Knockdown of CDK2AP1 in human embryonic stem cells reduces the threshold of differentiation

GUIDE deconstructs genetic architectures using association studies

Genome-wide association studies have revealed that the genetic architecture of most complex traits is characterized by a large number of distinct effects scattered across the genome. Functional enrichment analyses of these results suggest that the associations for any given complex trait are not purely random. Thus, we set out to leverage the genetic association results from many traits with a view to identifying the set of modules, or latent factors, that mediate these associations. The identification of such modules may aid in disease classification as well as the elucidation of complex disease mechanisms. We propose a method, Genetic Unmixing by Independent Decomposition (GUIDE), to estimate a set of statistically independent latent factors that best express the patterns of association across many traits. The resulting latent factors not only have desirable mathematical properties, such as sparsity and a higher variance explained (for both traits and variants), but are also able to single out and prioritize key biological features or pathophysiological mechanisms underlying a given trait or disease. Moreover, we show that these latent factors can index biological pathways as well as epidemiological and environmental influences that compose the genetic architecture of complex traits.

Generation of iPSC lines (KAIMRCi003A, KAIMRCi003B) from a Saudi patient with Dravet syndrome carrying homozygous mutation in the CPLX1 gene and heterozygous mutation in SCN9A

The most prevalent form of epileptic encephalopathy is Dravet syndrome (DRVT), which is triggered by the pathogenic variant SCN1A in 80% of cases. iPSCs with different SCN1A mutations have been constructed by several groups to model DRVT syndrome. However, no studies involving DRVT-iPSCs with rare genetic variants have been conducted. Here, we established two DRVT-iPSC lines harboring a homozygous mutation in the CPLX1 gene and heterozygous mutation in SCN9A gene. Therefore, the derivation of these iPSC lines provides a unique cellular platform to dissect the molecular mechanisms underlying the cellular dysfunctions consequent to CPLX1 and SCN9A mutations.

A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development

Retrotransposons mediate gene regulation in important developmental and pathological processes. Here, we characterized the transient retrotransposon induction during preimplantation development of eight mammals. Induced retrotransposons exhibit similar preimplantation profiles across species, conferring gene regulatory activities, particularly through long terminal repeat (LTR) retrotransposon promoters. A mouse-specific MT2B2 retrotransposon promoter generates an N-terminally truncated Cdk2ap1ΔN that peaks in preimplantation embryos and promotes proliferation. In contrast, the canonical Cdk2ap1 peaks in mid-gestation and represses cell proliferation. This MT2B2 promoter, whose deletion abolishes Cdk2ap1ΔN production, reduces cell proliferation and impairs embryo implantation, is developmentally essential. Intriguingly, Cdk2ap1ΔN is evolutionarily conserved in sequence and function yet is driven by different promoters across mammals. The distinct preimplantation Cdk2ap1ΔN expression in each mammalian species correlates with the duration of its preimplantation development. Hence, species-specific transposon promoters can yield evolutionarily conserved, alternative protein isoforms, bestowing them with new functions and species-specific expression to govern essential biological divergence.

Generation of induced pluripotent stem cell Line KAIMRCi001-A by reprogramming erythroid progenitors from peripheral blood of a healthy Saudi donor

In this study we isolated and enriched erythroid progenitor cells (EPCs) from a 10 ml peripheral blood sample from a 37-year old healthy Saudi donor. After expansion, these EPCs were reprogrammed using episomal plasmids to generate an induced pluripotent stem (iPS) cell line, KAIMRCi001-A. The pluripotency of this line was confirmed by measuring the expression of typical pluripotency markers and assessing differentiation potential in vitro.

MicroRNA-21 is involved in oocyte maturation, blastocyst formation, and pre-implantation embryo development

Follicular fluid is one source of microRNAs (miRNAs). These miRNAs originate from oocytes and their neighboring cells. The changes in the miRNAs profile in the follicular fluid could alter folliculogenesis and oocyte maturation, and lead to infertility. Polycystic ovary syndrome (PCOS) patients have increased miR-21 levels in their sera, granulosa cells, and follicular fluid, and this mi-RNA plays a role in the pathophysiology and follicular dysfunction of PCOS patients. In the current study, we intend to examine whether expression levels of miR-21 influence oocyte maturation and embryo development. We examined miR-21 over-expression and down-regulation of miR-21 by miR-off 21 during in vitro maturation (IVM) to assess its influence on oocyte maturation and embryo development in mice. Over-expression of miR-21 in cumulus cells decreased expansion, meiotic progression, Glutathione-S-transferase GSH levels, and decreased expressions of Bmpr2 and Ptx3 genes. Subsequently, we noted that in vitro fertilization, and the cleavage rate and blastocyst formation significantly increased in cumulus oocyte complexes (COCs) that over-expressed miR-21. Inhibition of miR-21 by miR-off 21 led to increased cumulus expansion and GSH levels, along with decreased cleavage rate and blastocyst formation by alterations in Cdk2ap1 and Oct4 gene expressions. However, oocyte progression from the germinal vesicle (GV) to the metaphase II (MII) stage was not significant. miR-21 altered the gene expression levels in cumulus cells and influenced cytoplasmic oocyte maturation, cumulus expansion, and subsequent embryonic development in mice.

Genes in immune pathways associated with abnormal white matter integrity in first-episode and treatment-naïve patients with schizophrenia

BACKGROUND

Previous studies have inferred a strong genetic component in schizophrenia. However, the genetic variants involved in the susceptibility to schizophrenia remain unclear.AimsTo detect potential gene pathways and networks associated with schizophrenia, and to explore the relationship between common and rare variants in these pathways and abnormal white matter integrity in schizophrenia.

METHOD

The analysis included 100 first-episode treatment-naïve patients with schizophrenia and 140 healthy controls. A network-based analysis was carried out on the data collected from the Psychiatric Genomics Consortium Phase I (PGC-I). Based on our genome-wide association study and whole-exome sequencing data-sets, we performed a gene-set analysis to detect associations between the combining effects of common and rare genetic variants and abnormal white matter integrity in schizophrenia.

RESULTS

Patients had significantly reduced functional anisotropy in the left and right anterior cingulate cortex, left and right precuneus and extra-nuclear (t = 4.61-5.10, PFDR < 0.01), compared with controls. Generated from co-expression network analysis of the PGC-1 summary statistics of schizophrenia, a subnetwork of 207 genes associated with schizophrenia was identified (P < 0.01), and 176 genes were co-expressed in four gene modules. Functional enrichment analysis for genes in each module revealed that the yellow module was enriched with highly co-expressed, innate immune response genes. Furthermore, rare variants of enriched genes in the yellow module were associated with reduced functional anisotropy in the left anterior cingulate cortex (P = 0.006; Padjusted = 0.024) in patients only.

CONCLUSIONS

The pathogenesis of schizophrenia may be substantially influenced by genes involved in the immune system, via both pathway and network.Declaration of interestsNone.