Discovery of New Candidate Genes Related to Brain Development Using Protein Interaction Information

Human brain development is a dramatic process composed of a series of complex and fine-tuned spatiotemporal gene expressions. A good comprehension of this process can assist us in developing the potential of our brain. However, we have only limited knowledge about the genes and gene functions that are involved in this biological process. Therefore, a substantial demand remains to discover new brain development-related genes and identify their biological functions. In this study, we aimed to discover new brain-development related genes by building a computational method. We referred to a series of computational methods used to discover new disease-related genes and developed a similar method. In this method, the shortest path algorithm was executed on a weighted graph that was constructed using protein-protein interactions. New candidate genes fell on at least one of the shortest paths connecting two known genes that are related to brain development. A randomization test was then adopted to filter positive discoveries. Of the final identified genes, several have been reported to be associated with brain development, indicating the effectiveness of the method, whereas several of the others may have potential roles in brain development.     

Programming of the adult psychoneuroendocrine qualities by gene expression early-life

Ontogeny of the mechanisms of physiological functions and behavior are adjusted --"programmed" during early development to match predicted conditions of future life environment. The discrepancies between anticipated and actual environmental conditions provoke endocrine, cardiovascular, metabolic and psychiatric pathologies. Alterations in gene expression and of subsequent regulation of the gene activities, as well as morphogenetic abnormalities due to changes in cell migration and apoptosis could be the mechanisms of this phenomenon. Inhibition of a targeted-gene expression by short interfering RNA in the developing mammalian brain in vivo have revealed programming of the adult animal psychophysiological qualities by the neurogene during critical period of the brain development. Mechanism of early-life programming evidently has adaptive evolutionary-genetic basis and is capable of transmitting effects of adverse treatments endued by ancestors to subsequent generations.     

脑机接口：现状，问题与展望

本文综述现有脑机接口技术的最新发展,并讨论这些脑机接口技术的局限和存在的问题,如高估人类个体大脑的功能、对大脑信息存储方式缺乏了解等.基于大脑信息存储的"二维码"模型,我们认为目前的脑机接口技术方案仅适用于一些简单的应用场景,如了解受测者的情绪变化、生命活动的状态,以及控制体外器械等,而无法通过脑机接口技术获取脑内诸如记忆与思考等信息的精准细节.我们也提出,向大脑输入信息的脑机接口技术有较大的发展空间,比如发展具有多种调控效果、物理和生化技术结合的深脑刺激装置,有可能广泛应用于抑郁症、癫痫等脑疾病的治疗,以及应用于短期脑力的增强.本文对于目前的脑机接口研究领域具有一定的警示和启发意义.     

Synthesis of 2'-O-modified adenosine building blocks and application for RNA interference

RNA-interference has been recognized as a powerful tool to control gene function and has been used for gene silencing by knocking down mRNA. Chemically modified RNAs, especially 2'-O-modification, successfully improved their physicochemical and pharmaceutical properties such as stability, nuclease resistance and delivery. Here, we report the synthesis of adenosine building blocks with different 2'-tethered modifications like aminoethyl and guanidinoethyl and show that they are compatible with RNAi function. They enhance the half life of the siRNA in serum suggesting that these modifications can enhance the pharmacokinetic properties and knock down activity of siRNAs in vivo.     

Differential display reveals downregulation of the phospholipid transfer protein (PLTP) at the mRNA level in brains of patients with Down syndrome

The phospholipid transfer protein (PLTP) shows a wide variety of functions including transfer of phospholipids and other lipid-like substances. Performing gene hunting in brain of patients with Down syndrome (DS) we detected the absence of a fragment identified as PLTP. Cerebellum of 4 controls, 7 patients with DS, 5 patients with Alzheimer's disease (AD) were used for differential display and for quantification of mRNA steady state levels of the isomer PLTP-1 by blotting methods. Differential display showed the absence of a cDNA fragment and cloning, sequencing and gene bank work revealed 100% homology with human PAC 337018 on chromosome 20q containing the PLTP gene. The PLTP gene in turn consists of at least three different PLTP-isomers. Based on these results, a 450 bp cDNA fragment of the PLTP-isomer I (PLTP I) was isolated and amplified by PCR, serving as probe for the PLTP-1 isomer and its expression level was found to be significantly reduced in cerebellum of patients with DS. Biologically, the downregulation of PLTP maybe involved in the pathology of DS as phospholipids not only are of importance for membrane biogenesis and structure but also in the regulation of cellular metabolism, signaling and growth. In the brain, phospholipids in addition are integral constituents of myelins and synaptosomes (Johnson etc) and deficient PLTP levels may account for the deteriorated functions described to occur in DS brain.     

