Spatial and temporal localization during embryonic and fetal human development of the transcription factor SIM2 in brain regions altered in Down syndrome

Parity is associated with long-term differences in DNA methylation at genes related to neural plasticity in multiple sclerosis

BACKGROUND

Pregnancy in women with multiple sclerosis (wwMS) is associated with a reduction of long-term disability progression. The mechanism that drives this effect is unknown, but converging evidence suggests a role for epigenetic mechanisms altering immune and/or central nervous system function. In this study, we aimed to identify whole blood and immune cell-specific DNA methylation patterns associated with parity in relapse-onset MS.

RESULTS

We investigated the association between whole blood and immune cell-type-specific genome-wide methylation patterns and parity in 192 women with relapse-onset MS, matched for age and disease severity. The median time from last pregnancy to blood collection was 16.7 years (range = 1.5-44.4 years). We identified 2965 differentially methylated positions in whole blood, 68.5% of which were hypermethylated in parous women; together with two differentially methylated regions on Chromosomes 17 and 19 which mapped to TMC8 and ZNF577, respectively. Our findings validated 22 DMPs and 366 differentially methylated genes from existing literature on epigenetic changes associated with parity in wwMS. Differentially methylated genes in whole blood were enriched in neuronal structure and growth-related pathways. Immune cell-type-specific analysis using cell-type proportion estimates from statistical deconvolution of whole blood revealed further differential methylation in T cells specifically (four in CD4⁺ and eight in CD8⁺ T cells). We further identified reduced methylation age acceleration in parous women, demonstrating slower biological aging compared to nulligravida women.

CONCLUSION

Differential methylation at genes related to neural plasticity offers a potential molecular mechanism driving the long-term effect of pregnancy on MS outcomes. Our results point to a potential 'CNS signature' of methylation in peripheral immune cells, as previously described in relation to MS progression, induced by parity. As the first epigenome-wide association study of parity in wwMS reported, validation studies are needed to confirm our findings.

Developmental Neuropathology and Neurodegeneration of Down Syndrome: Current Knowledge in Humans

Individuals with Down syndrome (DS) suffer from developmental delay, intellectual disability, and an early-onset of neurodegeneration, Alzheimer’s-like disease, or precocious dementia due to an extra chromosome 21. Studying the changes in anatomical, cellular, and molecular levels involved may help to understand the pathogenesis and develop target treatments, not just medical, but also surgical, cell and gene therapy, etc., for individuals with DS. Here we aim to identify key neurodevelopmental manifestations, locate knowledge gaps, and try to build molecular networks to better understand the mechanisms and clinical importance. We summarize current information about the neuropathology and neurodegeneration of the brain from conception to adulthood of foetuses and individuals with DS at anatomical, cellular, and molecular levels in humans. Understanding the alterations and characteristics of developing Down syndrome will help target treatment to improve the clinical outcomes. Early targeted intervention/therapy for the manifestations associated with DS in either the prenatal or postnatal period may be useful to rescue the neuropathology and neurodegeneration in DS.

A recessive variant in SIM2 in a child with complex craniofacial anomalies and global developmental delay

Rare deletions and duplications on the long arm of Chromosome 21 have previously been reported in many patients with craniofacial and developmental phenotypes. However, this Down Syndrome Critical Region (DSCR) contains multiple genes, making identifying a single causative gene difficult. Here, we report a case of a boy with bicoronal craniosynostosis, facial dysmorphism, developmental delay, and intellectual impairment who was found by whole genome sequencing to have a homozygous missense mutation in the Single-Minded Homolog 2 (SIM2) gene (c.461 A  >  G, p.Tyr154Cys) within the DSCR. SIM2 encodes an essential bHLH and PAS domain transcription factor expressed during fetal brain development and acts as a master regulator of neurogenesis. This variant is globally very rare, segregates in the family, and is predicted to be highly deleterious by in silico analysis, 3D molecular modeling of protein structure, and functional analysis of zebrafish models. Zebrafish expressing the human SIM2^p.Y154C variant displayed a progressed microcephaly-like phenotype and head shape abnormalities. When combined with careful phenotyping of the patient vis-à-vis previously reported cases harboring structural variants in this critical 21q22 region, the data support a pathogenic role of SIM2 in this complex syndrome and demonstrates the utility of next-generation sequencing in prioritizing genes in contiguous deletions/duplications syndromes and diagnosing microarray-negative patients in the craniofacial clinic.

