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CYD-4-61 Suppresses Gastric Tumor Growth by Targeting SOX9–CDK4–Driven Oncogenic Programs and Enhances Anti-PD-1 Therapy

GSE316970 Homo sapiens (human) Single-cell RNA-seq 18 samples Submitted 2026/05/01 Platform GPL16791
At a glance

Single-cell RNA-seq · human · 18 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Topic
Gastric cancerThis series is part of our curated briefing on it.
Samples
18 samples: 6 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.
Summary (written by the submitters)
Gastric adenocarcinoma (GAC), particularly with peritoneal carcinomatosis, remains highly lethal and therapeutically refractory. We investigated the anti-tumor activity and mechanisms of CYD-4-61, a small-molecule BAX activator, with emphasis on the SOX9–CDK4 oncogenic axis and tumor immune microenvironment. CYD-4-61 efficacy was evaluated using in vitro GAC models and in vivo xenograft, genetically engineered, and syngeneic mouse models.
Read the full summary ↓
Bulk, single-cell, and spatial transcriptomics, along with molecular and functional assays, were used to define apoptotic, cell-cycle, and immune-related mechanisms. CYD-4-61 induced BAX-dependent apoptosis and suppressed proliferation, stem-like properties, and tumor growth across multiple GAC models. Transcriptomic analyses revealed inhibition of SOX9-dependent programs, including CDK4, and activation of apoptotic and inflammatory pathways. CYD-4-61 destabilized SOX9 via caspase-dependent cleavage, inhibited cell-cycle progression, activated STING signaling, and enhanced response to PD-1 blockade in immunocompetent models. CYD-4-61 exerts potent anti-tumor effects in GAC by targeting SOX9–CDK4–driven oncogenic programs and modulating immune signaling, supporting its development as a therapeutic agent alone or in combination with immunotherapy.
This dataset
Open GSE316970 in finder → Find more human RNA-seq datasets → Gastric cancer 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 GSE316970_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1405615 and SRA study SRP664751. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
CYD-4-61 treated GA0518 cells biol ×3 CYD-4-61 treated GA0518 SOX9 KO cells biol ×3 AGS CYD-4-61 treatment biol ×3 AGS control biol ×3 GA0518 CYD-4-61 treatment biol ×3 GA0518 Control biol ×3

Supports a case/control comparison: 6 samples read as cases, 6 as controls.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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 Gastric cancer datasets

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