Nature Cardiovascular Research January, 2023 by Marie A. C. Dupuydt et al.
Single-cell T cell receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T cells

Atherosclerosis might have autoimmune components, Depuydt et al. conclude after 10x Genomics Single Cell Immune Profiling human patient’s atherosclerotic plaques and blood. They observed signs of autoreactivity with foam cells in clonally expanded T-cell subsets.

Clinical & Translational Immunology September, 2022 by Lisanne Lutter et al.
Human regulatory T cells locally differentiate and are functionally heterogeneous within the inflamed arthritic joint

The authors combined SORT-seq and T cell receptor sequencing to investigate the heterogeneity of regulatory T cells (Tregs) derived from synovial fluid of three patients with juvenile idiopathic arthritis. Results indicate Tregs differentiate to classical effector Tregs or GRP56+CD161+CXCL13+ Tregs. They also found novel predicted drivers of local Treg differentiation.

JCI Insight September, 2022 by Viviana Valeri et al.
The whole-cell pertussis vaccine imposes a broad effector B-cell response in mouse heterologous prime-boost settings

The authors compare effector and memory B cells induced by the two classes of pertussis vaccines (whole cell and acellular versions) using SORT-seq among other techniques. They show that a whole-cell pertussis vaccine prime achieves a more potent and broader memory B cell and plasma-cell response.

Nature Communications August, 2022 by Mathieu Claireaux et al.
A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike

Claireaux et al. aimed to guide vaccine improvement by finding out how the unexposed immune system reacts to the SARS-CoV-2 spike protein. Single-cell RNA sequencing and flow cytometry helped them describe the reactive B cell repertoire. They identified a non-neutralizing antibody class as a main factor in the unexposed SARS-CoV-2 response.

Nature Biotechnology July, 2022 by Johanna F. Dekkers et al.
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.

Viruses April, 2022 by Stephanie B.H. Gumbs et al.
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.

The Journal of Immunology January, 2022 by Florencia Morgana et al.
Single-Cell Transcriptomics Reveals Discrete Steps in Regulatory T Cell Development in the Human Thymus

By using SORT-seq, the authors delineated three major regulatory T cell developmental stages in the human thymus. Cells from these stages can be distinguished using the surface markers CD1a, CD27, CCR7, and CD39, allowing for their viable isolation. These insights help identify fully mature regulatory T cells cells for adoptive cell therapy.

PNAS December, 2021 by Jelte van der Vaart et al.
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.

Nature Communications October, 2021 by Lydia Krabbendam et al.
CD127+ CD94+ innate lymphoid cells expressing granulysin and perforin are expanded in patients with Crohn’s disease

The researchers designate two distinct innate lymphoid cell subtypes. Then, using single-cell RNA sequencing and further characterization methods, one subtype was found to express toxic compounds granulysin and perforin in the intestines of Chron’s disease patients.

Nature Communications September, 2021 by Emilie Crouchet et al.
A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery

A lack of suitable experimental models hampers drug discovery for chronic liver disease and hepatocellular carcinoma. So Crouchet et al. developed a human liver cell–based model predicting long-term liver disease progression toward hepatocellular carcinoma. They identified nizatidine as a potential therapeutic and, with single-cell RNA sequencing, could identify hepatocytes and certain liver macrophage subtypes as a potential therapeutical targets.