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Reduced expression of UPF1 promotes tumor progression through stabilizing COX-2 mRNA in nasopharyngeal carcinoma

GSE305669 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/10/31 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × NC vs 3 × UPF1Groups 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.
Paper
Reduced expression of UPF1 promotes tumor progression through stabilizing COX-2 mRNA in nasopharyngeal carcinomaFrontiers in immunology · 2025
Summary (written by the submitters)
Nonsense-mediated mRNA decay (NMD) is conserved mRNA surveillance pathway that targeted and degraded one-third of aberrant and non-aberrant cellular transcripts. Recently, growing evidences have shown that NMD pathway is implicated in multiple cancer types. However, the activity and function of NMD in nasopharyngeal carcinoma (NPC) remains unclear.
Read the full summary ↓
Here we demonstrated that the expression level of the core NMD factors UPF1 (up-frameshift) was significantly downregulated in NPC tissues compared with adjacent noncancerous tissues and predicted poor prognosis. Knockdown of UPF1 expression enhanced tumor growth and metastasis of NPC cells in vitro and in vivo. UPF1 down-regulated genes revealed by RNA sequencing were selectively upregulated in NPC tissues. COX-2 and PD-L1 were identified as NMD targets. UPF1 knockdown activated ERK/MAPK and JAK2/STAT3 pathways through stabilizing COX-2 in NPC cells. Importantly, co-culture with UPF1 knockdown NPC cells promotes M2 polarization and migration of macrophages, and suppressed proliferation and activation of CD8+ T cell. Our findings suggested that UPF1 expression level and NMD efficiency were impaired in NPC tissues, which contributed to tumor progression and immune modulation.
Published in
Reduced expression of UPF1 promotes tumor progression through stabilizing COX-2 mRNA in nasopharyngeal carcinoma
Wu C, Xiao R, Zhang L et al. · Frontiers in immunology 2025 · PMID 41293174 · doi:10.3389/fimmu.2025.1617864
This dataset
Open GSE305669 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 GSE305669_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 PRJNA1307433 and SRA study SRP610054. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41293174) ↗
Study design
3 × NC vs 3 × UPF1

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 12 sample titles; they account for 6 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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