Manipulating gene expressions by electroporation in the developing brain of mammalian embryos

One of the goals of developmental neuroscience in the post-genomic era is to clarify functions of a huge number of anonymous genes of which only DNA sequences are identified. More convenient methods for genetic manipulation in vertebrates, especially mammals, could help us to identify functions of the novel genes. Here we introduce a novel gene transfer technology using electroporation (EP), which is a simple and powerful strategy for genetic analysis. We have applied this method to cultured mammalian embryos in order to understand the function of specific genes in the developing brain. We have also performed EP in developing fetuses in utero guided by ultrasound image. The combination of these techniques in addition to analysis of genetic mutants will clarify functions of individual genes, gene interactions, and the molecular mechanisms underlying the brain development.     

用基因工程方法研制廿二碳六烯酸

廿二碳六烯酸(DHA)能促进脑细胞的生长发育,改善大脑机能和行为学习,防治中枢神经疾病,是人及其它动物重要的必需多不饱和脂肪酸。目前,DHA主要来自深海鱼油的分离制备。利用微生物发酵生产DHA仍处于实验室阶段。破囊壶菌(Thraustochytriumroseum)是合成DHA的优良海洋真菌。研究与筛选破囊壶菌DHA合成突变株,克隆破囊壶菌DHA合成关键酶基因,进而在酵母真核表达系统中表达,可为今后对该酶进行更深入的研究及应用建立良好的基础。用基因工程方法研制重组DHA,将开拓广阔的应用前景。     

Target validation and biomarker identification in oncology : the example of aurora kinases

The strong link between gene expression of mitotic Aurora kinases and cancer has stimulated a very high interest in developing Aurora kinase inhibitors for cancer therapy. Validation of Aurora kinases as targets, and development of pharmacodynamic biomarkers for inhibitors of Aurora kinases, provides an example of how target validation can help the drug discovery process, and also of how to interpret results depending on the technology used. In this review, we outline the principal tools, concepts, and strategies of target and biomarker validation for Aurora kinases, with emphasis on validation results derived from RNA-interference experiments. These data were essential for the decision to enter the next steps in drug development and for the selection of the appropriate biomarkers for clinical trials.     

Classifying mild traumatic brain injuries with functional network analysis

Background

Traumatic brain injury (TBI) represents a critical health problem of which timely diagnosis and treatment remain challenging. TBI is a result of an external force damaging brain tissue, accompanied by delayed pathogenic events which aggravate the injury. Molecular responses to different mild TBI subtypes have not been well characterized. TBI subtype classification is an important step towards the development and application of novel treatments. The computational systems biology approach is proved to be a promising tool in biomarker discovery for central nervous system injury.

Results

In this study, we have performed a network-based analysis on gene expression profiles to identify functional gene subnetworks. The gene expression profiles were obtained from two experimental models of injury in rats: the controlled cortical impact and the fluid percussion injury. Our method integrates protein interaction information with gene expression profiles to identify subnetworks of genes as biomarkers. We have demonstrated that the selected gene subnetworks are more accurate to classify the heterogeneous responses to different injury models, compared to conventional analysis using individual marker genes selected without network information.

Conclusions

The systems approach can lead to a better understanding of the underlying complexities of the molecular responses after TBI and the identified subnetworks will have important prognostic functions for patients who sustain mild TBIs.

     

Role of siRNAs and miRNAs in the processes of RNA-mediated gene silencing during viral infections

Phenomenon of RNA-induced gene silencing is a highly conservative mechanism among eukaryotic organisms. Several classes of small RNAs (siRNAs and miRNAs) 21–25 nt in length, which play a significant role in the processes of development of an organism, occurred important components of antiviral defence in animals and plants. This review shortly describes the main stages of gene silencing mechanism, features of antiviral RNA silencing in plants, invertebrates, mammals, ways of suppression of RNA-interference by viruses, as well as possible approaches of utilization of abovementioned phenomenon for struggling against viral infections. The article is published in the original.     

The Nature and Composition of the Internal Environment of the Developing Brain

1. The fetal brain develops within its own environment, which is protected from free exchange of most molecules among its extracellular fluid, blood plasma, and cerebrospinal fluid (CSF) by a set of mechanisms described collectively as brain barriers.2. There are high concentrations of proteins in fetal CSF, which are due not to immaturity of the blood–CSF barrier (tight junctions between the epithelial cells of the choroid plexus), but to a specialized transcellular mechanism that specifically transfers some proteins across choroid plexus epithelial cells in the immature brain.3. The proteins in CSF are excluded from the extracellular fluid of the immature brain by the presence of barriers at the CSF–brain interfaces on the inner and outer surfaces of the immature brain. These barriers are not present in the adult.4. Some plasma proteins are present within the cells of the developing brain. Their presence may be explained by a combination of specific uptake from the CSF and synthesis in situ. 5. Information about the composition of the CSF (electrolytes as well as proteins) in the developing brain is of importance for the culture conditions used for experiments with fetal brain tissue in vitro, as neurons in the developing brain are exposed to relatively high concentrations of proteins only when they have cell surface membrane contact with CSF.6. The developmental importance of high protein concentrations in CSF of the immature brain is not understood but may be involved in providing the physical force (colloid osmotic pressure) for expansion of the cerebral ventricles during brain development, as well as possibly having nutritive and specific cell development functions.     

