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An Integrated Human/Murine Transcriptome and Pathway Approach To Identify Prenatal Treatments For Down Syndrome.

ABSTRACT: Anatomical and functional brain abnormalities begin during fetal life in Down syndrome (DS). We hypothesize that novel prenatal treatments can be identified by targeting signaling pathways that are consistently perturbed in cell types/tissues obtained from human fetuses with DS and mouse embryos. We analyzed transcriptome data from fetuses with trisomy 21, age and sex-matched euploid controls, and embryonic day 15.5 forebrains from Ts1Cje, Ts65Dn, and Dp16 mice. The new datasets were compared to other publicly available datasets from humans with DS. We used the human Connectivity Map (CMap) database and created a murine adaptation to identify FDA-approved drugs that can rescue affected pathways. USP16 and TTC3 were dysregulated in all affected human cells and two mouse models. DS-associated pathway abnormalities were either the result of gene dosage specific effects or the consequence of a global cell stress response with activation of compensatory mechanisms. CMap analyses identified 56 molecules with high predictive scores to rescue abnormal gene expression in both species. Our novel integrated human/murine systems biology approach identified commonly dysregulated genes and pathways. This can help to prioritize therapeutic molecules on which to further test safety and efficacy. Additional studies in human cells are ongoing prior to pre-clinical prenatal treatment in mice.

SUBMITTER: Guedj F

PROVIDER: S-EPMC5009456 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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An Integrated Human/Murine Transcriptome and Pathway Approach To Identify Prenatal Treatments For Down Syndrome.

Guedj Faycal F Pennings Jeroen LA JL Massingham Lauren J LJ Wick Heather C HC Siegel Ashley E AE Tantravahi Umadevi U Bianchi Diana W DW

Scientific reports 20160902

Anatomical and functional brain abnormalities begin during fetal life in Down syndrome (DS). We hypothesize that novel prenatal treatments can be identified by targeting signaling pathways that are consistently perturbed in cell types/tissues obtained from human fetuses with DS and mouse embryos. We analyzed transcriptome data from fetuses with trisomy 21, age and sex-matched euploid controls, and embryonic day 15.5 forebrains from Ts1Cje, Ts65Dn, and Dp16 mice. The new datasets were compared to ...[more]

PMID: 27586445

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Project description:BACKGROUND:Long non-coding RNAs (lncRNAs) have previously been emerged as key players in a series of biological processes. Dysregulation of lncRNA is correlated to human diseases including neurological disorders. Here, we developed a multi-step bioinformatics analysis to study the functions of a particular Down syndrome-associated gene DSCR9 including the lncRNAs. The method is named correlation-interaction-network (COIN), based on which a pipeline is implemented. Co-expression gene network analysis and biological network analysis results are presented. METHODS:We identified the regulation function of DSCR9, a lncRNA transcribed from the Down syndrome critical region (DSCR) of chromosome 21, by analyzing its co-expression genes from over 1700 sets and nearly 60,000 public Affymetrix human U133-Plus 2 transcriptional profiling microarrays. After proper evaluations, a threshold is chosen to filter the data and get satisfactory results. Microarray data resource is from EBI database and protein-protein interaction (PPI) network information is incorporated from the most complete network databases. PPI integration strategy guarantees complete information regarding DSCR9. Enrichment analysis is performed to identify significantly correlated pathways. RESULTS:We found that the most significant pathways associated with the top DSCR9 co-expressed genes were shown to be involved in neuro-active ligand-receptor interaction (GLP1R, HTR4, P2RX2, UCN3, and UTS2R), calcium signaling pathway (CACNA1F, CACNG4, HTR4, P2RX2, and SLC8A3), neuronal system (KCNJ5 and SYN1) by the KEGG, and GO analysis. The A549 and U251 cell lines with stable DSCR9 overexpression were constructed. We validated 10 DSCR9 co-expression genes by qPCR in both cell lines with over 70% accuracy. CONCLUSIONS:DSCR9 was highly correlated with genes that were known as important factors in the developments and functions of nervous system, indicating that DSCR9 may regulate neurological proteins regarding Down syndrome and other neurological-related diseases. The pipeline can be properly adjusted to other applications.

