Exploring new dimensions of tumor heterogeneity: the application of single cell analysis to organoid-based 3D in vitro models.

Abstract

Modelling the heterogeneity of the tumor microenvironment (TME) in vitro is essential to investigating fundamental cancer biology and developing novel treatment strategies that holistically address the factors affecting tumor progression and therapeutic response. Thus, the development of new tools for both in vitro modelling, such as patient-derived organoids (PDOs) and complex 3D in vitro models, and single cell omics analysis, such as single-cell RNA-sequencing, represents a new frontier for investigating tumor heterogeneity. Specifically, the integration of PDO-based 3D in vitro models and single cell analysis offers a unique opportunity to explore the intersecting effects of interpatient, microenvironmental, and tumor cell heterogeneity on cell phenotypes in the TME. In this review, we discuss the current use of PDOs in complex 3D in vitro models of the TME and highlight emerging directions in the development of these models. Next, we examine work that has successfully applied single cell analysis to PDO-based models and identify important experimental considerations for this approach. Finally, we highlight open questions that may be amenable to exploration using the integration of PDO-based models and single cell analysis. Ultimately, such investigations may facilitate the identification of novel therapeutic targets for cancer that address the significant influence of tumor-TME interactions. This article is protected by copyright. All rights reserved.