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 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.

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.

Science September, 2022 by Samuel J. Wattrus et al.
Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality

Wattrus et al. establish that hematopoietic stem and progenitor cells (HSPC) are quality assured for stress levels during development. Calreticulin is revealed as an “eat-me” molecule that initiates macrophage-HSPC interaction and leads to programmed cell clearance or stem cell expansion. They used SORT-seq to characterize the macrophage and HSPC subpopulations involved.

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.

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.