Single-minded 2 is required for left-right asymmetric stomach morphogenesis

The morphogenesis of left-right (LR) asymmetry is a crucial phase of organogenesis. In the digestive tract, the development of anatomical asymmetry is first evident in the leftward curvature of the stomach. To elucidate the molecular events that shape this archetypal laterality, we performed transcriptome analyses of the left versus right sides of the developing stomach in frog embryos. Besides the known LR gene pitx2, the only gene found to be expressed asymmetrically throughout all stages of curvature was single-minded 2 (sim2), a Down Syndrome-related transcription factor and homolog of a Drosophila gene (sim) required for LR asymmetric looping of the fly gut. We demonstrate that sim2 functions downstream of LR patterning cues to regulate key cellular properties and behaviors in the left stomach epithelium that drive asymmetric curvature. Our results reveal unexpected convergent cooption of single-minded genes during the evolution of LR asymmetric morphogenesis, and have implications for dose-dependent roles of laterality factors in non-laterality-related birth defects.

Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells

Treatment of prostate cancer confronts resistance to androgen receptor (AR)-targeted therapies. AR-associated coregulators and chromatin proteins hold a great potential for novel therapy targets. Here, we employed a powerful chromatin-directed proteomics approach termed ChIP-SICAP to uncover the composition of chromatin protein network, the chromatome, around endogenous AR in castration resistant prostate cancer (CRPC) cells. In addition to several expected AR coregulators, the chromatome contained many nuclear proteins not previously associated with the AR. In the context of androgen signaling in CRPC cells, we further investigated the role of a known AR-associated protein, a chromatin remodeler SMARCA4 and that of SIM2, a transcription factor without a previous association with AR. To understand their role in chromatin accessibility and AR target gene expression, we integrated data from ChIP-seq, RNA-seq, ATAC-seq and functional experiments. Despite the wide co-occurrence of SMARCA4 and AR on chromatin, depletion of SMARCA4 influenced chromatin accessibility and expression of a restricted set of AR target genes, especially those involved in cell morphogenetic changes in epithelial-mesenchymal transition. The depletion also inhibited the CRPC cell growth, validating SMARCA4's functional role in CRPC cells. Although silencing of SIM2 reduced chromatin accessibility similarly, it affected the expression of a much larger group of androgen-regulated genes, including those involved in cellular responses to external stimuli and steroid hormone stimulus. The silencing also reduced proliferation of CRPC cells and tumor size in chick embryo chorioallantoic membrane assay, further emphasizing the importance of SIM2 in CRPC cells and pointing to the functional relevance of this potential prostate cancer biomarker in CRPC cells. Overall, the chromatome of AR identified in this work is an important resource for the field focusing on this important drug target.

Treatment of Epilepsy Associated with Common Chromosomal Developmental Diseases

Chromosomal diseases are heterogeneous conditions with complex phenotypes, which include also epileptic seizures. Each chromosomal syndrome has a range of specific characteristics regarding the type of seizures, EEG findings and specific response to antiepileptic drugs, significant in the context of the respective genetic etiology. Therefore, it is very important to know these particularities, in order to avoid an exacerbation of seizures or some side effects. In this paper we will present a review of the epileptic seizures and antiepileptic treatment in some of the most common chromosomal syndromes.

DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

Background

Down syndrome (DS) is characterized by neurodevelopmental abnormalities caused by partial or complete trisomy of human chromosome 21 (T21). Analysis of Down syndrome brain specimens has shown global epigenetic and transcriptional changes but their interplay during early neurogenesis remains largely unknown. We differentiated induced pluripotent stem cells (iPSCs) established from two DS patients with complete T21 and matched euploid donors into two distinct neural stages corresponding to early- and mid-gestational ages.

Results

Using the Illumina Infinium 450K array, we assessed the DNA methylation pattern of known CpG regions and promoters across the genome in trisomic neural iPSC derivatives, and we identified a total of 500 stably and differentially methylated CpGs that were annotated to CpG islands of 151 genes. The genes were enriched within the DNA binding category, uncovering 37 factors of importance for transcriptional regulation and chromatin structure. In particular, we observed regional epigenetic changes of the transcription factor genes ZNF69, ZNF700 and ZNF763 as well as the HOXA3, HOXB3 and HOXD3 genes. A similar clustering of differential methylation was found in the CpG islands of the HIST1 genes suggesting effects on chromatin remodeling.

Conclusions

The study shows that early established differential methylation in neural iPSC derivatives with T21 are associated with a set of genes relevant for DS brain development, providing a novel framework for further studies on epigenetic changes and transcriptional dysregulation during T21 neurogenesis.

