Abstract

   Neuronal migration constitutes an important step in corticogenesis;
   dysregulation of the molecular mechanisms mediating this crucial step
   in neurodevelopment may result in various neuropsychiatric disorders.
   By curating experimental data from published literature, we identified
   eight functional modules involving Disrupted-in-schizophrenia 1 (DISC1)
   and its interacting proteins that regulate neuronal migration. We then
   identified miRNAs and transcription factors (TFs) that form functional
   feedback loops and regulate gene expression of the DISC1 interactome.
   Using this curated data, we conducted in-silico modeling of the DISC1
   interactome involved in neuronal migration and identified the proteins
   that either facilitate or inhibit neuronal migrational processes. We
   also studied the effect of perturbation of miRNAs and TFs in feedback
   loops on the DISC1 interactome. From these analyses, we discovered that
   STAT3, TCF3, and TAL1 (through feedback loop with miRNAs) play a
   critical role in the transcriptional control of DISC1 interactome
   thereby regulating neuronal migration. To the best of our knowledge,
   regulation of the DISC1 interactome mediating neuronal migration by
   these TFs has not been previously reported. These potentially important
   TFs can serve as targets for undertaking validation studies, which in
   turn can reveal the molecular processes that cause neuronal migration
   defects underlying neurodevelopmental disorders. This underscores the
   importance of the use of in-silico techniques in aiding the discovery
   of mechanistic evidence governing important molecular and cellular
   processes. The present work is one such step towards the discovery of
   regulatory factors of the DISC1 interactome that mediates neuronal
   migration.

   Subject terms: Computational biology and bioinformatics, Neuroscience,
   Logic gates

Neuroinformatics: Framework for simulating regulation of neurodevelopment

   Computer simulation (in-silico) methods offer a potent approach to deal
   with the enormous complexity of regulatory interactions mediating
   neurodevelopment. John P. John and Priyadarshini Thirunavukkarasu
   (National Institute of Mental Health and Neurosciences, India) and
   Akira Sawa (Johns Hopkins University, USA), along with their
   colleagues, developed an in-silico simulation of the regulation of
   genes interacting with Disrupted-in-schizophrenia 1 gene (the DISC1
   interactome) that mediate neuronal migration. Through in-silico
   perturbation of microRNAs and transcription factors (TFs), they
   discovered three TFs, namely, STAT3, TCF3 and TAL1, that play a
   critical role in the regulation of the DISC1 interactome. Further
   experimental validation studies can confirm the role of these TFs in
   neuronal migration. This framework for discovery of critical factors
   that can be targets for in-vivo studies may aid in advancing our
   understanding regarding molecular pathophysiology of neurodevelopmental
   disorders.

Introduction

   Neuronal migration is one of the most crucial steps of
   neurodevelopment. Any disturbance of this process can lead to cortical
   dysgenesis, i.e., abnormal development of the cerebral cortex.^[32]1
   Disrupted-in-schizophrenia 1 (DISC1) is an extensively studied molecule
   in its regulation of neuronal migration and other stages of
   neurodevelopment, as well as its mediation of higher brain
   functions.^[33]2 It performs its role through its interactions with
   multiple other proteins.^[34]3 Although genetic implication of DISC1
   has turned out to be very specific to the original Scottish pedigree,
   and not for sporadic cases of schizophrenia, biological perturbation of
   DISC1 clearly leads to neurodevelopmental and behavioral
   deficits.^[35]4 Therefore, the importance of DISC1, originally proposed
   on the basis of a rare genetic case, is very high in neurobiology.

   There is considerable evidence for interplay between transcriptional
   and post-transcriptional regulators of gene expression underlying the
   molecular pathology of various diseases.^[36]5 MicroRNA (miRNA) and
   transcription factors (TF) in miRNA-TF feedback loops strongly regulate
   each other and many target genes.^[37]5 Furthermore, miRNAs and TFs in
   these feedback loops have higher in-degree and out-degree in comparison
   to those that are not involved in these feedback loops.^[38]6 Thus, the
   miRNA-TF feedback loop is suggested as a common mechanism of gene
   regulation at a systems level.^[39]7

   Network models that integrate protein−protein interactions (PPIs)
   involving DISC1 (the DISC1 interactome) and the regulation of
   expression of genes encoding these proteins by miRNA-TF feedback loops
   can advance our understanding of the complex molecular mechanisms that
   regulate neuronal migration. Several mathematical approaches have been
   used to model such interactions.^[40]8–[41]11 Boolean network models
   are one of the most widely used discrete mathematical models in
   contexts where the biological kinetic parameters are not known^[42]12;
   e.g., colitis-associated colon cancer,^[43]13 apoptosis,^[44]14
   survival signaling of T-cell large granular lymphocyte leukemia^[45]15
   and p53 regulatory circuit.^[46]16 Using real-world data, Boolean
   network models allow simulation of interactions between genes and
   identification of the most important gene regulatory elements in the
   network.^[47]17,[48]18 Multiple regulators determining the activity of
   a given gene are combined using logical operators and a Boolean
   function determines the next state of a gene, based on the current
   state of its regulators. Boolean models provide insight about the
   dynamics of biological systems such as multiple cell fates and cellular
   phenotypes.^[49]19

   In this study, we constructed a Boolean network integrating the DISC1
   interactome that mediates neuronal migration using experimental
   evidence curated from relevant databases. We determined the
   stable-states reached by PPIs between proteins constituting the DISC1
   interactome regulating neuronal migration and determined the modes of
   neuronal migration that are facilitated or inhibited in each stable
   state. We then demonstrated how perturbation of each miRNA, gene, and
   TF affects neuronal migration in each functional module (FM). We also
   examined the influence of miRNA and TF in feedback loops regulating two
   or more FMs of migration. Finally, we constructed a comprehensive
   network model of regulation of proteins in the DISC1 interactome by
   miRNA-TF feedback loops, which can provide a framework for further
   examination of the molecular mechanisms that regulate neuronal
   migration in experimental studies.

Results

DISC1 protein−protein interactions/functional modules (the DISC1 interactome)
involved in neuronal migration

   We observed that DISC1 interacts with 87 proteins as well as with DISC1
   fusion partner 1 (DISC1FP1) regulating various neurodevelopmental
   functions (Supplementary Table [50]S1 and Supplementary
   [51]References). Of these, 18 proteins regulated eight FMs of neuronal