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Effect of the different isoforms of RPL22L1 protein on the transcriptome of human glioblastoma cells.

ABSTRACT: Effect of the different isoforms of RPL22L1 protein on the transcriptome of human glioblastoma cells.

PROVIDER: PRJNA748368 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15197942_1.fastq.gz	Fastqsanger.gz
	SRR15197942_2.fastq.gz	Fastqsanger.gz
	SRR15197943_1.fastq.gz	Fastqsanger.gz
	SRR15197943_2.fastq.gz	Fastqsanger.gz
	SRR15197944_1.fastq.gz	Fastqsanger.gz

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Interactome of different isoforms of RPL22L1 protein in human glioblastoma cells

Project description:Interactome of different isoforms of RPL22L1 protein in human glioblastoma cells

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Effect of the different isoforms of RPL22L1 protein on the transcriptome of human glioblastoma cells and their interactome

Project description:Effect of the different isoforms of RPL22L1 protein on the transcriptome of human glioblastoma cells and their interactome

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Effect of the different isoforms of RPL22L1 protein on the transcriptome of human glioblastoma cells.

Project description:Glioblastoma multiforme (GBM) is characterized by an exceptionally high intratumoral heterogeneity. However, the molecular mechanisms underlying the origin of different GBM cell populations remain unclear. Here we found that the composition of ribosomes of GBM cells in the tumor core and edge differ due to alternative RNA splicing. The acidic pH in the core switches pre-mRNA splicing of the ribosomal gene RPL22L1 toward the RPL22L1b isoform. This allows cells to survive acidosis, increases stemness and correlates with worse patient outcome. Mechanistically, RPL22L1b promotes RNA splicing by binding to lncMALAT1 in the nucleus, resulting in its degradation. Contrarily, in the tumor edge region, RPL22L1a interacts with ribosomes in cytoplasm and upregulates translation of multiple mRNAs including TP53. We found that RPL22L1 isoform switch is regulated by SRSF4 and identified the compound, that inhibits this process and decreases tumor growth. These findings demonstrate how distinct GBM cell populations arise during tumor growth. Targeting this mechanism may decrease GBM heterogeneity and facilitate therapy.

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Interactome of different isoforms of RPL22L1 protein in human glioblastoma cells

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LC-MS/MS identification of proteins that were co-purified with Fc-tagged isoforms of RPL22L1

Project description:Glioblastoma (GBM) is characterized by an exceptionally high intratumoral heterogeneity. However, the molecular mechanisms underlying the origin of different GBM cell populations remain unclear. Here we found that the composition of ribosomes of GBM cells in the tumor core and edge differ due to alternative RNA splicing. The acidic pH in the core switches pre-mRNA splicing of the ribosomal gene RPL22L1 toward the RPL22L1b isoform. To elucidate the functions of RPL22L1 isoforms we identified proteins that interact with RPL22L1a and RPL22L1b. First, we generated GBM cells with stable expression of Fc-tagged RPL22L1 isoforms. Fc-RPL22L1a and Fc-RPL22L1b together with their binding partners were isolated from neurospheres using magnetic beads and analyzed by LC-MS/MS.

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LC-MS/MS identification of proteins that were bound to recombinant His-tagged isoforms of RPL22L1

Project description:Glioblastoma (GBM) is characterized by an exceptionally high intratumoral heterogeneity. However, the molecular mechanisms underlying the origin of different GBM cell populations remain unclear. Here we found that the composition of ribosomes of GBM cells in the tumor core and edge differ due to alternative RNA splicing. The acidic pH in the core switches pre-mRNA splicing of the ribosomal gene RPL22L1 toward the RPL22L1b isoform. To elucidate the functions of RPL22L1 isoforms we identified proteins that interact with RPL22L1a and RPL22L1b. First, each isoform was expressed in E. coli and immobilized on magnetic beads. The beads were incubated with GBM cell lysates and proteins bound to the beads were identified using LC-MS/MS.

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Differential effects of estrogen receptor beta isoforms on glioblastoma progression

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Truncated protein isoforms generate diversity of protein localization and function in yeast

Project description:Genome-wide measurements of ribosome occupancy on mRNA transcripts have enabled global empirical identification of translated regions. These approaches have revealed an unexpected diversity of protein products, but high-confidence identification of new coding regions that entirely overlap annotated coding regions – including those that encode truncated protein isoforms – has remained challenging. Here, we develop a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms, a more than 30-fold increase in the number known in budding yeast. We perform extensive experimental validation of these truncated proteins and define two general classes. The first set lack large portions of the annotated protein sequence and tend to be produced from a truncated transcript. We show two such cases, Yap5truncation and Pus1truncation, to have condition-specific regulation and functions that appear distinct from their respective annotated isoforms. The second set of N-terminally truncated proteins lack only a small region of the annotated protein and are less likely to be regulated by an alternative transcript isoform. Many localize to different subcellular compartments than their annotated counterpart, representing a common strategy for achieving dual localization of otherwise functionally identical proteins.

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