Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A cooperative organelle biogenesis program in mammalian cells

ABSTRACT: The compartmentalisation of distinct organelles within eukaryotic cells is essential for their diverse functions, however, how their structures and functions depend on each other has not been systematically explored. We combined a fluorescent reporter of mitochondrial stress with genome-wide CRISPR knockout screening and identified networks of genes involved in the biogenesis and metabolism of diverse organelles. Targeted organelle gene knockouts identified that defects in peroxisomes, Golgi, and ER cause mitochondrial fragmentation and dysfunction. Correlative light and electron microscopy analysed using artificial intelligence-directed voxel extraction revealed in unprecedented detail how impaired mitochondrial interactions with diverse organelles caused cell-wide defects in their morphology and biogenesis. Multi-omics analyses identified a unified proteome stress response and global shifts in lipid and glycoprotein homeostasis that are elicited when organelle biogenesis is compromised. Our comprehensive resource has defined metabolic and morphological interactions between organelles that can be mined to understand how changes in organelle components drive diverse cellular pathologies.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Timothy McCubbin

LAB HEAD: Aleksandra Filipovska

PROVIDER: PXD033871 | Pride | 2023-10-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

A cooperative organelle biogenesis program in mammalian cells

Project description:The compartmentalisation of distinct organelles within eukaryotic cells is essential for their diverse functions, however, how their structures and functions depend on each other has not been systematically explored. We combined a fluorescent reporter of mitochondrial stress with genome-wide CRISPR knockout screening and identified networks of genes involved in the biogenesis and metabolism of diverse organelles. Targeted organelle gene knockouts identified that defects in peroxisomes, Golgi, and ER cause mitochondrial fragmentation and dysfunction. Correlative light and electron microscopy analysed using artificial intelligence-directed voxel extraction revealed in unprecedented detail how impaired mitochondrial interactions with diverse organelles caused cell-wide defects in their morphology and biogenesis. Multi-omics analyses identified a unified proteome stress response and global shifts in lipid and glycoprotein homeostasis that are elicited when organelle biogenesis is compromised. Our comprehensive resource has defined metabolic and morphological interactions between organelles that can be mined to understand how changes in organelle components drive diverse cellular pathologies.

2023-10-13 | GSE201573 | GEO

Endolysosomal protease leakage reprograms macrophage mitochondrial metabolism

Project description:Organelle crosstalk plays important functions in metabolic processes and is relevant to immunity, neurodegeneration, and cancer. The permeabilisation and rupture of endolysosomes during stress can induce inflammation and cell death. There is growing evidence that endomembrane damage does not always result in cell death and that important cellular functions can be regulated by limited endolysosomal damage. However, the effect of limited cytosolic leakage of endolysosomal contents on the function of other cytoplasmic organelles is poorly understood. Here, we show that sterile and non-sterile endolysosomal damage triggers remodelling of the mitochondrial proteome and metabolic reprogramming of human macrophages. Mitochondrial metabolic reprogramming was associated with endolysosomal leakage independently of proteasome degradation and mitophagy. Furthermore, single-cell RNA-sequencing and metabolic analysis of lung macrophages undergoing endomembrane damage showed altered mitochondrial metabolism in mice. We, therefore, uncover an inter-organelle communication mechanism between mitochondria and endolysosomes with limited proteolytic leakage, providing a general mechanism by which macrophages undergo mitochondrial metabolic reprogramming in response to infection or injury.

