Impaired fatty acid import and metabolism in macrophages restricts intracellular growth of Mycobacterium tuberculosis
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ABSTRACT:
PROVIDER: PRJNA1127515 | ENA |
REPOSITORIES: ENA
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Project description:Mycobacterium tuberculosis (Mtb) infection of macrophages reprograms cellular lipid metabolism to promote the formation of cytosolic lipid droplets. While it is clearly known that intracellular Mtb utilize host derived fatty acids and cholesterol to fuel a majority of its biosynthetic demands, the role of macrophage lipid metabolism on the bacteria’s ability to access the intracellular lipid pool remains controversial. We have utilized a CRISPR genetic knockdown approach to, systematically and comprehensively, characterize the role of macrophage fatty acid metabolism on the intracellular growth of Mtb. Our analyzes demonstrate that knockdown of lipid import, sequestration and metabolism genes collectively impair the intracellular growth of Mtb in macrophages. We further demonstrate that modulating fatty acids homeostasis in macrophages impair Mtb replication by enhancing production of pro-inflammatory cytokines, restricting the bacteria access to nutrients and increasing oxidative stress in a manner which is surprisingly divergent. We also demonstrate that impaired macrophage lipid droplet biogenesis is restrictive to intracellular Mtb growth. However, increased induction of lipid droplet formation by downstream blockade of fatty acid oxidation does not rescue the impaired Mtb growth phenotypes. Our work provides a characterization of macrophage fatty acid homeostasis and how its modulation impacts Mtb intracellular growth.
2024-06-24 | GSE270571 | GEO
Project description:Mitochondrial functions are largely performed by proteins imported from cytosol. Impaired protein import in mitochondria affects the maintenance of intra-mitochondrial anabolic and energy metabolic pathways. It leads to cytosolic accumulation of mistargeted proteins and activation of cellular stress responses. To explore the communication between these mechanism in mammalian system, we targeted the co-chaperone of mitochondrial Hsp70, a GrpE Like protein 1 (Grpel1), in mice. We show that loss of protein import into mitochondrial matrix results in mitochondrial dysfunction, which triggers stress responses. The total shut down of mtHSP70 function by overall knockout of Grpel1 resulted in early embryonic lethality, and tamoxifen-induced skeletal muscle-specific knockout of Grpel1 caused rapid muscular atrophy. We show here, with transcriptomics analysis, that protein-import failure in mitochondria increased cellular proteotoxic stress due to mitochondrial dysfunction. As a control mechanism, it triggered adaptive stress responses, including unfolded protein responses and integrated stress responses. Metabolic profiling of skeletal muscle-specific knockout mice revealed amino acid and TCA cycle intermediates shuttle between serum and muscle.
2022-10-04 | GSE198540 | GEO
Project description:Inter-organellar and systemic survival responses to impaired mitochondrial matrix protein import in skeletal muscle
| PRJNA815842 | ENA
Project description:Mitophagy is essential to maintain mitochondrial function and prevent diseases. It activates upon mitochondria depolarization, which causes PINK1 stabilization on the mitochondrial outer membrane. Strikingly, a number of conditions, including mitochondrial protein misfolding, can induce mitophagy without a loss in membrane potential. The underlying molecular details remain unclear. Here, we report that a loss of mitochondrial protein import, mediated by the pre-sequence translocase-associated motor complex PAM, is sufficient to induce mitophagy in polarized mitochondria. A genome-wide CRISPR/Cas9 screen for mitophagy inducers identifies components of the PAM complex. Protein import defects are able to induce mitophagy without a need for depolarization. Upon mitochondrial protein misfolding, PAM dissociates from the import machinery resulting in decreased protein import and mitophagy induction. Our findings extend the current mitophagy model to explain mitophagy induction upon conditions that do not affect membrane polarization, such as mitochondrial protein misfolding.
2022-08-04 | GSE207212 | GEO
Project description:The relevance of adipose-derived long noncoding RNAs (lncRNAs) to the regulation of gene expression patterns related to the obese phenotype remains elusive. Here, the analysis of transcriptomes of adipose tissue before-after significant weight loss led to the identification of 496 putative lncRNAs (FDR p-values <0.05). Only the nonconserved linc-GALNTL6-4 displayed a fold-change above 2 plus adjusted p-value <0.0001. Exploration of additional omental and subcutaneous fat samples confirmed diminished linc-GALNTL6-4 in obese subjects, while lncRNA-mRNA co-expression analyses highlighted its association with fatty acid metabolism. Concurrently, the expression of this unique lncRNA towered in ex vivo isolated and in vitro differentiated adipocytes, being compromised under conditions that mimicked inflammation in obese adipocytes. On the other hand, the knockdown of linc-GALNTL6-4 in fat cell progenitors conveys impaired differentiation, fostering deranged expression patterns in differentiated adipocytes, including the increased expression of genes devoted to the transport of lipids, such as Apolipoprotein C1 (APOC1) and the intracellular fatty acid-binding protein FABP3. Conversely, overexpression of linc-GALNTL6-4 ameliorated adipocyte performance through the specific control of the short-chain fatty acid receptor FFAR3. Current data unveil the unforeseen relevance of linc-GALNTL6-4 as a modulator of fatty acid sensing in adipocytes deeply challenged by body weight and meta-inflammation.
