Stem cell-based embryo models offer a powerful window into the principles of self-organization that guide early development. In this talk, I will explore how we can reconstruct these processes from the bottom up—starting with simple stem cell–based models that mimic specific regions or lineages, and progressing toward integrated systems that capture the full complexity of the mammalian embryo. Using both mouse and human systems, I will highlight how these models allow us to probe critical stages of development that are otherwise inaccessible in natural embryos. Through them, we can observe how cells communicate, cooperate, and compete to form organized tissues and establish body plans. I will also discuss the surprising self-regulatory capacities of these systems and the emergent behaviors that arise during symmetry breaking, pattern formation, and lineage specification. Together, these insights illuminate conserved strategies and species-specific differences in early development. Ultimately, they offer new tools to decode the logic of embryo formation—and to guide regenerative and reproductive medicine.

Embryonic development establishes the body plan, yet human post-implantation stages remain a “black box” due to ethical and technical constraints. We harness the self-organizing capacity of pluripotent stem cells to generate stem-cell-based embryo models, termed peri-gastruloids, that recapitulate key features of human peri-gastrulation and early organogenesis. Peri-gastruloids robustly model amniotic and yolk sac cavity formation, bilaminar and trilaminar disc development, primordial germ cell specification, and early neurulation and organogenesis. Single-cell RNA-seq demonstrates strong transcriptomic similarity between peri-gastruloids and in vivo peri-gastrulation cell types in humans and non-human primates. In parallel, we apply spatial transcriptomics to human embryos to build a three-dimensional, single-cell–resolved atlas of early organogenesis. Guided by in vivo insights, we further establish a self-organizing embryo model that captures neural tube–notochord interactions. Together, these complementary in vitro and in vivo strategies open a path to mechanistically dissect human post-implantation development and to build stem-cell–based models of early development and disease.

Human embryos undergo profound cellular and molecular change over the first two weeks of development. An example of this is the widespread epigenome programming that occurs over this period, which is a topic that forms the primary focus of our research. Gamete-inherited epigenetic information is erased, followed by the coordinated establishment of new, long-lived epigenetic programmes that persist through development and into later life. These events affect many key processes such as gene regulation, control of repetitive elements in the genome, as well as DNA replication and repair. Towards a better understanding of how epigenomes are initiated and controlled in early human development, we have developed new cellular models and molecular approaches. I will present our current efforts in creating a culture system that permits the in vitro development of human embryos and embryo models over the first two weeks. Insights from these studies are beginning to reveal information about the emergence of embryo lineages and the molecular interactions between cell types that guide embryogenesis. I will also discuss our new mechanistic leads that provide robustness to epigenetic states in early human development.

Tissue morphogenesis requires coordinated movement of the component cells. One such morphogenetic event in the mouse embryo is the migration of the distal visceral endoderm (DVE) within the visceral endoderm (VE), that positions it correctly to specify axial pattern in the underlying pluripotent epiblast. It is unknown how these epithelial cells negotiate their way through surrounding cells, and how they stop once they reach their destination.

Using lightsheet microscopy, machine learning based image analysis approaches and a data-informed computational framework, we characterised morphological, behavioural and molecular parameters of every VE cell during DVE migration, that we refer to as single-cell phenomics. This revealed previously unappreciated phenomic heterogeneity within the VE, that mapped to spatially distinct regions. Laser-ablation and fluorescence lifetime imaging of a tension sensor revealed differences in the mechanical properties of these regions. DVE cells showed elevated cortical tension, while the cells immediately ahead showed reduced tension. Genetic and pharmacological intervention showed that these differences are dependent on actomyosin function. Optopharmacological inhibition of myosin specifically in DVE cells is sufficient to arrest their migration. In such embryos and in multiple mutants where the DVE fails to migrate, the cells ahead of the DVE do not show their normal anisotropy of shape, indicating that active DVE migration drives their deformation. DVE cells stop migrating upon reaching a region of VE with matching elevated tension that is dependent on LEFTY1, a secreted inhibitor of NODAL signalling. Lefty1 mutants show abnormal over-migration of DVE cells, as well as a reduction in phosphorylated MyosinIIA and membrane tension in the VE region where DVE cells normally stop migrating.

Our results show that the migration of DVE cells is facilitated, but also circumscribed, by patterned heterogeneities in the mechanical properties of surrounding cells. It suggests a paradigm by which signalling molecules can regulate both specification of cell identity and morphogenesis by modulating the mechanical properties of the tissues through which cells migrate.

