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Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression

Abstract

Papillary thyroid cancer (PTC) is the most common endocrine cancer, with a good prognosis in most cases. However, aggressive PTC can metastasise or reoccur and become refractory disease. Therefore, it’s urgent to uncover new biomarkers for aggressive PTC. Accumulating evidence suggests that aberrant enhancers and targeted gene transcription drive the progression of PTC. To identify the cancer-specific enhancers and their downstream genes in PTC, we profiled the transcriptomes (RNA-seq) and enhancer-based epigenomic reorganisation (ChIP-seq) of cancer tissues and matched normal tissues from three PTC patients. Importantly, six candidate genes (RHBDF1, FAM20C, PHLDA2, TMPRSS6, LAD1, and BGN) were identified to be consistently upregulated by enhancers in PTC and correlated with prognosis. Further experiments verified the function of enhancers governing FAM20C in regulating PTC tumorigenesis, thereby unveiling a FAM20C-governed oncogenic mechanism for suppressing two cytokines (TNF-α and TGF-β) in PTC. Additionally, we demonstrated that a FAM20C inhibitor (3r) suppressed the proliferation and invasion of thyroid cancer cells in vitro and vivo. Moreover, FAM20C is driven by KLF12 through its enhancer. Collectively, our study uncovers the potential correlations between the aberrant activation of cancer-specific enhancers and PTC tumorigenesis and identifies FAM20C as a novel target for PTC.

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Fig. 1: Enhancer landscape of papillary thyroid carcinoma (PTC).
Fig. 2: Transcriptome analysis of gene expression in PTC tissues and paired normal tissues.
Fig. 3: Identification of target genes that may be regulated by cancer-specific enhancers.
Fig. 4: Further screening for oncogenes was performed using The Cancer Genome Atlas (TCGA) database.
Fig. 5: FAM20C is an enhancer-driven gene.
Fig. 6: FAM20C knockdown inhibits thyroid cancer progression in vitro and in vivo.
Fig. 7: FAM20C knockdown activates the TNF signalling pathway while inhibiting the TGF-β signalling pathway in thyroid cancer.
Fig. 8: Antitumour effects of 3r in thyroid cancer cells.
Fig. 9: Transcription factor KLF12 increases FAM20C expression in PTC.

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Data availability

The ChIP-seq and RNA-seq data generated in this study have been deposited to the NCBI Gene Expression Omnibus (GEO) with the accession codes GSE224355, GSE224356 and Sequence Read Archive (SRA) under accession number PRJNA1070988. The corresponding author can provide all other data to support this study upon reasonable request. The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

We thank Prof. Yupeng Chen (Tianjin Medical University) and Prof. Nan Qin (Tianjin Medical University) for generously providing technical support and helpful discussion and suggestions.

Funding

This work was supported by grants from the National Natural Science Foundation of China (82172821, 82103386, 82272721, 82103234), Tianjin Municipal Science and Technology Project (19JCYBJC27400, 21JCZDJC00360), and Beijing-Tianjin-Hebei Basic Research Cooperation Project (20JCZXJC00120), The Science & Technology Development Fund of Tianjin Education Commission for Higher Education (2021ZD033), Tianjin Medical Key Discipline (Specialty) Construction Project (TJYXZDXK-058B), Tianjin Health Research Project (TJWJ2022XK024).

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Contributions

Xiangqian Zheng: writing—review & editing, writing—original draft, validation, software, resources, methodology, investigation, funding acquisition. Xianhui Ruan: writing—review & editing, validation, software, resources, methodology, investigation, data curation, conceptualisation, funding acquisition. Wei Zhang: writing—review & editing, resources, methodology, investigation, conceptualisation. Xiukun Hou: writing—original draft, validation, software, investigation, formal analysis, data curation. Guiming Fu: resources. Weike Ma: supervision, software, resources, investigation. Jianfeng Huang: writing—original draft, supervision, resources, methodology, investigation. Yuyang Qian: software, project administration, investigation, data curation. Mengran Tian: software, methodology, formal analysis, data curation. Nan Qin: validation, software, investigation. Yupeng Chen: writing—review & editing. Ming Gao: writing—review & editing, supervision, project administration, funding acquisition, conceptualisation. Dapeng Li: writing—review & editing, validation, supervision, project administration, funding acquisition.

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Correspondence to Dapeng Li or Xiangqian Zheng.

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The present study was approved by the Ethics Committee of the Tianjin Medical University Cancer Institute and Hospital (EK2021149), and was performed according to the Declaration of Helsinki.

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Ruan, X., Zhang, W., Hou, X. et al. Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression. Cancer Gene Ther 32, 854–869 (2025). https://doi.org/10.1038/s41417-025-00930-8

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