4. Perspectives for the coming years: from the use of new in-vitro 3Dbrain tissue models, single cell strategies to big-data systems biology

The majority of transcriptome or related studies in human brain used postmortem tissues as source of material. As consequence, technical concerns like the potential RNA degradation following pre- and postmortem factors as environment, collection methods, or postmortem interval could directly influence the quality of the readouts [75–77]. The use of animal models as an alternative is losing interest due to the reported differences, for instance in human corticogenesis relative to mouse models, which are further supported by human specific gene signature and/ or divergences in gene regulatory programs [78–80]. Even if few percentages of genes have different trajectories in non-human primate and human in contrast to rodent, this model can help to understand brain development, but it cannot model all features found in human [79, 81]. In fact, comparison between non-human

primate and human brains transcriptome analysis showed human specificity in gene expression profiling [82–84] with demonstration that genes differentially expressed are principally upregulated in human brains in contrast to other organs [85, 86]. In addition, the transcriptome remodeling during postnatal periods appears delayed in human brain comparing to non-human primate [87].

genome, and in the particular case of the human brain, it is enhancing the comprehension of neurological disorders. In this chapter, we have discussed the use of transcriptomes, exome sequencing, and gene regulatory network strategies for revealing the influence of multiple genes. Furthermore, we have highlighted the arrival of cerebral organoids as a novel model system for studying human nervous system, which in combination with further developments (single-cell strategies, CRISPR-Cas9 engineering, etc.) is a promising major progress for understanding the brain function. This enthusiasm is further supported with the major advancements in computational developments, notably the artificial intelligence, which together with the major amounts of data (issued from omics strategies) is expected to accelerate discoveries. Overall, we expect that this chapter will open the mind to young readers to further explore the multidisciplinary approaches described herein to directly participate in the exploration of the human brain in the following years.

Systems Biology Perspectives for Studying Neurodevelopmental Events

DOI: http://dx.doi.org/10.5772/intechopen.85072

We thank all members of the SysFate lab for discussions related to the elaboration of this chapter. SysFate is supported by the "Genopole Thematic Incentive Actions" funding (referred to by their French acronym "ATIGE") and by the institutional bodies CEA, CNRS, and Université d'Evry, Université Paris-Saclay.

The authors declare that there is no conflict of interest.

RT-PCR reverse transcription polymerase chain reaction

RMST rhabdomyosarcoma 2-associated transcript

PsychENCODE psychiatric encyclopedia of DNA elements

Auts2 activator of transcription and developmental regulator

CHD8 chromodomain helicase DNA binding protein 8


DNA deoxyribonucleic acid

ASD autism spectrum disorder

SOX2 sex determining region Y-box 2 GTex genotype tissue expression ENCODE encyclopedia of DNA elements

PET positron emission tomography SNV single nucleotide variants CNV copy number variants

GWAS genome-wide association studies ChIP chromatin immunoprecipitation

lncRNA long non-coding RNA

TF transcription factor TBR1 T-box, brain 1

RNA ribonucleic acid RNA-Seq RNA sequencing EdU 5-ethynyl-2<sup>0</sup>

miRNA micro-RNA

Acknowledgements

Conflict of interest

Nomenclature

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More recently, the use of human-induced pluripotent stem cells (hIPSCs) combined with in-vitro culture strategies for generating two- or three-dimensional nervous tissue appears as an alternative to animal model systems. In fact, nowadays it is possible to generate hIPSCs from tissue samples collected from patients presenting neurological disorders which can be differentiated toward nervous tissue. In this context, a recent study compared the transcriptome of neural stem cells driven in-vitro toward corticogenesis and discovered a strong conservation with invivo gene expression with the conservation of cortical gene network implicated in ASD [73]. In contrast to the in-vitro neuronal differentiation in two dimensions, the generation of three-dimensional models (known as cerebral organoids) appears as a more relevant physiological model to study neurodevelopment [88–91]. Comparing human cerebral organoids and fetal brain development demonstrated the similarity in gene expression programs and epigenomic signatures [92–94]. Furthermore, single-cell transcriptome analysis over cerebral organoids revealed an important cellular heterogeneity, reminiscent to what is observed in the human brain [95]. As a consequence, the use of human cerebral organoids corresponds to a new approach for modeling the neuronal development and providing means to study neurogenesis from a systems biology perspective. For example, Mariani et al. generated cerebral organoids from hIPSCs derived from patients with ASD and recapitulated transcriptional programs present in fetal cortical development. In this study, the use of gene network analyses allowed to identify upregulated gene programs implicated in cell proliferation, neuronal differentiation and synaptic process [90]. Similarly, Amiri et al. identified gene modules implicated in ASD that overlap those described previously in postmortem data. This study supported the idea that cerebral organoids provide means to reveal gene regulatory elements contributing to ASD [94]. Due to these success, major efforts focused on the development of protocols to generate tissues reminiscent to different brain structures like forebrain [90, 96], midbrain [96, 97], or hypothalamus [96] were developed. Recently, chimeric organoids issued from the fusion different regionalized organoids (like dorsalventral forebrain organoids) were generated to increase the complexity of the generated tissues [98].

The use of cerebral organoids as a model system for studying neurodevelopment and related diseases is in its infancy. This approach still requires improvements, for instance in the context of the reproducibility, but due to its alternative to human postmortem samples and animal models, it is expected to continue to evolve over the coming years. In fact, this tendency is also boosted by multiple other developments, including the use of CRISPR/CAS9 system to engineer organoids [99], the democratization of single cell omics strategies [95], as well as the gain in multidisciplinary approaches, specifically by the incorporation of computational approaches for modeling brain tissue organization [74].