Among the rising spatial-omics technologies, a missing tool is for locating proteins in tissues in an untargeted manner at high spatial resolution and coverage. We introduce iPEX, a method for spatial proteomic mapping at high-resolution and detection depth. iPEX provides scalable spatial resolution improvement down to micron-scale, and substantially boosts protein identification sensitivity by one order of magnitude. In mouse retina, iPEX enables construction of spatial proteomic maps at high-precision, visualization of single-cell layers and extra-somatic structures, and identification of colocalized proteins. iPEX readily applies to diverse tissues including brain, intestine, liver and organoids, detecting ~1000 proteins at micron resolution. We used iPEX to depict spatial proteomic maps in 5xFAD Alzheimer’s disease (AD) mouse brains and revealed an early-onset mitochondrial aberrancy, and uncovered early alterations in lipid metabolic genes that are relevant to human AD pathogenesis. We envision iPEX will be readily adaptable to diverse biomedical applications.

Ludovic Vallier and colleagues

The liver is a unique organ by the broad spectrum of its functions which include drugs detoxification and, glycogen storage, lipid metabolisms and secretion of protein such as Albumin. End stage liver diseases are life threatening and orthoptic liver transplantation is the only treatment available. However, transplantation entails high risk of surgical complications, immunosuppression associated with severe side effects, and ultimately organ dysfunction. More importantly, the number of organ donors remains constant the past 10 years while the demand for liver transplantation has more than doubled. Thus, alternative therapies are urgently needed to address this growing health care challenge.

Understanding liver development could help to develop alternative therapies by providing the knowledge necessary to control regenerative process in chronic liver diseases. However, the study of human liver organogenesis has been impaired by technical and ethical challenges. Consequently, little is known about the mechanisms directing the cellular composition of the human liver and how this cellular diversity results into tightly regulated hepatic activity. Here, we start to address this gap by combining new in vitro models and single cell transcriptomic analyses to investigate the mechanisms controlling early liver organogenesis. Our approach shows the importance of cellular diversity in the human foetal liver and the developmental trajectory of key cell types such as cholangiocytes and hepatocytes. The resulting knowledge reveals new developmental mechanisms which could inform process of differentiation in vitro for the production of cell types with a clinical interest.

The kidney develops from the intermediate mesoderm and exhibits a higher-order structure consisting of multiple branched collecting ducts that are connected to numerous nephrons located on the periphery. The kidney is also connected to the ureter, which drains urine. This complicated organ develops through interactions among the nephron progenitor, the ureteric bud, and the stromal progenitor. We have developed induction protocols for these progenitors from pluripotent stem cells (PSCs) (Cell Stem Cell, 2014 & 2017; Nature Communications, 2022). When these three progenitors were assembled, the fully PSC-derived organoids reproduced the higher-order kidney structure, featuring branched collecting ducts connected to multiple nephrons, with stromal cells distributed between the epithelia, at least in mice (Nature Communications, 2022). Furthermore, we recently generated ureteral organoids from PSCs by combining two ureter progenitors (Nature Communications, 2025). Our goal is to connect the kidney and ureter organoids; however, they are currently immature. Overcoming this immaturity is essential for the future clinical application of organoids in transplantation therapy. Thus, we will also discuss our preliminary results on kidney maturation.

The lack of relevant models has constrained human cerebellar development research. We present a novel human cerebellar organoid (hCerO) system that recapitulates the cellular diversity and distinct functional features of the fetal cerebellum. Our hCerOs develop complex cytoarchitecture, including transient laminar organization, and demonstrate functional neuronal connections with coordinated network activity. Long-term culture allows for the maturation of Purkinje cells exhibiting molecular and electrophysiological characteristics of their in vivo counterparts. By integrating these organoids with single-cell -omics techniques and bioengineering methods, our goals are to 1. reconstruct the developmental lineage and dynamic events of individual cells during human cerebellar neurogenesis in both health and disease, and 2. identify disease mechanisms specific to brain regions and cell types. Ultimately, our aim is to provide new insights and tools to understand cerebellar development and disease mechanisms, contributing to foundational knowledge in the field.

