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J. Adv. Res., Available online 1 October 2023 | https://doi.org/10.1016/j.jare.2023.09.043 Immune response and mesenchymal transition of papillary thyroid carcinoma reflected in ultrasonography features assessed by radiologists and deep learning.

Jandee Lee ^a, Jung Hyun Yoon ^b,1, Eunjung Lee ^c, Hwa Young Lee ^a, Seonhyang Jeong ^d, Sunmi Park ^d, Young Suk Jo ^d, Jin Young Kwak ^b

^aDepartment of Surgery, Open NBI Convergence Technology Research Laboratory, Yonsei Cancer Center, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, South Korea

^bDepartment of Radiology, Severance Hospital, Research Institute of Radiological Science, Yonsei University, College of Medicine, Seoul 03722, South Korea

^cSchool of Mathematics and Computing (Computational Science and Engineering), Yonsei University, Seoul 03722, South Korea

^dDepartment of Internal Medicine, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul 03722, South Korea

¹These authors contributed equally to this work.

Corresponding authors : Young Suk Jo, Jin Young Kwak

Abstract

Ultrasonography (US) features of papillary thyroid cancers (PTCs) are used to select nodules for biopsy due to their association with tumor behavior. However, the molecular biological mechanisms that lead to the characteristic US features of PTCs are largely unknown. This study aimed to investigate the molecular biological mechanisms behind US features assessed by radiologists and three convolutional neural networks (CNN) through transcriptome analysis. Transcriptome data from 273 PTC tissue samples were generated and differentially expressed genes (DEGs) were identified according to US feature. Pathway enrichment analyses were also conducted by gene set enrichment analysis (GSEA) and ClusterProfiler according to assessments made by radiologists and three CNNs - CNN1 (ResNet50), CNN2 (ResNet101) and CNN3 (VGG16). Signature gene scores for PTCs were calculated by single-sample GSEA (ssGSEA). Individual suspicious US features consistently suggested an upregulation of genes related to immune response and epithelial-mesenchymal transition (EMT). Likewise, PTCs assessed as positive by radiologists and three CNNs showed the coordinate enrichment of similar gene sets with abundant immune and stromal components. However, PTCs assessed as positive by radiologists had the highest number of DEGs, and those assessed as positive by CNN3 had more diverse DEGs and gene sets compared to CNN1 or CNN2. The percentage of PTCs assessed as positive or negative concordantly by radiologists and three CNNs was 85.6% (231/273) and 7.1% (3/273), respectively. US features assessed by radiologists and CNNs revealed molecular biologic features and tumor microenvironment in PTCs.

논문정보

형식Research article
게재일2023년 10월 (BRIC 등록일 2023-10-05)
연구진국내 연구진
분야 의약학 > 종양의학

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