SIM2l attenuates resistance to hypoxia and tumor growth by transcriptional suppression of HIF1A in uterine cervical squamous cell carcinoma

Despite chemoradiotherapy being one of the most important modalities in advanced cervical cancer, there is a lack of both usable biomarkers to predict treatment outcome and of knowledge about the mechanism of refractoriness to the therapy. Here we identified a transcriptional factor Single-minded homolog 2 (SIM2) as an independent predictive biomarker for uterine cervical squamous cell carcinoma (CvSCC). The retrospective study showed that high expression level of SIM2 was correlated to good survival in CvSCC patients. SIM2 knockdown in CvSCC cell lines showed resistance to hypoxia with increased expression of HIF1A and its target genes. Loss of SIM2 also caused growth promotion, resistance to ROS, and radiation in 3D culture. Furthermore, SIM2 knockdown suppressed tumor growth with increased HIF-1α expression and angiogenesis in vivo. On the other hand, SIM2 long isoform (SIM2l)-overexpressed cells had contrary results, indicating the long isoform plays a key role for maintenance of these phenotypes. These data indicated that SIM2l has a potential to be precision medicine for CvSCC patients and that anti-angiogenesis therapy might be usable for SIM2l^Low poor survivors.

A small pons as a characteristic finding in Down syndrome: A quantitative MRI study

BACKGROUND

Down syndrome (DS) is the most common chromosomal aberration, but the characteristics of the brainstem component in this condition during childhood (from newborn to preteen stages) have not been clarified.

OBJECTIVE

To evaluate the morphological features of the brainstem in DS on magnetic resonance imaging (MRI).

MATERIALS AND METHODS

MRIs for 32 children with DS (16 boys and girls each; age range, 0-11years) without major brain insults, and 32 age-matched controls (16 boys and girls each) were retrospectively analyzed. Height, width, and area of the midbrain, pons, and medulla oblongata were measured on sagittal T1-weighted images; these were compared in children with DS and age-matched controls. The ratios of the brainstem to the size of the posterior fossa (BS/PF index) were calculated; these were also compared in the children with DS and the control group.

RESULTS

The width and area of the midbrain; height, width, area of the pons; and area of the medulla oblongata were significantly smaller in children with DS than in control children (P<0.05); the area of the pons, particularly for the ventral part, showed the largest differences in the mean relative differences. The BS/PF indices of the height, width, and area of the pons were significantly smaller in children with DS than in the control group (P<0.01). However, the BS/PF indices for the midbrain and the medulla oblongata did not differ between these two groups.

CONCLUSIONS

Children with DS may have small brainstems, particularly in the pons; this may be a characteristic morphological feature of the brainstem on MRI in childhood including neonates.

HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells

The HSA21 encoded Single-minded 2 (SIM2) transcription factor has key neurological functions and is a good candidate to be involved in the cognitive impairment of Down syndrome. We aimed to explore the functional capacity of SIM2 by mapping its DNA binding sites in mouse embryonic stem cells. ChIP-sequencing revealed 1229 high-confidence SIM2-binding sites. Analysis of the SIM2 target genes confirmed the importance of SIM2 in developmental and neuronal processes and indicated that SIM2 may be a master transcription regulator. Indeed, SIM2 DNA binding sites share sequence specificity and overlapping domains of occupancy with master transcription factors such as SOX2, OCT4 (Pou5f1), NANOG or KLF4. The association between SIM2 and these pioneer factors is supported by co-immunoprecipitation of SIM2 with SOX2, OCT4, NANOG or KLF4. Furthermore, the binding of SIM2 marks a particular sub-category of enhancers known as super-enhancers. These regions are characterized by typical DNA modifications and Mediator co-occupancy (MED1 and MED12). Altogether, we provide evidence that SIM2 binds a specific set of enhancer elements thus explaining how SIM2 can regulate its gene network in neuronal features.

Down syndrome: the brain in trisomic mode

Down syndrome is the most common form of intellectual disability and results from one of the most complex genetic perturbations that is compatible with survival, trisomy 21. The study of brain dysfunction in this disorder has largely been based on a gene discovery approach, but we are now moving into an era of functional genome exploration, in which the effects of individual genes are being studied alongside the effects of deregulated non-coding genetic elements and epigenetic influences. Also, new data from functional neuroimaging studies are challenging our views of the cognitive phenotypes associated with Down syndrome and their pathophysiological correlates. These advances hold promise for the development of treatments for intellectual disability.

Methylation alterations of WT1 and homeobox genes in inflamed muscle biopsy samples from patients with untreated juvenile dermatomyositis suggest self-renewal capacity

OBJECTIVE

To determine the effect of methylation alteration in inflamed muscles from children with juvenile dermatomyositis (DM) and other idiopathic inflammatory myopathies (IIMs).

