A novel transcript from a pseudogene for human glucocerebrosidase in non-Gaucher disease cells

GBA, Gaucher Disease, and Parkinson's Disease: From Genetic to Clinic to New Therapeutic Approaches

Parkinson’s disease (PD) is the second most common degenerative disorder. Although the disease was described more than 200 years ago, its pathogenetic mechanisms have not yet been fully described. In recent years, the discovery of the association between mutations of the GBA gene (encoding for the lysosomal enzyme glucocerebrosidase) and PD facilitated a better understating of this disorder. GBA mutations are the most common genetic risk factor of the disease. However, mutations of this gene can be found in different phenotypes, such as Gaucher’s disease (GD), PD, dementia with Lewy bodies (DLB) and rapid eye movements (REM) sleep behavior disorders (RBDs). Understanding the pathogenic role of this mutation and its different manifestations is crucial for geneticists and scientists to guide their research and to select proper cohorts of patients. Moreover, knowing the implications of the GBA mutation in the context of PD and the other associated phenotypes is also important for clinicians to properly counsel their patients and to implement their care. With the present review we aim to describe the genetic, clinical, and therapeutic features related to the mutation of the GBA gene.

Competing Endogenous RNA Regulations in Neurodegenerative Disorders: Current Challenges and Emerging Insights

The past decade has witnessed exciting breakthroughs that have contributed to the richness and complexity of a burgeoning modern RNA world, and one particular breakthrough-the competing endogenous RNA (ceRNA) hypothesis-has been described as the "Rosetta Stone" for decoding the RNA language used in regulating RNA crosstalk and modulating biological functions. The proposed far-reaching mechanism unites diverse RNA species and provides new insights into previously unrecognized RNA-RNA interactions and RNA regulatory networks that perhaps determine gene expression in an organized, hierarchical manner. The recently uncovered ceRNA regulatory loops and networks have emphasized the power of ceRNA regulation in a wide range of developmental stages and pathological contexts, such as in tumorigenesis and neurodegenerative disorders. Although the ceRNA hypothesis drastically enhanced our understanding of RNA biology, shortly after the hypothesis was proposed, disputes arose in relation mainly to minor discrepancies in the reported effects of ceRNA regulation under physiological conditions, and this resulted in ceRNA regulation becoming an extensively studied and fast-growing research field. Here, we focus on the evidence supporting ceRNA regulation in neurodegenerative disorders and address three critical points related to the ceRNA regulatory mechanism: the microRNA (miRNA) and ceRNA hierarchies in cross-regulations; the balance between destabilization and stable binding in ceRNA-miRNA interactions; and the true extent to which ceRNA regulatory mechanisms are involved in both health and disease, and the experimental shortcomings in current ceRNA studies.

The GBAP1 pseudogene acts as a ceRNA for the glucocerebrosidase gene GBA by sponging miR-22-3p

Mutations in the GBA gene, encoding lysosomal glucocerebrosidase, represent the major predisposing factor for Parkinson's disease (PD), and modulation of the glucocerebrosidase activity is an emerging PD therapy. However, little is known about mechanisms regulating GBA expression. We explored the existence of a regulatory network involving GBA, its expressed pseudogene GBAP1, and microRNAs. The high level of sequence identity between GBA and GBAP1 makes the pseudogene a promising competing-endogenous RNA (ceRNA), functioning as a microRNA sponge. After selecting microRNAs potentially targeting both transcripts, we demonstrated that miR-22-3p binds to and down-regulates GBA and GBAP1, and decreases their endogenous mRNA levels up to 70%. Moreover, over-expression of GBAP1 3'-untranslated region was able to sequester miR-22-3p, thus increasing GBA mRNA and glucocerebrosidase levels. The characterization of GBAP1 splicing identified multiple out-of-frame isoforms down-regulated by the nonsense-mediated mRNA decay, suggesting that GBAP1 levels and, accordingly, its ceRNA effect, are significantly modulated by this degradation process. Using skin-derived induced pluripotent stem cells of PD patients with GBA mutations and controls, we observed a significant GBA up-regulation during dopaminergic differentiation, paralleled by down-regulation of miR-22-3p. Our results describe the first microRNA controlling GBA and suggest that the GBAP1 non-coding RNA functions as a GBA ceRNA.

