Isolation of two novel genes, DSCR5 and DSCR6, from Down syndrome critical region on human chromosome 21q22.2

Integrating copy number data of 64 iAMP21 BCP-ALL patients narrows the common region of amplification to 1.57 Mb

Background and purpose

Intrachromosomal amplification of chromosome 21 (iAMP21) is a rare subtype of B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). It is unknown how iAMP21 contributes to leukaemia. The currently known commonly amplified region is 5.1 Mb.

Methods

We aimed to narrow down the common region of amplification by using high resolution techniques. Array comparative genomic hybridization (aCGH) was used to determine copy number aberrations, Affymetrix U133 Plus2 expression arrays were used to determine gene expression. Genome-wide expression correlations were evaluated using Globaltest.

Results

We narrowed down the common region of amplification by combining copy number data from 12 iAMP21 cases with 52 cases from literature. The combined common region of amplification was 1.57 Mb, located from 36.07 to 37.64 Mb (GRCh38). This region is located telomeric from, but not including, RUNX1, which is the locus commonly used to diagnose iAMP21. This narrow region, which falls inside the Down Syndrome critical region, includes 13 genes of which the expression of eight genes was significantly upregulated compared with 143 non-iAMP21 B-other cases. Among these, transcriptional repressor RIPPLY3 (also known as DSCR6) was the highest overexpressed gene (fold change = 4.2, FDR < 0.001) and most strongly correlated (R = 0.58) with iAMP21-related genome-wide expression changes.

Discussion

The more precise definition of the common region of amplification could be beneficial in the diagnosis of iAMP21 based on copy number analysis from DNA sequencing or arrays as well as stimulate functional research into the role of the included genes in iAMP21 biology.

HDAC1-mediated repression of the retinoic acid-responsive gene ripply3 promotes second heart field development

Coordinated transcriptional and epigenetic mechanisms that direct development of the later differentiating second heart field (SHF) progenitors remain largely unknown. Here, we show that a novel zebrafish histone deacetylase 1 (hdac1) mutant allele cardiac really gone (crg) has a deficit of ventricular cardiomyocytes (VCs) and smooth muscle within the outflow tract (OFT) due to both cell and non-cell autonomous loss in SHF progenitor proliferation. Cyp26-deficient embryos, which have increased retinoic acid (RA) levels, have similar defects in SHF-derived OFT development. We found that nkx2.5⁺ progenitors from Hdac1 and Cyp26-deficient embryos have ectopic expression of ripply3, a transcriptional co-repressor of T-box transcription factors that is normally restricted to the posterior pharyngeal endoderm. Furthermore, the ripply3 expression domain is expanded anteriorly into the posterior nkx2.5⁺ progenitor domain in crg mutants. Importantly, excess ripply3 is sufficient to repress VC development, while genetic depletion of Ripply3 and Tbx1 in crg mutants can partially restore VC number. We find that the epigenetic signature at RA response elements (RAREs) that can associate with Hdac1 and RA receptors (RARs) becomes indicative of transcriptional activation in crg mutants. Our study highlights that transcriptional repression via the epigenetic regulator Hdac1 facilitates OFT development through directly preventing expression of the RA-responsive gene ripply3 within SHF progenitors.

Congenital heart defects are the most common malformations found in newborns, with many of these defects disrupting development of the outflow tract, the structure where blood is expelled from the heart. Despite their frequency, we do not have a grasp of the molecular and genetic mechanisms that underlie most congenital heart defects. Here, we show that zebrafish embryos containing a mutation in a gene called histone deacetylase 1 (hdac1) have smaller hearts with a reduction in the size of the ventricle and outflow tract. Hdac1 proteins limit accessibility to DNA and repress gene expression. We find that loss of Hdac1 in zebrafish embryos leads to increased expression of genes that are also induced by excess retinoic acid, a teratogen that induces similar outflow tract defects. Genetic loss-of-function studies support that ectopic expression of ripply3, a common target of both Hdac1 and retinoic acid signaling that is normally restricted to a subset of posterior pharyngeal cells, contributes to the smaller hearts found in zebrafish hdac1 mutants. Our study establishes a mechanism whereby the coordinated repression of genes downstream of Hdac1 and retinoic acid signaling is necessary for normal vertebrate outflow tract development.

