Deep Learning–Based Retinoblastoma Protein Subtyping of Pulmonary Large-Cell Neuroendocrine Carcinoma on Small Hematoxylin and Eosin–Stained Specimens

Trandafir, Teodora E. and Heijboer, Frank W.J. and Akram, Farhan and Derks, Jules L. and Li, Yunlei and Hillen, Lisa M. and Speel, Ernst-Jan M. and Megyesfalvi, Zsolt and Dome, Balazs and Stubbs, Andrew P. and Dingemans, Anne-Marie C. and von der Thüsen, Jan H. (2025) Deep Learning–Based Retinoblastoma Protein Subtyping of Pulmonary Large-Cell Neuroendocrine Carcinoma on Small Hematoxylin and Eosin–Stained Specimens. LABORATORY INVESTIGATION, 105 (9). No. 104192. ISSN 00236837

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Abstract

Molecular subtyping of pulmonary large-cell neuroendocrine carcinoma (LCNEC) based on retinoblastoma protein (pRb) expression may influence systemic treatment decisions. Current histomorphologic assessments of hematoxylin and eosinestained tissue samples cannot reliably differentiate LCNEC molecular subtypes. This study explores the potential of deep learning (DL) to identify histologic patterns that distinguish these subtypes, by developing a custom convolutional neural network to predict the binary expression of pRb in small LCNEC tissue samples. Our model was trained, cross-validated, and tested on tissue microarray cores from 143 resection specimens and biopsies from 21 additional patients, with corresponding immunohistochemical pRb status. The best-performing DL model achieved a patient-wise balanced accuracy value of 0.75 and an area under the receiver operating characteristic curve value of 0.77 when tested on biopsies, significantly outperforming the hematoxylin and eosinebased subtype classification by lung pathologists. Explainable artificial intelligence techniques further highlighted coarse chromatin patterns and distinct nucleoli as distinguishing features for pRb retained status. Meanwhile, pRb lost cases were characterized by limited cytoplasm and morphologic similarities with small cell lung cancer. These findings suggest that DL analysis of small histopathology samples could ultimately replace immunohistochemical pRb testing. Such a development may assist in guiding chemotherapy decisions, particularly in metastatic cases.

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