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.

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.

Linking the genotypes and phenotypes of cancer cells in heterogenous populations via real-time optical tagging and image analysis

This paper describes how cells can be optically tagged in real-time based on specific functional cell dynamics, such as fast migration or morphological variation. Moreover, it documents how you can combine optical tagging with single-cell RNA sequencing to link the genotypes and phenotypes of heterogenous tumor populations.

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.

Molecular characterization of Barrett’s esophagus at single-cell resolution

Barrett’s esophagus is the premalignant condition of esophageal adenocarcinoma. It is categorized into different stages which correlate with the risk of developing carcinoma. Busslinger et al. performed single-cell RNA sequencing to identify seven genes that facilitate the distinction between different Barrett’s esophagus stages on histological sections.

Collection of cells for single-cell RNA sequencing using high-resolution fluorescence microscopy

Segeren et al. describe a workflow to capture, image, and collect fluorescent human retina pigment epithelium cells for SORT-seq using the VYCAP puncher system. This protocol is relevant for cells that cannot be FACS-sorted.

Hepatitis B virus compartmentalization and single-cell differentiation in hepatocellular carcinoma

The authors applied SORT-seq and Smart-seq2 to study the interactions between hepatitis B virus and patient-derived hepatocellular carcinoma host cells. They detected active virus replication correlated with host factor expression at the single-cell level.

The Prognostic Potential of Human Prostate Cancer-Associated Macrophage Subtypes as Revealed by Single-Cell Transcriptomics

Siefert et al. performed single-cell transcriptomic analysis of human prostate cancer-resident macrophages. They identified three populations. The genes associated with each macrophage populations were used to develop a gene signature which was highly associated with both recurrence-free and metastasis-free survival.