Transcriptome analysis and artificial intelligence for predicting lymph node metastasis of esophageal squamous cell
Zhengang Zhao1, Yujie Xie2, Dongmei Lai3
1Department of Thoracic Surgery, Gaozhou People's Hospital Affiliated to Guangdong Medical University, Maoming, China.
Background:
Lymph node metastasis (LNM) is the most common route of metastasis in esophageal squamous cell carcinoma (ESCC), and the treatment of patients with ESCC largely depends on the LNM status. The methods for diagnosing LNM in ESCC are still not accurate enough, and accurate LNM staging is crucial for clinical practice. The purpose of this study was to investigate the value of combining transcriptome analysis with artificial intelligence (AI) in predicting LNM and to construct an effective predictive model for LNM in ESCC.
Methods:
We first enrolled 36 patients with ESCC for RNA sequencing (RNA-seq) to identify the differentially expressed messenger RNA (mRNAs), and then selected candidate genes via a random forest machine learning algorithm. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression of three candidate genes. For the assessment of the overall survival (OS) of patients with ESCC, we used the Kaplan-Meier method and the log-rank test. Univariate and multivariate logistic regression analyses were performed to screen for risk model factors. The model was validated with the area under the curve (AUC) and visualized through a nomogram. For AI model building, random forest was conducted. We included five variables to create the AI model, and divided the data from 209 patients into a training set and a validation set to evaluate the model's performance. Thereafter, receiver operating characteristic (ROC) curves and the AUC were used to validate the AI system and to conduct subgroup analyses.
Results:
RNA-seq identified 2,837 genes that were differentially expressed in ESCC tissues with LNM. We used a random forest machine learning algorithm to eliminate candidate diagnostic genes for patients with ESCC with LNM, with the three most diagnostic genes being SIM2, CUX1, and CYP4B1. Analysis of OS indicated that patients with LNM had a worse prognosis. Low expression levels of SIM2 were negatively correlated with OS. However, high expression levels of CUX1 or CYP4B1 were negatively correlated with OS. We added five independent influencing factors to the risk model via univariate and multivariate logistic regression analyses. In the ROC curve analysis, the AUC for the most effective logistic regression model was 0.83. A nomogram was used to display the predictive variables. Finally, these five variables were used to create the AI model, and the AUC was 0.78. Moreover, the subgroup analysis indicated that the AI model that incorporated only the T3 clinical tumor stage yielded an AUC of 0.78.
Conclusions:
AI and transcriptome analysis can be used to create a risk model for predicting LNM, and it can enhance prediction accuracy and inform clinical staging and decision-making before surgery.