METHODS

Magnetic resonance imaging-directed diagnostic muscle biopsies yielded samples from 20 children with juvenile DM, which were used for genome-wide DNA methylation profiling, as were muscle biopsy samples from 4 healthy controls. Bisulfite treatment followed by pyrosequencing confirmed methylation status in juvenile DM and other IIMs. Immunohistochemistry defined localization and expression levels of WT1.

RESULTS

Comparison of genome-wide DNA methylation profiling between juvenile DM muscle and normal control muscle revealed 27 genes with a significant methylation difference between the groups. These genes were enriched with transcription factors and/or cell cycle regulators and were unrelated to duration of untreated disease. Six homeobox genes were among them; ALX4, HOXC11, HOXD3, and HOXD4 were hypomethylated, while EMX2 and HOXB1 were hypermethylated. WT1 was significantly hypomethylated in juvenile DM (Δβ = -0.41, P < 0.001). Bisulfite pyrosequencing verification in samples from 56 patients with juvenile DM confirmed the methylation alterations of these genes. Similar methylation alterations were observed in juvenile polymyositis (n = 5) and other IIMs (n = 9). Concordant with the other findings, WT1 protein was increased in juvenile DM muscle, with average positive staining of 11.6%, but was undetectable in normal muscle (P < 0.001).

CONCLUSION

These results suggest that affected muscles of children with juvenile DM and IIMs have the capacity to be repaired, and that homeobox and WT1 genes are epigenetically marked to facilitate this repair process, potentially suggesting new avenues of therapeutic intervention.

A 1 Mb de novo deletion within 11q13.1q13.2 in a boy with mild intellectual disability and minor dysmorphic features

We report a 11 year old male patient ascertained for mild intellectual disability and minor dysmorphic features, carrying a 1 Mb de novo deletion on chromosome 11q13.1q13.2 detected by aCGH. This is the first report of a deletion in this region in a patient presenting with intellectual impairment and mild dysmorphic traits. The 1 Mb deleted area encompasses 47 RefSeq genes, including Cornichon homologue 2 (CNIH2), Cofilin-1 (CFL1) and neuronal PAS domain-containing protein 4 (NPAS4), which are highly expressed in the central nervous system. Knockout of the CNIH2 and CFL1 orthologues in animals results in migration disturbances, while low or no expression of Npas4 in mice results in impairment of memory and learning. These three genes have previously been suggested as candidate genes for neurological disorders.

Genomic determinants in the phenotypic variability of Down syndrome

Down syndrome caused by trisomy 21 is a collection of phenotypes with variable expressivity and penetrance. The significant advances in exploring the human genome now provide the tools to better understand the contribution of trisomy 21 in the different manifestations of Down syndrome, and the functional links between the genome variability and the phenotypic variability.

Down syndrome: searching for the genetic culprits

Down syndrome (DS) is caused by trisomy of human chromosome 21 (Hsa21) and results in a large number of phenotypes, including learning difficulties, cardiac defects, distinguishing facial features and leukaemia. These are likely to result from an increased dosage of one or more of the ∼310 genes present on Hsa21. The identification of these dosage-sensitive genes has become a major focus in DS research because it is essential for a full understanding of the molecular mechanisms underlying pathology, and might eventually lead to more effective therapy. The search for these dosage-sensitive genes is being carried out using both human and mouse genetics. Studies of humans with partial trisomy of Hsa21 have identified regions of this chromosome that contribute to different phenotypes. In addition, novel engineered mouse models are being used to map the location of dosage-sensitive genes, which, in a few cases, has led to the identification of individual genes that are causative for certain phenotypes. These studies have revealed a complex genetic interplay, showing that the diverse DS phenotypes are likely to be caused by increased copies of many genes, with individual genes contributing in different proportions to the variance in different aspects of the pathology.

Variants in RET associated with Hirschsprung's disease affect binding of transcription factors and gene expression

BACKGROUND & AIMS

Two noncoding variations in RET-the T allele of the single nucleotide polymorphism (SNP) rs2435357 (Enh1:C>T) and the A allele of the SNP rs2506004 (Enh2:C>A)-are associated with Hirschsprung's disease. These SNPs are in strong linkage disequilibrium and located in an enhancer element in intron 1 of the RET gene. The T allele of the Enh1 variant results in reduced expression of RET, compared with the C allele, because the T allele disrupts binding to the transcription factor SOX10. We studied whether the A allele of Enh2 (Enh2-A) also affects RET gene expression.

