ArticleEndocrine2025
Consensus nonnegative matrix factorization reveals metastatic gene expression program and identifies E74-like ETS transcription factor 3 confers to the lymph nodes metastasis in papillary thyroid cancer.
Article in Endocrine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Cell-state transitions and microenvironmental remodeling in thyroid cancer progression revealed by single-cell and spatial transcriptomics.Frontiers in immunology · 2026Review
- ScLineageAtlas: a comprehensive single-cell genomics database for characterizing cellular clones in cancer.Database : the journal of biological databases and curation · 2025Article
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Authors and funding
11 authors.
Funding
Abstract
backgroundAdvanced papillary thyroid carcinoma (PTC) exhibits significant heterogeneity. Understanding the gene expression programs underlying tumor heterogeneity is crucial for improving diagnostic and therapeutic strategies.
methodsWe integrated single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data to explore transcriptional heterogeneity in PTC. Using consensus nonnegative matrix factorization (cNMF), we identified gene expression programs (GEPs) within malignant cells. A machine learning framework was applied to establish a lymph node metastasis (LNM) signature. Functional validation of key genes was performed through in vitro experiments, and drug screening was conducted to identify potential therapeutic candidates.
resultsWe identified an epithelial-mesenchymal transition (EMT)-related gene expression program, GEP3, which was strongly associated with LNM and poor clinical outcomes in PTC. Within the GEP3
conclusionsThis study highlights the critical role of GEP and ELF3 in driving PTC progression and metastasis. Drug screening revealed that tanespimycin and vemurafenib were effective in targeting GEP3
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