Deep learning-based quantitative assessment of renal chronicity indices in lupus nephritis

Renal chronicity indices (CI) have been identified as strong predictors of long-term outcomes in lupus nephritis (LN) patients. However, assessment by pathologists is hindered by challenges such as substantial time requirements, high interobserver variation, and susceptibility to fatigue. This study aims to develop an effective deep learning (DL) pipeline that automates the assessment of CI and provides valuable prognostic insights from a disease-specific perspective. We curated a dataset comprising 282 slides obtained from 141 patients across two independent cohorts with a complete 10-years follow-up. Our DL pipeline was developed on 60 slides (22,410 patch images) from 30 patients in the training cohort and evaluated on both an internal testing set (148 slides, 77,605 patch images) and an external testing set (74 slides, 27,522 patch images). The study included two cohorts with slight demographic differences, particularly in age and hemoglobin levels. The DL pipeline showed high segmentation performance across tissue compartments and histopathologic lesions, outperforming state-of-the-art methods. The DL pipeline also demonstrated a strong correlation with pathologists in assessing CI, significantly improving interobserver agreement. Additionally, the DL pipeline enhanced prognostic accuracy, particularly in outcome prediction, when combined with clinical parameters and pathologist-assessed CIs. The DL pipeline demonstrated accuracy and efficiency in assessing CI in LN, showing promise in improving interobserver agreement among pathologists. It also exhibited significant value in prognostic analysis and enhancing outcome prediction in LN patients, offering a valuable tool for clinical decision-making.