RIPPLY3 is a retinoic acid-inducible repressor required for setting the borders of the pre-placodal ectoderm

Retinoic acid signaling is a major component of the neural posteriorizing process in vertebrate development. Here, we identify a new role for the retinoic acid receptor (RAR) in the anterior of the embryo, where RAR regulates Fgf8 expression and formation of the pre-placodal ectoderm (PPE). RARα2 signaling induces key pre-placodal genes and establishes the posterolateral borders of the PPE. RAR signaling upregulates two important genes, Tbx1 and Ripply3, during early PPE development. In the absence of RIPPLY3, TBX1 is required for the expression of Fgf8 and hence, PPE formation. In the presence of RIPPLY3, TBX1 acts as a transcriptional repressor, and functions to restrict the positional expression of Fgf8, a key regulator of PPE gene expression. These results establish a novel role for RAR as a regulator of spatial patterning of the PPE through Tbx1 and RIPPLY3. Moreover, we demonstrate that Ripply3, acting downstream of RAR signaling, is a key player in establishing boundaries in the PPE.

Ripply3, a Tbx1 repressor, is required for development of the pharyngeal apparatus and its derivatives in mice

The pharyngeal apparatus is a transient structure that gives rise to the thymus and the parathyroid glands and also contributes to the development of arteries and the cardiac outflow tract. A typical developmental disorder of the pharyngeal apparatus is the 22q11 deletion syndrome (22q11DS), for which Tbx1 is responsible. Here, we show that Ripply3 can modulate Tbx1 activity and plays a role in the development of the pharyngeal apparatus. Ripply3 expression is observed in the pharyngeal ectoderm and endoderm and overlaps with strong expression of Tbx1 in the caudal pharyngeal endoderm. Ripply3 suppresses transcriptional activation by Tbx1 in luciferase assays in vitro. Ripply3-deficient mice exhibit abnormal development of pharyngeal derivatives, including ectopic formation of the thymus and the parathyroid gland, as well as cardiovascular malformation. Corresponding with these defects, Ripply3-deficient embryos show hypotrophy of the caudal pharyngeal apparatus. Ripply3 represses Tbx1-induced expression of Pax9 in luciferase assays in vitro, and Ripply3-deficient embryos exhibit upregulated Pax9 expression. Together, our results show that Ripply3 plays a role in pharyngeal development, probably by regulating Tbx1 activity.

Down syndrome critical region protein 5 regulates membrane localization of Wnt receptors, Dishevelled stability and convergent extension in vertebrate embryos

The Glypican family of heparan sulfate proteoglycans regulates Wnt signaling and convergent extension (CE) in vertebrate embryos. They are predicted to be glycosylphosphatidylinositol (GPI)-tethered membrane-bound proteins, but there is no functional evidence of their regulation by the GPI synthesis complex. Down syndrome critical region protein 5 (Dscr5, also known as Pigp) is a component of the GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex, and is associated with specific features of Down syndrome. Here we report that Dscr5 regulates CE movements through the non-canonical Wnt pathway. Both dscr5 overexpression and knockdown impaired convergence and extension movements. Dscr5 functionally interacted with Knypek/Glypican 4 and was required for its localization at the cell surface. Knockdown of dscr5 disrupted Knypek membrane localization and caused an enhanced Frizzled 7 receptor endocytosis in a Caveolin-dependent manner. Furthermore, dscr5 knockdown promoted specific Dishevelled degradation by the ubiquitin-proteosome pathway. These results reveal a functional link between Knypek/Glypican 4 and the GPI synthesis complex in the non-canonical Wnt pathway, and provide the new mechanistic insight that Dscr5 regulates CE in vertebrate embryos by anchoring different Wnt receptors at the cell surface and maintaining Dishevelled stability.

