GEO series

SMAD nucleocytoplasmic shuttling relies on nucleoporin RanBP2 and VIM-AS1 long non-coding RNA during TGF-β signaling

GSE281521 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/12/22 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)
Samples: 12 samples: 3 × Ctrl vs 3 × TGFβ vs 3 × VIM-AS1 vs 3 × VIM-AS1+TGFβGroups 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: The long noncoding RNA VIM-AS1 and nucleoporin Nup358/RanBP2 regulate SMAD nuclear accumulation during TGF-β signalingNucleic acids research · 2026

Summary (written by the submitters)

Activation of the transforming growth factor β (TGF-β) signaling leads to established hallmarks of cancer such as the epithelial-to-mesenchymal transition (EMT), initiating cancer dissemination and increasing chemoresistance. TGF-β signal by binding to its type I and II receptors, leading to parallel activation of SMAD proteins, ubiquitin ligases and protein kinases.

Read the full summary ↓

Here, using a panel of tumor cells we show that TGF-β activation induces the expression of the mammalian nuclear long non-coding RNA (lncRNA) VIM-AS1 (Vimentin antisense RNA 1) variant 2 (v.2) via the formation of a complex among the transcriptional factors GATA6-SMAD-SPI1. Furthermore, transcriptomic analysis indicated VIM-AS1 enhancing TGF-β signaling and EMT, as further validated by functional gain or loss assays. Mechanistically, the TGF-β-induced VIM-AS1 v.2 enhanced SMAD nucleocytoplasmic shuttling by interacting with the N-terminus domain of the nucleoporin RanBP2 (Nup358), whereby acting as a scaffold molecule, facilitates the binding of RanBP2 with SMAD2/3 and its further nuclear import. Finally, VIM-AS1 increases invasion and motility of tumor cells and emerges as a promising therapeutic target to sensitize cancer cells to chemotherapeutic drugs. Hence, we delineated a novel signaling mechanism for VIM-AS1 v.2 facilitating TGF-β response in tumor cells via SMAD nucleocytoplasmic shuttling.

Published in

The long noncoding RNA VIM-AS1 and nucleoporin Nup358/RanBP2 regulate SMAD nuclear accumulation during TGF-β signaling

Rodrigues-Junior DM, Ali MM, Itoh Y et al. · Nucleic acids research 2026 · PMID 41556346 · doi:10.1093/nar/gkaf1526

This dataset

Open GSE281521 in finder → Find more human RNA-seq datasets →

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 GSE281521_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 PRJNA1184177 and SRA study SRP544249. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41556346) ↗

Study design

3 × Ctrl vs 3 × TGFβ vs 3 × VIM-AS1 vs 3 × VIM-AS1+TGFβ

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 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

GSM8622592 Ctrl_1 Ctrl
GSM8622593 Ctrl_2 Ctrl
GSM8622594 Ctrl_3 Ctrl
GSM8622595 TGFβ_1 TGFβ
GSM8622596 TGFβ_2 TGFβ
GSM8622597 TGFβ_3 TGFβ
GSM8622598 VIM-AS1_1 VIM-AS1
GSM8622599 VIM-AS1_2 VIM-AS1
GSM8622600 VIM-AS1_3 VIM-AS1
GSM8622601 VIM-AS1+TGFβ_1 VIM-AS1+TGFβ
GSM8622602 VIM-AS1+TGFβ_2 VIM-AS1+TGFβ
GSM8622603 VIM-AS1+TGFβ_3 VIM-AS1+TGFβ

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