Hypoxia and inflammation induce synergistic transcriptome turnover in macrophages

Cell Reports, Journal Year: 2024, Volume and Issue: 43(7), P. 114452 - 114452

Published: July 1, 2024

Macrophages are effector immune cells that experience substantial changes to oxygenation when transiting through tissues, especially entering tumors or infected wounds. How hypoxia alters gene expression and macrophage function at the post-transcriptional level remains poorly understood. Here, we use TimeLapse-seq measure how inflammatory activation modifies hypoxic response in primary macrophages. Nucleoside recoding sequencing allows derivation of steady-state transcript levels, degradation rates, transcriptional synthesis rates from same dataset. We find produces distinct responses resting Hypoxia induces destabilization mRNA transcripts, though macrophages substantially increase compared Increased RNA turnover results upregulation ribosomal protein genes downregulation extracellular matrix components Pathways regulated by decay vitro differentially tumor-associated implying mixed stimuli could induce regulation solid tumors.

Language: Английский

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LARP1 binds ribosomes and TOP mRNAs in repressed complexes

The EMBO Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 12, 2024

Abstract Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis cell state. Previous studies have implicated LARP1 40S- or 80S-ribosome complexes that thought repress stabilize TOPs. However, a molecular understanding of how TOPs interact with these is lacking. Here, we show directly binds non-translating subunits. Cryo-EM structures reveal previously uncharacterized domain bound occluding the mRNA channel 40S subunit. Increased availability free subunits downstream various stresses promote 60S joining at same interface form LARP1-80S complexes. Simultaneously, engages TOP via its characterized La/PAM2 DM15 domains. Contrary expectations, binding within not required for LARP1-mediated repression stabilization, two canonical functions. Together, this work provides insight into challenges existing models describing function repressed LARP1-40S/80S-TOP

Language: Английский

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Structural Features of 5′ Untranslated Region in Translational Control of Eukaryotes

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(5), P. 1979 - 1979

Published: Feb. 25, 2025

Gene expression is a complex process regulated at multiple levels in eukaryotic cells. Translation frequently represents pivotal step the control of gene expression. Among stages translation, initiation particularly important, as it governs ribosome recruitment and efficiency protein synthesis. The 5' untranslated region (5' UTR) mRNA plays key role this process, often exhibiting complicated structured landscape. Numerous mRNAs possess long UTRs that contain diverse regulatory elements, including RNA secondary structures, specific nucleotide motifs, chemical modifications. These structural features can independently modulate translation through their intrinsic properties or by serving platforms for trans-acting factors such RNA-binding proteins. dynamic nature UTR elements allows cells to fine-tune response environmental cellular signals. Understanding these mechanisms not only fundamental molecular biology but also holds significant biomedical potential. Insights into UTR-mediated regulation could drive advancements synthetic mRNA-based targeted therapies. This review outlines current knowledge UTR, interplay between them, combined functional impact on translation.

Language: Английский

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Hypoxia and the endometrium: An indispensable role for HIF-1α as therapeutic strategies

Redox Biology, Journal Year: 2024, Volume and Issue: 73, P. 103205 - 103205

Published: May 21, 2024

Hypoxia-inducible factor 1 alpha (HIF-1α) is a major molecular mediator of the hypoxic response. In endometrium, local conditions induced by hormonal fluctuations and endometrial vascular remodeling contribute to production HIF-1α, which plays an indispensable role in series physiological activities, such as menstruation metamorphosis. The sensitive regulation HIF-1α maintains cellular viability regenerative capacity endometrium against stresses hypoxia excess reactive oxygen species. contrast, abnormal levels exacerbate development various pathologies. This knowledge opens important possibilities for promising HIF-1α-centered strategies ameliorate disease. Nonetheless, additional efforts are required elucidate regulatory network promote applications human endometrium. Here, we summarize HIF-1α-mediated pathway physiology pathology, highlight latest treating diseases, improve receptivity.

Language: Английский

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The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(3)

Published: Jan. 24, 2025

LARP4 interacts with poly(A)-binding protein (PABP) to protect messenger RNAs (mRNAs) from deadenylation and decay, recent data indicate it can direct the translation of functionally related mRNA subsets. was known bind RACK1, a ribosome-associated protein, although specific regions involved relevance had been undetermined. Here, through combination in-cell in vitro methodologies, we identified positions 615-625 conserved region-2 (CR2) (and 646-656 LARP4B) as directly binding RACK1. Consistent these results, AlphaFold2-Multimer predicted high-confidence interaction CR2 RACK1 propellers 5 6. mutations strongly decreased association cellular ribosomes by multiple assays, whereas PABP less affected, consistent independent interactions. The LARP4's ability stabilize β-globin reporter containing an AU-rich element (ARE) higher degree than GFP (green fluorescent protein) mRNAs lacking ARE. We show robustly increases β-glo-ARE mRNA, mutant is impaired. Analysis nanoLuc-ARE for production luciferase activity confirmed promotes efficiency, while are disabling. Thus, CR2-mediated promote translational efficiency some mRNAs.

