NEURAL TUBE NETWORK

Systematic analysis and modeling of the gene regulatory network underlying neural tube patterning

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 Obiettivo del progetto (Objective)

'In many developing tissues, initially equipotent cells acquire their intended identity by exposure to extrinsic, graded signals termed morphogens, such as Sonic Hedgehog (Shh). In the ventral neural tube, Shh induces 5 progenitor domains in a precise spatial order along the dorsoventral axis of the developing spinal cord. These domains can be distinguished by the expression of different combinations of transcription factors (TFs). During their specification, the progenitors transit through several metastable states, exhibited by the expression of different combinations of TFs. In network analysis terminology these states define so-called attractors – states of equilibrium towards which global gene expression profile tends to move. We predict that ventral neural tube progenitor states correspond to such attractor states that are generated by a gene regulatory network (GRN) controlled by graded Shh signalling. We will use a series of experimental and in silico approaches to systematically decipher and model this GRN. We will perturb the GRN in the developing chick neural tube using in ovo electroporation of constructs that change the level of Shh signalling and/or the expression of specific TFs. The consequences on the transcriptome of neural cells will be assayed systematically. Factors newly identified in this analysis will be examined and their function in the transcriptional response of neural cells assessed. We will use this approach iteratively to build, challenge and refine our model, and progressively understand the principles of the network. This will define the attractor states of the system and identify the TFs that contribute to the establishment of these states. By extending our knowledge of basic mechanisms of neural tube development we hope to provide new insight that will guide therapeutic approaches to the diseased or damaged spinal cord.'

Introduzione (Teaser)

Elucidating neural tube patterning

Descrizione progetto (Article)

The EU-funded project 'Systematic analysis and modeling of the gene regulatory network underlying neural tube patterning' (NEURAL TUBE NETWORK) was initiated to elucidate the gene regulatory network (GRN) involved in neural tube patterning. The researchers used the chick embryo for transcriptional profiling.

Neural tube patterning involves the expression of different types of transcription factors (TFs) and signalling molecules such as sonic hedgehog (Shh) to produce functionally-distinct neuronal subtypes. The Shh-controlled GRN is a major player in controlling this process and determines the fate of these neuronal subtypes.

Scientists performed high throughput mRNA sequencing (HTS) on chick neural tube cells for transcriptome analyses at different time-points of Shh signalling. Differentially expressed genes were successfully identified and results were validated using data from Nanostring nCounter, a fully automated system to profile RNA and DNA.

A chick TF database was generated and used to annotate the transcriptome data obtained previously. The researchers then compared the profiles of differentially expressed TFs from altered Shh signalling at different periods.

Results revealed that a combination of specific TFs need to be expressed to generate distinct neuronal progenitor domains (e.g. p3 and pMN) during neural tube patterning. These p3 and pMN domains are spatially distinct in the ventral spinal cord where the p3 domain produces V3 interneurons and pMN generates somatic motoneurons.

In parallel, work is ongoing to develop computational approaches to model the Shh-controlled GRN to represent gene regulation by TFs during ventral neural tube patterning.

Project outcomes have revealed that neural tube TFs act alone or in combination to produce different progenitor gene expression profiles in response to Shh concentration.

Validation of these findings will have important implications with regard to understanding the dynamics of gene regulation and its role in spinal cord development. Study results could also be extrapolated to other developing tissues and used to develop innovative medical interventions through stem cell therapy or artificial bone or skin grafts.