Gene expression in organoids: an expanding horizon

Abstract

Recent development of human three-dimensional organoid cultures has opened new doors and opportunities ranging from modelling human development in vitro to personalised cancer therapies. These new in vitro systems are opening new horizons to the classic understanding of human development and disease. However, the complexity and heterogeneity of these models requires cutting-edge techniques to capture and trace global changes in gene expression to enable identification of key players and uncover the underlying molecular mechanisms. Rapid development of sequencing approaches made possible global transcriptome analyses and epigenetic profiling. Despite challenges in organoid culture and handling, these techniques are now being adapted to embrace organoids derived from a wide range of human tissues. Here, we review current state-of-the-art multi-omics technologies, such as single-cell transcriptomics and chromatin accessibility assays, employed to study organoids as a model for development and a platform for precision medicine.

Molecular profiling of a bladder cancer with very high tumour mutational burden

“…In the era of 4 P (Predictive, Personalized, Preventive and Participatory) medicine [ 75 – 78 ], the molecular profiling of single cancer entity represents a great opportunity for the development of patient-tailored therapies. Hence, this case report highlights the complex molecular landscape of an infiltrating urothelial bladder cancer characterized by very high TMB.…”

Human-Organoid-Based In Vitro Modeling for Environmental Toxicology

“…This induced gain of pluripotency is achieved through retrovirus-mediated transfection of a combination of four transcription factors, commonly known as the Yamanaka factors, including Oct3/4, Sox2, Klf4, and c-Myc . Many applications of hiPSCs involve obtaining terminally differentiated cells from patients as their cellular source, which serve as valuable resources for understanding the molecular mechanisms underlying disease progression, such as tumorigenesis. In addition, tumor organoids generated from tumor tissues have recently emerged as preclinical models that can represent patient-specific intra- and intertumoral biological heterogeneity. , This offers excellent research opportunities to understand cancer heterogeneity and its implications for personalized medicine (Figure ).…”

“…The stable and scalable derivation of in vitro models from stem cells facilitates the creation of platforms suitable for reliable toxicology tests. , Since the cellular origin of organoids is PSCs, both organoids and stem cells face common obstacles due to their pluripotent nature. The failure to maintain reproducibility is increasingly recognized as one of the significant challenges in stem-cell-based in vitro models.…”

“…In addition, the use of chromatin immunoprecipitation (ChIP-seq) allows the identification of certain transcription factors occupying various regions of the genome. This analysis, in conjunction with other multiomics approaches, enables a more sensitive determination of specific transcriptional regions of interest . It is important to note that the transition in pluripotency exists as a continuum rather than a series of distinct biological reactions.…”

Exploring New Dimensions of Tumor Heterogeneity: The Application of Single Cell Analysis to Organoid‐Based 3D In Vitro Models

“…Though this technology has largely been optimized for fresh-frozen tissue sections, it is possible to prepare PDOs in hydrogels for spatial transcriptomic investigations where preserving the tissue structure and cellular organization within the hydrogel is desired. [214][215][216] However, where spatial transcriptomics is not feasible, models that isolate individual organoids, such as micromolded ECM microwells, [107] and spatially-resolved models, such as TRACER and other stacked paper-supported models, [145,146] may be valuable to ensure analysis of PDOs with phenotypes of interest and minimize the loss of information related to tissue organization. Additionally, though not widely used for analysis of PDOs at present, emerging tools for spatial proteomics such as imaging mass cytometry and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) may prove valuable for spatial single cell analysis of complex PDO-based 3D in vitro models in the future.…”