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

Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries

Summary: Recombination of repeat elements is an important source of genomic variation in human tissues. Here, we describe steps to prepare libraries enriched for repeat elements starting from the genomic DNA of any species. We also detail the computational post-processing of the TE-reX pipeline output to generate datasets of putative somatic and polymorphic recombination events.For complete details on the use and execution of this protocol, please refer to Pascarella et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics

SLC25A46 mutations in patients with Parkinson's Disease and optic atrophy

Mutations in the gene encoding the mitochondrial carrier protein SLC25A46 are known to cause optic atrophy associated with peripheral neuropathy and congenital pontocerebellar hypoplasia. We found novel biallelic SLC25A46 mutations (p.H137R, p.A401Sfs*17) in a patient with Parkinson's disease and optic atrophy. Screening of six unrelated patients with parkinsonism and optic atrophy allowed us to identify two additional mutations (p.A176V, p.K256R) in a second patient. All identified variants are predicted likely pathogenic and affect very conserved protein residues. These findings suggest for the first time a possible link between Parkinson's Disease and SLC25A46 mutations. Replication in additional studies is needed to conclusively prove this link

DNAJC12 and dopa-responsive nonprogressive parkinsonism

Biallelic DNAJC12 mutations were described in children with hyperphenylalaninemia, neurodevelopmental delay, and dystonia. We identified DNAJC12 homozygous null variants (c.187A>T;p.K63* and c.79-2A>G;p.V27Wfs*14) in two kindreds with early-onset parkinsonism. Both probands had mild intellectual disability, mild nonprogressive, motor symptoms, sustained benefit from small dose of levodopa, and substantial worsening of symptoms after levodopa discontinuation. Neuropathology (Proband-A) revealed no alpha-synuclein pathology, and substantia nigra depigmentation with moderate cell loss. DNAJC12 transcripts were reduced in both patients. Our results suggest that DNAJC12 mutations (absent in 500 early-onset patients with Parkinson's disease) rarely cause dopa-responsive nonprogressive parkinsonism in adulthood, but broaden the clinical spectrum of DNAJC12 deficiency. Ann Neurol 2017;82:640-646

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<p>Mutations in leucine-rich repeat kinase 2 gene (LRRK2) are associated with familial and sporadic Parkinson’s disease (PD). LRRK2 is a complex protein that consists of multiple domains, including 13 putative armadillo-type repeats at the N-terminus. In this study, we analyzed the functional and molecular consequences of a novel variant, E193K, identified in an Italian family. E193K substitution does not influence LRRK2 kinase activity. Instead it affects LRRK2 biochemical properties, such as phosphorylation at Ser935 and affinity for 14-3-3ε. Primary fibroblasts obtained from an E193K carrier demonstrated increased cellular toxicity and abnormal mitochondrial fission upon 1-methyl-4-phenylpyridinium treatment. We found that E193K alters LRRK2 binding to DRP1, a crucial mediator of mitochondrial fission. Our data support a role for LRRK2 as a scaffolding protein influencing mitochondrial fission.</p

Evolution of thermally pulsing asymptotic giant branch stars - I. The COLIBRI code

We present the COLIBRI code for computing the evolution of stars along the thermally pulsing asymptotic giant branch (TP-AGB) phase. Compared to purely synthetic TP-AGB codes, COLIBRI relaxes a significant part of their analytic formalism in favour of a detailed physics applied to a complete envelope model, in which the stellar structure equations are integrated from the atmosphere down to the bottom of the hydrogen-burning shell. This allows us to predict self-consistently: (i) the effective temperature, and more generally the convective envelope and atmosphere structures, correctly coupled to the changes in the surface chemical abundances and gas opacities; (ii) the conditions under which sphericity effects may significantly affect the atmospheres of giant stars; (iii) the core mass-luminosity relation and its possible breakdown due to the occurrence of hot-bottom burning (HBB) in the most massive AGB stars, by taking properly into account the nuclear energy generation in the H-burning shell and in the deepest layers of the convective envelope; (iv) the HBB nucleosynthesis via the solution of a complete nuclear network (including the pp chains, and the CNO, NeNa and MgAl cycles) coupled to a diffusive description of mixing, suitable to follow also the synthesis of Li-7 via the Cameron-Fowler beryllium transport mechanism; (v) the intershell abundances left by each thermal pulse via the solution of a complete nuclear network applied to a simple model of the pulse-driven convective zone (PDCZ); (vi) the onset and quenching of the third dredge-up, with a temperature criterion that is applied, at each thermal pulse, to the result of envelope integrations at the stage of the post-flash luminosity peak. At the same time, colibri pioneers new techniques in the treatment of the physics of stellar interiors, not yet adopted in full TP-AGB models. It is the first evolutionary code ever to use accurate on-the-fly computation of the equation of state (EoS) for roughly 800 atoms, ions, molecules and of the Rosseland mean opacities throughout the atmosphere and the deep envelope. This ensures a complete consistency, step by step, of both EoS and opacity with the evolution of the chemical abundances caused by the third dredge-up and HBB. Another distinguishing aspect of colibri is its high computational speed, which allows to generate complete grids of TP-AGB models in just a few hours. This feature is absolutely necessary for calibrating the many uncertain parameters and processes that characterize the TP-AGB phase. We illustrate the many unique features of colibri by means of detailed evolutionary tracks computed for several choices of model parameters, including initial star masses, chemical abundances, nuclear reaction rates, efficiency of the third dredge-up, overshooting at the base of the PDCZ, etc. Future papers in this series will deal with the calibration of all these and other parameters using observational data of AGB stars in the Galaxy and in nearby systems, a step that is of paramount importance for producing reliable stellar population synthesis models of galaxies up to high redshift

The LRRK2 variant E193K prevents mitochondrial fission upon MPP+ treatment by altering LRRK2 binding to DRP1

Mutations in leucine-rich repeat kinase 2 gene (LRRK2) are associated with familial and sporadic Parkinson’s disease (PD). LRRK2 is a complex protein that consists of multiple domains, including 13 putative armadillo-type repeats at the N-terminus. In this study, we analyzed the functional and molecular consequences of a novel variant, E193K, identified in an Italian family. E193K substitution does not influence LRRK2 kinase activity. Instead it affects LRRK2 biochemical properties, such as phosphorylation at Ser935 and affinity for 14-3-3ε. Primary fibroblasts obtained from an E193K carrier demonstrated increased cellular toxicity and abnormal mitochondrial fission upon 1-methyl-4-phenylpyridinium treatment. We found that E193K alters LRRK2 binding to DRP1, a crucial mediator of mitochondrial fission. Our data support a role for LRRK2 as a scaffolding protein influencing mitochondrial fission