Investigating the genetic basis of Down Syndrome
1. Introduction
The traditional approach for this type of goal is a function-based case and control study. For DS function-based studies in mouse models (DSM), one prepares contrasting groups from Ts65Dn mice [a translocation trisomic mouse now widely used as the model available from the Jackson laboratory] and control littermates. The understanding that a copy number variation was a heterozygous condition, not a haploinsufficiency, leads to Ts65Dn work that concerns the genetic map of the trisomy chromosome or its downstream effects. There was still initial confusion and then little attention to the observed phenotypes to DS ones. Analysis of trisomy-related phenotypes in other Ts65Dn model analyses started when the methods, e.g., the Pdio8 gene that if mutated may lead to Spongiform encephalopathy, could be generalized from the mouse to DS patients. In two other studies, some information was taken from previous simple Ts65Dn studies but substantial attention was given to comparisons with patients.
Down syndrome (DS) is the major genetic cause of significant intellectual disability, with a worldwide incidence of approximately 1 in 732 live births. DS occurs due to triplication of chromosome 21 (HSA21, HSA for Homo Sapiens Autosome), but the underlying genetic bases of the clinical characteristics are not well known. Studies of rare patients with HSA21 anomalies suggest that some of the observed DS characteristics are due to trisomy for particular chromosomal regions, but what genes are involved and their contributions to the DS clinical patience are not well defined. The only information that would enable inferring the phenotypic effect of a HSA21 trisomy, finding the dosage-sensitive genes, would be a list of HSA21 genes and their respective roles in normal development and function. The latest human genome annotation list 231 mRNA-coding genes on HSA21, and it is unrealistic to sequence the genes for follow-up analyses on the patients where they map. Therefore, who is going to find which gene(s) are somehow related to a particular clinical feature of DS patients?
2. Causes of Down Syndrome
Down syndrome can arise from different errors in cell division. The different causes of the disorder lead to the existence of three groups: the most frequent is Trisomy Down syndrome (95%), which is also the one first described (cell contains three copies of chromosome 21) and it is estimated to appear in 1.5 in 1,000 babies. Then there is Translocation Down syndrome (3-4%), in which part of chromosome 21 is attached to a different chromosome (and the person has two complete sets of it as well as an additional full or partial final 21). Finally, Mosaicism Down syndrome (1-2%) in which the person has a mix of two types of cells (some with two chromosomes 21 and some with three chromosomes 21). In very rare cases, people with Down syndrome are not Trisomic, but rather have two chromosomes 21, but a segment of chromosome 21 has another copy in a part of another chromosome. It is believed that Mosaicism is the rarest form, but this has not yet been properly studied since few people carrying this type of Down syndrome are ascertained.
Down syndrome is usually caused by an error in cell division called non-disjunction. This leaves a sperm or egg cell with an extra copy or lack of a copy of chromosome 21 before or at the time of conception. Non-disjunction can prevent a chromosome from taking part in the formation of a normal pair of chromosomes, which is necessary for cell division. This means that another egg or sperm cell would contain a duplicate chromosome, which would later set and correctly pair to form a normal set of 46 chromosomes after fertilization. If the gamete with an extra chromosome is fertilized, then the zygote will contain three instead of two chromosomes as usual.
All cells with a nucleus have inherited genetic material from the parents. This genetic information is contained in 46 threadlike structures called chromosomes. We inherit 23 chromosomes from our mother and 23 chromosomes from our father.
Down syndrome was first described by a British doctor, John Langdon, at the end of the 19th century. However, it was Jane Lejeune from Paris who managed to demonstrate the genetic cause of the disorder in 1959. She observed an additional odd-shaped chromosome under the microscope of a child with Down syndrome.
3. Genetic Abnormalities in Down Syndrome
Recent findings employing a new mouse model with a reciprocal translocation between mouse chromosome 16 and 17 (Tc1 mice) have significant implications for our understanding of the etiology of cardiac disease in Down syndrome. Tc1 mice are mouse models for Down syndrome as they carry an extra copy of human chromosome 21 and show some of the salient features of Down syndrome in human beings. Tc1 mice have demonstrated cardiac abnormalities that have some overlap with the phenotypes of human subjects with Down syndrome. These mice show significantly less activity, decreased grip strength, hyperactivity, and impaired grip strength. Such results provide further experimental support to the concept of a dosage effect from chromosome 21 gene on heart development and function in Down syndrome and have significant implications for future therapeutic treatment and diagnosis for congenital heart disease cases in Down syndrome.
