Identifying convergent pathomechanisms in ALS using hiPSC-derived motor neurons
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 480, Q Exactive HF
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Motor Neuron, Cell Culture
DISEASE(S): Amyotrophic Lateral Sclerosis
SUBMITTER: 
Mirita Franz-Wachtel
LAB HEAD: Alberto Catanese
PROVIDER: PXD041543 | Pride | 2023-07-28
REPOSITORIES: Pride
Similar Datasets
Project description:Analysis of changes in the phosphoproteome upon transient siRNA-mediated knockdown of ABL1/ABL2 or DDR1 for 48 hours. CILAC phosphoproteome analysis was conducted after 48hrs using human U-2 OS cells.
2023-10-24 | PXD023146 | Pride
Project description:The sudden global emergence of SARS-CoV-2 urgently requires an in-depth understanding of 39 molecular functions of viral proteins and their interactions with the host proteome. Several omics studies have extended our knowledge of COVID-19 pathophysiology, including some focused on proteomic aspects1–3. To understand how SARS-CoV-2 and related coronaviruses manipulate the host we here characterized interactome, proteome and signaling processes in a systems-wide manner. This identified connections between the corresponding cellular events, revealed functional effects of the individual viral proteins and put these findings into the context of host signaling pathways. We investigated the closely related SARS-CoV-2 and SARS-CoV viruses as well as the influence of SARS-CoV-2 on transcriptome, proteome, ubiquitinome and phosphoproteome of a lung-derived human cell line. Projecting these data onto the global network of cellular interactions revealed 48 relationships between the perturbations taking place upon SARS-CoV-2 infection at different layers and identified unique and common molecular mechanisms of SARS coronaviruses. The results highlight the functionality of individual proteins as well as vulnerability hotspots of SARS-CoV-2, which we targeted with clinically approved drugs. We exemplify this by identification of kinase inhibitors as well as MMPase inhibitors with significant antiviral effects against SARS-CoV-2
2021-02-15 | PXD020461 | Pride
Project description:Streptomyces rimosus is an industrial streptomycete, best known as a producer of oxytetracycline, one of the most widely used antibiotics. Despite the significant contribution of Streptomyces species to the pharmaceutical industry, most omics analyses have only been conducted on the model organism, Streptomyces coelicolor. In recent years, protein phosphorylation on serine, threonine and tyrosine (Ser/Thr/Tyr) has been shown to play a crucial role in the regulation of numerous cellular processes, including metabolic changes leading to antibiotic production and morphological changes. In this study, we performed a comprehensive quantitative (phospho)proteomic analysis during the growth of S. rimosus under conditions of oxytetracycline production and pellet fragmentation. LC-MS/MS analysis combined with phosphopeptide enrichment detected a total of 3,725 proteins, corresponding to 45.6% of the proteome and 417 phosphorylation sites from 230 phosphoproteins. Significant changes in abundance during three distinct growth phases were determined for 494 proteins and 98 phosphorylation sites. Functional analysis revealed changes in phosphorylation events of proteins involved in important cellular processes, including regulatory mechanisms, primary and secondary metabolism, cell division and stress response. About 80% of the phosphoproteins detected during submerged growth of S. rimosus have not yet been reported in streptomycetes, and 55 phosphoproteins were not reported in any prokaryote studied so far. This enabled the creation of a unique resource that provides novel insights into the dynamics of (phospho)proteins and reveals many potential regulatory events during antibiotic production in liquid culture of an industrially-important bacterium.
