Systematic genetic analyses of genome-wide association study data reveal an association between the key nucleosome remodeling and deacetylase complex and bipolar disorder development

Neurodevelopmental functions of CHD8: new insights and questions

Heterozygous, de novo, loss-of-function variants of the CHD8 gene are associated with a high penetrance of autism and other neurodevelopmental phenotypes. Identifying the neurodevelopmental functions of high-confidence autism risk genes like CHD8 may improve our understanding of the neurodevelopmental mechanisms that underlie autism spectrum disorders. Over the last decade, a complex picture of pleiotropic CHD8 functions and mechanisms of action has emerged. Multiple brain and non-brain cell types and progenitors appear to be affected by CHD8 haploinsufficiency. Behavioural, cellular and synaptic phenotypes are dependent on the nature of the gene mutation and are modified by sex and genetic background. Here, I review some of the CHD8-interacting proteins and molecular mechanisms identified to date, as well as the impacts of CHD8 deficiency on cellular processes relevant to neurodevelopment. I endeavour to highlight some of the critical questions that still require careful and concerted attention over the next decade to bring us closer to the goal of understanding the salient mechanisms whereby CHD8 deficiency causes neurodevelopmental disorders.

Unveiling the Pathogenesis of Psychiatric Disorders Using Network Models

Psychiatric disorders are complex brain disorders with a high degree of genetic heterogeneity, affecting millions of people worldwide. Despite advances in psychiatric genetics, the underlying pathogenic mechanisms of psychiatric disorders are still largely elusive, which impedes the development of novel rational therapies. There has been accumulating evidence suggesting that the genetics of complex disorders can be viewed through an omnigenic lens, which involves contextualizing genes in highly interconnected networks. Thus, applying network-based multi-omics integration methods could cast new light on the pathophysiology of psychiatric disorders. In this review, we first provide an overview of the recent advances in psychiatric genetics and highlight gaps in translating molecular associations into mechanistic insights. We then present an overview of network methodologies and review previous applications of network methods in the study of psychiatric disorders. Lastly, we describe the potential of such methodologies within a multi-tissue, multi-omics approach, and summarize the future directions in adopting diverse network approaches.

Implications of Gut-Brain axis in the pathogenesis of Psychiatric disorders

<abstract> <p>Psychiatric disorders may extremely impair the quality of life with patients and are important reasons of social disability. Several data have shown that psychiatric disorders are associated with an altered composition of gut microbiota. Dietary intake could determine the microbiota, which contribute to produce various metabolites of fermentation such as short chain fatty acids. Some of the metabolites could result in epigenetic alterations leading to the disease susceptibility. Epigenetic dysfunction is in fact implicated in various psychiatric and neurologic disorders. For example, it has been shown that neuroepigenetic dysregulation occurs in psychiatric disorders including schizophrenia. Several studies have demonstrated that the intestinal microbiome may influence the function of central nervous system. Furthermore, it has been proved that the alterations in the gut microbiota-composition might affect in the bidirectional communication between gut and brain. Similarly, evidences demonstrating the association between psychiatric disorders and the gut microbiota have come from preclinical studies. It is clear that an intricate symbiotic relationship might exist between host and microbe, although the practical significance of the gut microbiota has not yet to be determined. In this review, we have summarized the function of gut microbiota in main psychiatric disorders with respect to the mental health. In addition, we would like to discuss the potential mechanisms of the disorders for the practical diagnosis and future treatment by using bioengineering of microbiota and their metabolites.</p> </abstract>

In vivo human brain expression of histone deacetylases in bipolar disorder

The etiology of bipolar disorder (BD) is unknown and the neurobiological underpinnings are not fully understood. Both genetic and environmental factors contribute to the risk of BD, which may be linked through epigenetic mechanisms, including those regulated by histone deacetylase (HDAC) enzymes. This study measures in vivo HDAC expression in individuals with BD for the first time using the HDAC-specific radiotracer [¹¹C]Martinostat. Eleven participants with BD and 11 age- and sex-matched control participants (CON) completed a simultaneous magnetic resonance - positron emission tomography (MR-PET) scan with [¹¹C]Martinostat. Lower [¹¹C]Martinostat uptake was found in the right amygdala of BD compared to CON. We assessed uptake in the dorsolateral prefrontal cortex (DLPFC) to compare previous findings of lower uptake in the DLPFC in schizophrenia and found no group differences in BD. Exploratory whole-brain voxelwise analysis showed lower [¹¹C]Martinostat uptake in the bilateral thalamus, orbitofrontal cortex, right hippocampus, and right amygdala in BD compared to CON. Furthermore, regional [¹¹C]Martinostat uptake was associated with emotion regulation in BD in fronto-limbic areas, which aligns with findings from previous structural, functional, and molecular neuroimaging studies in BD. Regional [¹¹C]Martinostat uptake was associated with attention in BD in fronto-parietal and temporal regions. These findings indicate a potential role of HDACs in BD pathophysiology. In particular, HDAC expression levels may modulate attention and emotion regulation, which represent two core clinical features of BD.

