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.

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.

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.