et al.  Flow-Based Network Analysis of the Caenorhabditis elegans Connectome , 2015, PLoS Comput. Biol..

[36]  Eli Shlizerman,et al.  Whole integration of neural connectomics, dynamics and bio-mechanics for identification of behavioral sensorimotor pathways in Caenorhabditis elegans , 2019 .

[37]  Alexander Gottschalk,et al.  Functionally asymmetric motor neurons contribute to coordinating locomotion of Caenorhabditis elegans , 2018, eLife.

[38]  J. Sulston,et al.  Developmental genetics of the mechanosensory neurons of Caenorhabditis elegans. , 1981, Developmental biology.

[39]  J. Coron Control and Nonlinearity , 2007 .

[40]  Jie Ren,et al.  Controlling complex networks: How much energy is needed? , 2012, Physical review letters.

[41]  Andrew M. Leifer,et al.  Monoaminergic Orchestration of Motor Programs in a Complex C. elegans Behavior , 2013, PLoS biology.

[42]  Yee Lian Chew,et al.  Recordings of Caenorhabditis elegans locomotor behaviour following targeted ablation of single motorneurons , 2017, Scientific data.

[43]  S. Brenner,et al.  The neural circuit for touch sensitivity in Caenorhabditis elegans , 1985, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[44]  Yi Wang,et al.  Whole-animal connectomes of both Caenorhabditis elegans sexes , 2019, Nature.

[45]  Albert-László Barabási,et al.  Control Principles of Complex Networks , 2015, ArXiv.

[46]  W. Kaelin The Concept of Synthetic Lethality in the Context of Anticancer Therapy , 2005, Nature Reviews Cancer.

[47]  A. Goffeau,et al.  The uses of genome-wide yeast mutant collections , 2004, Genome Biology.

[48]  Aravinthan D. T. Samuel,et al.  Proprioceptive Coupling within Motor Neurons Drives C. elegans Forward Locomotion , 2012, Neuron.

[49]  Danielle S. Bassett,et al.  Two's company, three (or more) is a simplex - Algebraic-topological tools for understanding higher-order structure in neural data , 2016, J. Comput. Neurosci..

[50]  P. Hieter,et al.  Synthetic lethality and cancer , 2017, Nature Reviews Genetics.

[51]  A. Rose,et al.  Synthetic Lethal Interactions Identify Phenotypic “Interologs” of the Spindle Assembly Checkpoint Components , 2007, Genetics.

[52]  Michael J. O'Donovan,et al.  A Perimotor Framework Reveals Functional Segmentation in the Motoneuronal Network Controlling Locomotion in Caenorhabditis elegans , 2011, The Journal of Neuroscience.

[53]  Steven B Augustine,et al.  A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans , 2016, eLife.

[54]  O. Sporns,et al.  Identification and Classification of Hubs in Brain Networks , 2007, PloS one.

[55]  Olaf Sporns,et al.  Modeling the Impact of Lesions in the Human Brain , 2009, PLoS Comput. Biol..

[56]  J. Moffat,et al.  Global Genetic Networks and the Genotype-to-Phenotype Relationship , 2019, Cell.

[57]  Fabio Pasqualetti,et al.  Optimally controlling the human connectome: the role of network topology , 2016, Scientific Reports.

[58]  Kazushi Yoshida,et al.  Parallel Use of Two Behavioral Mechanisms for Chemotaxis in Caenorhabditis elegans , 2009, The Journal of Neuroscience.

[59]  A. Barabasi,et al.  Predicting synthetic rescues in metabolic networks , 2008, Molecular systems biology.