Neurodevelopmental pathways in bipolar disorder

Aberrations in neurodevelopmental trajectories have been implicated in the neurobiology of several mental disorders and evidence indicates a pathophysiological and genetic overlap of schizophrenia and bipolar disorder (BD). In this narrative review, we summarize findings related to developmental and perinatal factors as well as epidemiological, clinical, neuropsychological, brain imaging, postmortem brain and genomic studies that provide evidence for a putative neurodevelopmental pathogenesis and etiology of BD. Overall, aberrations in neurodevelopmental pathways have been more consistently implicated in the pathophysiology of schizophrenia compared to BD. Nevertheless, an accumulating body of evidence indicates that dysfunctional neurodevelopmental pathways may be implicated in the underlying pathophysiology of at least a subset of individuals with BD particularly those with an early age of illness onset and those exhibiting psychotic symptoms. A heuristic neurodevelopmental model for the pathophysiology of BD based on the findings of this review is proposed. Furthermore, we critically discuss clinical and research implications of this model. Finally, further research directions for this emerging field are provided.

An integrative analysis of genome-wide association study and regulatory SNP annotation datasets identified candidate genes for bipolar disorder

Background

Bipolar disorder (BD) is a complex mood disorder. The genetic mechanism of BD remains largely unknown.

Methods

We conducted an integrative analysis of genome-wide association study (GWAS) and regulatory SNP (rSNP) annotation datasets, including transcription factor binding regions (TFBRs), chromatin interactive regions (CIRs), mature microRNA regions (miRNAs), long non-coding RNA regions (lncRNAs), topologically associated domains (TADs) and circular RNAs (circRNAs). Firstly, GWAS dataset 1 of BD (including 20,352 cases and 31,358 controls) and GWAS dataset 2 of BD (including 7481 BD patients and 9250 controls) were integrated with rSNP annotation database to obtain BD associated SNP regulatory elements and SNP regulatory element-target gene (E–G) pairs, respectively. Secondly, a comparative analysis of the two datasets results was conducted to identify the common rSNPs and also their target genes. Then, gene sets enrichment analysis (FUMA GWAS) and HumanNet-XC analysis were conducted to explore the functional relevance of identified target genes with BD.

Results

After the integrative analysis, we identified 52 TFBRs target genes, 44 TADs target genes, 55 CIRs target genes and 21 lncRNAs target genes for BD, such as ITIH4 (P_dataset1 = 6.68 × 10⁻⁸, P_dataset2 = 6.64 × 10⁻⁷), ITIH3 (P_dataset1 = 1.09 × 10⁻⁸, P_dataset2 = 2.00 × 10⁻⁷), SYNE1 (P_dataset1 = 1.80 × 10⁻⁶, P_dataset2 = 4.33 × 10⁻⁹) and OPRM1 (P_dataset1 = 1.80 × 10⁻⁶, P_dataset2 = 4.33 × 10⁻⁹).

Conclusion

We conducted a large-scale integrative analysis of GWAS and 6 common rSNP information datasets to explore the potential roles of rSNPs in the genetic mechanism of BD. We identified multiple candidate genes for BD, supporting the importance of rSNP in the development of BD.

Chromatin Remodeling Complex NuRD in Neurodevelopment and Neurodevelopmental Disorders

The nucleosome remodeling and deacetylase (NuRD) complex presents one of the major chromatin remodeling complexes in mammalian cells. Here, we discuss current evidence for NuRD's role as an important epigenetic regulator of gene expression in neural stem cell (NSC) and neural progenitor cell (NPC) fate decisions in brain development. With the formation of the cerebellar and cerebral cortex, NuRD facilitates experience-dependent cerebellar plasticity and regulates additionally cerebral subtype specification and connectivity in postmitotic neurons. Consistent with these properties, genetic variation in NuRD's subunits emerges as important risk factor in common polygenic forms of neurodevelopmental disorders (NDDs) and neurodevelopment-related psychiatric disorders such as schizophrenia (SCZ) and bipolar disorder (BD). Overall, these findings highlight the critical role of NuRD in chromatin regulation in brain development and in mental health and disease.