2022-10-30 | PXD026045 | Pride

Multi-omic profiling reveals an RNA processing rheostat that predisposes to prostate cancer

Project description:Prostate cancer is the most commonly diagnosed malignancy and the second leading cause of cancer deaths in men. GWAS studies have identified variants associated with prostate cancer susceptibility, however, mechanistic and functional validation of these mutations are lacking. Mitochondrial energy metabolism plays an important role in the onset and development of cancer. A missense variant was identified in the ELAC2 gene, which encodes a dually localized nuclear and mitochondrial RNA processing enzyme, with predicted impact on metabolism and tumorigenesis. We used CRISPR/Cas9 genome editing to introduce this variant into the mouse Elac2 gene as well as to generate a prostate-specific gene knockout of Elac2. The mutations caused enlargement and inflammation in the prostate and nodule formation. Multi-omic profiling revealed defects in RNA and energy metabolism that activated proinflammatory and tumorigenic pathways as a consequence of impaired processing of mitochondrial and nuclear encoded non-coding RNAs and reduced protein synthesis. The Elac2 variant or knockout mice on the background of the transgenic adenocarcinoma of the mouse prostate (TRAMP) model show that Elac2 mutation with a secondary genetic insult exacerbated the onset and progression of prostate cancer and led to metastasis. Our systems biology analyses reveal a miRNA-mediated molecular mechanism by which specific non-coding RNAs elicit metabolic changes that drive prostate tumorigenesis and metastasis. We conclude that the ELAC2 variant is a predisposing factor for prostate cancer and provide a detailed molecular mechanism and physiologically relevant models of this cancer.

2023-04-19 | PXD033891 | Pride

Characterisation of a novel CRLS1 variant in multi-system mitochondrial disease pathogenesis identifies mitochondrial and endoplasmic reticular stress responses to cardiolipin dysfunction

Project description:Mitochondrial diseases (MD) are a group of inherited diseases with highly varied and complex clinical presentations and their molecular diagnosis has been improved through next generation sequencing. Here, we report four individuals, two of whom are siblings, affected by a progressive mitochondrial encephalopathy who carry biallelic variants in the cardiolipin biosynthesis gene CRLS1. Using patient fibroblasts, we characterised defects in mitochondrial function that were reflective of CRLS1 dysfunctions, providing functional evidence that the CRLS1 I109N variant causes the MD phenotype observed in this patient. Lipid profiling highlighted that the CRLS1 variants reduced cardiolipin levels, altered its acyl-chain composition and caused a significant increase in phosphatidylglycerol, the substrate of cardiolipin synthase. Proteomic profiling of patient cells and Crls1 knockout cell lines identified both endoplasmic reticular and mitochondrial stress responses, and key features that distinguish between varying degrees of cardiolipin insufficiency. Our findings support that deleterious variants in CRLS1 cause a novel autosomal recessive MD, presenting as a severe encephalopathy with multisystemic involvement. Furthermore, we have identified key changes in cardiolipin and proteome profiles across various degrees of cardiolipin dysfunction, facilitating future advances in diagnostic technologies based on curated signatures in high-throughput datasets.

2023-03-06 | PXD029861 | Pride

Transcription profiling of yeast mutants Gal-YAH1, Gal-ATM1 and Gal-NBP35 to investigate responses to defects in cellular Fe-S protein maturation

Project description:The biogenesis of iron-sulfur proteins in eukaryotes is an essential process involving the mitochondrial iron-sulfur cluster (ISC) assembly and export machineries and the cytosolic Fe/S protein assembly (CIA) apparatus. To define the integration of Fe/S protein biogenesis into cellular homeostasis, we compared the global transcriptional responses to defects in the three biogenesis systems in S. cerevisiae using DNA microarrays. Microarray analyses were carried out with regulatable yeast mutants in which representatives of each of the three biosynthetic systems could be depleted. In particular, we used the mutants Gal-YAH1, Gal-ATM1 and Gal-NBP35.

2007-12-14 | E-MEXP-1215 | biostudies-arrayexpress

Copy number variation in tRNA isodecoders impairs mammalian development and balanced translation

Project description:The number of tRNA isodecoder genes has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-seq, RNA-seq and proteomics we observed distinct molecular consequences of individual tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoders compensate for the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least four tRNA-Phe isodecoders is required for embryonic development and survival. The loss of tRNA-Phe-1-1 and any other three tRNA-Phe genes causes embryonic lethality indicating that tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA isodecoder genes is required to buffer translation and viability in mammals.