Kidney organoid is a miniature 3D kidney-like structure and provides a very useful platform to directly interrogate human kidney regeneration. However, current organoids do not recapitulate the kidney's complex spatial patterning and function, which greatly limit the extensive applications of kidney organoid. The function unit of mammalian kidney is nephron that derived from nephron progenitor cell (NPCs), and connect to tree-like collecting system that derived from ureteric progenitor cell (UPCs). Here, we successfully leveraged expandable NPCs and UPCs to generate spatially organized mouse and human kidney progenitor assembloid (KPA) in which multiple nephrons fully develop as in vivo and fuse to one collecting system located in center, and kidney progenitor self-assembly processes happen as in vivo. KPAs present dramatical cellular complexity and improved maturity, and exhibit several aspects of major kidney functions in vitro and in vivo. Surprisedly, PKD2^-/- human KPAs in vivo developed a markedly size comparable to host mouse kidney and recapitulated the cystic phenotype and the molecular and cellular hallmarks of human autosomal dominant polycystic kidney disease (ADPKD), and highlighted the crosstalk among cyst epithelium, stroma, and macrophages. The KPA platform offers a very useful approach for high-fidelity kidney disease modeling and interrogating kidney regenerative medicine.

Adult stem cells support tissue homeostasis and repair throughout the life of an individual. Numerous changes occur with age that result in altered stem cell behavior and reduced tissue maintenance and regeneration. In Drosophila melanogaster, advanced age leads to changes in the intestine, including an increase in intestinal stem cell (ISC) proliferation, accumulation of mis-differentiated cells, an increase in bacterial load, activation of inflammatory pathways, increases in ROS levels, and loss of intestinal barrier function. However, there is a lack of consensus regarding the impact of aging on the mammalian intestine and colon. Environmental interventions, such as dietary changes and exercise can influence adult stem cell behavior in both humans and mice. We have begun exploring how exercise impacts ISC number and behavior, crypt morphology, and hallmarks of aging in young and aged male and female mice. These experiments will expand on the usefulness of exercise as a non-invasive intervention to rejuvenate endogenous stem cell pools, as well as provide a new paradigm to study intestinal aging.

The cumulative burden of lifelong environmental exposures—the exposome—profoundly shapes tissue ageing and cancer risk. In mammalian hair follicles, melanocyte stem cells (McSCs) generate pigment-producing melanocytes but are susceptible to genotoxic stress and ageing. Using longitudinal single-cell fate-tracking in mice combined with niche perturbations, we show that the fate of individual McSC clones depends on an antagonistic interplay between the type of DNA damage and niche-derived signals. DNA double-strand breaks (DSBs) activate a senescence-associated differentiation program that drives McSC exhaustion and selective loss, producing hair graying while enhancing cancer defence. By contrast, certain carcinogenic exposures can suppress this program and, via a niche-derived master factor that enforces self-renewal, rescue DSB-bearing clones and promote clonal expansion—thereby increasing tumorigenic risk. These findings reveal how stress-responsive, niche-mediated pathways at the single-cell level govern opposing outcomes—exhaustion versus expansion—with direct implications for understanding age-related tissue decline and mechanisms of tumorigenesis.

Biomechanical changes might contribute to the decreased regenerative capacity of aged stem cells. Small RhoGTPases are key regulators of mechanosignalling, but their specific role for mechanotransduction in stem cell aging remains unknown. Here, we show that a specific small RhoGTPase is necessary to survive mechanical insults in hematopoietic stem cells, which cell intrinsically induce its activation. Interestingly, we measure a 2-fold higher activity level of this small RhoGTPase in aged hematopoietic stem cells, associated with altered nuclear architecture. Reducing the activity of this small RhoGTPase with a selective inhibitor influenced nuclear mechanostransduction and improved the regenerative capacity of aged stem cells in vivo. Moreover, we developed an imaged-based computational framework to reveal the chromatin changes that are reverted in aged stem cells upon treatment with the selective small RhoGTPase inhibitor. Reducing the smallRhoGTPase activity in aged stem cells decreased chromatin accessibility and transcription of several repetitive elements (REs), downregulating inflammation and interferon response and inducing partial reprogramming. Overall, our data support that an intrinsic small RhoGTPase mechanosignalling axis is necessary for adult stem cells to survive mechanical insults and can be pharmacologically targeted to rejuvenate aged stem cell function.