METHODS

We evaluated the function of Enh1 and Enh2 using luciferase reporter assays with constructs that contained each allele, separately or in combination. We performed in silico analysis to identify transcription activators or repressors that bind to Enh2-C.

RESULTS

The Enh1-T and the Enh2-A alleles reduced expression of the luciferase reporter gene. In silico analysis identified the sequence of Enh2-C and its surrounding sequence (ACGTG) as a potential binding site for the NXF-ARNT2 and SIM2-ARNT2 transcription factor heterodimers. The affinity of NXF-ARNT2 for Enh2-C was confirmed by electrophoresis mobility shift and supershift assays. Transfection of neuroblastoma cell lines with NXF-ARNT2 or SIM2-ARNT2 increased and decreased expression of RET, respectively.

CONCLUSIONS

More than one SNP on an associated haplotype can influence gene expression and ultimately disease phenotype. Binding of the transcription factors NXF, ARNT2, and SIM2 to RET depend on the RET polymorphism of Enh2 and affect RET expression and the development of Hirschsprung's disease.

A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes

Background

Dosage imbalance is responsible for several genetic diseases, among which Down syndrome is caused by the trisomy of human chromosome 21.

Results

To elucidate the extent to which the dosage imbalance of specific human chromosome 21 genes perturb distinct molecular pathways, we developed the first mouse embryonic stem (ES) cell bank of human chromosome 21 genes. The human chromosome 21-mouse ES cell bank includes, in triplicate clones, 32 human chromosome 21 genes, which can be overexpressed in an inducible manner. Each clone was transcriptionally profiled in inducing versus non-inducing conditions. Analysis of the transcriptional response yielded results that were consistent with the perturbed gene's known function. Comparison between mouse ES cells containing the whole human chromosome 21 (trisomic mouse ES cells) and mouse ES cells overexpressing single human chromosome 21 genes allowed us to evaluate the contribution of single genes to the trisomic mouse ES cell transcriptome. In addition, for the clones overexpressing the Runx1 gene, we compared the transcriptome changes with the corresponding protein changes by mass spectroscopy analysis.

Conclusions

We determined that only a subset of genes produces a strong transcriptional response when overexpressed in mouse ES cells and that this effect can be predicted taking into account the basal gene expression level and the protein secondary structure. We showed that the human chromosome 21-mouse ES cell bank is an important resource, which may be instrumental towards a better understanding of Down syndrome and other human aneuploidy disorders.

Molecular and cellular mechanisms elucidating neurocognitive basis of functional impairments associated with intellectual disability in Down syndrome

Down syndrome, the most common genetic cause of intellectual disability, is associated with brain disorders due to chromosome 21 gene overdosage. Molecular and cellular mechanisms involved in the neuromorphological alterations and cognitive impairments are reported herein in a global model. Recent advances in Down syndrome research have lead to the identification of altered molecular pathways involved in intellectual disability, such as Calcineurin/NFATs pathways, that are of crucial importance in understanding the molecular basis of intellectual disability pathogenesis in this syndrome. Potential treatments in mouse models of Down syndrome, including antagonists of NMDA or GABA(A) receptors, and microRNAs provide new avenues to develop treatments of intellectual disability. Nevertheless, understanding the links between molecular pathways and treatment strategies in human beings requires further research.

A quantitative assessment of gene expression (QAGE) reveals differential overexpression of DOPEY2, a candidate gene for mental retardation, in Down syndrome brain regions

The brain alterations and mental retardation in Down syndrome are associated with overdosage of chromosome 21 genes. To shed light on the understanding of the molecular effect of this genetic overdosage, gene expression studies have crucial importance to quantify expression variations in Down syndrome tissues compared to normal ones. Herein, an in situ Quantitative Assessment of Gene Expression (QAGE) was used to quantify and statistically analyze, for the first time, DOPEY2 expression variations in different regions of the Down syndrome human fetal brains and to compare them to corresponding normal brains. DOPEY2, which is localized in the Down Syndrome Critical Region (DSCR) and is a candidate gene for neurological alterations in Down syndrome, showed a delimited regional and cellular expression pattern in the cortex, hippocampus and cerebellum, characterized by different transcriptional intensities in both normal and trisomic brains. DOPEY2 is overexpressed more than 50% (1.79-, 1.97- and 2.12-folds in the cortex, cerebellum and hippocampus, respectively), and showed statistically significant differences in the overexpression ratios in the three brain regions expressing DOPEY2. The demonstration of differential DOPEY2 expression and overexpression in human fetal brains suggests that this gene is submitted to a complex transcriptional control and could depend from other human chromosome 21 genes. Moreover, DOPEY2 overexpression in the brain regions, that are altered in Down syndrome patients and involved in learning and memory processes, is in agreement to the hypothesis that this gene plays a potential role in functional brain alterations and in the pathogenesis of mental retardation in Down syndrome. This new in situ QAGE approach allowed quantitative measurements of transcriptional changes and statistical evaluations of the expression and overexpression patterns of DOPEY2 at specific regions of the brain, which is a complementary approach to qRT-PCR and microarray for transcriptome study. Moreover, this approach could be a powerful tool to study the candidate chromosome 21 genes for Down syndrome and other pathologies caused by regionalized quantitative transcriptional alterations, for greater interpretation of functional processes driving gene expression.

