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Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1 (RNA-Seq of HuCC-A1 CDX tumors short treatment)

GSE298420 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2026/06/08 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 12 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)
Samples
12 samples: 3 × CDX, HuCC-A1, Isotype 48h, batch1, vs 3 × CDX, HuCC-A1, Isotype 48h, batch2, vs 3 × CDX, HuCC-A1, H3L3 48h, batch1, vs 3 × CDX, HuCC-A1, H3L3 48h, batch2,Groups 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
Claudin-1 targeting suppresses tumor growth, invasion, and metastasis in patient-derived cholangiocarcinoma modelsScience translational medicine · 2026
Summary (written by the submitters)
Cholangiocarcinoma (CCA) is an adenocarcinoma of the hepatobiliary system showing an alarming rise in incidence and mortality with unsatisfactory treatment options. Claudin-1 (CLDN1) is a transmembrane protein expressed in tight junctions and exposed on the cell surface in liver fibrosis and cancer. Using single cell RNA-sequencing (scRNA-Seq) and spatial transcriptomics of CCA patient tissues, we show that CLDN1 expression is highly upregulated in cancer cells and is associated with stemness and cell fate.
Read the full summary ↓
Gain-of-function studies in CCA orthotopic in vivo mouse models showed decreased survival and enhanced tumor growth, unraveling a functional role of CLDN1 as an oncogenic driver. Targeting exposed CLDN1 using highly specific CLDN1 monoclonal antibodies (mAbs) robustly inhibited tumor growth across CCA CDX and PDX mouse models and patient-derived CCA organoids including tumors with medium or low CLDN1 expression. Moreover, antibody treatment markedly inhibited tumor cell migration, invasion, and extrahepatic metastasis. Mechanistically, targeting exposed CLDN1 on CCA tumors inhibited Notch1, FAK/SRC, and Hippo-YAP signaling, resulting in decreased cancer cell stemness, EMT and extracellular matrix remodeling. In conclusion, these results uncover CLDN1 as a previously undiscovered CCA driver and therapeutic target, paving the way for the clinical development of CLDN1 mAbs to improve the dismal outcome of patients with advanced CCA.
Published in
Claudin-1 targeting suppresses tumor growth, invasion, and metastasis in patient-derived cholangiocarcinoma models
Nehme Z, Muller M, Brochon J et al. · Science translational medicine 2026 · PMID 42234772 · doi:10.1126/scitranslmed.adp2595
This dataset
Open GSE298420 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 GSE298420_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 PRJNA1269320 and SRA study SRP588491. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42234772) ↗
Study design
3 × CDX, HuCC-A1, Isotype 48h, batch1, vs 3 × CDX, HuCC-A1, Isotype 48h, batch2, vs 3 × CDX, HuCC-A1, H3L3 48h, batch1, vs 3 × CDX, HuCC-A1, H3L3 48h, batch2,

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
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