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Interactome of different isoforms of RPL22L1 protein in human glioblastoma cells

ABSTRACT: Interactome of different isoforms of RPL22L1 protein in human glioblastoma cells

PROVIDER: PRJNA748369 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15197939_1.fastq.gz	Fastqsanger.gz
	SRR15197939_2.fastq.gz	Fastqsanger.gz
	SRR15197940_1.fastq.gz	Fastqsanger.gz
	SRR15197940_2.fastq.gz	Fastqsanger.gz
	SRR15197941_1.fastq.gz	Fastqsanger.gz

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

Project description:Effect of the different isoforms of RPL22L1 protein on the transcriptome of 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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Project description:Glioblastoma (GBM) is the most aggressive of all primary brain tumours. Here, we perform a multi-omics approach to map the promoter-enhancer interactome and the regulatory landscape of glioblastoma, including RNA-seq, ChIP-seq of histone marks (H3K4me3, H3K27ac, H3K27me3), H3K4me3 HiChIP and ATAC-seq.

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