A pendulum of induction between the epiblast and extra-embryonic endoderm supports post-implantation progression

Vrij et al. aim to elucidate the principles of epiblast and extraembryonic endoderm co-development in mice. SORT-seq and immunofluorescence microscopy analysis indicate a process of lineage bifurcation and the two layers sequentially inducing developmental progression in each other.

Molecular signatures and cellular diversity during mouse habenula development

The authors performed SORT-seq on mouse habenular neurons at critical developmental stages, instructed by detailed 3D anatomical data. The data reveal cellular and molecular trajectories during embryonic and postnatal development, leading to different habenular subtypes. Among these, the Cartpt+ neuron subtype was studied in-depth and successfully linked to specific molecular and functional properties.

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.

Epicutaneous allergen immunotherapy induces a profound and selective modulation in skin dendritic cell subsets

A fast-expanding method in food allergy health is the epicutaneous allergen immunotherapy or patch test (“plakproef”). Laoubi et al. used SORT-seq, among other methods, to study the contribution of skin dendritic cells to T cell remodeling during patch tests. Their results emphasize that the cornerstone of food allergy desensitization is skin dendritic cells acquiring distinct specializations during the patch test.

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.

p57Kip2 imposes the reserve stem cell state of gastric chief cells

Gastric chief cells are referred to as ‘reserve’ stem cells because they become proliferative and take part in regeneration after injury. The authors employed SORT-seq and doxycycline-based lineage tracing to reveal that p57Kip2 is a molecular switch for the reserve stem cell state of chief cells in mice.

Inflammatory response in hematopoietic stem and progenitor cells triggered by activating SHP2 mutations evokes blood defects

Hematopoietic stem and progenitor cells (HSPCs) are the disease-propagating cells of juvenile myelomonocytic leukemia (JMML). A SHP2 mutation is common in these patients, and Solman et al. reproduced it in zebrafish. Single-cell mRNA sequencing of HSPCs from mutant zebrafish embryos and bulk sequencing of HSPCs from JMML patients revealed an overlapping inflammatory gene expression pattern. Pharmacological inhibition of the inflammatory response positively impacted mutant zebrafish, suggesting therapeutic possibilities in JMML patients.

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.

Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy

Wehrens et al. perform single-cell RNA sequencing on the hearts of patients who suffer from hypertrophic cardiomyopathy (HCM). This reveals cardiomyocyte subpopulations, gene regulatory networks, transcription factors, and hypertrophy-related genes that might be relevant to the pathogenesis of the disease.

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.