Project description:Overexpression of Dual-specificity tyrosine-phosphorylated regulated kinase 1A (DYRK1A), located on human chromosome 21, may alter molecular processes linked to developmental deficits in Down syndrome (DS). Trisomic DYRK1A is a rational therapeutic target, and although reductions in Dyrk1a genetic dosage have shown improvements in trisomic mouse models, attempts to reduce Dyrk1a activity by pharmacological mechanisms and correct these DS-associated phenotypes have been largely unsuccessful. Epigallocatechin-3-gallate (EGCG) inhibits DYRK1A activity in vitro and this action has been postulated to account for improvement of some DS-associated phenotypes that have been reported in preclinical studies and clinical trials. However, the beneficial effects of EGCG are inconsistent and there is no direct evidence that any observed improvement actually occurs through Dyrk1a inhibition. Inconclusive outcomes likely reflect a lack of knowledge about the tissue-specific patterns of spatial and temporal overexpression and elevated activity of Dyrk1a that may contribute to emerging DS traits during development. Emerging evidence indicates that Dyrk1a expression varies over the life span in DS mouse models, yet preclinical therapeutic treatments targeting Dyrk1a have largely not considered these developmental changes. Therapies intended to improve DS phenotypes through normalizing trisomic Dyrk1a need to optimize the timing and dose of treatment to match the spatiotemporal patterning of excessive Dyrk1a activity in relevant tissues. This will require more precise identification of developmental periods of vulnerability to enduring adverse effects of elevated Dyrk1a, representing the concurrence of increased Dyrk1a expression together with hypothesized tissue-specific-sensitive periods when Dyrk1a regulates cellular processes that shape the long-term functional properties of the tissue. Future efforts targeting inhibition of trisomic Dyrk1a should identify these putative spatiotemporally specific developmental sensitive periods and determine whether normalizing Dyrk1a activity then can lead to improved outcomes in DS phenotypes.

Project description:BackgroundOur team has developed a decision aid to help pregnant women and their partners make informed decisions about Down syndrome prenatal screening. However, the decision aid is not yet widely available in Quebec's prenatal care pathways.ObjectiveWe sought to identify knowledge translation strategies and develop an implementation plan to promote the use of the decision aid in prenatal care services in Quebec, Canada.MethodsGuided by the Knowledge-to-Action Framework and the Theoretical Domains Framework, we performed a synthesis of our research (11 publications) on prenatal screening in Quebec and on the decision aid. Two authors independently reviewed the 11 articles, extracted information, and mapped it onto the Knowledge-to-Action framework. Using participatory action research methods, we then recruited pregnant women, health professionals, managers of three prenatal care services, and researchers to (a) identify the different clinical pathways followed by pregnant women and (b) select knowledge translation strategies for a clinical implementation plan. Then, based on all the information gathered, the authors established a consensus on strategies to include in the plan.ResultsOur knowledge synthesis showed that pregnant women and their partners are not sufficiently involved in the decision-making process about prenatal screening and that there are numerous barriers and facilitators of the use of the decision aid in clinical practice (e.g., low intention to use it among health providers). Using a participatory action approach, we met with five pregnant women, three managers, and six health professionals. They informed us about three of Quebec's prenatal care pathways and helped us identify 20 knowledge translation strategies (e.g., nurse discusses decision aid with women before they meet the doctor) to include in a clinical implementation plan. The research team reached a consensus about the clinical plan and also about broader organizational strategies, such as training healthcare providers in the use of the decision aid, monitoring its impact (e.g., measure decisional conflict) and sustaining its use (e.g., engage key stakeholders in the implementation process).ConclusionNext steps are to pilot our implementation plan while further identifying global strategies that target institutional, policy, and systemic supports for implementation.

Dataset Information

An Integrated Human/Murine Transcriptome and Pathway Approach To Identify Prenatal Treatments For Down Syndrome.

Publications

An Integrated Human/Murine Transcriptome and Pathway Approach To Identify Prenatal Treatments For Down Syndrome.

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