Predicting breast cancer molecular subtypes from H &E-stained histopathological images using a spatial-transcriptomics-based patch filter

The molecular subtype of breast cancer plays an important role in the prognosis of patients and guides physicians to develop scientific therapeutic regimes. In clinical practice, physicians classify molecular subtypes of breast cancer with immunohistochemistry(IHC) technology, which requires a long cycle for diagnosis, resulting in a delay in effective treatment of patients with breast cancer. To improve the diagnostic rate, we proposed a machine learning method that predicted molecular subtypes of breast cancer from H&E-stained histopathological images. Although some molecular subtype prediction methods have been suggested, they are noisy and lack clinical evidence. To address these issues, we introduced a patch filter-based molecular subtype prediction (PFMSP) method using spatial transcriptomics data, training a patch filter with spatial transcriptomics data first, and then the trained filter was used to select valuable patches for molecular subtype prediction in other H&E-stained histopathological images. These valuable patches contained one or more genes expressed of ESR1, ESR2, PGR, and ERBB2. We evaluated the performance of our method on the spatial transcriptomics(ST) dataset and the TCGA-BRCA dataset, and the patches filtered by the patch filter achieved accuracies of 80% and 73.91% in predicting molecular subtypes on the ST and TCGA-BRCA datasets, respectively. Experimental results showed that the use of the trained patch filter to filter patches was beneficial to improving precision in predicting molecular subtypes of breast cancer.