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18S rRNA N6-methyladenosine (m6A) modification promotes tumorigenesis and chemoresistance via gain-of-function mutant p53 in nasopharyngeal carcinoma

GSE186485 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2024/10/24 Platform GPL20795Platform GPL23227
At a glance

RNA-seq (gene expression) · human · 16 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Nasopharyngeal carcinomaThis series is part of our curated briefing on it.
Samples
16 samples: 3 × Vector_Input vs 3 × Vector_Polyribosome vs 3 × KO_Input vs 3 × KO_PolyribosomeGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Mis-regulated mRNA translation and hyperactivation of ribosome biogenesis are the two main hallmarks of cancer cells, whereas their intrinsic links and molecular mechanisms remain poorly understood. Our current study revealed that METTL5 and its mediated 18S rRNA N6-methyladenosine modification at 1832 position (m6A1832) are elevated in nasopharyngeal carcinoma (NPC) and correlated with disease progression.
Read the full summary ↓
Gain-of-function and loss-of-function assays showed that METTL5 mediated 18S rRNA m6A1832 modification promotes NPC cells proliferation and metastasis in vitro and in vivo. Mechanistically, loss of 18S rRNA m6A1832 modification impairs the assembly of 80S ribosome and therefore affecting global mRNA translation. Furthermore, polyribosome-bound mRNA sequencing (Polyribosome-RNA-seq), ribosome profiling sequencing (Ribo-seq) and whole exome sequencing (WES) data identified a METTL5/HSF4b/HSP90B1/mutant p53 (mutp53) axis which contributed to NPC tumorigenesis and chemoresistance. Our findings uncovered a novel mechanism underlying rRNA epigenetic modification in regulating mRNA translation and mutp53 pathway in cancer.
This dataset
Open GSE186485 in finder → Find more human RNA-seq datasets → Nasopharyngeal carcinoma landscape →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE186485_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA774057 and SRA study SRP342986. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × Vector_Input vs 3 × Vector_Polyribosome vs 3 × KO_Input vs 3 × KO_Polyribosome

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
More Nasopharyngeal carcinoma datasets

Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.