Molecular and Functional Characterization of Human Intestinal Organoids and Monolayers for Modeling Epithelial Barrier

Patient-derived organoid models can transform drug discovery for inflammatory bowel disease, but differentiation and functional characterization inconsistencies limit that transformation. Jelinsky et al. profiled molecular and cellular features across a range of intestinal organoid models using bulk RNA sequencing, among other technologies, and examined differentiation and establishing a functional epithelial barrier.

Uncovering the mode of action of engineered T cells in patient cancer organoids

The authors developed a system called BEHAV3D to study the dynamic interactions of engineered T cells cultured with patient-derived solid-tumor organoids by imaging and (single-cell) transcriptomics. They identified a ‘super engager’ behavioral cluster of T cells with potent serial killing capacity. Then, they uncovered a behavior-specific gene expression signature in cancer metabolome-sensing engineered T cells and, finally, showed that type I interferon can prime resistant tumors for T cell killing.

Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer

This paper documents the discovery of a new driver mutation in bladder cancer, present in ~10% of the studied cancer patients. The mutation is a deletion of exons 8 and 9 in the aryl hydrocarbon receptor (AHR) gene. SORT-seq analysis confirmed that a transformed, tumor-related expression profile arose due to mutated AHR in mouse bladder organoids.

Exposure to the Amino Acids Histidine, Lysine, and Threonine Reduces mTOR Activity and Affects Neurodevelopment in a Human Cerebral Organoid Model

The authors pioneered the use of human cerebral organoids to investigate the impact of amino acid supplementation on neurodevelopment. RNA sequencing identified gene expression changes after supplementation, with enrichment in genes related to mTOR signaling and immune function, a.o., and to specific cell types, including proliferative precursor cells, microglia, and astrocytes.

Characterization of HIV-1 Infection in Microglia-Containing Human Cerebral Organoids

Gumbs et al. study the molecular mechanisms of HIV entry into central nervous system organoids and identify microglia as the primary target cell. Single-cell RNA sequencing confirmed the presence of microglia, among other cell types, and HIV-entry receptor expression in brain organoids.

BMP gradient along the intestinal villus axis controls zonated enterocyte and goblet cell states

Beumer et al. show that the bone morphogenetic protein (BMP) signaling pathway controls the creation of functional zones along the crypt-villus axis. A gene lipid uptake gene signature is enriched in the villus tip and could be therapeutically exploited with BMP inhibitors.

Adult mouse and human organoids derived from thyroid follicular cells and modeling of Graves’ hyperthyroidism

This study describes an organoid-based model system to study mouse and human thyroid biology. SORT-seq and transmission electron microscopy confirmed that thyroid follicular cell organoids phenocopy primary thyroid tissue. Moreover, the study explores the potential of human organoids for modeling an autoimmune disease, the anti-TSH receptor antibody-driven Graves’ hyperthyroidism.

EWSR1-WT1 Target Genes and Therapeutic Options Identified in a Novel DSRCT In Vitro Model

Bleijs et al. established a patient-derived in vitro model of the rare and life-threatening cancer desmoplastic small round cell tumor. They used SORT-seq to check how the model’s heterogeneity compared to the original tumor’s. Then, the authors identified tyrosine kinase MERTK as a potential therapeutic target.