GEO series

Characterization of cholangiocarcinoma cell line-derived xenograft (CDX) tumors

GSE298419 Homo sapiens (human) Single-cell RNA-seq 15 samples Submitted 2026/06/08 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 15 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: 15 samples: 5 × CDX, HuCC-A1, vs 5 × CDX, EGI-1, vs 5 × CDX, HuCC-T1,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 GSE298419 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 GSE298419_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 PRJNA1269319 and SRA study SRP588490. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42234772) ↗

Study design

5 × CDX, HuCC-A1, vs 5 × CDX, EGI-1, vs 5 × CDX, HuCC-T1,

Supports a between-group comparison across 15 samples.

How we read this: 3 replicated groups read from 15 sample titles; they account for 15 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

GSM9014046 CDX, HuCC-A1, rep1 CDX, HuCC-A1,
GSM9014047 CDX, HuCC-A1, rep2 CDX, HuCC-A1,
GSM9014048 CDX, HuCC-A1, rep3 CDX, HuCC-A1,
GSM9014049 CDX, HuCC-A1, rep4 CDX, HuCC-A1,
GSM9014050 CDX, HuCC-A1, rep5 CDX, HuCC-A1,
GSM9014051 CDX, EGI-1, rep1 CDX, EGI-1,
GSM9014052 CDX, EGI-1, rep2 CDX, EGI-1,
GSM9014053 CDX, EGI-1, rep3 CDX, EGI-1,
GSM9014054 CDX, EGI-1, rep4 CDX, EGI-1,
GSM9014055 CDX, EGI-1, rep5 CDX, EGI-1,
GSM9014056 CDX, HuCC-T1, rep1 CDX, HuCC-T1,
GSM9014057 CDX, HuCC-T1, rep2 CDX, HuCC-T1,
GSM9014058 CDX, HuCC-T1, rep3 CDX, HuCC-T1,
GSM9014059 CDX, HuCC-T1, rep4 CDX, HuCC-T1,
GSM9014060 CDX, HuCC-T1, rep5 CDX, HuCC-T1,

Datasets on a similar topic

GSE298420 Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1 (RNA-Seq of HuCC-A1 CDX tumors short treatment) 12 samples shares cdx, cholangiocarcinoma
GSE261998 Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1(HuCC-A1 CDX tumors) 10 samples shares cdx, cholangiocarcinoma
GSE277629 RNA-seq of AsPC-1 cell line-derived xenograft mouse tumors treated with a MEK-RAF molecular glue, IK-595 24 samples shares line-derived, xenograft
GSE237624 Induction of CDX2 as a differentiation therapy in colorectal cancers [cell lines] 12 samples shares cdx
GSE237626 Induction of CDX2 as a differentiation therapy in colorectal cancers 57 samples shares cdx
GSE237623 Induction of CDX2 as a differentiation therapy in colorectal cancers [CRC organoids] 39 samples shares cdx
GSE319124 Next-GenerationPediatric Cancer Models: Patient-Matched Orthotopic Xenografts, 3D Organoids, 2D Cultures, and Cell Lines for Identification of Therapeutic Vulnerabilities in Pediatric Solid Tumors [scRNAseq] 59 samples shares xenograft
GSE276348 The olfactory receptor OR51E2 regulates prostate cancer aggressiveness and modulates STAT3 in prostate cancer cells and in xenograft tumors 17 samples shares xenograft

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