2024-01-31 | GSE218895 | GEO
Project description:The relevance of adipose-derived long noncoding RNAs (lncRNAs) to the regulation of gene expression patterns related to the obese phenotype remains elusive. Here, the analysis of transcriptomes of adipose tissue before-after significant weight loss led to the identification of 496 putative lncRNAs (FDR p-values <0.05). Only the nonconserved linc-GALNTL6-4 displayed a fold-change above 2 plus adjusted p-value <0.0001. Exploration of additional omental and subcutaneous fat samples confirmed diminished linc-GALNTL6-4 in obese subjects, while lncRNA-mRNA co-expression analyses highlighted its association with fatty acid metabolism. Concurrently, the expression of this unique lncRNA towered in ex vivo isolated and in vitro differentiated adipocytes, being compromised under conditions that mimicked inflammation in obese adipocytes. On the other hand, the knockdown of linc-GALNTL6-4 in fat cell progenitors conveys impaired differentiation, fostering deranged expression patterns in differentiated adipocytes, including the increased expression of genes devoted to the transport of lipids, such as Apolipoprotein C1 (APOC1) and the intracellular fatty acid-binding protein FABP3. Conversely, overexpression of linc-GALNTL6-4 ameliorated adipocyte performance through the specific control of the short-chain fatty acid receptor FFAR3. Current data unveil the unforeseen relevance of linc-GALNTL6-4 as a modulator of fatty acid sensing in adipocytes deeply challenged by body weight and meta-inflammation.
2024-01-31 | GSE218896 | GEO
Project description:Peroxisome biogenesis diseases (PBDs) are characterized by global defects in peroxisomal function and can result in severe brain, liver, kidney, and bone malfunctions. PBDs are due to mutations in peroxisome biogenesis factors (PEX genes) that are responsible for peroxisome assembly and function. Increasing evidence suggests that peroxisome import functions decline during aging. However, the transcriptome profiling of peroxisome import defects and how they affect disease development are still lacking. PEX5 encodes the cytoplasmic receptors for peroxisome-targeting signal types 1. We generate knock-in human HEK293 cells mutant using CRISPR to transiently express PEX5 cysteine 11 to alanine mutant (PEX5C11A), which blocks PEX5 recycling and exerts dominant negative effect on PEX5 mediated peroxisome import. To identify conserved responses, we perform transcriptomic analysis on Drosophila oenocyte-specific Pex1, Pex12 and Pex5 knockdowns and on human cells with impaired peroxisome import (through expressing PEX5C11A and applying PEX5 siRNA respectively). PEX5C11A induction triggers vast transcriptomic changes, including decreased oxidative phosphorylation, increased MAPK signaling and HIPPO signaling. PEX5 siRNA specifically decreases spliceosome activity and increases cholesterol metabolism. Using gene set enrichment analysis (GSEA), we identify protein processing in endoplasmic reticulum pathway, specifically ER-associated protein degradation (ERAD) pathway is induced in all PEX knockdowns in Drosophila. Peroxisome dysfunction elevates eIF2α phosphorylation in both Drosophila and human cell culture independent of XBP1 activation, suggesting increased integrative stress response (ISR). Moreover, peroxisome stress decreases ribosome biogenesis genes and impairs ribosome biogenesis in flies and human cells. Specifically, peroxisome stress impairs the 5'-ETS cleavage activity during the ribosome biogenesis and dampens 40S small ribosomal export in both flies and human. Our results suggest that reduced ribosome biogenesis and elevated ISR could be conserved cellular response to peroxisome import stress.
2021-02-23 | GSE167197 | GEO
Project description:UBE2D3 is an Intracellular Checkpoint in Pancreatic Ductal Carcinoma that Restricts CD8+ T-Cell Antitumor Immunity
| PRJNA1124987 | ENA
Project description:Mitochondrial protein import through the outer and inner membranes is key to mitochondrial biogenesis. Recent studies have explored how cells respond when import is impaired by a variety of different insults. Here, we developed a mammalian import blocking system using dihydrofolate reductase (DHFR) fused to the N-terminus of the inner membrane protein MIC60. While stabilization of the DHFR domain by methotrexate inhibited endogenous mitochondrial protein import, it neither activated the transcription factor ATF4, nor was affected by ATAD1 expression or by VCP/p97 inhibition. On the other hand, surprisingly, plugging the channel of translocase of the outer membrane (TOM) induced YME1L1, an ATP-dependent protease, to eliminate translocase of the inner membrane (TIM23) channel components TIMM17A and TIMM23. The data suggest that unoccupied TIM23 complexes expose a C-terminal degron on TIMM17A to YME1L1 for degradation. Import plugging caused a cell growth defect and loss of YME1L1 exacerbated the growth inhibition, showing the protective effect of YME1L1 activity. YME1L1 appears to play a crucial role in mitochondrial quality control to counteract precursor stalling in the TOM complex and unoccupied TIM23 channels.
2024-10-24 | MSV000096201 | MassIVE
Project description:Protein expression and turnover are controlled through a complex interplay of transcriptional, post-transcriptional and post-translational mechanisms to enable spatial and temporal regulation of cellular processes. To systematically elucidate such gene regulatory networks, we developed a CRISPR screening assay based on time-controlled Cas9 mutagenesis, intracellular immunostaining and fluorescence-activated cell sorting that enables the identification of regulatory factors independent of their effects on cellular fitness. We pioneered this approach by systematically probing the regulation of the transcription factor MYC, a master regulator of cell growth. Our screens uncover a highly conserved protein, AKIRIN2, that is essentially required for nuclear protein degradation. We found that AKIRIN2 forms homodimers that directly bind to fully assembled 20S proteasomes to mediate their nuclear import. During mitosis, proteasomes are excluded from condensing chromatin and re-imported into newly formed daughter nuclei in a highly dynamic, AKIRIN2-dependent process. Cells undergoing mitosis in the absence of AKIRIN2 become devoid of nuclear proteasomes, rapidly causing accumulation of MYC and other nuclear proteins. Collectively, our study reveals a dedicated pathway controlling the nuclear import of proteasomes in vertebrates and establishes a scalable approach to decipher regulators in essential cellular processes.
2021-08-27 | GSE157663 | GEO