GEO series

FKBP9 Enhances IGF2BP1 Mediated m6A Recognition and Promotes Hepatocellular Carcinoma Progression

GSE289122 Homo sapiens (human) RNA-seq (gene expression) 13 samples Submitted 2025/12/09 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 13 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: Hepatocellular carcinomaThis series is part of our curated briefing on it.
Samples: 13 samples: 5 conditions, mostly in triplicateGroups 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: FKBP9 enhances IGF2BP1-mediated m(6)A recognition to promote hepatocellular carcinoma progressionJHEP reports : innovation in hepatology · 2025

Summary (written by the submitters)

Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal malignancies worldwide, with intricate molecular mechanisms driving its progression. Among various post-transcriptional regulatory mechanisms, N6-methyladenosine (m6A) modification has emerged as a critical factor influencing mRNA stability and translation, thereby impacting tumorigenesis.

Read the full summary ↓

FK506-binding protein 9 (FKBP9), a peptidyl-prolyl isomerase (PPIase), has been implicated in several cancers; however, its specific role in HCC remains largely unexplored, and existing studies have not fully elucidated the molecular interactions and downstream effects of FKBP9 in HCC. In this study, we employed a combination of biochemical, molecular, and cellular techniques, including immunoprecipitation, RNA immunoprecipitation, luciferase reporter assays, and in vivo tumor models, to investigate the functional relationship between FKBP9 and the m6A reader protein Insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1). Our findings demonstrate that FKBP9 directly interacts with IGF2BP1, enhancing its recognition of m6A-modified transcripts, particularly oncogenes such as MYC and Platelet-Derived Growth Factor Subunit B (PDGFB). Functional assays revealed that FKBP9 promotes HCC cell proliferation, migration, and invasion by stabilizing m6A-tagged oncogenic mRNAs. Furthermore, in vivo experiments confirmed that FKBP9 overexpression accelerates tumor growth, whereas MYC inhibition mitigates this effect. This study provides novel insights into the oncogenic role of FKBP9 in HCC by uncovering its regulatory influence on IGF2BP1-mediated m6A RNA recognition. These findings suggest that targeting the FKBP9-IGF2BP1 axis could be a promising therapeutic strategy for HCC.

Published in

FKBP9 enhances IGF2BP1-mediated m(6)A recognition to promote hepatocellular carcinoma progression

Yang F, Si A, Chi C et al. · JHEP reports : innovation in hepatology 2025 · PMID 41281450 · doi:10.1016/j.jhepr.2025.101584

This dataset

Open GSE289122 in finder → Find more human RNA-seq datasets → Hepatocellular 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 GSE289122_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 PRJNA1220380 and SRA study SRP562149. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41281450) ↗

Study design

5 conditions, mostly in triplicate

Huh7 cells, shControl, ×3 Huh7 cells, shFKBP9, ×3 Huh7 cells, shIGF2BP1, ×3 HepG2 cells, Input, ×2 HepG2 cells, m6A, ×2

Supports a between-group comparison across 13 samples.

How we read this: 5 replicated groups read from 13 sample titles; they account for 13 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

GSM8784065 Huh7 cells, shControl, Rep1 Huh7 cells, shControl,
GSM8784066 Huh7 cells, shControl, Rep2 Huh7 cells, shControl,
GSM8784067 Huh7 cells, shControl, Rep3 Huh7 cells, shControl,
GSM8784068 Huh7 cells, shFKBP9, Rep1 Huh7 cells, shFKBP9,
GSM8784069 Huh7 cells, shFKBP9, Rep2 Huh7 cells, shFKBP9,
GSM8784070 Huh7 cells, shFKBP9, Rep3 Huh7 cells, shFKBP9,
GSM8784071 Huh7 cells, shIGF2BP1, Rep1 Huh7 cells, shIGF2BP1,
GSM8784072 Huh7 cells, shIGF2BP1, Rep2 Huh7 cells, shIGF2BP1,
GSM8784073 Huh7 cells, shIGF2BP1, Rep3 Huh7 cells, shIGF2BP1,
GSM8784074 HepG2 cells, Input, Rep1 HepG2 cells, Input,
GSM8784075 HepG2 cells, Input, Rep2 HepG2 cells, Input,
GSM8784076 HepG2 cells, m6A, Rep1 HepG2 cells, m6A,
GSM8784077 HepG2 cells, m6A, Rep2 HepG2 cells, m6A,

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GSE114564 Identification of novel serum biomarkers in early-stage HCC patients. 118 samples same disease briefing

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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.