Spaceflight multi-omics reveals vulnerabilities of human germ cell development

Single-cell spatial mapping of human kidney development implicates the microenvironment in guiding cell fate decisions

Evolution has used cell–cell communication as a strategy to coordinate organ development, enabling the reproducible generation of intricate structures. Classically, these interactions have been studied one at a time in model organisms, limiting our understanding of how cellular interplay coordinates human development. We investigated human kidney development using single-cell RNA sequencing and spatial transcriptomics, analyzing over 700,000 cells. By mapping gene expression and differentiation trajectories in space, we define the spatial organization of kidney development. Our analysis revealed unrecognized plasticity, showing that cell fate established during early patterning can be later revised. This plasticity provides a potential mechanism for how cell fate is robustly established in complex patterned tissues. Additionally, through a genome-wide, spatially aware cell–cell interaction analysis, we link localized ligand signals to cell fate decisions. We also define biologically meaningful cellular neighborhoods based on aggregated extracellular cues, providing a blueprint to understand the coordination of human development at scale. The spatial organization of human kidney development is explored using single-cell RNA sequencing and spatial transcriptomics, highlighting the crucial role of microenvironmental signals in guiding cell fate.

Reversible epiblast regionalization determines differentiation potential of human pluripotent stem cells.

Although human pluripotent stem cells (hPSCs) can generate all tissues of the body, hPSCs in vitro frequently exhibit differentiation biases or failure that pose substantial challenges for disease modeling and regenerative medicine. The origins of these biases remain incompletely understood and extend beyond reprogramming artifacts. Here we show that loss of default neural differentiation capacity and failure to form brain organoids are linked to erosion of bivalent chromatin marks at developmental gene loci, independent of DNA methylation, driving acquisition of a posterior epiblast-like state and premature developmental gene expression. We develop a chemical chromatin restoration (CHR) approach that rescues this differentiation bias by reinstating transcriptional programs and chromatin landscapes characteristic of the competent anterior epiblast-like state, restoring broad differentiation potential. These findings establish locus-specific patterns of repressive and activating histone post-translational modifications as a tractable and experimentally targetable determinant of hPSC fate competency, and offer an effective route to rescue differentiation-compromised hPSC lines for applications in disease modeling and regenerative medicine.

hiPSC-derived Organoids and Organ-on-chip Systems: New Frontiers in Neural Tube Defect Research.

Rapid Generation of Functional Oligodendrocytes From Human Induced Pluripotent Stem Cells Through Small Molecule Guided Differentiation.

Oligodendrocytes (OLs) are essential for central nervous system (CNS) function through their role in axon myelination, and their dysfunction is implicated in a range of neurological disorders. Despite this, in vitro modeling of human OL biology remains limited by the scarcity of primary human OLs. Furthermore, while induced pluripotent stem cells (iPSCs) offer a promising source of human OLs, current differentiation protocols remain complex, inefficient, and time-consuming. Here, we present an optimized protocol to generate OLs from iPSCs (iOLs) using defined soluble factors supplemented in the culture media. Within 28 days, cultures yielded an average of 85% O4+ iOLs, and by Day 38, approximately 70% expressed MBP, a key marker of mature OLs. Bulk RNA-seq analysis confirmed a stepwise transcriptional progression consistent with OL lineage identity, with upregulation of key OL-specific transcripts and gene expression profiles. Comparative transcriptomic analyses further revealed increased expression of gene networks associated with myelination, extracellular matrix remodeling, and gliogenesis when iOLs were cultured on aligned nanofiber scaffolds. Importantly, iOLs formed compact myelin sheaths around axons and showed enhanced maturation in a three-dimensional (3D) environment, highlighting the importance of spatial and matrix-derived cues in OL development. This study establishes a cost- and time-efficient approach for generating functional OLs from iPSCs, with broad applicability for disease modeling, drug screening, and the development of regenerative therapies.