2023-04-19 | PXD029684 | Pride

Autophagy driven by a master regulator of hematopoiesis

Project description:Developmental and homeostatic remodeling of cellular organelles is mediated by a complex process termed autophagy. The cohort of proteins that constitute the autophagy machinery function in a multistep biochemical pathway. Though components of the autophagy machinery are broadly expressed, autophagy can occur in specialized cellular contexts, and mechanisms underlying cell type-specific autophagy are poorly understood. We demonstrate that the master regulator of hematopoiesis GATA-1 directly activates transcription of genes encoding the essential autophagy component Microtubule Associated Protein 1 Light Chain 3B (LC3B) and its homologs (MAP1LC3A, GABARAP, GABARAPL1, GATE-16). In addition, GATA-1 directly activates genes involved in the biogenesis/function of lysosomes, which mediate autophagic protein turnover. We demonstrate that GATA-1 utilizes the forkhead protein FoxO3 to activate select autophagy genes. GATA-1-dependent LC3B induction is tightly coupled to accumulation of the active form of LC3B and autophagosomes, which mediate mitochondrial clearance as a critical step in erythropoiesis. These results illustrate a novel mechanism by which a master regulator of development establishes a genetic network to instigate cell type-specific autophagy. Genome-wide maps of GATA1 factor occupancy in primary human PBMC derived erythroblasts

2011-09-30 | E-GEOD-32491 | biostudies-arrayexpress

A trans-generational epigenetic process defines piRNA biogenesis in Drosophila virilis

Project description:Piwi interacting (pi)RNAs repress diverse transposable elements in the germ cells of metazoans and are essential for fertility in both invertebrates and vertebrates. The precursors of piRNAs are transcribed from distinct genomic regions, the so-called piRNA clusters; however, how piRNA clusters are differentiated from the rest of the genome is not known. To address this question, we studied piRNA biogenesis in two Drosophila virilis strains that show differential ability to generate piRNAs from several genomic regions. We found that active piRNA biogenesis correlates with high levels of histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Furthermore, piRNA biogenesis in the progeny requires the trans-generational inheritance of an epigenetic signal, presumably in form of homologous piRNAs that are generated in the maternal germline and deposited into the oocyte. The inherited piRNAs enhance piRNA biogenesis by installment of H3K9me3 mark on piRNA clusters and by promoting ping-pong processing of homologous transcripts into mature piRNAs. We submitted the resequencing data together with the functional genomic datasets because it was generated with the sole purpose of supporting those. The SRA accession numbers are SRR1536176 and SRR1536175. ChIP-seq against H3K9me3 and Pol2, Total RNA-seq, in Drosophila virilis Strain9 and Strain160 as well as crosses between them

2014-09-01 | E-GEOD-59965 | biostudies-arrayexpress

Charting Organellar Importomes by Quantitative Mass Spectrometry - ERV1 organelle-enriched fractions

Project description:Protein import into organelles is essential for all eukaryotes and facilitated by multi-protein translocation machineries. Analyzing whether a protein is transported into an organelle is largely restricted to single constituents. This renders knowledge about imported proteins incomplete, limiting our understanding of organellar biogenesis and function. Here, we introduce a method that enables to chart an organelle’s importome. Our method relies on inducible RNAi-mediated knockdown of an essential subunit of a translocase to impair import, metabolic labeling and quantitative mass spectrometry. To highlight its potential, we established the mitochondrial importome of Trypanosoma brucei, comprising 1,120 proteins including 331 new candidates. An exciting feature of this method is that it overcomes limitations in identifying proteins with dual or multiple locations. We demonstrate the specificity and versatility of this novel ImportOmics method by targeting import machineries in mitochondria and glycosomes demonstrating its high potential for globally studying protein import and inventories of organelles.

2017-06-14 | PXD005730 | Pride

Charting Organellar Importomes by Quantitative Mass Spectrometry - ATOM40 whole cells

2017-06-14 | PXD005725 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data