2022-08-22 | PXD034565 | Pride
Project description:Bacterial type III secretion systems are cell envelope-spanning effector protein-delivery machines essential for colonization and survival of many Gram-negative pathogens and symbionts. The membrane-embedded core unit of these secretion systems is termed needle complex. The needle complex is composed of a base that anchors the machinery to the inner and outer membranes, a hollow filament formed by inner rod and needle subunits that serves as conduit for substrate proteins, and a membrane-embedded export apparatus facilitating substrate translocation. While the stoichiometry of the base and of the major export apparatus protein have been revealed by structural analyses, the stoichiometries of the other export apparatus components and of the inner rod remain unknown. We employed peptide concatenated standard and absolute quantification-based strategies to analyze the stoichiometry of the entire needle complex by mass spectrometry. Here we provide evidence that the export apparatus of the type III secretion system encoded on Salmonella pathogenicity island 1 contains 5 SpaP, 1 SpaQ, 1 SpaR, and 1 SpaS. We have corroborated the previously suggested stoichiometry of 9 InvA per needle complex and describe a loose association of InvA with other needle complex components that may reflect its function. These numbers indicate that the inner membrane patch of the needle complex base houses 104 transmembrane domains in total, a dense assembly whose function in the secretion process we merely understand. Furthermore, we present evidence that not more than 6 PrgJ form the inner rod of the needle complex.
2016-02-25 | PXD003113 | Pride
Project description:Amyotrophic Lateral Sclerosis (ALS) is a rare neurodegenerative disease characterized by motor neuron dysfunction and loss, leading to progressive paralysis and death. A portion of ALS cases is caused by mutation of the proteasome shuttle factor Ubiquilin 2 (UBQLN2), but the molecular pathway leading from UBQLN2 dysfunction to neurodegenerative disease remains unclear. Here, we demonstrate a major function of UBQLN2 in regulating activity of the domesticated gag-pol retrotransposon ‘paternally expressed gene 10’ (PEG10) in human cells and tissues. UBQLN2 exclusively facilitates degradation of the frameshifted gag-pol form of PEG10 through recognition of a unique polyproline repeat. In cells, the PEG10 gag-pol protein cleaves itself in a mechanism reminiscent of retrotransposon self-processing to generate a liberated ‘nucleocapsid’ fragment, which uniquely localizes to the nucleus. Overexpression of the nucleocapsid fragment upregulates transcription of neuronal genes involved in axon remodeling, which were also affected in sporadic ALS (sALS) patient tissues. Finally, proteomics of spinal cords from ALS patients revealed that PEG10 gag-pol is significantly elevated in disease compared to healthy controls. These findings implicate the retrotransposon-like activity of PEG10 as a contributing mechanism in ALS through regulation of neuronal gene expression, and restraint of PEG10 as a primary function of UBQLN2.
2023-03-24 | PXD031964 | Pride
Project description:In the United States, high grade serous ovarian cancer (HGSOC) is the most lethal gynecologic malignancy and tumor response to platinum-based chemotherapy is a major determinant of clinical outcome. Although recent efforts have dramatically improved the median survival of advanced ovarian cancer, the initial treatment of the disease has remained the same. The initial therapy includes surgery and chemotherapy and the response rate is very high (85%). Unfortunately, 15% of patients do not respond to this therapy and have platinum-refractory disease. These patients have a very short survival and there is an urgent need to identify novel pharmaceutically targetable pathways to treat these patients. We generated extensive proteomic (global, phospho, ubiquitin, acetylation, pTyr) and RNASeq-based dynamic molecular profiles (+/-carboplatin at 8 and 24 hours) from HGSOC intra-patient cell line pairs (PEA1/PEA2, PEO1/PEO4, PEO14/PEO23) derived from 3 patients before and after acquiring platinum resistance. The molecular profiles revealed a multi-faceted response to carboplatin (e.g., induction of a DNA damage response, ubiquitination of ribosomal proteins, and metabolic changes), as well as novel carboplatin-induced post-translational modifications. Higher oxidative phosphorylation (OXPHOS) and fatty acid beta-oxidation (FAO) pathway expression was observed in resistant compared with sensitive cells. These expression findings were validated via metabolite profiling of cell lines and proteomic profiling of platinum sensitive and refractory HGSOC patient derived xenograft (PDX) models. Both pharmacologic inhibition and CRISPR knockout of CPT1A, which represents the rate limiting step of FAO, sensitizes HGSOC cells to platinum. The metabolic signature identified in the cell line and PDX models is correlated with survival in a previously reported proteomic analysis of HGSOC, and thus FAO is a candidate druggable pathway to overcome platinum resistance.
