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Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (Polysomal RNA-Seq)

ABSTRACT: Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (Polysomal RNA-Seq)

PROVIDER: PRJNA988807 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25055800_1.fastq.gz	Fastqsanger.gz
	SRR25055800_2.fastq.gz	Fastqsanger.gz
	SRR25055801_1.fastq.gz	Fastqsanger.gz
	SRR25055801_2.fastq.gz	Fastqsanger.gz
	SRR25055802_1.fastq.gz	Fastqsanger.gz

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Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (Polysomal RNA-Seq)

Project description:Lung metastases are detected in more than half of patients with metastatic tumors. However, it remains largely unknown why the lung environment is a permissive niche for metastases. Here, we discover that pulmonary aspartate triggers a cellular signaling cascade in disseminated cancer cells resulting in a translational program that boosts lung metastasis. Specifically, we observe that patients and mice with breast cancer have high concentrations of aspartate in their lung interstitial fluid. This extracellular aspartate activates the ionotropic N-methyl-D-aspartate (NMDA) receptor in cancer cells, which induces CREB-dependent mRNA expression of deoxyhypusine hydroxylase (DOHH). The latter is essential for hypusination, a posttranslational modification required for the activity of the non-classical translation initiation factor eIF5A. In turn, a translational program with TGF-β signaling as a central hub promotes collagen remodeling in the disseminated breast cancer cells. We detect key aspects of this mechanism in lung metastases from patients with breast cancer. In summary, we discover that pulmonary aspartate increases with breast cancer and induces a signaling cascade promoting the growth of lung metastases.

2024-10-04 | GSE236086 | GEO

Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)

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Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation

Project description:Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation

| PRJNA988804 | ENA

Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (Total RNA-Seq)

2024-10-04 | GSE277634 | GEO

Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)

Project description:Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)

| PRJNA988806 | ENA

Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (Total RNA-Seq)

Project description:Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (Total RNA-Seq)

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Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-04 | GSE236087 | GEO

Ribosome profiling study of eIF5A depletion strain

Project description:The eukaryotic translation factor eIF5A, originally identified as an initiation factor, was later shown to promote translation elongation of iterated proline sequences. Using a combination of ribosome profiling and in vitro biochemistry, we report a much broader role for eIF5A in elongation and uncover a substantial function for eIF5A in termination. Ribosome profiling of an eIF5A-depleted strain reveals a global elongation defect, with abundant ribosomes stalling at many sequences, not limited to proline stretches. Our data also show accumulation at stop codons and in the 3’-UTR, suggesting a global defect in termination in the absence of eIF5A. Using an in vitro reconstituted translation system, we find that eIF5A strongly promotes the translation of novel stalling sequences and increases the rate of peptidyl-tRNA hydrolysis more than 17-fold. We conclude that eIF5A functions broadly in elongation and termination, rationalizing its great cellular abundance and essential nature.

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Transcription profiling of S. cerevisiae temperature sensitive eIF5A mutant shows accumulation of transcripts targeted to the Nonsense Mediated Decay pathway

Project description:The highly conserved protein eIF5A found in archaea and all eucaryotes uniquely contains the posttranslationally formed amino acid hypusine. Despite being essential the functions of this protein and its modification remain unclear. To gain more insight into these functions temperature sensitive mutants of the human EIF5A1 were characterized in the yeast Saccharomyces cerevisiae. EIF5A is proposed to be an RNA binding protein. Thus, we used microarrays to identify special RNA subsets of up- and downregulation that are influenced by a limited eIF5A function in strains expressing a point mutated form of eIF5A. Experiment Overall Design: Wild-type and mutant yeast strains were grown at 25Â°C following total RNA extraction and hybridization on Affymetrix microarrays. cRNA probes derived from RNA preparations were obtained from four isogenic, haploid strains from each of the wild-type and the mutant. This ensured that changes in the transcriptome could be attributed to the impaired HYP function of V81G rather than to differences in the genetic background. Therefore, two groups of 4 datasets (per wild-type W303-WT and mutant W303-V81G strains) were generated after hybridisation to the micro arrays.

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Study of ribosome dynamics after eIF5A depletion in budding yeast

Project description:eIF5A is an essential translation elongation factor present in all eukaryotes, and the only known protein to follow a post-translational modification called hypusination. Here, we performed a wide analysis of ribosome dynamics in S. cerevisiae eIF5A depleted cells using 5Pseq (Pelechano et al. 2015 PMID 26046441). This method allows the study of ribosome dynamics, by sequencing 5’ phosphorylated mRNA co-translational degradation intermediates. Since eIF5A is an essential protein in yeast, we used two eIF5A temperature-sensitive strains containing a single Pro83 to Ser mutation (tif51A-1) and double Cys39 to Tyr and Gly118 to Asp mutations (tif51A-3) in the highly expressed gene TIF51A (HYP2) that encodes eIF5A protein (Li et al. 2011 PMID: 24923804).

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