FRET-SAM: SAM_Med2D-based automatic FRET two-hybrid analysis

Abstract

Background and objective: The fluorescence resonance energy transfer (FRET) two-hybrid assay enables quantification of the stoichiometry and binding affinity of protein interactions directly in living cells, but its broader application remains constrained by labor-intensive manual image analysis and high computational complexity. This study leverages deep learning to accurately extract FRET two-hybrid image signals and automate the FRET two-hybrid analysis process, thereby eliminating subjective bias and enhancing the method's efficiency and accuracy.

Methods: Based on the Segment Anything Model (SAM), we developed FRET-SAM, an optimized analysis method adapting SAM_Med2D's structure for automated regions of interest (ROI) selection and fluorescence signal extraction in FRET two-hybrid images. A comprehensive FRET image dataset was established, including six model plasmids (C4Y, C10Y, C40Y, C80Y, C32V and CVC) and three functional FRET pairs (Bcl-XL-CFP/Bak-YFP, EGFR-CFP/Grb2-YFP and RAF-CFP/RAS-YFP), for model training and validation. Model segmentation performance was assessed by comparing its mean pixel accuracy (MPA), mean intersection over union (MIoU), and Dice coefficient against the original SAM_Med2D model. To assess protein interaction results, FRET-SAM-derived values were compared to established literature values, using relative error as a key metric of consistency.

Results: The FRET-SAM model exhibited enhanced segmentation accuracy, with MPA, MIoU, and Dice coefficient increasing by 2.88%, 2.36%, and 2.19%, respectively, compared to the original SAM_Med2D model. Validation experiments demonstrated high consistency between FRET-SAM-derived results and literature values, with all plasmid models exhibiting relative errors that were individually calculated and confirmed to be under 5%. Furthermore, FRET-SAM exhibited robust drug screening potential in three biomedical case studies: (1) EGFR-Grb2-targeted lung cancer intervention (gefitinib), (2) RAS-RAF-mediated hepatocellular carcinoma suppression (sorafenib), and (3) Bcl-XL inhibitors discovery (A-1331852). Mechanistic studies confirmed its ability to resolve drug-target interactions.

Conclusions: By enabling automated analysis of FRET images, FRET-SAM significantly enhances the efficiency and accuracy of FRET two-hybrid assays, while eliminating subjective bias. The capability of FRET-SAM to resolve drug-target interactions establishes it as a promising tool for drug discovery.

Keywords: Automatic image processing; FRET; FRET two-hybrid analysis; SAM_Med2D.