Systematic genetic analyses of GWAS data reveal an association between the immune system and insomnia

BACKGROUND

Previous studies have inferred a strong genetic component for insomnia. However, the etiology of insomnia is still unclear. The aim of the current study was to explore potential biological pathways, gene networks, and brain regions associated with insomnia.

METHODS

Using pathways (gene sets) from Reactome, we carried out a two-stage gene set enrichment analysis strategy. From a large genome-wide association studies (GWASs) of insomnia symptoms (32,155 cases/26,973 controls), significant gene sets were tested for replication in other large GWASs of insomnia complaints (32,384 cases/80,622 controls). After the network analysis of unique genes within the replicated pathways, a gene set analysis for genes in each cluster/module of the enhancing neuroimaging genetics through meta-analysis GWAS data was performed for the volumes of the intracranial and seven subcortical regions.

RESULTS

A total of 31 of 1,816 Reactome pathways were identified and showed associations with insomnia risk. In addition, seven functionally and topologically interconnected clusters (clusters 0-6) and six gene modules (named Yellow, Blue, Brown, Green, Red, and Turquoise) were associated with insomnia. Moreover, significant associations were detected between common variants of the genes in Cluster 2 with hippocampal volume (p = 0.035; family wise error [FWE] correction) and the red module with intracranial volume (p = 0.047; FWE correction). Functional enrichment for genes in the Cluster 2 and the Red module revealed the involvement of immune responses, nervous system development, NIK/NF-kappaB signaling, and I-kappaB kinase/NF-kappaB signaling. Core genes (UBC, UBB, and UBA52) in the interconnected functional network were found to be involved in regulating brain development.

CONCLUSIONS

The current study demonstrates that the immune system and the hippocampus may play central roles in neurodevelopment and insomnia risk.

Tumor suppressor MCPH1 regulates gene expression profiles related to malignant conversion and chromosomal assembly

Strong inherited predisposition to breast cancer is estimated to cause about 5–10% of all breast cancer cases. As the known susceptibility genes, such as BRCA1 and BRCA2, explain only a fraction of this, additional predisposing genes and related biological mechanisms are actively being searched for. We have recently identified a recurrent MCPH1 germline mutation, p.Arg304ValfsTer3, as a breast cancer susceptibility allele. MCPH1 encodes a multifunctional protein involved in maintenance of genomic integrity and it is also somatically altered in various cancer types, including breast cancer. Additionally, biallelic MCPH1 mutations are causative for microcephaly and at cellular level premature chromosome condensation. To study the molecular mechanisms leading to cancer predisposition and malignant conversion, here we have modeled the effect of MCPH1 p.Arg304ValfsTer3 mutation using gene‐edited MCF10A breast epithelial cells. As a complementary approach, we also sought for additional potential cancer driver mutations in MCPH1 p.Arg304ValfsTer3 carrier breast tumors. We show that mutated MCPH1 de‐regulates transcriptional programs related to invasion and metastasis and leads to downregulation of histone genes. These global transcriptional changes are mirrored by significantly increased migration and invasion potential of the cells as well as abnormal chromosomal condensation both before and after mitosis. These findings provide novel molecular insights to MCPH1 tumor suppressor functions and establish a role in regulation of transcriptional programs related to malignant conversion and chromosomal assembly. The MCPH1 p.Arg304ValfsTer3 carrier breast tumors showed recurrent tumor suppressor gene TP53 mutations, which were also significantly over‐represented in breast tumors with somatically inactivated MCPH1.

What's new?

Even though several breast cancer susceptibility genes have been identified, additional molecular mechanisms behind predisposition and the promotion of malignant conversion remain obscure. Here, the authors show that a previously‐identified breast cancer predisposing allele in tumor suppressor MCPH1 deregulates transcriptional programs related to invasion and metastasis and leads to down‐regulation of histone genes. These global transcriptional changes are mirrored by increased cell migration and invasion potential and abnormal chromosomal condensation. The findings provide novel molecular insights into MCPH1 tumor suppressor functions and establish a role in the regulation of transcriptional programs related to malignant conversion and chromosomal assembly.