Prenatal diagnosis of trisomy 21 without the Down syndrome phenotype

OBJECTIVE

To report a patient with the prenatal diagnosis of trisomy 21 without the clinical Down syndrome (DS) phenotype secondary to the absence of the Down syndrome chromosomal region (DSCR) in a derivative chromosome 21.

CASE REPORT AND METHODS

A newborn patient with prenatal diagnosis of duodenal atresia. Cytogenetic studies revealed a regular trisomy 21. At birth, she did not present the clinical features of DS. FISH analysis was performed in the patient with the LSI spectrum probe for the DSCR and in the mother with FISH multicolor analysis using painting probes for chromosomes 20 and 21.

RESULTS

FISH analysis in the patient showed two hybridization signals suggesting that the third chromosome 21 did not have the DSCR region explaining the absence of the DS phenotype. FISH multicolor analysis in the mother showed three hybridization signals for chromosomes 20 and 21, concluding a maternal karyotype, 46,XX,t(20;21)(p11.2;q22.1).

CONCLUSIONS

The patient was found to have a derivative chromosome 21 secondary to a nondisjunction error in meiosis II without the DS critical region and the phenotype was mostly secondary to the combination of the two partial trisomies.

Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution

Sequence comparison of humans and chimpanzees is of interest to understand the mechanisms behind primate evolution. Here we present an independent analysis of human chromosome 21 and the high-quality BAC clone sequences of the homologous chimpanzee chromosome 22. In contrast to previous studies, we have used global alignment methods and Ensembl predictions of protein coding genes (n = 224) for the analysis. Divergence due to insertions and deletions (indels) along with substitutions was examined separately for different genomic features (coding, noncoding genic, and intergenic sequence). The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%. When excluding repeats and low-complexity DNA the total divergence decreased to 2.37%. The chromosomal distribution of nucleotide substitutions and indel events was significantly correlated. To further examine the role of indels in primate evolution we focused on coding sequences. Indels were found within the coding sequence of 13% of the genes and approximately half of the indels have not been reported previously. In 5% of the chimpanzee genes, indels or substitutions caused premature stop codons that rendered the affected transcripts nonfunctional. Taken together, our findings demonstrate that indels comprise the majority of the genomic divergence. Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.

Ledgerline, a Novel Xenopus laevis Gene, Regulates Differentiation of Presomitic Mesoderm During Somitogenesis

Segmentation of the vertebrate body via the sequential formation of somites is an important process in embryogenesis. This sequential process is governed by the activation and regulation of Notch-related molecular oscillators by fibroblast growth factor and retinoic acid (RA) signaling. In this study, we identified ledgerline, a novel gene of Xenopus laevis expressed specifically in the presomitic mesoderm. Knockdown of ledgerline using antisense morpholino oligonucleotides shifted the developing somite front and altered the expression of genes that regulate molecular oscillation, including Delta2, ESR5, Hairy2a, and Thylacine1. Knockdown of ledgerline also downregulated RALDH-2 expression. Injection of RARalpha-CA, a constitutively active mutant of the RA receptor RARalpha, subsequently reduced the altered Thylacine1 expression. These results strongly suggest that ledgerline is essential for mesodermal RA activity and differentiation of the presomitic mesoderm during Xenopus somitogenesis.

Production of inbred and hybrid transgenic mice carrying large (> 200 kb) foreign DNA fragments by intracytoplasmic sperm injection

We have developed a mouse transgenesis technique that facilitates the insertion of large (approximately 200 kilo base pairs) DNA fragments into host genomes of both inbred and hybrid mice. Six inbred and three hybrid transgenic mice carrying a single bacterial artificial chromosome (BAC) clone with genes located in the Down syndrome critical region of human chromosome 21 were produced using this technology.

Protein Dysregulation in Mouse Hippocampus Polytransgenic for Chromosome 21 Structures in the Down Syndrome Critical Region

Mice polytransgenic for chromosome 21 genes DSCR3, 5, 6, 9, and TTC3 within the Down Syndrome Critical Region-1 represent an animal model for Down Syndrome (DS). In a proteomic approach, we show a series of altered hippocampal protein levels that may be caused by overexpression of at least one of the five chromosome 21 genes and that fit fear-conditioned memory defects and were observed to be dysregulated in human fetal DS.