Eutherians dominate vertebrates through reproductive strategies requiring significant maternal investment, which intricately links offspring development with maternal resource allocation. This dynamic creates an evolutionary conflict: paternal genes drive enhanced resource extraction, while maternal genes prioritize conservation for future reproduction. Genomic imprinting, an epigenetic mechanism with parent-of-origin-specific monoallelic expression, evolved to balance these competing interests. Here, we present the first comprehensive spatiotemporal map of genomic imprinting in the developing mouse brain, revealing the hypothalamus as an imprinting hub. Our study reveals that imprinted genes regulate hypothalamus size by controlling neural progenitor cell expansion, providing the structural foundation for efficient mother–offspring interactions. Our work uncovers the pivotal role of genomic imprinting in coordinating hypothalamic development with neonatal behavior, offering new insights into its contribution to the co-evolution of reproductive strategies, neural development, and social behaviors in mammals.

Stem cells support homeostasis and injury repair of adult organs. It remains unclear when and how adult stem cells form during development. Here, we discover that incisor mesenchymal stem cells, marked by an extracellular matrix molecule Smoc2, establish their identity and quiescence between E14.5 and E16.5, and maintain into adulthood. They support both embryonic tooth development and postnatal organ turnover. Concurrently, the incisor mesenchyme evolves from a homogenous dental papilla into a heterogeneous dental pulp consisting of a complete lineage hierarchy, which persists into adulthood. Smoc2, along with its homologous molecule Smoc1, is indispensable for maintaining the quiescence and hierarchy formation of mesenchymal stem cells. They function by disrupting the binding between canonical WNT ligands and glypican, a process critical for transporting hydrophobic WNT ligands within the aqueous niche. In conclusion, MSCs establish their quiescence during development through autocrine extracellular matrix molecules to keep canonical WNT ligands from accessing themselves.

In vivo lineage tracing holds great potential to reveal fundamental principles of tissue development and homeostasis. However, current lineage tracing in humans relies on extremely rare somatic mutations, which has limited temporal resolution and lineage accuracy. Here, we developed a generic lineage-tracing tool based on frequent epimutations on DNA methylation, enabled by our computational method MethylTree. MethylTree reconstructed lineage histories at nearly 100% accuracy across different cell types, developmental stages, and species. In this talk, I will discuss some ongoing progress on both tool development and biological application along this direction, including an extensive study of human blood aging using DNA methylation and MethylTree. We believe that MethylTree opens the door for high-resolution, noninvasive and multi-omic lineage tracing in humans and beyond.

Longevity research aims to extend the healthspan while minimizing the duration of disability and morbidity, known as the sickspan. Most longevity interventions in model organisms extend healthspan, but it is not known whether they compress sickspan relative to the lifespan. Here, we present a theory that predicts which interventions compress relative sickspan, based on the shape of the survival curve. Interventions such as caloric restriction that extend mean lifespan while preserving the shape of the survival curve, are predicted to extend the sickspan proportionally, without compressing it. Conversely, a subset of interventions that extend lifespan and steepen the shape of the survival curve are predicted to compress the relative sickspan. We explain this based on the saturating-removal mathematical model of aging, and present evidence from longitudinal health data in mice, Caenorhabditis elegans and Drosophila melanogaster. We apply this theory to identify potential interventions for compressing the sickspan in mice, and to combinations of longevity interventions. This approach offers potential strategies for compressing morbidity and extending healthspan.

Totipotency, defined as the ability to form a fully functional organism from a single cell, is restricted to zygotes and 2-cell blastomeres in mice. As development proceeds, 4-cell and later-stage blastomeres gradually lose this potential. Strategies to enhance totipotency of blastomeres remain limited. Here, we identified a mixture of signaling inhibitors (MSi) that enhanced totipotency in 4-cell blastomeres. Remarkably, a single MSi-treated 4-cell blastomere, without any helper "carrier" cells, developed into morphologically normal embryos with substantially improved implantation and post-implantation developmental success. In addition, MSi treatment significantly increased epiblast cell numbers and improved the proportion of complete blastocysts in quarter-embryos. Furthermore, MSi-treated 4-cell blastomeres displayed enhanced efficiency in deriving epiblast, primitive endoderm, and trophectoderm-like cell lines, facilitating the reconstruction of stem-cell-based embryo models with identical genetic backgrounds. Together, these findings provide a strategy to extend totipotent potential in vivo and deepen our understanding of the signaling pathway modulation underlying totipotency.

