Project description:This SuperSeries is composed of the SubSeries listed below. The BioProject ID on this superSeries record also encompasses a genome sequencing project under BioProject PRJNA213010.
Project description:Objective: Lysosomal acid lipase (LAL) is the only enzyme known to hydrolyze cholesteryl esters (CE) and triacylglycerols in lysosomes at an acidic pH. Despite the importance of lysosomal hydrolysis in skeletal muscle (SM), research in this area is limited. We hypothesized that LAL may play an important role in SM development, function, and metabolism as a result of lipid and/or carbohydrate metabolism disruptions. Results: Mice with systemic LAL deficiency (Lal-/-) had markedly lower SM mass, cross-sectional area, and Feret diameter despite unchanged proteolysis or protein synthesis markers in all SM examined. In addition, Lal-/- SM showed increased total cholesterol and CE concentrations, especially during fasting and maturation. Regardless of increased glucose uptake, expression of the slow oxidative fiber marker MYH7 was markedly increased in Lal-/-SM, indicating a fiber switch from glycolytic, fast-twitch fibers to oxidative, slow-twitch fibers. Proteomic analysis of the oxidative and glycolytic parts of the SM confirmed the transition between fast- and slow-twitch fibers, consistent with the decreased Lal-/- muscle size due to the “fiber paradox”. Decreased oxidative capacity and ATP concentration were associated with reduced mitochondrial function of Lal-/- SM, particularly affecting oxidative phosphorylation, despite unchanged structure and number of mitochondria. Impairment in muscle function was reflected by increased exhaustion in the treadmill peak effort test in vivo. Conclusion: We conclude that whole-body loss of LAL is associated with a profound remodeling of the muscular phenotype, manifested by fiber type switch and a decline in muscle mass, most likely due to dysfunctional mitochondria and impaired energy metabolism, at least in mice.
Project description:Background: Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of Sm RNPs is critical for understanding their functions. Results: We developed a multi-targeting RNA-immunoprecipitation sequencing (RIP-seq) strategy to reliably identify Sm-associated RNAs from Drosophila ovaries and cultured human cells. Using this method, we discovered three major categories of Sm-associated transcripts: small nuclear (sn)RNAs, small Cajal body (sca)RNAs and mRNAs. Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-independent function for Sm RNPs. Conclusions: This study represents the first comprehensive analysis of eukaryotic Sm-containing RNPs, and provides a basis for additional functional analyses of Sm proteins and their associated snRNPs outside of the context of pre-mRNA splicing. Our findings expand the repertoire of eukaryotic Sm-containing RNPs and suggest new functions for snRNPs in mRNA metabolism.
Project description:This SuperSeries is composed of the SubSeries listed below. The BioProject ID on this superSeries record also encompasses a genome sequencing project under BioProject PRJNA213010. Refer to individual Series
Project description:We have previously reported on two brothers, PM and SM, that carry identical compound heterozygous PRKN mutations but show significantly different clinical Parkinson disease (PD) phenotypes. The occurrence of juvenile cases demonstrates that PD is not necessarily an age-associated disease; indeed, evidence is accumulating that there is a developmental component to PD pathogenesis. The divergence in the clinical presentations between PM and SM lead us to hypothesize that an additional genetic modifier(s) may influence the risk conferred by PRKN. To test our hypothesis, we differentiated human induced pluripotent stem cells (iPSCs) from SM and PM into mitotically active mesencephalic neural precursor cells (floor plate cells) and early postmitotic dopaminergic neurons, and performed whole exome sequencing, and transcriptomic and metabolomics analysis. Our transcriptomic analysis revealed a significant down regulation of three known neurodevelopmentally relevant cell adhesion molecules in PM compared to SM cultures on days 11 and 25 of differentiation, CNTN4, CNTN6, and CHL1. In addition, several HLA genes, known to play a role in neurodevelopment, independent of their well-established function in immunity, were differentially regulated in developing dopamine neurons. EN2, a transcription factor crucial for mesencephalic dopamine neuron development, was also differentially regulated. We further report on a single nucleotide polymorphism in DBH, a gene encoding an enzyme involved in dopamine metabolism, as well as differential expression. Our metabolomics data reveal differential biosynthesis of tyrosine, the precursor for dopamine synthesis. Lastly, our whole exome sequencing revealed the homozygous deletion in SM of two glutathione S-transferases, GSTM1 and GSTT1, which encode enzymes involved in glutathione (GSH) metabolism. Moreover, our RNA sequencing analysis shows a lack of expression of these two enzymes in SM cells and our metabolomics analysis indicates differences in GSH homeostasis between SM and PM neurons. This finding builds on previous evidence of glutathione dysregulation being implicated in PD pathogenesis. Our data support our hypothesis that additional genetic differences at least partially underlie the differential clinical PD presentation between PM and SM.