Search

Roser Vento-Tormo highlights the synergy of single-cell omics and organoids by Camp et al., who used single-cell RNA sequencing to characterize the cell–cell communication events driving tissue formation in human liver organoids.

A machine learning model was trained to quantify how closely neurons differentiated in a dish from stem cells resemble those found in the brain.

The HuBMAP consortium has generated spatially resolved cell atlases for the human intestine, kidney and placenta, which enable analysis of tissue organization in unprecedented detail.

Common variable immunodeficiency (CVID) is a prevalent primary immunodeficiency characterized by hypogammaglobulinemia, poor antibody responses, and enhanced susceptibility to infection. Here the authors examine CVID patients infected by SARS-CoV-2 and describe broad immune dysregulation, sustained type I IFN responses, altered B/T cell signaling, impaired NK cell differentiation, and persistent inflammasome activation.

Transcriptomes of about 70,000 single cells from first-trimester deciduas and placentas reveal subsets of perivascular, stromal and natural killer cells in the decidua, with distinct immunomodulatory profiles that regulate the environment necessary for successful placentation.

Hu et al. use single-cell RNA sequencing to explore the transcriptional profile of human amnion samples spanning the developmental window from Carnegie stage (CS)16 to CS23.

Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency. Here the authors perform single-cell omics analyses in CVID-discordant monozygotic twins and show epigenetic and transcriptional alterations associated with activation in memory B cells.

Single-cell and spatial transcriptomic profiling of the human endometrium highlights pathways governing the proliferative and secretory phases of the menstrual cycle. Analyses of endometrial organoids show that WNT and NOTCH signaling modulate differentiation into the secretory and ciliated epithelial lineages, respectively.

A computational pipeline enables differential V(D)J usage analysis and pseudotime trajectory inference from single-cell AIR sequencing.

The myeloid lineage is central to homeostasis and immunity. The authors provide an atlas of human iPSC-to-myeloid cell differentiation and demonstrate that the in vitro system recapitulates yolk sac differentiation, opening new avenues to human myelopoiesis.

CellPhoneDB combines an interactive database and a statistical framework for the exploration of ligand–receptor interactions inferred from single-cell transcriptomics measurements.

A comprehensive multi-omics reference atlas of prenatal human skin shows that innate immune cells crosstalk with non-immune cells to perform pivotal roles in skin morphogenesis, including the formation of hair follicles.

The Human Endometrial Cell Atlas integrates single-cell transcriptomic datasets from women with and without endometriosis. Novel and known cell types are registered using spatial transcriptomics to provide a comprehensive map of the human endometrium in controls and endometriosis cases.

A transcriptomic analysis of endometriosis and comparison tissues has been conducted, revealing a rich and complex catalogue of single-cell-based expression data. This resource is an invaluable building block towards single cell profiling at scale, aiding research into endometriosis pathogenesis and new ways of diagnosing and treating the disease.

Here Sarah Teichmann and colleagues provide a Perspective on the exponential scaling of single-cell RNA-sequencing experiments over the last decade, commenting on the methodological developments that have underpinned the advances in this technology.

Single cell analysis of early human embryos identifies key changes in pluripotency, the requirement of FGF signalling for embryo survival, and defines a putative anterior-like region of hypoblast cells, providing insights into how early human development is regulated.

Phylogenies of human placental cells based on whole-genome sequencing of bulk samples and microdissections reveal extensive mutagenesis in placental tissue, and suggest that mosaicism is a typical part of normal placental development.

Irie, Lee et al. report a role for DMRT1 in human germline development and show that induction of DMRT1 in primordial germ cell-like cells triggers germline commitment, but suppresses pluripotency genes, thus promoting the onset of gametogenesis.

CellPhoneDB combines a curated database of receptor–ligand interactions with methods to infer cell–cell communication from single-cell expression data. This protocol update describes an expanded database and new methods to infer, prioritize and visualize the results.

A multiomics single-cell atlas of the human maternal–fetal interface including the myometrium, combining spatial transcriptomics data with chromatin accessibility, provides a comprehensive analysis of cell states as placental cells infiltrate the uterus during early pregnancy.

This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy, which can guide in vitro gonadogenesis.

A Bayesian model maps the location of cell types in tissues with higher sensitivity.

Systematic measurements of the interactions between proteins found on the surfaces of human leukocytes provides a global view of the way that immune cells are dynamically connected by receptors.

Single-cell transcriptomics reveals immune and stromal compartment remodeling, including the enrichment of unique populations of epithelial cells and CD4⁺ T cells, in asthmatic lungs

Single-cell transcriptomic profiling of fetal liver, skin, kidney and yolk sac reveals the differentiation trajectories of human haematopoietic stem cells and multipotent progenitors, which are validated to produce an integrated map of fetal liver haematopoiesis.

In this Review, the authors describe the key epigenetic events that are associated with the differentiation and function of cells of the myeloid lineage, with a particular emphasis on monocytes and macrophages. They detail the epigenetic enzymes that control these events and discuss emerging data that show the importance of epigenetic regulation for 'memory-like' behaviour in innate immune cells.

This Perspective outlines the Human Developmental Cell Atlas initiative, which uses state-of-the-art technologies to map and model human development across gestation, and discusses the early milestones that have been achieved.