Functional characterization of basic helix-loop-helix-PAS type transcription factor NXF in vivo: putative involvement in an "on demand" neuroprotection system

NXF, a member of the basic helix-loop-helix-PAS transcription factor family, is thought to be involved in functional regulation of neurons, because significant expression is found in the mature brain. To elucidate functions of NXF in vivo, here we generated mice lacking NXF using homologous recombination with embryonic stem cells. NXF(-/-) mice were morphologically indistinguishable (with no growth retardation) from their littermates (wild type) at birth. However, they started to die at a rate of 1 death/20-30 animals per week under specific pathogen-free grade breeding conditions when over 3 months old. Histological analyses revealed age-dependent neurodegeneration in brain, and only 20-30% of the NXF(-/-) mice survived for 16 months. To clarify the role of NXF in protection against neurodegeneration in normal cells, we analyzed gene expression under several conditions in vitro and in vivo. The NXF gene was up-regulated by several neurodegenerative cell-stress inducers such as thapsigargin (endoplasmic reticulum stress), SIN-1 (oxidative stress), and sorbitol (osmotic stress) in cultured cells. Furthermore, elevated NXF gene expression was apparent with in vivo stroke models featuring kainate-induced hippocampal injury and transient global ischemia. When NXF(-/-) mice were evaluated in the glutamate excitotoxicity model, they proved more susceptible to hippocampal injury at 15 weeks after birth. The findings in this study suggest that the NXF gene could be induced in response to several neurodegenerative stimuli/excitations for the cell protection, and thus provide an "on demand" cell-protection system in nervous tissue.

Mental retardation and associated neurological dysfunctions in Down syndrome: a consequence of dysregulation in critical chromosome 21 genes and associated molecular pathways

Down syndrome (DS), affecting 1/700 live births, is the major genetic cause of mental retardation (MR), a cognitive disorder with hard impact on public health. DS brain is characterized by a reduced cerebellar volume and number of granular cells, defective cortical lamination and reduced cortical neurons, malformed dendritic trees and spines, and abnormal synapses. These neurological alterations, also found in trisomic mouse models, result from gene-dosage effects of Human Chromosome 21 (HC21) on the expression of critical developmental genes. HC21 sequencing, mouse ortholog gene identification and DS mouse model generation lead to determine HC21 gene functions and the effects of protein-dosage alterations in neurodevelopmental and metabolic pathways in DS individuals. Trisomic brain transcriptome of DS patients and trisomic mouse models identified some molecular changes determined by gene-overdosage and associated dysregulation of some disomic gene expression in DS brains. These transcriptional variations cause developmental alterations in neural patterning and signal transduction pathways that may lead to defective neuronal circuits responsible for the pathogenesis of MR in DS. Recently, the first altered molecular pathway responsible of some DS phenotypes, including neurological and cognitive disorders has been identified. In this pathway, two critical HC21 genes (DYRK1A and DSCR1) act synergistically to control the phosphorylation levels of NFATc and NFATc-regulated gene expression. Interestingly, the NFATc mice show neurological dysfunctions similar to those seen in DS patients and trisomic mouse models. Treatment of DS mouse model Ts65Dn with GABA(A) antagonists allowed post-drug rescue of cognitive defects, indicating a hopeful direction in clinical therapies for MR in children with DS.

