Deep learning radiomics model related with genomics phenotypes for lymph node metastasis prediction in colorectal cancer

• Published in: Radiotherapy and oncology 2022-02, Vol.167, p.195-202
• Main Authors: Zhao, Jiaojiao, Wang, Han, Zhang, Yin, Wang, Rui, Liu, Qin, Li, Jie, Li, Xue, Huang, Hanyu, Zhang, Jie, Zeng, Zhaoping, Zhang, Jun, Yi, Zhang, Zeng, Fanxin
• Format: Article
• Language: English
• Subjects: Colorectal cancer; Colorectal Neoplasms - diagnostic imaging; Colorectal Neoplasms - genetics; Colorectal Neoplasms - pathology; Deep Learning; Deep learning model; Genomics; Humans; Lymph node metastasis; Lymph Nodes - diagnostic imaging; Lymph Nodes - pathology; Lymphatic Metastasis - pathology; Phenotype; Retrospective Studies; Transcriptomics
• ISSN: 0167-8140; 1879-0887
• DOI: 10.1016/j.radonc.2021.12.031

•The deep learning radiomics model showed good performance in lymph node metastasis (LNM) prediction of colorectal cancer (CRC) patients.•The genes correlated to selected deep learning features mainly enriched in catabolic processes and immune-related pathways in CRC patients.•The genes in the immune pathways significantly decreased from non-LNM to LNM in CRC patients. The preoperative lymph node (LN) status is important for the treatment of colorectal cancer (CRC). Here, we established and validated a deep learning (DPL) model for predicting lymph node metastasis (LNM) in CRC. A total of 423 CRC patients were divided into cohort 1 (training set, n = 238, testing set, n = 101) and cohort 2 (validation set, n = 84). Among them, 84 patients’ tumour tissues were collected for RNA sequencing. The DPL features were extracted from enhanced venous-phase computed tomography of CRC using an autoencoder. A DPL model was constructed with the least absolute shrinkage and selection operator algorithm. Carcinoembryonic antigen and carbohydrate antigen 19-9 were incorporated into the DPL model to construct a combined model. The model performance was assessed by receiver operating characteristic curves, calibration curves and decision curves. The correlations between DPL features, which have been selected, and genes were analysed by Spearman' correlation, and the genes correlated with DPL features were used to transcriptomic analysis. The DPL model, integrated with 20 DPL features, showed a good discrimination performance in predicting the LNM, with areas under the curves (AUCs) of 0.79, 0.73 and 0.70 in the training set, testing set and validation set, respectively. The combined model had a better performance, with AUCs of 0.81, 0.77 and 0.73 in the three sets, respectively. Decision curve analysis confirmed the clinical application value of the DPL model and combined model. Furthermore, catabolic processes and immune-related pathways were identified and related with the selected DPL features. This study presented a DPL model and a combined model for LNM prediction. We explored the potential genomic phenotypes related with DPL features. In addition, the model could potentially be utilized to facilitate the individualized prediction of LNM in CRC.