A novel pathological feature that can affect the prognosis of IgA nephropathy was found by pathomics

 

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A novel pathological feature that can affect the prognosis of IgA nephropathy was found by pathomics

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Zhenliang
FAN
Zhenliang FAN fanmlov@sina.cn The First Affiliated Hospital of Zhejiang Chinese Medical University Nephrology Department Hangzhou China *
Yan LIU ly06012025@163.com The First Affiliated Hospital of Zhejiang Chinese Medical University Nephrology Department Hangzhou China -
Wenze JIANG jiangwenze1997@163.com The Third Affiliated Hospital of Zhejiang Chinese Medical University Nephrology Department Hangzhou China -
Qiaorui YANG qiaorui.rui@163.com Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine Department of Gynecology Shanghai China -
Hong XIA xiahongaini@126.com The First Affiliated Hospital of Zhejiang Chinese Medical University Nephrology Department Hangzhou China -
Keda LU lukedaq@126.com The Third Affiliated Hospital of Zhejiang Chinese Medical University Nephrology Department Hangzhou China -
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IgA nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. However, there are still many limitations in using renal pathology to assess the risk of progression of IgAN. As emerging technologies, pathomics can assist renal pathologists in discovering subvisual features, and becoming an important tool for assessing the risk of IgAN progression. This study utilize pathomics to identify valuable subvisual features in renal pathology for the prognosis of IgAN, and further validate the clinical value of these features.

In this study, we selected 285 patients who underwent renal biopsy at Zhejiang Provincial Hospital of Chinese Medicine, Zhejiang Provincial Zhongshan Hospital, Zhejiang Provincial Dongfang Hospital, and Jiangshan Hospital of Chinese Medicine from January 1, 2017 to January 1, 2020 and were diagnosed with primary IgAN. We randomly selected 200 patients to train the deep learning model, and the remaining 85 patients were used for validation. We obtained whole-slide images (WSI) for HE, PAS, Masson and PASM of this patients and divided the WSI into 512×512 pixel patches at magnification of 100x, 200x, and 400x. After removing the blank patches, we applied the Vahadane method to standardize the color of all patches. The Residual Network 18 is utilized for deep learning to predict the risk of each patch experiencing the study outcome, and then the prediction probabilities of each patch are aggregated onto the corresponding WSI using the multi-instance learning. We used principal component analysis to reduce the dimension of the data and selected the optimal magnification rate based on the C-index of the Cox model. We also used visualization techniques to project the prediction of the patch on the optimal condition onto the WSI. Finally, we invited renal pathologists to summarize all the patches and identify the pathological features with prognostic value. Additionally, we invited another renal pathologist to conduct independent validation on the validation set patients to confirm the value of the features discovered by the pathomics.

We found the prognostic model constructed using deep learning  (0.837±0.051) significantly outperforms the Lee grading(0.676±0.059) and Oxford classification(0.766±0.055) in predicting the occurrence of the adverse study outcome in IgAN. And we found that the pathological features of deep learning mainly focused on ‘renal tubular atrophy with inflammatory cell infiltration’, and through independent validation by renal pathologists on patients in the validation set, this feature proved to be of great value in predicting the prognosis of patients with IgAN.

This study utilized pathomics to identify renal tubular atrophy with inflammatory cell infiltration is associated with the progression risk of IgAN. It is expected to complement the Oxford Classification (MEST-CL), thereby enabling a more accurate assessment of the prognosis of patients with IgAN. 

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