GEO series

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

GSE261998 Homo sapiens (human) Single-cell RNA-seq 10 samples Submitted 2026/06/08 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 10 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: 10 samples
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 GSE261998 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 GSE261998_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 PRJNA1090012 and SRA study SRP496689. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42234772) ↗

Samples in this study

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+ 10 more — browse all 10 samples with per-sample file links →

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 claudin-1, hucc-a1, cdx, cholangiocarcinoma, monoclonal, antibodies, treatment, humanized
GSE261999 Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1(PDX tumors) 8 samples shares claudin-1, cholangiocarcinoma, monoclonal, antibodies, treatment, humanized
GSE261997 Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1(CCA organoids) 6 samples shares claudin-1, cholangiocarcinoma, monoclonal, antibodies, treatment, humanized
GSE262166 Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1 77 samples shares claudin-1, cholangiocarcinoma, monoclonal, antibodies, treatment, humanized
GSE196393 Targeting non-junctional Claudin-1 with monoclonal antibodies to treat hepatocellular carcinoma 33 samples shares claudin-1, monoclonal, antibodies
GSE196390 Targeting non-junctional Claudin-1 with monoclonal antibodies to treat hepatocellular carcinoma [RNA-seq] 31 samples shares claudin-1, monoclonal, antibodies
GSE196392 Targeting non-junctional Claudin-1 with monoclonal antibodies to treat hepatocellular carcinoma [scRNA-seq] 2 samples shares claudin-1, monoclonal, antibodies
GSE298419 Characterization of cholangiocarcinoma cell line-derived xenograft (CDX) tumors 15 samples shares cdx, cholangiocarcinoma

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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.