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.

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.

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.

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.

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.

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.

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.

p57Kip2 imposes the reserve stem cell state of gastric chief cells

Gastric chief cells are referred to as ‘reserve’ stem cells because they become proliferative and take part in regeneration after injury. The authors employed SORT-seq and doxycycline-based lineage tracing to reveal that p57Kip2 is a molecular switch for the reserve stem cell state of chief cells in mice.

Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma

Prummel et al. studied the early embryonic origins of mesothelia in zebrafish, mice, and humans. Single-cell RNA sequencing of zebrafish early lateral plate mesoderm revealed a heterogeneous progenitor pool. Hand2 was found as a marker for mesothelial progenitors. These progenitors form visceral and parietal mesothelium.

BMP gradient along the intestinal villus axis controls zonated enterocyte and goblet cell states

Beumer et al. show that the bone morphogenetic protein (BMP) signaling pathway controls the creation of functional zones along the crypt-villus axis. A gene lipid uptake gene signature is enriched in the villus tip and could be therapeutically exploited with BMP inhibitors.

Time-resolved single-cell sequencing identifies multiple waves of mRNA decay during the mitosis-to-G1 phase transition

The authors show that scheduled mRNA decay helps to reshape cell cycle gene expression as cells move from mitosis into G1 phase. To obtain a detailed view of mRNA levels as cells progress from M phase into G1 phase, they developed an original method that connects live-cell microscopy with SORT-seq.

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.