biostudies-arrayexpressFlorian WegwitzMus musculusnahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15010We employed high-throughput sequencing with spatial resolution in the WAP-T mouse model of basal-like breast cancer (BLBC) to investigate the transcriptomic response to radiation therapy (RT). Our analysis revealed a distinct spatial pattern of gene expression (10X visium platform), with irradiated BLBC tumors exhibiting a strong enrichment of epithelial genes and a hybrid epithelial/mesenchymal (E/M) state. Notably, MUC1 expression was upregulated in response to RT, suggesting its role as a key driver of cell survival. These findings provide new insights into the spatial transcriptomic landscape of BLBC under RT and highlight the potential of MUC1 as a therapeutic target or prognostic marker for optimizing patient response to RT.biostudies-arrayexpressSample Collection - Tumor samples were embedded in cryomatrix, sectioned at 10 µm thickness using a Leica cryostat, and mounted onto Visium Spatial Gene Expression Slides (PN-2000233). Slide Serial Number: V21S08-020-A1Sequencing - Libraries were sequenced at the BGI facility in Hong-Kong using the DNBSEQ-G400 platform. The sequencing method utilized was paired-end (PE), with read lengths of 28 bases for the first read, 100 bases for the second read, and 10 bases each for the index and UMI reads, respectively.Growth Protocol - 1x10^6 pH8N8 tumor cells were orthotopically implanted into the right abdominal mammary gland of syngeneic female WAP-T-NP8 mice. The mice were housed under standard laboratory conditions with controlled temperature and humidity, and they were given ad libitum access to food and water.Nucleic Acid Extraction - RNA was extracted from the cryosections using the Visium Spatial Gene Expression kit following the manufacturer's instructions, specifically optimized for spatial transcriptomics applications.Library Construction - cDNA libraries were constructed using the Visium Spatial Gene Expression Kit, following the manufacturer's protocol (Rev A).Sample Treatment - When tumor volumes reached 300 mm³, four female mice (average body mass 25.8±4.6 g, age 131.4±42.1 days) received irradiation with the XCELL RS225 device. The total dose of 11 Gy was administered as 1.1 Gy daily for 5 days, followed by 2 resting days, and another 5 days of 1.1 Gy. Five untreated tumor-bearing mice (average body mass 25.7±6.5 g, age 118.9±44.4 days) served as controls, evaluating the irradiation effects on tumor development. Tumors were harvested 24H after the last treatment.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Data normalization and transformation were performed in the R environment (v 4.4.1) using the Seurat package (v 5.1.0).Sequence Alignment - Transcriptomic data were aligned to the mouse genome reference mm10-2020-A using the Space Ranger pipeline, version 3.0.0.UnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G400RNA-seq of coding RNA from single cellsMus musculusFlorian WegwitzfalseBasal-like breast cancer stimulates MUC1 to support an epithelial/mesenchymal hybrid state and survive radiotherapyWe employed high-throughput sequencing with spatial resolution in the WAP-T mouse model of basal-like breast cancer (BLBC) to investigate the transcriptomic response to radiation therapy (RT). Our analysis revealed a distinct spatial pattern of gene expression (10X visium platform), with irradiated BLBC tumors exhibiting a strong enrichment of epithelial genes and a hybrid epithelial/mesenchymal (E/M) state. Notably, MUC1 expression was upregulated in response to RT, suggesting its role as a key driver of cell survival. These findings provide new insights into the spatial transcriptomic landscape of BLBC under RT and highlight the potential of MUC1 as a therapeutic target or prognostic marker for optimizing patient response to RT.2026-03-19T00:00:00Z2026-03-19T02:03:21.372Z2025-04-04T12:13:41.772ZE-MTAB-15010ERP171270EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969