Groucho-Associated Transcriptional Repressor Ripply1 Is Required for Proper Transition from the Presomitic Mesoderm to Somites

Concomitant with the transition from the presomitic mesoderm (PSM) to somites, the periodical gene expression characteristic of the PSM is drastically changed and translated into the segmental structure. However, the molecular mechanism underlying this transition has remained obscure. Here, we show that ripply1, encoding a nuclear protein associated with the transcriptional corepressor Groucho, is required for this transition. Zebrafish ripply1 is expressed in the anterior PSM and in several newly formed somites. Ripply1 represses mesp-b expression in the PSM through a Groucho-interacting motif. In ripply1-deficient embryos, somite boundaries do not form, the characteristic gene expression in the PSM is not properly terminated, and the initially established rostrocaudal polarity in the segmental unit is not maintained, whereas paraxial mesoderm cells become differentiated. Thus, ripply1 plays dual roles in the transition from the PSM to somites: termination of the segmentation program in the PSM and maintenance of the rostrocaudal polarity.

Identification of a novel zinc finger protein gene (ZNF298) in the GAP2 of human chromosome 21q

We have isolated a novel zinc finger protein gene, designated ZNF298, as a candidate gene for a particular phenotype of Down syndrome or bipolar affective disorder (BPAD) which maps to human chromosome 21q22.3. ZNF298 gene consists of 25 exons spanning approximately 80kb in a direction from the telomere to centromere. There are four kinds of transcripts that harbor three types of 3' UTR. These four transcripts (ZNF298a, ZNF298b, ZNF298c, and ZNF298d) contain putative open reading frames encoding 1178, 1198, 555, and 515 amino acids, respectively. ZNF298 gene was ubiquitously expressed in various tissues at very low level. The protein motif analysis revealed that ZNF298 proteins contain a SET [Su(var)3-9, Enhancer-of-zeste, Trithorax] domain, multiple C2H2-type zinc finger (ZnF_C2H2) domains, several nuclear localization signals (NLSs), and PEST sequences. Nuclear localization of ZNF298 protein was confirmed by transfection of expression vector of GFP-tagged protein into two human cell lines. Interestingly, this gene crosses over a clone gap (GAP2) remaining in the band 21q22.3. We obtained the DNA fragments corresponding to GAP2 using ZNF298 cDNA sequence as anchor primers for PCR and determined its genomic DNA sequence.

Molecular and cellular characterization of the Down syndrome critical region protein 2

Down syndrome (DS) is caused by trisomy for human chromosome 21 and is the most common genetic cause of mental retardation. The distal 10 Mb region of the long arm of the chromosome has been proposed to be associated with many of the abnormalities seen in DS. This region is often referred to as the Down syndrome critical region (DSCR). We report here the results of our analyses of the DSCR protein 2 (DSCR2). Results from transiently transfected COS-1 and HEK293 cells suggest that DSCR2 is synthesized as a 43 kDa precursor protein, from which the N-terminus is cleaved resulting in a polypeptide of 41 kDa. The polypeptide is modified by still uncharacterized co- or post-translational modifications increasing the predicted molecular weight of 32.8 kDa by about 10 kDa. Analyses of the only putative N-glycosylation site by in vitro mutagenesis excluded the possibility of the contribution of N-glycosylation to this increase in molecular weight. Further, the results of intracellular localization studies and membrane fractionation assays indicate that DSCR2 is targeted to a cytoplasmic compartment as a soluble form.

Down syndrome with pure partial trisomy 21q22 due to a paternal insertion (4;21) uncovered by uncultured amniotic fluid interphase FISH

OBJECTIVE

To emphasize the usefulness and reliability of fluorescence in situ hybridization (FISH) on uncultured amniotic fluid cells in the prenatal diagnosis of common chromosomal aneuploidies.

METHODS

FISH analyses utilizing centromeric, locus-specific or whole chromosome paint DNA probes specific for chromosomes X, Y, 13, 18, 21, and 4 were performed on uncultured amniotic fluid cells or the peripheral blood specimen from the father. Routine chromosome analysis was carried out as well.

