Gene expression in organoids: An expanding horizon

Introduction

Organoid cultures offer diverse research opportunities, from studying organ development, mimicking biological processes, assessing drug toxicity and creating experimental models. The complexity and heterogeneity of organoid models demands gene expression analysis to identify global molecular mechanisims and key players, using methods like RT-qPCR, gene arrays, spatial transcriptomics and RNA ssequencing.

Main Points

• RT-qPCR, gene arrays, and bulk RNA sequencing provide insight into global gene expression changes in organoid models, helping to assess drug effects by identifying expression changes linked to efficacy, resistance and toxicity. These techniques enable biomarker discovery, improving drug screening and precision medicine.
• Single-cell sequencing enables cell type identification, molecular pathways enrichment, cell communication and gene expression. Reg4 has been identified as a novel marker for enteroendocrine cells, a rare population of hormone-producing intestinal cells.
• Spatial transcriptomics allows differentiation of cell types across regions and developmental stages of organoids. Similarities between gastruloids and mammalian embryos have been found making them an attractive model for embryonic development, bypassing ethical concerns.
• ChIP-seq analysis of specific histone modifications allows the identification of active or inactive chromatin regions genome-wide, a new powerful tool for understanding molecular mechanisms of disease progression and the development of precision medicine. A study using mouse liver organoids model examined how different isoforms of the bile acid receptor (FXR) influence the transcription of genes involved in bile acid, fat, sugar, and amino acid metabolism. It was found that only two isoforms, FXRα2 and FXRα4, bound to FXR loci.

Conclusion

Advancements in sequencing and gene expression studies have expanded the potential of organoids as research models. While still in early development as research models, studies showed they closely mimic tissue architecture with high fidelity, and their contributions highlight the complex network of events driving disease progression.

EPISTEM SERVICES

Organoids

Epistem provides 3D intestinal organoid models from several species offering valuable insights into biology, disease, and drug induced effects. These are also used to derive 2D cultures to assess barrier function and transport effects.

Gene Expression

Furthermore, Epistem regularly employs qPCR and NGS platforms for gene expression, whole-exome, genotyping and epigenetic analysis. Full bioinformatics supported is provided, along with correlation with in vivo data.

Epistem has extensive experience processing different sample types, including fresh, frozen or FFPE tissues, ranging from good to degraded quality and from nano to ultra-low RNA or DNA input.