SecProGNN: Predicting Bronchoalveolar Lavage Fluid Secreted Protein Using Graph Neural Network

Bronchoalveolar lavage fluid (BALF) is a liquid obtained from the alveoli and bronchi, often used to study pulmonary diseases. So far, proteomic analyses have identified over three thousand proteins in BALF. However, the comprehensive characterization of these proteins remains challenging due to their complexity and technological limitations. This paper presented a novel deep learning framework called SecProGNN, designed to predict secretory proteins in BALF. Firstly, SecProGNN represented proteins as graph-structured data, with amino acids connected based on their interactions. Then, these graphs were processed through graph neural networks (GNNs) model to extract graph features. Finally, the extracted feature vectors were fed into a multi-layer perceptron (MLP) module to predict BALF secreted proteins. Additionally, by utilizing SecProGNN, we investigated potential biomarkers for lung adenocarcinoma and identified 16 promising candidates that may be secreted into BALF.