Language: Английский

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Biased regulation of protein synthesis and hypoxic death by a conditional raptor mutation

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Language: Английский

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Oocyte‐specific deletion of eukaryotic translation initiation factor 5 causes apoptosis of mouse oocytes within the early‐growing follicles by mitochondrial fission defect‐reactive oxygen species‐DNA damage

Clinical and Translational Medicine, Journal Year: 2024, Volume and Issue: 14(8)

Published: Aug. 1, 2024

Abstract Background Mutations in several translation initiation factors are closely associated with premature ovarian insufficiency (POI), but the underlying pathogenesis remains largely unknown. Methods and results We generated eukaryotic factor 5 ( Eif5 ) conditional knockout mice aiming to investigate function of eIF5 during oocyte growth follicle development. Here, we demonstrated that deletion mouse primordial growing oocytes both resulted apoptosis within early‐growing follicles. Further studies revealed downregulated levels mitochondrial fission‐related proteins (p‐DRP1, FIS1, MFF MTFR) upregulated integrated stress response‐related (AARS1, SHMT2 SLC7A1) genes Atf4 , Ddit3 Fgf21 ). Consistent this, dysfunction characterized by elongated form, aggregated distribution beneath membrane, decreased adenosine triphosphate content mtDNA copy numbers, excessive accumulation reactive oxygen species (ROS) superoxide. Meanwhile, led a significant increase DNA damage response (γH2AX, p‐CHK2 p‐p53) proapoptotic (PUMA BAX), as well decrease anti‐apoptotic protein BCL‐xL. Conclusion These findings indicate follicles via fission defects, ROS damage. This study provides new insights into pathogenesis, genetic diagnosis potential therapeutic targets for POI. Key points leads arrest impairs proteins, followed dysfunction. Depletion causes pathway.

Language: Английский

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LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 2, 2023

Abstract Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis cell state. Previous studies implicate LARP1 40S- or 80S-ribosome complexes that repress stabilize TOPs. However, a mechanistic understanding of how TOPs interact with these coordinate TOP outcomes is lacking. Here, we show senses the cellular supply ribosomes by directly binding non-translating subunits. Cryo-EM structures reveal previously uncharacterized domain bound occluding 40S mRNA channel. Free cytosolic induce sequestration repressed 80S-LARP1-TOP independent alterations mTOR signaling. Together, this work demonstrates general ribosome-sensing function allows it protein demand. One-Sentence Summary binds free subunits

Language: Английский

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Fer governs mTORC1 regulating pathways and sustains viability of pancreatic ductal adenocarcinoma cells

Frontiers in Oncology, Journal Year: 2024, Volume and Issue: 14

Published: Aug. 14, 2024

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with a high percentage morbidity. The deciphering and identification novel targets tools for intervening its adverse progression are therefore immense importance. To address this goal we adopted specific inhibitor intracellular tyrosine kinase Fer, whose expression level upregulated in PDAC tumors, associated poor prognosis patients. Subjecting cells to E260-Fer inhibitor, unraveled simultaneous effects on mitochondria, non-mitochondrial ERK1/2 regulatory cascade. E260 caused severe mitochondrial deformation, resulting cellular- aspartate ATP depletion, followed by activation metabolic sensor AMPK. This led phosphorylation deactivation bona fide AMPK substrate, RAPTOR, which serves as positive regulator mTORC1 hub. Accordingly, resulted inhibition activity. In parallel, downregulated state kinases, their ability neutralize suppressor TSC2, thereby accentuating mTORC1. Importantly, both downregulation were also achieved upon knockdown corroborating role Fer these processes. Concomitantly, tumors not healthy pancreatic tissues, levels demonstrate moderate but statistically significant correlation mTOR downstream effector LARP1. Finally, targeting driven mTORC1, culminated necrotic death treated cells, envisaging new intervention tool challenging disease.

Language: Английский

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Comparative analysis of the LARP1 C-terminal DM15 region through Coelomate evolution

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(8), P. e0308574 - e0308574

Published: Aug. 27, 2024

TOR (target of rapamycin), a ubiquitous protein kinase central to cellular homeostasis maintenance, fundamentally regulates ribosome biogenesis in part by its target La-related 1 (LARP1). Among other transcripts, LARP1 specifically binds TOP (terminal oligopyrimidine) mRNAs encoding all 80 ribosomal proteins TOR-dependent manner through C-terminal region containing the DM15 module. Though functional implications interaction with is controversial, it clear that TOP-LARP1-TOR axis critical health humans. Its existence and role evolutionarily divergent animals remain less understood. We focused our work on expanding knowledge first arm axis: connection between LARP1-DM15 5’ motif. show overall architecture observed humans conserved fruit fly zebrafish. Both adopt familiar curved arrangements HEAT-like repeats bind same surface, although molecular dynamics simulations suggest N-terminal fold predicted be unstable unfold. demonstrate each ortholog interacts sequences varying affinities. Importantly, we determine ability some but not others might amount context RNA structure, rather than module recognize others. propose may retain similar secondary structures regulate recognition.

Language: Английский

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