The study of human embryogenesis has been limited by the reliance on totipotent pluripotent stem cells (PSCs) or transgenic strategies to derive extraembryonic lineages such as the extraembryonic endoderm (ExEn). Here, we demonstrate that precise spatiotemporal modulation of specific signaling pathways—with carefully controlled concentrations and duration—enables efficient induction of multiple early embryonic lineages directly from conventional primed human PSCs, including ExEn and extraembryonic mesoderm cells. The resulting ExEn-like cells closely resemble human Carnegie Stage 7 visceral endoderm at the transcriptomic level, co-express canonical ExEn markers (SOX17, GATA4, GATA6, HNF4α, and PDGFRα), and exhibit functional capacity to support epiblast lumenogenesis and amnion formation. Leveraging this scalable system, we generated self-assembling yolk sac-like organoids that recapitulate primitive hematopoiesis, including the emergence of erythro-myeloid progenitors. Further deconstruction of this model into a minimal 2D co-culture of ExEn and extraembryonic mesoderm revealed a previously unrecognized instructive role for ExEn in initiating hematopoietic programs. This defined co-culture system also provides a robust source of tissue-resident immune cells for constructing immune-composite organoids. Collectively, our work establishes a foundational platform for generating extraembryonic endoderm from human PSCs to model yolk sac organogenesis and primitive hematopoiesis, thereby opening new avenues for developmental studies and in vitro disease modeling.

Drastic transcription and epigenetic reprogramming occur during mammalian early embryogenesis. Deciphering the molecular events underlying these processes is crucial for understanding how life really begins. Probing these questions was previously hindered by the scarce experimental materials that are available from early embryos. By developing a set of ultra-sensitive chromatin analysis technologies, we investigated epigenetic reprogramming during early mouse development for chromatin accessibility, histone modifications, and 3D chromatin architecture. These studies unveiled highly dynamic and non-canonical chromatin regulation during the maternal-to-zygotic transition. Recently, we also identified a number of key transcription factors (TFs) that govern mammalian zygotic genome activation (ZGA) and the first cell fate commitment. However, how the embryonic transcription program is established amid the non-canonical, immature epigenome, and how the embryonic epigenomes are correctly restored still remain enigmatic. In this talk, I will present data on how TFs and epigenetic factors may cooperatively establish embryonic gene program, and how the embryonic epigenomes including DNA methylation, histone modifications, and the 3D chromatin organization are properly restored in early mammalian development.

Tumors represent dynamically evolving populations of mutant cells and many advances have been made in understanding the biology of their progression. However, key unresolved questions remain about the conditions that support their initial transformation, which cannot be easily captured in patient populations but are instead modeled using transgenic cellular or animal systems. We present extensive patient atlas data to define common features of the tumor DNA methylation landscape as they compare to healthy human cells, and used this benchmark to screen engineered human and mouse models for their ability to reproduce these patterns.

In addition, we will present data on new models to study the early epigenetic transformation.

Aging is the major risk factor for a number of diseases, including neurodegeneration and several types of cancer. Yet, our understanding of the mechanisms responsible for aging at the molecular level remains limited. Identifying the factors that accelerate the aging process, as well as those that confer resilience, will influence quality of life in the elderly and lead to treatments for age-associated diseases. The focus of our research is on the molecular mechanisms of brain aging. We take an interdisciplinary approach to study physiological aging and age-associated disease, using a combination of mouse models, cell culture approaches, and genomics technologies. More specifically, we investigate the epigenetic, transcriptional, and metabolic mechanisms that preserve healthy cellular function, and how changes in these processes impair cellular processes in the aged brain. One major line of investigation is to discover the mechanisms that support the formation of new neurons from stem cells in the adult brain. We have made discoveries on how relatively dormant stem cells in the brain accumulate epigenetic changes that impact homeostatic transcriptional networks with age. Most recently, we have extended our work to models of Alzheimer’s disease and applied cutting-edge technologies such as single cell and spatial transcriptomics to delve into mechanisms of aging and disease at the single cell level. In the long-term, our work will advance our understanding of the molecular and cellular mechanisms that accelerate brain aging, and reveal new strategies to promote healthy aging and prevent age-associated disease.

