GEO series

Development of novel Hepatocellular Carcinoma drugs, JNK-IN-5A derivatives simultaneously induce Apoptosis and Necrosis

GSE255617 Homo sapiens (human) RNA-seq (gene expression) 40 samples Submitted 2026/04/22 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 40 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: 40 samples: 10 conditions, mostly with about 4 replicates eachGroups 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: Phospho-JNK agonists show promising effects for the treatment of hepatocellular carcinomaiScience · 2026

Summary (written by the submitters)

In our previous study, we repurposed JNK-IN-5A to targeting PKLR gene which most co-related to hepatocellular carcinoma (HCC). Here, We showed anti HCC effect of JNK-IN-5A and its six derivative compounds SET135, SET156, SET158, SET159, SET171, and SET172 in HepG2 human HCC cell line. Compare to multi-target kinase inhibitor sorafenib and regorafenib, JNK-IN-5A and its 6 derivatives showed p53 induced cell cycle arrest, autophagy, apoptosis and reduced invasiveness.

Read the full summary ↓

We found two derivatives which also has its own necrotic cell death pathway. SET135 showed p62/SQSTM1 induced autophgic necrotic cell death, and SET171 increased cellular ROS and lipid peroxidation induced necrotic cell death. Bioinformatics analysis also confirmed new derivatives has distinctive different cellular effect with stronger cell cycle arrest and apoptosis compare to sorafenib and regorfenib. Our new derivatives of JNK-IN-5A which has apoptotic and necrotic cell death inducer can be suggested as a new HCC drug candidate.

Published in

Phospho-JNK agonists show promising effects for the treatment of hepatocellular carcinoma

Kim W, Jin H, Miao P et al. · iScience 2026 · PMID 42211113 · doi:10.1016/j.isci.2026.116005

This dataset

Open GSE255617 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 GSE255617_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 PRJNA1075778 and SRA study SRP489485. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42211113) ↗

Study design

10 conditions, mostly with about 4 replicates each

HepG2, Control, ×4 HepG2, SET135, ×4 HepG2, SET156, ×4 HepG2, SET158, ×4 HepG2, SET159, ×4 HepG2, SET171, ×4 HepG2, SET172, ×4 HepG2, JNK-IN-5A, ×4 +2 more

Supports a between-group comparison across 40 samples.

How we read this: 10 replicated groups read from 40 sample titles; they account for 40 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

GSM8076112 HepG2, Control, rep1 HepG2, Control,
GSM8076113 HepG2, Control, rep2 HepG2, Control,
GSM8076114 HepG2, Control, rep3 HepG2, Control,
GSM8076115 HepG2, Control, rep4 HepG2, Control,
GSM8076116 HepG2, SET135, rep1 HepG2, SET135,
GSM8076117 HepG2, SET135, rep2 HepG2, SET135,
GSM8076118 HepG2, SET135, rep3 HepG2, SET135,
GSM8076119 HepG2, SET135, rep4 HepG2, SET135,
GSM8076120 HepG2, SET156, rep1 HepG2, SET156,
GSM8076121 HepG2, SET156, rep2 HepG2, SET156,
GSM8076122 HepG2, SET156, rep3 HepG2, SET156,
GSM8076123 HepG2, SET156, rep4 HepG2, SET156,
GSM8076124 HepG2, SET158, rep1 HepG2, SET158,
GSM8076125 HepG2, SET158, rep2 HepG2, SET158,
GSM8076126 HepG2, SET158, rep3 HepG2, SET158,
GSM8076127 HepG2, SET158, rep4 HepG2, SET158,
GSM8076128 HepG2, SET159, rep1 HepG2, SET159,
GSM8076129 HepG2, SET159, rep2 HepG2, SET159,
GSM8076130 HepG2, SET159, rep3 HepG2, SET159,
GSM8076131 HepG2, SET159, rep4 HepG2, SET159,
GSM8076132 HepG2, SET171, rep1 HepG2, SET171,
GSM8076133 HepG2, SET171, rep2 HepG2, SET171,
GSM8076134 HepG2, SET171, rep3 HepG2, SET171,
GSM8076135 HepG2, SET171, rep4 HepG2, SET171,
GSM8076136 HepG2, SET172, rep1 HepG2, SET172,
GSM8076137 HepG2, SET172, rep2 HepG2, SET172,
GSM8076138 HepG2, SET172, rep3 HepG2, SET172,
GSM8076139 HepG2, SET172, rep4 HepG2, SET172,
GSM8076140 HepG2, JNK-IN-5A, rep1 HepG2, JNK-IN-5A,
GSM8076141 HepG2, JNK-IN-5A, rep2 HepG2, JNK-IN-5A,
GSM8076142 HepG2, JNK-IN-5A, rep3 HepG2, JNK-IN-5A,
GSM8076143 HepG2, JNK-IN-5A, rep4 HepG2, JNK-IN-5A,
GSM8076144 HepG2, Regorafenib, rep1 HepG2, Regorafenib,
GSM8076145 HepG2, Regorafenib, rep2 HepG2, Regorafenib,
GSM8076146 HepG2, Regorafenib, rep3 HepG2, Regorafenib,
GSM8076147 HepG2, Regorafenib, rep4 HepG2, Regorafenib,
GSM8076148 HepG2, Sorafenib, rep1 HepG2, Sorafenib,
GSM8076149 HepG2, Sorafenib, rep2 HepG2, Sorafenib,
GSM8076150 HepG2, Sorafenib, rep3 HepG2, Sorafenib,
GSM8076151 HepG2, Sorafenib, rep4 HepG2, Sorafenib,

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