2021-12-22 | PXD020764 | Pride
Project description:We report the identification of a heat-stress mediated mRNA decay in arabidopsis that is mediated by the XRN4 exonuclease and LARP1 RNA-binding protein. mRNA population in WT and larp1 mutant at 20C or 15 min at 38C
2014-03-28 | E-GEOD-51879 | biostudies-arrayexpress
Project description:Protein Ser/Thr kinases are post-translational regulators of key molecular processes in bacteria, such as cell division and antibiotic tolerance. Here we characterize the E. coli toxin YjjJ (HipH), a putative protein kinase annotated as a member of the family of HipA-like Ser/Thr kinases which are involved in antibiotic tolerance. Using SILAC-based phosphoproteomics we provide experimental evidence that YjjJ is a Ser/Thr protein kinase and its primary protein substrates are the ribosomal protein RpmE (L31) and the carbon storage regulator CsrA. YjjJ activity impacts ribosome assembly, cell division and central carbon metabolism but it does not increase antibiotic tolerance as does its homologue HipA. Intriguingly, overproduction of YjjJ and its kinase-deficient variant can activate HipA and other kinases, pointing to a crosstalk between Ser/Thr kinases in E. coli.
2022-11-28 | PXD033071 | Pride
Project description:Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative condition characterized by loss of motor neurons in the brain and spinal cord. Expansions of a hexanucleotide repeat (GGGGCC) in the noncoding region of the C9ORF72 gene are the most common cause of the familial form of ALS (C9-ALS), as well as frontotemporal lobar degeneration and other neurological diseases. How the repeat expansion causes disease remains unclear, with both loss of function (haploinsufficiency) and gain of function (either toxic RNA or protein products) proposed. We report a cellular model of C9-ALS with motor neurons differentiated from induced pluripotent stem cells (iPSCs) derived from ALS patients carrying the C9ORF72 repeat expansion. No significant loss of C9ORF72 expression was observed, and knockdown of the transcript was not toxic to cultured human motor neurons. Transcription of the repeat was increased, leading to accumulation of GGGGCC repeat–containing RNA foci selectively in C9-ALS iPSC-derived motor neurons. Repeat-containing RNA foci colocalized with hnRNPA1 and Pur-?, suggesting that they may be able to alter RNA metabolism. C9-ALS motor neurons showed altered expression of genes involved in membrane excitability including DPP6, and demonstrated a diminished capacity to fire continuous spikes upon depolarization compared to control motor neurons. Antisense oligonucleotides targeting the C9ORF72 transcript suppressed RNA foci formation and reversed gene expression alterations in C9-ALS motor neurons. These data show that patient-derived motor neurons can be used to delineate pathogenic events in ALS. Transcriptome profiling from iPSC derived motor neurons compared to controls
2013-11-07 | E-GEOD-52202 | biostudies-arrayexpress
Project description:Depending on their environment and their exposure to various factors, dendritic cells (DCs) exist in different activation and maturation states. The versatility of DCs allows them to shape the immune system towards an inflammatory or tolerant state depending on the antigens and the environment they encounter. In this study we aimed to provide a proteomic catalogue of differentially expressed and differentially phosphorylated proteins between distinct DC maturation states, brought about by bacteria that differ in their endotoxicity. To achieve this, we have performed unlabeled shotgun proteomics and phosphoproteomics on cell fractions obtained from murine bone marrow DC cultures. The symbiont B. vulgatus stimulation was used to obtain semi-mature DCs, and the pathobiont E. coli stimulation was used to obtain mature DCs. For both shotgun proteome and phosphoproteome analysis two biological replicates consisting of 8 mice were used. Each biological replicate were run as 3 technical replicates.
2017-11-27 | PXD003738 | Pride