RESULTS

A prenatal case with partial trisomy 21 due to a paternal cryptic insertion (4;21) was ascertained by a rapid overnight FISH on uncultured amniotic fluid cells. The fetus was delivered at term and had classical features of Down syndrome.

CONCLUSION

Our results stress the importance of FISH on uncultured amniotic fluid cells to supplement routine cytogenetics, especially in cases with abnormal ultrasound findings.

Initial characterization of an uromodulin-like 1 gene on human chromosome 21q22.3

We have isolated a novel gene, designated UMODL1, similar to uromodulin (UMOD)/Tamm-Horsfall glycoprotein, on human chromosome 21q22.3. Uromodulin like-1 (UMODL1) consists of 22 exons and spans approximately 80 kb in a direction from centromere to telomere. Two major transcripts produced by alternative splicing have been identified. These transcripts contain open reading frames of 4125 and 3741 bp encoding proteins of 1374 and 1246 amino acids, respectively. Expression of UMODL1 mRNA was detected only in 14 human tissues, e.g., kidney, testis, and fetal thymus at low level. Interestingly, two gene products (UMODL1L and UMODL1S) contain multiple domains including whey acidic protein, sea urchin sperm protein, enterokinase, and agrin, zona pellucida domain, and so on. Both proteins seemed to localize in cytoplasm, but UMODL1 is likely to be ubiquitinated and rapidly degraded in HEK293 cells. This gene may be a potent candidate for Down syndrome or bipolar affective disorder.

A cluster of 21 keratin-associated protein genes within introns of another gene on human chromosome 21q22.3

Recently, we identified multiple unique sequences in the 21q22.3 region and predicted them to be a cluster of genes encoding hair-specific keratin-associated proteins (KAPs). Detailed computer-aided analysis of these clustered genes revealed that the cluster spans over 165 kb and consists of 21 KAP-related sequences including 16 putative genes and 5 pseudogenes. These were further divided into two subfamilies, KRTAP12 (KRTAP12.1-12.4 and KRTAP12.5P) and KRTAP18 (KRTAP18.1-18.12 and KRTAP18.13P-18.16P). All 16 putative genes possess several intragenic repeat sequences and apparently belong to the high-sulfur KAP gene family (16-30% cysteine content) known for nonhuman mammalian species. Transcripts were detected by RT-PCR analysis for all 16 putative KAP genes and their expression was restricted to hair root cells (radix pili cells) and not found in 28 other tissues, including skin. All 16 KAP genes produced unspliced transcripts, indicating their nature to be that of active intronless genes. Interestingly, all these KAP-related genes are located within introns of the recently identified gene TSPEAR (approved gene symbol C21orf29), 214 kb in size. Surprisingly, the transcriptional direction of 8 of the 16 active genes is the same as that of C21orf29/TSPEAR. This finding suggests a novel transcription mechanism in which C21orf29/TSPEAR gene transcription passes over the multiple transcriptional termination sites of the KAP genes.

Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins

GPI lipid anchoring is an important post-translational modification of eukaryote proteins in the endoplasmic reticulum. In total, 19 genes have been directly implicated in the anchor synthesis and the substrate protein modification pathway. Here, the molecular functions of the respective proteins and their evolution are analyzed in the context of reported literature data and sequence analysis studies for the complete pathway (http://mendel.imp.univie.ac.at/SEQUENCES/gpi-biosynthesis/) and questions for future experimental investigation are discussed. Studies of two of these proteins have provided new mechanistic insights. The cytosolic part of PIG-A/GPI3 has a two-domain alpha/beta/alpha-layered structure; it is suggested that its C-terminal subsegment binds UDP-GlcNAc whereas the N-terminal domain interacts with the phosphatidylinositol moiety. The lumenal part of PIG-T/GPI16 apparently consists of a beta-propeller with a central hole that regulates the access of substrate protein C termini to the active site of the cysteine protease PIG-K/GPI8 (gating mechanism) as well as of a polypeptide hook that embraces PIG-K/GPI8. This structural proposal would explain the paradoxical properties of the GPI lipid anchor signal motif and of PIG-K/GPI8 orthologs without membrane insertion regions in some species.