Besides this, another segmental trisomy model, Ts1Rhr, has been developed. This mouse carries an extra chromosome 16 as well as an extra copy of Gart (phosphoribosylglycinamide formyltransferase) genes. Ts1Rhr mice show increased Gart gene expression and reduced GSAM enzymatic activity, as well as craniofacial defects. While these models provide important information pertaining to the pathogenesis of craniofacial defects, the number of cases reported with this etiology alone is limited.
The Ts65Dn mouse is the segmental trisomy model for Down syndrome in mice, showing many of the phenotypes consistent with Down syndrome in human beings. The Ts65Dn mouse carries a partial triplication of mouse chromosome 16. This chromosome shares many synteny homologies with human chromosome 21. The Ts65Dn mouse is widely used to study canine neurogenesis, craniofacial development, neural development, wound healing, learning, memory, and cognitive abilities of Down syndrome.
Down syndrome is a complex syndrome caused by the presence of an extra copy of chromosome 21. The genetic mechanisms of Down syndrome phenotypes are still unclear, but many of them are thought to be inherited. Because of the important genetic homology between human chromosome 21 and proteins in homologous mammals, the mouse is often employed to study the underlying molecular basis of Down syndrome.
4. Current Research and Findings
The expression of genes potentially responsible for sex phenotype differences was measured in the cortex and the hippocampus of wild type (WT) and Ts65Dn mice. Genes involved in chromatin reorganization were found to be differentially expressed in the hippocampus of Ts65Dn male and female mice. Using the ISB approach, we are able to delineate the dynamics of chromatin reorganization leading to the DS differentiation of cortical and hippocampal neuroblasts. We found the up-regulation of Nhlh1, Parp9, Bzrp, and Rcan between E14.5 and E15.5 of Ts65Dn embryos that could inactivate histone H1.0 and consequently block the G1 phase of the cell cycle leading to the dysregulation of DNA replication, chromatin remodeling, cell cycle, G1/S transition, R-loop formation, gene transcription, and neural differentiation.
In silico Systems Biology (ISB) approach has been developed by combining transcriptomics, in silico analysis, and Systems Biology to identify the genetic basis of Down Syndrome (DS) phenotypes. In this approach, unique and differentially expressed genes, or gerontogenes, involved in the development of the DS phenotypes are overlapped with genetic interactions. New gerontogenes are identified, and these findings are analyzed with Systems Biology tools to understand novel molecular mechanisms that, with high probability, develop and drive the DS phenotypes. This novel approach was applied to study the sex-related differences previously identified in the brain and the heart of DS mice carrying the partial trisomy of chromosome 16 (Ts65Dn). The idea is based on the fact that DS carriers are affected by hypogonadism and had alterations of the gonadal-hypothalamic-pituitary axis.
5. Conclusion and Future Directions
An extended version of our study is also available for further investigation where we have also included gene products not associated with protein coding genes such as lncRNA or miRNA. Overall, we expect that additional evidence (e.g. OMICs data) combined with knowledge on genome wide associations studies, as well as advanced biological models such as Single Cell Biology studies, will help identifying new scopes and relevant molecular players in DS. Future directions encompass systems biology analysis performed on different DS cohort including age, sex and disease progression as well as further prioritization and validation process that might benefit from novel bioinformatics and experimental economics-friendly technologies.
In this paper, we identified and ranked the importance of protein coding genes likely involved in the Down Syndrome (DS) based on empirical evidence in humans, and in mouse models. We found that most DS-associated genes are highly expressed in the brain and are functionally linked to signal transduction, cell proliferation, and neurogenesis. Using protein-protein interaction networks, we also identified several hub genes (namely, APP, PPP2R2A, and DYRK1A) that play a key role in the network connectivity of DS genes, indicating that they potentially define central points for DS biological foundation. Furthermore, our investigation revealed that DS genes are more likely to be associated with cancer and potentially with neurodegenerative disorders such as Alzheimer disease. Pathway enrichment analysis identified a number of relevant and highly significant pathways in which DS genes are involved. For example, cAMP signaling, VEGF signaling, and ECM-receptor interaction, known to play a key role in the physiological alterations associated with DS. However, we also found that DS genes play a significant role in unexpected biological processes such as ribosome biogenesis in eukaryotes, and the spliceosome which are difficult to reconcile with current knowledge on DS phenotypes.