Mental retardation in Down syndrome: From gene dosage imbalance to molecular and cellular mechanisms

Down syndrome (DS), the most frequent genetic disorder leading to mental retardation (MR), is caused by three copies of human chromosome 21 (HC21). Trisomic and transgenic mouse models for DS allow genetic dissection of DS neurological and cognitive disorders in view to identify genes responsible for these phenotypes. The effects of the gene dosage imbalance on DS phenotypes are explained by two hypotheses: the "gene dosage effect" hypothesis claims that a DS critical region, containing a subset of dosage-sensitive genes, determines DS phenotypes, and the "amplified developmental instability" hypothesis holds that HC21 trisomy determines general alteration in developmental homeostasis. Transcriptome and expression studies showed different up- or down-expression levels of genes located on HC21 and the other disomic chromosomes. HC21 genes, characterized by their overexpression in brain regions affected in DS patients and by their contribution to neurological and cognitive defects when overexpressed in mouse models, are proposed herein as good candidates for MR. In this article, we propose a new molecular and cellular mechanism explaining MR pathogenesis in DS. In this model, gene dosage imbalance effects on transcriptional variations are described considering the nature of gene products and their functional relationships. These transcriptional variations may affect different aspects of neuronal differentiation and metabolism and finally, determine the brain neuropathologies and mental retardation in DS.

Increased Expression of SIM2-s Protein Is a Novel Marker of Aggressive Prostate Cancer

PURPOSE

The human SIM2 gene is located within the Down's syndrome critical region of chromosome 21 and encodes transcription factors involved in brain development and neuronal differentiation. SIM2 has been assigned a possible role in the pathogenesis of solid tumors, and the SIM2-short isoform (SIM2-s) was recently proposed as a molecular target for cancer therapy. We previously reported SIM2 among the highly up-regulated genes in 29 prostate cancers, and the purpose of our present study was to examine the expression status of SIM2 at the transcriptional and protein level as related to outcome in prostate cancer.

EXPERIMENTAL DESIGN

By quantitative PCR, mRNA in situ hybridization, and immunohistochemistry, we evaluated the expression and significance of SIM2 isoforms in 39 patients with clinically localized prostate cancer and validated the expression of SIM2-s protein in an independent cohort of 103 radical prostatectomies from patients with long and complete follow-up.

RESULTS

The SIM2 isoforms (SIM2-s and SIM2-l) were significantly coexpressed and increased in prostate cancer. Tumor cell expression of SIM2-s protein was associated with adverse clinicopathologic factors like increased preoperative serum prostate-specific antigen, high histologic grade, invasive tumor growth with extra-prostatic extension, and increased tumor cell proliferation by Ki-67 expression. SIM2-s protein expression was significantly associated with reduced cancer-specific survival in multivariate analyses.

CONCLUSIONS

These novel findings indicate for the first time that SIM2 expression might be important for clinical progress of human cancer and support the recent proposal of SIM2-s as a candidate for targeted therapy in prostate cancer.

Using mouse models to explore genotype–phenotype relationship in Down syndrome

Down Syndrome (DS) caused by trisomy 21 is characterized by a variety of phenotypes and involves multiple organs. Sequencing of human chromosome 21 (HSA21) and subsequently of its orthologues on mouse chromosome 16 have created an unprecedented opportunity to explore the complex relationship between various DS phenotypes and the extra copy of approximately 300 genes on HSA21. Advances in genetics together with the ability to generate genetically well-defined mouse models have been instrumental in understanding the relationships between genotype and phenotype in DS. Indeed, elucidation of these relationships will play an important role in understanding the pathophysiological basis of this disorder and helping to develop therapeutic interventions. A successful example of using such a strategy is our recent studies exploring the relationship between failed nerve growth factor (NGF) transport and amyloid precursor protein (App) overexpression. We found that increased dosage of the gene for App is linked to failed NGF signaling and cholinergic neurodegeneration in a mouse model of DS. Herein, we discuss several mouse models of DS and explore the emergence of exciting new insights into genotype-phenotype relationships, particularly those related to nervous system abnormalities. An important conclusion is that uncovering these relationships is enhanced by working from carefully defined phenotypes to the genes responsible.

Genetic mechanisms involved in the phenotype of Down syndrome

Down syndrome (DS) is the most common genetic cause of significant intellectual disability in the human population, occurring in roughly 1 in 700 live births. The ultimate cause of DS is trisomy of all or part of the set of genes located on chromosome 21. How this trisomy leads to the phenotype of DS is unclear. The completion of the DNA sequencing and annotation of the long arm of chromosome 21 was a critical step towards understanding the genetics of the phenotype. However, annotation of the chromosome continues and the functions of many genes on chromosome 21 remain uncertain. Recent findings about the structure of the human genome and of chromosome 21, in particular, and studies on mechanisms of gene regulation indicate that various genetic mechanisms may be contributors to the phenotype of DS and to the variability of the phenotype. These include variability of gene expression, the activity of transcription factors both encoded on chromosome 21 and encoded elsewhere in the genome, copy number polymorphisms, the function of conserved nongenic regions, microRNA activities, RNA editing, and perhaps DNA methylation. In this manuscript, we describe current knowledge about these genetic complexities and their likely importance in the context of DS. We identify gaps in current knowledge and suggest priorities to fill these gaps.

