BioRxiv February, 2023 by Pere Català et al.
A Single-Cell RNA-seq Analysis Unravels the Heterogeneity of Primary Cultured Human Corneal Endothelial Cells

Català et al. used 10x Genomics Single Cell Gene Expression to profile 42,220 primary human corneal endothelial cells. They identify their variable transcriptomic fingerprint, provide a pseudotemporal reconstruction of the changes arising from primary culture, and suggest markers to assess the quality of primary cornea cell cultures.

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.

Cell Death Discovery January, 2023 by Marlene Geyer et al.
A microfluidic-based PDAC organoid system reveals the impact of hypoxia in response to treatment

This team from Mimetas created patient-derived pancreatic ductal adenocarcinoma (PDAC) organoids-on-a-chip, under different oxygen pressure conditions. They evaluated gene expression changes with bulk RNA sequencing under low-oxygen conditions. Then, the team tested standard-of-care chemotherapeutics to analyze drug response in the organoids-on-a-chip. They found oxygen pressure conditions impacted the responses, so doctors may adjust therapy choice based on the PDAC’s oxygen pressure conditions.

Cell Reports December, 2022 by Harald Shuhwerk et al.
The EMT transcription factor ZEB1 governs a fitness-promoting but vulnerable DNA replication stress response

The authors discover a chemoresistant ZEB1-high-expressing subpopulation of cancer cells. Then, they use SORT-seq to study the transcriptomes of ZEB1-high- and low-expressing cells. They find changes in cell cycle progression and DNA damage response, which creates stress resistance. This is found to, at the same time, create a targetable vulnerability in chemoresistant ZEB1-high-expressing cancer cells, which could be exploited in therapy.

Inflammatory Bowel Diseases November, 2022 by Scott A. Jelinsky et al.
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.

eLife October, 2022 by Alexandra Wiesinger et al.
A single cell transcriptional roadmap of human pacemaker cell differentiation

Wiesinger et al. combine SORT-seq analysis with trajectory inference to reconstruct lineage decisions of sinoatrial node–like cardiomyocytes (derived from induced pluripotent stem cells). WNT and TGFb signaling seem to play a role in these lineage decisions, the authors find.

Journal of Tissue Engineering October, 2022 by Jiuru Li et al.
Molecular and electrophysiological evaluation of human cardiomyocyte subtypes to facilitate generation of composite cardiac models

The authors directed the differentiation of human induced pluripotent stem cells to three types of heart cell: sinoatrial nodal, atrial and ventricular cardyomyocytes. SORT-seq established that the protocols indeed yielded distinct cell populations in line with expected identities. Such models can progress the use of cardiomyocytes in drug development.

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.

Immunity September, 2022 by Pascal Chappert et al.
Human anti-smallpox long-lived memory B cells are defined by dynamic interactions in the splenic niche and long-lasting germinal center imprinting

Immune memory in humans has been shown to extend well beyond decades. Using SORT-seq, Chappert et al. elucidate an extensive functional characterization of human splenic smallpox/vaccinia protein B5-specific memory B cells generated more than 40 years ago. This can be used to decipher the distinct selection and survival mechanisms associated with their longevity.

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.

Nutrients May, 2022 by Amber Berdenis van Berlekom et al.
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.