Cell Regeneration最新文献

Advanced imaging and single-cell omics technologies are fundamentally transforming developmental biology research, shifting it from static observation to dynamic, spatially resolved systems biology. Super-resolution microscopy breaks the diffraction barrier to visualize nanoscale subcellular dynamics, while light-sheet fluorescence microscopy enables long-term, multi-scale volumetric imaging of living specimens. In parallel, single-cell omics (e.g., transcriptomics and proteomics) decipher molecular heterogeneity and lineage trajectories, and spatially resolved transcriptomics maps gene expression within native tissue contexts at subcellular resolution. However, each approach has inherent limitations: imaging lacks deep molecular profiling, while dissociation-based omics loses spatial context. This review highlights how the integration of these technologies bridges cellular behaviors with molecular mechanisms, providing unprecedented multi-scale perspectives on key developmental processes-including embryogenesis, organogenesis, neural patterning, and disease progression. By synergistically capturing the "when," "where," and "how" of developmental processes, this convergence resolves longstanding questions and establishes a new mechanistic and predictive paradigm in developmental biology.

Maintaining the odontogenic potential of dental mesenchymal cells (DMCs) in vitro remains a critical challenge in tooth regeneration research. Current culture systems fail to sustain DMC functionality beyond short-term periods, limiting their utility for tissue engineering applications. Here, we developed an optimized N2B27-based culture medium that preserves the odontogenic capacity of mouse DMCs (mDMCs) for up to 14 days with passaging-a significant improvement over conventional methods (≤ 24 h). Single-cell RNA sequencing (scRNA-seq) revealed distinct transcriptional profiles and cellular trajectories between traditionally cultured (FBS-based) and N2B27-cultured DMCs. Mechanistically, excessive BMP4 signaling in standard media suppressed odontogenesis, whereas elevated Spp1 (osteopontin, OPN) expression in the N2B27 system enhanced regenerative potential. We demonstrate that optimal maintenance of DMC functionality requires balanced BMP4 activity and is enhanced by high OPN levels. Notably, supplementation with recombinant OPN or all-trans retinoic acid (ATRA) partially restored tooth-forming capacity in suboptimal cultures. Our findings establish a robust in vitro platform for DMC expansion while preserving odontogenic competence, advancing both mechanistic studies of tooth development and the generation of clinically relevant cell sources for bioengineered dental tissues. This work provides key insights on the features of a regenerative tooth germ and its odontogenic microenvironment for future translational applications in tooth regeneration.

The interaction between hematopoietic stem and progenitor cell (HSPC) and its vascular niche is essential for supporting the homeostasis and reconstitution of hematopoietic system in adult bone marrow (BM), but a comprehensive atlas covering this HSPC-vascular niche crosstalk in multiple developmental stages and species is lacking. Here, we integrated single-cell transcriptomic data of HSPC and its vascular niches from fetal liver until aged BM, covering two species, two organs, and six developmental time points. Comparative analyses revealed dramatic differences in the gene expression, enriched pathway, and cell-cell communication between human fetal and adult BM. Notably, many of these differences were conserved between humans and mice. Multi-timepoint profiling of murine BM vascular niches revealed a stepwise maturation of gene expression, including critical niche factors such as SCF and CXCL12. Furthermore, analysis of this dynamic vascular niche atlas highlighted organ-specific features between fetal liver and BM niches, significant transcriptional changes in aged BM endothelial cells, and identified midkine as a previously unknown niche factor. Functional validation showed that transplanting HSPC into midkine knockout mice or treating with a midkine inhibitor (iMDK) enhanced hematopoietic reconstitution. In contrast, recombinant midkine suppressed HSPC differentiation. Together, our work presents a cross-species and multi-stage atlas of HSPC-vascular niche interactions, offering valuable insights into the dynamic changes of vascular niche through lifelong HSPC development and a platform to identify unknown niche factors.

Oct4 is a key transcription factor essential for maintaining pluripotency and self-renewal in embryonic stem cells (ESCs), where it activates pluripotency-related genes and represses differentiation-associated genes. While previous studies have identified OCT4 target genes using methods such as chromatin immunoprecipitation sequencing (ChIP-seq) and RNA interference (RNAi), these approaches may not fully capture direct transcriptional regulation. The auxin-inducible degron (AID) system, which enables rapid and reversible protein degradation, combined with nascent RNA sequencing, provides a refined method for identifying direct transcriptional targets by detecting immediate transcriptional changes in both protein-coding genes and non-coding RNAs. In this study, we utilized mouse Oct4-mAID ESCs and nascent RNA sequencing with 5-ethynyl uridine (5-EU) labeling to systematically identify direct OCT4 targets. Our results uncovered novel potential OCT4 targets, providing a dataset for further research into the functions and regulatory networks of Oct4 and related transcription factors.