Using Brain Organoids to Explore Human Neurobiology

One of the major challenges in neuroscience is understanding how the human brain develops into a highly organized and functionally integrated organ, because many developmental processes cannot be investigated directly in humans and are not fully recapitulated in animal models. Brain organoids derived from human pluripotent stem cells have emerged as powerful three-dimensional (3D) experimental models that recapitulate key features of human neurodevelopment, including regional patterning, cellular diversification, and neural circuit assembly. Recent advances in long-term organoid culture, organoid bioengineering, vascularization, assembloid technology, transplantation, multi-omics, and artificial intelligence have substantially expanded the applications of brain organoids to investigate human neurodevelopment, model neurological disorders, support drug discovery, and advance therapeutic development. Integration of single-cell and spatial multi-omics with computational approaches has enabled robust molecular benchmarking, assessment of developmental fidelity, and evaluation of organoid reproducibility, facilitating direct comparison with primary human fetal brain tissue. However, current organoid systems remain limited owing to incomplete cellular and tissue complexity, inter-organoid variability, limited vascularization, limited functional maturation, and incomplete physiological integration. Continued advances in tissue engineering, computational biology, and standardized differentiation protocols are expected to enhance the biological fidelity and translational utility of brain organoids for basic and translational neuroscience, as well as mechanistic and translational research. Human Pluripotent Stem Cell-Derived Brain Organoids: From Directed Differentiation to Biomedical Applications. The graphic presented represents a summary of the overall workflow used for creating, characterizing, and medical uses of the brain organoids derived from stem cells. To create brain organoids, scientists utilize stem cells, and through controlling developmental signaling pathway processes bring forth the organoids that are organ-specific and exhibit distinct features of formation of human body. Depending on the technique that was used for creating organoids, different kinds of organoids can be generated, including, for instance, the organoids of the dorsal forebrain (one can also name it as the cortex), organoid of the ventral forebrain, organoids of different parts of the brain like stipular, hypothalamic, retinal, mesencephalic, rhombic, cerebellar, and spinal organoids. There are many methods that help with providing enough information about organoids. The methods used mostly can be characterized by their efficiency, using approaches that enable scientists to know more about cell heterogeneity through using scRNA-seq, understanding the tissue structure through the use of spatial transcriptomics, learning about neuron functioning through utilizing electroactivity tests and calcium imaging, and obtaining other information through applying multiple omics. Organ identity becomes interactive with many branches of science without exception, mostly forming large platform for research and applications in the field of neuroscience. But still, the process of applying brain-based approaches for research development requires the solution of some issues that need to be attended and solved. Most of the issues emerged can be explained by a lack of blood vessels, partial immune system efficiency, limitations in cell functioning, and variability of protocols. Summarizing the graphic provided, it is evident that it represents a detailed process of brain organoid research and its application. The information provided for making the above-mentioned graphic was based on numerous scientific works that deal with the issue of the generation of organoids and the general overview of the development, usage, and creation process of this material. Abbreviations: AI, artificial intelligence; hPSC, human pluripotent stem cell; scRNA-seq, single-cell RNA sequencing.

Characterization of the metabolome and proteome of stem cell-derived human primordial germ cell-like cells: a multi-omics approach.

Primordial germ cells (PGCs) are the population of cells that, in the human embryo, are initially specified at day 12 post-fertilization, and form the precursor cells for the future gametes. Although in vitro differentiation of PGCs from human stem cells has been achieved, these primordial germ cell-like cells (hPGCLCs) fail to completely mature without the use of ex vivo human or animal gonadal soma. Previous studies in mice revealed that several metabolic changes occur during the specification and maturation of these cells, which are essential for their developmental progress. However, little is known about the metabolic profile of human primordial germ cells. In the scarcity of human PGCs, particularly at the early specification stage, hPGCLCs serve as a research model to study PGC formation. To characterize the metabolic and proteomic profile of these cells, we differentiated hPGCLCs using induced-pluripotent stem cells and performed a mass spectrometry analysis to establish their metabolome and proteome. These cells revealed distinct metabolic profile, with changes particularly at the proteome level. This included a shift between canonical and non-canonical citric acid cycle in hPGCLCs, downregulation of late-stage glycolysis and reduction of nucleotide de novo synthesis. By providing an integrative map of these metabolic networks, we aim to provide insight on the metabolism of hPGCLC development that could help improve methods for fully in vitro differentiation and maturation of hPGCLCs.