Isolation of 2000-kDa complexes of N-methyl-D-aspartate receptor and postsynaptic density 95 from mouse brain

Neurotransmitter receptors in vivo are linked to intracellular adaptor proteins and signalling molecules driving downstream pathways. Methods for physical isolation are essential to answer fundamental questions about the size, structure and composition of in vivo complexes and complement the widely used yeast 2-hybrid method. The N-methyl-D-aspartate receptor (NMDAR) binds postsynaptic density 95 (PSD-95) protein; both are required for synaptic plasticity and learning and participate in other important pathophysiological functions. Here we describe the development and optimization of novel methods for large-scale isolation of NMDAR--PSD-95 complexes from mouse brain including immunoaffinity, immunoprecipitation, ligand-affinity and immobilized PSD-95 binding peptides. Short PDZ binding peptides modelled on NMDAR subunits were shown to isolate NMDAR complexes. Gel filtration indicated the native NMDAR--PSD-95 complexes were 2000 kDa, and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) revealed a complexity suggesting a huge network of both structural components and signalling enzymes. These methods can be used to define the structure of the complexes at different synapses and in mice carrying gene mutations as well as new tools for drug discovery.     

Adeno-associated virus vectors for gene transfer to the brain

Gene therapy is a novel method under investigation for the treatment of neurological disorders. Considerable interest has focused on the possibility of using viral vectors to deliver genes to the central nervous system. Adeno-associated virus (AAV) is a potentially useful gene transfer vehicle for neurologic gene therapies. The advantages of AAV vector include the lack of any associated disease with a wild-type virus, the ability to transduce nondividing cells, the possible integration of the gene into the host genome, and the long-term expression of transgenes. The development of novel therapeutic strategies for neurological disorder by using AAV vector has an increasing impact on gene therapy research. This article describes methods that can be used to generate rodent and nonhuman primate models for testing treatment strategies linked to pathophysiological events in the ischemic brain and neurodegenerative disorders such as Parkinson's disease.     

Insulin-like Growth Factor Binding Protein6 Associated with Neuronal Apoptosis Following Intracerebral Hemorrhage in Rats

The insulin-like growth factor (IGF) system is linked to CNS pathological states. The functions of IGFs are modulated by a family of binding proteins termed insulin-like growth factor binding proteins (IGFBPs). Here, we demonstrate that IGFBP-6 may be associated with neuronal apoptosis in the processes of intracerebral hemorrhage (ICH). We obtained a significant upregulation of IGFBP-6 in neurons adjacent to the hematoma following ICH with the results of Western blot, immunohistochemistry, and immunofluorescence. Increasing IGFBP-6 level was found to be accompanied by the upregulation of Bax, Bcl-2, and active caspase-3. Besides, IGFBP-6 co-localized well with active caspase-3 in neurons, indicating its potential role in neuronal apoptosis. Knocking down IGFBP-6 by RNA-interference in PC12 cells reduced active caspase-3 expression. Thus, IGFBP-6 may play a role in promoting the brain secondary damage following ICH.     

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

Background

Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes. Ideally, to assess the accuracy of gene expression analysis methods, one needs a set of genes which are known to be differentially expressed in the samples and which can be used as a "gold standard". We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods.

Results

Expression of sex-chromosome genes were used as true internal biological controls to compare alternate probe-level data extraction algorithms (Microarray Suite 5.0 [MAS5.0], Model Based Expression Index [MBEI] and Robust Multi-array Average [RMA]), to assess microarray data quality and to establish some statistical guidelines for analyzing large-scale gene expression. These approaches were implemented on a large new dataset of human brain samples. RMA-generated gene expression values were markedly less variable and more reliable than MAS5.0 and MBEI-derived values. A statistical technique controlling the false discovery rate was applied to adjust for multiple testing, as an alternative to the Bonferroni method, and showed no evidence of false negative results. Fourteen probesets, representing nine Y- and two X-chromosome linked genes, displayed significant sex differences in brain prefrontal cortex gene expression.

Conclusion

In this study, we have demonstrated the use of sex genes as true biological internal controls for genomic analysis of complex tissues, and suggested analytical guidelines for testing alternate oligonucleotide microarray data extraction protocols and for adjusting multiple statistical analysis of differentially expressed genes. Our results also provided evidence for sex differences in gene expression in the brain prefrontal cortex, supporting the notion of a putative direct role of sex-chromosome genes in differentiation and maintenance of sexual dimorphism of the central nervous system. Importantly, these analytical approaches are applicable to all microarray studies that include male and female human or animal subjects.