Eukaryotic mRNAs are polyadenylated at their 3'-ends, and the poly(A) tails play critical roles in post-transcriptional gene regulation by influencing mRNA stability and translation. Here, we describe the biological processes and major protein factors that control poly(A) tail synthesis and shortening. We also discuss recent breakthroughs in poly(A) tail sequencing methods that enable high throughput and accurate measurement of poly(A) tail lengths. Finally, we review how poly(A)-tail regulators and poly(A)-tail-mediated post-transcriptional mechanisms affect stem cell fate and early embryonic development.

METTL3 is a crucial mRNA methyltransferase in mammals, essential for the regulation of gene expression and various biological processes. Here, we demonstrate that Mettl3 knockout (KO) in mouse embryonic stem cells (mESCs) leads to widespread upregulation of transposable elements (TEs) and 2-cell (2C)-like genes in a m⁶A enzyme activity-dependent manner, independent of culture conditions. Furthermore, embryo chimera experiments using a transient METTL3 degradation system (dTAG) revealed that METTL3-deficient mESCs can contribute to trophectoderm lineages at the blastocyst stage, indicative of expanded developmental potential. These findings highlight the role of METTL3-mediated m⁶A modifications in regulating the transcriptional and developmental plasticity of mESCs and suggest a link between m⁶A loss and the acquisition of a 2C-like state with features of extended potency.

Aging profoundly impacts bone homeostasis and regeneration, yet the cellular and molecular mechanisms underlying periosteal aging remain poorly understood. Using single-cell RNA sequencing, we profiled the periosteum of 3-, 9-, and 18-month-old mice, which revealed age-related shifts in progenitor, neutrophil, and macrophage subpopulations. Aging reduced mesenchymal cell populations and impaired osteogenic potential, may contribute to periosteal homeostasis. Periosteal progenitor subsets exhibited distinct aging trajectories: Dpt⁺ fibrous-layer cells undergoing early senescence, while Postn⁺ progenitors showed osteogenic decline. Aging also shifted immune profiles, increasing inflammatory Cd38^hi macrophages and dysfunctional Nlrp3^hi neutrophils, further disrupting bone homeostasis. Notably, aged progenitor cells upregulated CSF1 and CXCL signaling, driving macrophage and neutrophil infiltration, exacerbating bone loss. Our findings provide a comprehensive periosteal aging atlas, revealing aging-associated alterations in progenitor-immune crosstalk that may influence bone tissue dynamics, and offering insights into potential targets for age-related skeletal conditions.

Hypoxia-ischemia plays a role in the physiological and pathological processes of various diseases and presents a common challenge for humans under extreme environmental conditions. Neurons are particularly sensitive to hypoxia-ischemia, and prolonged exposure may lead to irreversible brain damage. The primary mechanisms underlying this damage include energy depletion, mitochondrial dysfunction, oxidative stress, inflammation, and apoptosis. Mitochondria serve as primary organelles for adenosine triphosphate (ATP) production, and mitochondrial dysfunction plays a crucial role in mediating hypoxic pathophysiological processes. Hypoxic-ischemic preconditioning (H/IPC) is an endogenous cellular protective mechanism that reduces the damage caused by lethal hypoxic stressors. In this review, we summarize the potential role of H/IPC and its protective effects on mitochondrial quality control and function. This perspective offers a new approach for treating diseases caused by hypoxia-ischemia.

Vertebrate axis patterning requires precise control of the differentiation of neuromesodermal progenitors (NMPs), which generate spinal cord (SC) and presomitic mesoderm (PSM). Previously, we identified a gastrula-premarked posterior enhancer (p-Enh) that is essential for posterior tissue development by regulating somite and SC in organogenetic embryos, while its role in early NMPs cells remains elusive. Here, using a highly efficient in vitro differentiation system, we found that the genetic removal of p-Enh leads to the aberrantly up-regulated PSM-related genes during both PSM and SC differentiation. Time-resolved transcriptomic analysis and experimental characterization revealed the activated PSM transcriptomic signature arose from disorganized NMPs composition, with an over-representation of the T^highSOX2^low NMPs subtype. Besides, through a newly developed bioinformatic tool, ST-Pheno, which effectively bridges the in vitro samples to in vivo embryonic phenotypes within spatiotemporal context, we determined that the over-produced T^highSOX2^low NMPs subtype is predominantly enriched in the anterior primitive streak and adjacent mesoderm region at E7.5, which may disrupt the proper development of NMPs towards prospective PSM and SC, ultimately leading to the posterior development failure. In summary, this study demonstrates a critical role of p-Enh in regulating NMPs subtype composition, which will broaden the molecular understanding of mammalian embryogenesis.