Automatic quantification of breast cancer biomarkers from multiple 18F-FDG PET image segmentation

TL;DR

This paper presents an automated deep learning system for segmenting breast tumors in 18F-FDG PET scans and extracting biomarkers to assess tumor evolution after chemotherapy, showing high accuracy and strong correlation with manual methods.

Contribution

The study introduces a fine-tuned nnUNet-based pipeline for automatic breast tumor segmentation and biomarker extraction from PET scans, improving accuracy and enabling automated cancer progression assessment.

Findings

Deep learning model achieved DSC of 0.89 on baseline PET scans.

Automated biomarkers strongly correlated with manual measurements.

Significant decrease in SUVmax, MTV, and TLG after chemotherapy.

Abstract

Neoadjuvant chemotherapy (NAC) has become a standard clinical practice for tumor downsizing in breast cancer with 18F-FDG Positron Emission Tomography (PET). Our work aims to leverage PET imaging for the segmentation of breast lesions. The focus is on developing an automated system that accurately segments primary tumor regions and extracts key biomarkers from these areas to provide insights into the evolution of breast cancer following the first course of NAC. 243 baseline 18F-FDG PET scans (PET_Bl) and 180 follow-up 18F-FDG PET scans (PET_Fu) were acquired before and after the first course of NAC, respectively. Firstly, a deep learning-based breast tumor segmentation method was developed. The optimal baseline model (model trained on baseline exams) was fine-tuned on 15 follow-up exams and adapted using active learning to segment tumor areas in PET_Fu. The pipeline computes biomarkers such as maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), and total lesion glycolysis (TLG) to evaluate tumor evolution between PET_Fu and PET_Bl. Quality control measures were employed to exclude aberrant outliers. The nnUNet deep learning model outperformed in tumor segmentation on PET_Bl, achieved a Dice similarity coefficient (DSC) of 0.89 and a Hausdorff distance (HD) of 3.52 mm. After fine-tuning, the model demonstrated a DSC of 0.78 and a HD of 4.95 mm on PET_Fu exams. Biomarkers analysis revealed very strong correlations whatever the biomarker between manually segmented and automatically predicted regions. The significant average decrease of SUVmax, MTV and TLG were 5.22, 11.79 cm3 and 19.23 cm3, respectively. The presented approach demonstrates an automated system for breast tumor segmentation from 18F-FDG PET. Thanks to the extracted biomarkers, our method enables the automatic assessment of cancer progression.