Sequence variability of a human pseudogene

We have obtained haplotypes from the autosomal glucocerebrosidase pseudogene (psGBA) for 100 human chromosomes from worldwide populations, as well as for four chimpanzee and four gorilla chromosomes. In humans, in a 5420-nucleotide stretch analyzed, variation comprises 17 substitutions, a 3-bp deletion, and a length polymorphism at a polyadenine tract. The substitution rate on the pseudogene (1.23 +/- 0.22 x 10(-9) per nucleotide and year) is within the range of previous estimates considering phylogenetic estimations. Recombination within the pseudogene was recognized, although the low variability of this locus prevented an accurate measure of recombination rates. At least 13% of the psGBA sequence could be attributed to gene conversion from the contiguous GBA gene, whereas the reciprocal event has been shown to lead to Gaucher disease. Human psGBA sequences showed a recent coalescence time (approximately 200,000 yr ago), and the most ancestral haplotype was found only in Africans; both observations are compatible with the replacement hypothesis of human origins. In a deeper timeframe, phylogenetic analysis showed that the duplication event that created psGBA could be dated at approximately 27 million years ago, in agreement with previous estimates.

Simple PCR amplification of the entire glucocerebrosidase gene (GBA) coding region for diagnostic sequence analysis

Mutations in the human glucocerebrosidase gene (GBA) may lead to Gaucher disease-an autosomal recessive, lysosomal storage disease. In about 15-25% of Caucasian patients with Gaucher disease yet the disease-causing mutations remain to be identified. There exists 16kb downstream from the functional GBA gene (chromosome 1q21) a highly homologous transcribed pseudogene (GBAP) with some sequence differences to GBA. These sequence differences might erroneously imitate a true mutation in the functional gene if an unintentional co-investigation of the pseudogene occurred. We describe a protocol which allows the selective analysis of a PCR-amplified 7.1 kb genomic GBA-fragment encompassing the entire GBA coding region. Direct, nonradioactive double stranded cycle-sequencing procedure of nested PCR fragments from this long range GBA-specific product allowed the sequencing of the coding exons including the flanking splice sites. Several, so far unknown coding mutation were identified in non-Jewish families with Gaucher disease. This protocol allows the rapid detection of new GBA mutations.

Antisense transcription of a murine FGFR-3 psuedogene during fetal developement

In a search for new protein tyrosine kinases (PTKs) in early hemopoietic cells, we have identified a sequence closely related to the Fibroblast Growth Factor Receptor (FGFR) family. A cDNA isolated from a mouse embryo library was 89% identical to FGFR-3 in both its coding and 3' untranslated regions. However, the region homologous to exons 5 to 9 of FGFR-3 was missing. In addition, the ORF was interrupted by several stop codons and frame shifts, indicating that this sequence is not functional. These transcripts were therefore copied from a novel FGFR-3 pseudogene, that we called psiFGFR-3. Partial analysis of this gene showed the absence of introns, which is a characteristic feature of a processed pseudogene. psiFGFR-3 gene was localized on Chromosome 1H4-6. Its transcription was shown to be antisense and its expression was restricted to fetal tissues. These results indicate that psiFGFR-3 has been inserted in Chromosome 1 in antisense orientation close to a heterologous promoter.

Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases

The regions surrounding the catalytic amino acids previously identified in a few "retaining" O-glycosyl hydrolases (EC 3.2.1) have been analyzed by hydrophobic cluster analysis and have been used to define sequence motifs. These motifs have been found in more than 150 glycosyl hydrolase sequences representing at least eight established protein families that act on a large variety of substrates. This allows the localization and the precise role of the catalytic residues (nucleophile and acid catalyst) to be predicted for each of these enzymes, including several lysosomal glycosidases. An identical arrangement of the catalytic nucleophile was also found for S-glycosyl hydrolases (myrosinases; EC 3.2.3.1) for which the acid catalyst is lacking. A (beta/alpha)8 barrel structure has been reported for two of the eight families of proteins that have been grouped. It is suggested that the six other families also share this fold at their catalytic domain. These enzymes illustrate how evolutionary events led to a wide diversification of substrate specificity with a similar disposition of identical catalytic residues onto the same ancestral (beta/alpha)8 barrel structure.