RESUMEN
3D co-cultures are key tools for in vitro biomedical research as they recapitulate more closely the in vivo environment while allowing a tighter control on the culture's composition and experimental conditions. The limited technologies available for the analysis of these models, however, hamper their widespread application. The separation of the contribution of the different cell types, in particular, is a fundamental challenge. In this work, ORACLE (OvaRiAn Cancer ceLl rEcognition) is presented, a deep neural network trained to distinguish between ovarian cancer and healthy cells based on the shape of their nucleus. The extensive validation that are conducted includes multiple cell lines and patient-derived cultures to characterize the effect of all the major potential confounding factors. High accuracy and reliability are maintained throughout the analysis (F1score> 0.9 and Area under the ROC curve -ROC-AUC- score = 0.99) demonstrating ORACLE's effectiveness with this detection and classification task. ORACLE is freely available (https://github.com/MarilisaCortesi/ORACLE/tree/main) and can be used to recognize both ovarian cancer cell lines and primary patient-derived cells. This feature is unique to ORACLE and thus enables for the first time the analysis of in vitro co-cultures comprised solely of patient-derived cells.
RESUMEN
Air-liquid interface (ALI) culture models currently represent a valid instrument to recreate the typical aspects of the respiratory tract in vitro in both healthy and diseased state. They can help reducing the number of animal experiments, therefore, supporting the 3R principle. This review discusses ALI cultures and co-cultures derived from immortalized as well as primary cells, which are used to study the most common disorders of the respiratory tract, in terms of both pathophysiology and drug screening. The article displays ALI models used to simulate inflammatory lung diseases such as chronic obstructive pulmonary disease (COPD), asthma, cystic fibrosis, lung cancer, and viral infections. It also includes a focus on ALI cultures described in literature studying respiratory viruses such as SARS-CoV-2 causing the global Covid-19 pandemic at the time of writing this review. Additionally, commercially available models of ALI cultures are presented. Ultimately, the aim of this review is to provide a detailed overview of ALI models currently available and to critically discuss them in the context of the most prevalent diseases of the respiratory tract.