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.
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.
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.
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.
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.
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.
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.
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.
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.