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GLIOBLASTOMAS ARE CHARACTERIZED BY A REDUCED NUMBER OF M6A SITES IN LNCRNAs

ABSTRACT: GLIOBLASTOMAS ARE CHARACTERIZED BY A REDUCED NUMBER OF M6A SITES IN LNCRNAs

PROVIDER: PRJNA1189527 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31451017_1.fastq.gz	Fastqsanger.gz
	SRR31451018_1.fastq.gz	Fastqsanger.gz
	SRR31451019_1.fastq.gz	Fastqsanger.gz
	SRR31451020_1.fastq.gz	Fastqsanger.gz
	SRR31451021_1.fastq.gz	Fastqsanger.gz

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GLIOBLASTOMAS ARE CHARACTERIZED BY A REDUCED NUMBER OF M6A SITES IN LNCRNAs

Project description:Recent studies have suggested the potential role of posttranscriptional N6-methyladenosine (m6A) RNA modifications in diverse biological processes, including tumor development. In contrast to intensively studied mRNA modifications, insufficient information is known so far about the epitranscriptome of long non-coding RNAs (lncRNAs). Furthermore, an epitranscriptome of LncRNAs in glioma pathogenesis has not been previously presented. Thus, this study aimed to profile m6A modifications within lncRNAs in different grades of gliomas using direct RNA long-read sequencing, with the goal of yielding both nucleotide and transcript-resolved m6A hits as biomarkers for tumor progression. Here we explored ONT direct RNA-seq to detect N6-methyladenosine (m6A) sites within lncRNAs' RRACH motifs in 26 glioma tumor tissues. Generally, 98.5% of m6A-modified RRACH motifs were detected in mRNA transcripts, and 1.16% in lncRNAs. We identified 60-748 unique m6A-modified lncRNAs for individual gliomas. On average, 15.84% of all RRACH motifs within lncRNAs were modified in glioblastomas (GB), while the m6A frequency reached 23.73% in the low-grade glioma (LGG) group. Unsupervised clustering analysis based on lncRNAs' m6A status resulted in three m6A clusters. Patients within the highly modified lncRNAs cluster (C3) experienced significantly longer survival compared to patients with lower methylation rates who were clustered into C1/C2 (2901 days in C3 vs 439 days in C1, log-rank test p=0.019).  In summary, we discovered that lncRNAs are highly modified in LGG while multiple epi-marks, found in low-grade gliomas, are absent in GB tissues revealing m6A contribution to glioma pathology.

2025-05-20 | GSE282642 | GEO

Genome-wide gain-of-function screening characterized lncRNAs as tumor immune response regulators

Project description:Genome-wide gain-of-function screening characterized lncRNAs as tumor immune response regulators

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Genome-wide gain-of-function screening characterized lncRNAs as tumor immune response regulators [CRISPR_screen]

Project description:Genome-wide gain-of-function screening characterized lncRNAs as tumor immune response regulators [CRISPR_screen]

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Genome-wide gain-of-function screening characterized lncRNAs as tumor immune response regulators [CRISPR_screen]

Project description:The majority of lncRNAs’ roles in tumor immunology remain elusive. In this project, we performed a CRISPR activation screening of 9744 lncRNAs in melanoma cells co-culturing with human CD8+ T cells. We identified 16 novel lncRNAs potentially regulating tumor immune response. Further integrative analysis using tumor immunogenomics data revealed that IL10RB-DT and LINC01198 are significantly correlated with tumor immune response and survival in melanoma and breast cancer. Specifically, IL10RB-DT suppresses CD8+ T cells activation via inhibiting IFN-γ-JAK-STAT1 signaling and antigen presentation in melanoma and breast cancer cells. On the other hand, LINC01198’s upregulation sensitizes the killing of tumor cells by CD8+ T cells. Mechanistically, LINC01198 interacts and activates NF-κB component p65 to trigger the type I and type II interferon responses in melanoma and breast cancer cells. Our study systematically characterized novel lncRNAs involved in tumor immune response.

2022-12-12 | GSE202130 | GEO

Prevalence of Copy-number neutral LOH in glioblastomas revealed by analysis of laser-microdissected tissues

Project description:We have employed a laser capture microdissection technique and single nucleotide polymorphism arrays to characterize genomic alterations associated with the development of glioblastomas. Combined analysis of LOH and copy number revealed that more than half of the identified 254 LOH loci showed no copy number alteration, indicating the presence of copy-number neutral LOH Keywords: DNA copy number, Loss of heterozygosity Affymetrix 50K SNP mapping arrays were used to profile 14 primary glioblastomas (GBMs) with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair.

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Prevalence of Copy-number neutral LOH in glioblastomas revealed by analysis of laser-microdissected tissues

2009-03-01 | GSE10922 | GEO

Mutations in IDH1 are associated with DNA hypermethylation in glioblastomas

Project description:We compared the DNA methylation profiles of 26 glioblastomas harboring mutations in IDH1 with 36 glioblastomas without these mutations on the Illumina HumanMethylation450 BeadChip.

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2016-02-08 | E-GEOD-77675 | biostudies-arrayexpress

One-shot analysis of translated mammalian lncRNAs with AHARIBO

Project description:A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.

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Project description:The goal of this study was to investigate genomic aberrations of glioblastoma patients. Keywords: Comparative genomic hybridization We performed array comparative genomic hybridization of 7 glioblastomas using as a reference DNA from healthy donors.

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