The highly ordered assembly of retinal axons and their synaptic partners is regulated by Hedgehog/Single-minded in the Drosophila visual system

During development of the Drosophila visual center, photoreceptor cells extend their axons (R axons) to the lamina ganglion layer, and trigger proliferation and differentiation of synaptic partners (lamina neurons) by delivering the inductive signal Hedgehog (Hh). This inductive mechanism helps to establish an orderly arrangement of connections between the R axons and lamina neurons, termed a retinotopic map because it results in positioning the lamina neurons in close vicinity to the corresponding R axons. We found that the bHLH-PAS transcription factor Single-minded (Sim) is induced by Hh in the lamina neurons and is required for the association of lamina neurons with R axons. In sim mutant brains, lamina neurons undergo the first step of differentiation but fail to associate with R axons. As a result, lamina neurons are set aside from R axons. The data reveal a novel mechanism for regulation of the interaction between axons and neuronal cell bodies that establishes precise neuronal networks.

Differential transcription ofBarhl1homeobox gene in restricted functional domains of the central nervous system suggests a role in brain patterning

The mouse Barhl1 homeogene, member of the BarH subfamily, play a crucial role in the cerebellum development and its human ortholog BARHL1 has been proposed as a positional and functional candidate gene for the Joubert syndrome, a form of cerebellar ataxia. The Barhl1 expression has been demonstrated to be induced by the transcription factor Math1 involved in BMP responses. We isolated the mouse Barhl1 by screening of a cDNA library with the Xenopus Xvent-2, member of the BarH subfamily, which acts in the BMP4 pathway during embryonic patterning and neural plate differentiation. We studied the detailed Barhl1 expression pattern and showed its transcription in spatio-temporally and functionally restricted domains of the developing central nervous system (CNS). Using our new optical microscopy technology, we compare the transcript steady state level and cell density in the Barhl1-expressing regions. We found that Barhl1 was transcribed in superior and inferior colliculi in the dorsal mesencephalon at a relatively low transcriptional level. In the diencephalon, Barhl1 was found higher expressed first within the basal plate and later in the mammillary region. In the cerebellum, Barhl1 showed the highest transcriptional level restricted to the anterior and posterior rhombic lips giving rise to the external and internal cerebellar granular cells and to the deep nuclei. In the spinal cord, Barhl1 showed similar expression level than in the cerebellum and is delimited to a subset of dorsal interneurons. Therefore, our results indicated that Barhl1 homeodomain gene is exclusively transcribed in restricted CNS domain at differential transcription levels which suggest a highly regulated transcriptional mechanism. In addition, these regional and cellular specificities indicated that Barhl1 may be involved in the differentiation of the specific subsets of neuronal progenitors.

BARHL1 homeogene, the human ortholog of the mouse Barhl1 involved in cerebellum development, shows regional and cellular specificities in restricted domains of developing human central nervous system

The mouse homeobox gene Barhl1 plays a central role in cerebellum development and its expression is activated by the transcription factor Math1 which is involved in bone morphogenetic protein response pathways. We studied the human ortholog BARHL1 and we found that human, mouse, monkey, rat, and zebrafish orthologs were highly conserved and are members of the BarH homeogene family, containing Drosophila BarH1 and BarH2. The N-terminus of BARHL1 protein presents two FIL domains and an acidic domain rich in serine/threonine and proline, while the C-terminus contains a canonical proline-rich domain. Secondary structure analysis showed that outside the three helixes of the homeodomain, BARHL1 protein has essentially random coil structure. We isolated BARHL1 and defined its expression pattern in human embryonic and fetal central nervous system (CNS) and compared it to the mouse Barhl1 transcription. BARHL1 mRNA was found exclusively in the CNS restricted to p1-p4 prosomeres of the diencephalon, to the dorsal cells of the mesencephalon, to the dorsal dl1 sensory neurons of the spinal cord, and to the rhombic lips yielding the cerebellar anlage. Detailed analysis of BARHL1 expression in fetal cerebellar cell layers using our new optic microscopy technology showed BARHL1 expression in external and internal granular cells and also in mouse adult granular cells, in agreement to Barhl1 null mouse phenotype affecting the differentiation and migration of granular cells. These findings indicate that the regional and cellular specificities of BARHL1 transcriptional control well correspond to the mouse Barhl1 transcription and suggest a potential role of this gene in the differentiation of BARHL1-expressing neuronal progenitors involved in the pattern formation of human cerebral and cerebellar structures.