Viruses April, 2023 by Joana Daradoumis et al.
An Endogenous Retrovirus Vaccine Encoding an Envelope with a Mutated Immunosuppressive Domain in Combination with Anti-PD1 Treatment Eradicates Established Tumours in Mice

Targeting the endogenous retrovirus protein ‘Envelope’ may protect against cancer. Here, the authors document their development of a virus-like vaccine technology and employ SORT-seq to study the vaccine’s immunogenicity effect on dendritic cells.

Biosensors March, 2023 by Daan C. ´t Hart et al.
Co-Culture of Glomerular Endothelial Cells and Podocytes in a Custom-Designed Glomerulus-on-a-Chip Model Improves the Filtration Barrier Integrity and Affects the Glomerular Cell Phenotype

The authors delevoped co-culturing methods for glomerulus endothelial and epithelial cells for the glomerulus-on-a-chip technology. Specifically, with RNA-seq, they investigated the effect of crosstalk between the two cells on their transcriptome, which was shown to affect differentiation and adhesion programs.

Nature Biotechnology December, 2022 by Fredrik Salmén et al.
High-throughput total RNA sequencing in single cells using VASA-seq

Our R&D consultant Salmén developed VASA-seq to detect the total transcriptome in single cells, which is enabled by fragmenting and tailing all RNA molecules after cell lysis. Applied to developing mouse embryos, they found cell type markers, many based on non-coding RNAs, performed cell cycle analysis, and characterized important splicing events during development.

PNAS November, 2022 by Olimpia Alessandra Buoninfante et al.
Mammalian life depends on two distinct pathways of DNA damage tolerance

The team applied SORT-seq on mouse embryos to investigate how DNA damage toleration (DDT) deficiency affected the hematopoietic stem cell subset in the so-called LSK compartment. Ultimately, DDT deficiency results in DNA damage accumulation and depletion of hematopoietic stem cells. Meanwhile, it promotes the survival of cells expressing erythroid transcription factor KLF1. These insights indicate a novel molecular mechanism that regulates hematopoietic output in response to DNA damage.

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.

Cardiovascular Research September, 2022 by Monika M. Gladka et al.
Thymosin B4 and prothymosin A promote cardiac regeneration post-ischemic injury in mice

This study uses SORT-seq to reveal the transcriptional profile of proliferating cardiomyocytes in the ischemic heart. It shows that overexpression of the two identified factors, TMSB4 and PTMA, can promote cardiac regeneration. A supportive environment seems to be critical for regeneration in addition to activating cardiomyocyte proliferation.

Science Advances August, 2022 by Celine Souilhol et al.
JAG1-NOTCH4 mechanosensing drives atherosclerosis

Heart attack and stroke can be caused by endothelial cell–triggered atherosclerosis. This paper shows that disturbed blood flow activates the JAG1-NOTCH4 signaling pathway. SORT-seq analysis indicates Jag1 suppresses proliferative endothelial cells, enhancing atherosclerosis susceptibility.

Development August, 2022 by Erik J. Vrij et al.
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.

Cell Reports July, 2022 by Lieke L. van de Haar et al.
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.

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.

Journal of Allergy and Clinical Immunology June, 2022 by Leo Laoubi et al.
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.