Familial MCA/MR syndrome due to inherited submicroscopic translocation t(18;21)(q22.1q21.3) with breakpoint at the Down syndrome critical region

We report three generation family that includes two patients with severe mental retardation and additional anomalies who have been studied, clinically, cytogenetically, and molecular cytogenetically. A clinical diagnosis could not be made in the propositus, but facial anomalies of Down syndrome (DS) were recognized in the maternal uncle of the propositus. In view of a strong family history of recurrent miscarriage, a familial translocation was highly suggestive. Standard cytogenetic analysis did not reveal any abnormalities. Fluorescence in situ hybridization (FISH) using subtelomeric DNA probes identified a familial cryptic translocation of chromosomes 18 and 21, resulting in partial trisomy 21 and partial monosomy 18q in both patients. FISH analysis of obligate carriers demonstrated a balanced translocation between the terminal parts of 18q and 21q. Including this family, a total of six different familial cases with cryptic or subtle subtelomeric translocations of chromosome 21q has been reported, of which three involved terminal parts of chromosome 18q. The remarkable similarity of the chromosomal breakpoints of our patients and the described families prompted us to refine the breakpoints and to discuss phenotypic differences between these patients. Our results reinforce the role of cryptic subtelomeric rearrangements in patients with mental retardation associated with physical anomalies and stress the importance of FISH technology to supplement routine cytogenetics.

Comparative genomic sequence analysis of the human chromosome 21 Down syndrome critical region

Comprehensive knowledge of the gene content of human chromosome 21 (HSA21) is essential for understanding the etiology of Down syndrome (DS). Here we report the largest comparison of finished mouse and human sequence to date for a 1.35-Mb region of mouse chromosome 16 (MMU16) that corresponds to human chromosome 21q22.2. This includes a portion of the commonly described "DS critical region," thought to contain a gene or genes whose dosage imbalance contributes to a number of phenotypes associated with DS. We used comparative sequence analysis to construct a DNA feature map of this region that includes all known genes, plus 144 conserved sequences > or =100 bp long that show > or =80% identity between mouse and human but do not match known exons. Twenty of these have matches to expressed sequence tag and cDNA databases, indicating that they may be transcribed sequences from chromosome 21. Eight putative CpG islands are found at conserved positions. Models for two human genes, DSCR4 and DSCR8, are not supported by conserved sequence, and close examination indicates that low-level transcripts from these loci are unlikely to encode proteins. Gene prediction programs give different results when used to analyze the well-conserved regions between mouse and human sequences. Our findings have implications for evolution and for modeling the genetic basis of DS in mice.

Molecular neuropathology of transgenic mouse models of Down syndrome

Down syndrome (DS) is a complex, clinically heterogeneous disorder which shows both impairment of neurodevelopement and the neurodegenerative changes of Alzheimer's disease (AD). The phenotype of DS is caused by triplication of chromosome 21 and transgenic mouse models have been developed, and are being created, that carry single genes and chromosomal segments to excess. For example, transgenic mice containing additional copies of the amyloid precursor protein (APP) gene, have been useful in producing the Abeta deposition characteristic of AD and DS, but not the cytoskeletal changes that are the hallmarks of these human disorders. Such models are useful in replicating aspects of pathogenesis and allow for the testing of therapeutic agents to restore impaired function. Segmental trisomic mouse models, which survive to adulthood and possess three copies of multiple genes responsible for the DS phenotype, such as Ts1Cje and Ts65Dn, have been used to explore aspects of neurodevelopment and neurodegeneration. These animal models show some but not all the pathological, biochemical, and transcriptional changes seen in DS. They also have the advantage of allowing for the testing of therapeutic agents to restore impaired function. Analysis of the transcriptome and proteome of fetal and adult DS indicates that there is a complex relationship between gene dosage, gene and protein expression, and that data from animal models will need to be compared and evaluated in the light of data obtained from DS tissue.