Machine learning-based plasma-derived extracellular vesicle signatures for digestive system cancers prediction

Background

Digestive system cancers (DSCs) represent a heterogeneous group of malignancies characterized by a poor prognosis and a lack of accurate early diagnostic methods. While traditional serological biomarkers and non-coding RNA continue to be commonly diagnostic marker for these cancers, their sensitivity and specificity in detection are often limited. RNA in plasma-derived extracellular vesicles (PDEV) has emerged as a promising diagnostic tool for a variety of cancers, but its application in the detection of various DSCs has not yet been fully explored.

Methods

By integrating PDEV sequencing data from the exoRBase 2.0 database, a total of 444 participants were included in the study, including 326 patients of DSCs, and 118 healthy individuals. The dataset was divided into training and test sets. The PDEV-diagnostic model was constructed using various machine learning algorithms and underwent 5-fold cross-validation in the training sets. The model's performance metrics were further evaluated in the test set. Additionally, the features were assessed using bulk RNA-seq and single RNA-seq datasets for different DSCs.

Results

Based on various feature selection methods and a comparison of 10 machine learning algorithms using seven metrics, the XGBoost model was selected as the PDEV-diagnostic model, with an AUC of 0.83 and 0.94 in the training and test sets, respectively, and 9 exosome predictors, including BANK1, MALAT1, FGA, UBR4, ILR-7,FGB, PLPP5,PCAT19, and CIITA for DSCs prediction.

Conclusions

The machine learning-based PDEV diagnostic models exhibit remarkable accuracy in identifying patients of DSCs. These nine exosomal mRNAs/lncRNAs consequently showed promise as non-invasive biomarkers for DSCs diagnosis.