The vasculature and mesenchyme exhibit distinct organ-specific characteristics adapted to local physiological needs, shaped by microenvironmental and cell-cell interactions from early development. To recapitulate this entire process, we adopted a co-differentiation strategy to facilitate the differentiation of mesoderm and endoderm within the same spheroid, thereby vascularizing lung and intestinal organoids derived from pluripotent stem cells. Notably, BMP signaling determined the endoderm-to-mesoderm ratio necessary to generate appropriate proportions of endothelial and epithelial progenitors with tissue-specificity, as well as to ensure proper regionalization of the gut tube fate. The endothelium exhibited tissue-specific barrier function, enhanced organoid maturation, cellular diversity, and alveolar formation on the engineered lung scaffold. Leveraging these vascularized organoids, we uncovered abnormal endothelial-epithelial crosstalk in patients with congenital defects. Multilineage organoids provide an advanced platform for studying intricate cell-to-cell communication during human organogenesis and disease.

Aging is characterized by a chronic low-grade inflammation known as inflammaging in multiple tissues, representing a risk factor for age-related diseases and dysfunction. In the intestinal tissue, aging leads to a loss of homeostasis and epithelium regeneration. However, the molecular mechanisms underlying inflammaging and intestinal aging remain largely undetermined. We have characterized the multi-tissue gene network regulating inflammaging involving interferon signaling. At intestinal level, blocking interferon gamma activity rescues the aging-associated differentiation skew of the intestinal stem cells and their regenerative potential in old organisms.

Epigenetic drift is a key feature of aging and is associated with biological processes and diseases. Studies have shown that DNA methylation (DNAm) drifts in mammalian aging relate to cell division or lifestyle, but molecular mechanisms are still unclear. Here we identify an aging and colon cancer-associated (ACCA) DNAm drift starting in intestinal stem cells and showing cell-intrinsic and non-mitotic nature.

Our results present a comprehensive understanding of the molecular network regulating inflammation in aging and in intestinal tissues and provide anti-inflammaging therapeutic targets. Moreover, our research enhances our understanding of epigenetic mechanisms in aging suggesting a mechanistic basis for the hypermethylation observed in cancer.

Clonal hematopoiesis (CH) is characterized by expanding blood cell clones carrying somatic mutations in healthy aged individuals and is associated with various age-related diseases and all-cause mortality. While CH mutations affect diverse genes associated with myeloid malignancies, their underlying mechanisms of expansion and disease associations remain poorly understood. We investigate mechanisms driving clonal evolution and thereby disease outcomes over the lifespan by integrating data from three longitudinal aging cohorts. We demonstrate that clonal composition and competition influence clonal dynamics. Furthermore, it is important to consider the timing of mutation acquisition to determine the extent of clonal expansion reached during the host individual's lifetime. By combining these, we can better predict future clonal growth, outperforming traditional variant allele frequency (VAF) measurements in predicting clinical outcomes. Our study aids the understanding of underlying mechanisms that drive clonal evolution across the lifespan and identifies factors contributing to adverse clinical outcomes. This study helps explain why certain mutations, such as DNMT3A, can arise early without leading to significant clonal expansion later in life, while splicing mutations tend to occur at later stages.

The incidence of clonal hematopoiesis of indeterminate potential (CHIP) increases exponentially with aging, increasing the risk of hematological malignancies, cardiovascular disease and a multitude of sequelae associated with CHIP. We have proposed that aging or insult-driven alterations in cells and tissues drive selection for adaptive mutations, and some of these mutations can confer malignant phenotypes. We have been using mouse models to generate mutations in the common CHIP mutated genes DNMT3A, TET2 and U2AF1, and determine how aging impacts selection for such mutations. We show that while mutation of Dnmt3a initiated in hematopoietic stem cells (HSC) results in positive selection that is independent of the age of the HSCs or the host, that mutation of Tet2 in old HSC leads to stronger positive selection than when initiated in young HSC (largely independent of host age). Strikingly, point mutations in the splicing factor U2af1 (S34F) are potently selected against in HSC of young mice, while positively selected in old mice, and this differential selection is mediated by both HSC and host age. Through single cell RNAseq, we have revealed potential mechanisms that can explain differential selection for Tet2 mutations (through inhibition of Runx1-Trp53 dependent gene expression) and U2af1 S34F mutation (through reversing the aging-dependent upregulation of interferon pathways, while promoting oxidative phosphorylation). Notably, mutation-affected changes are different in young and old contexts. We propose a model whereby evolution has selected for tissue landscapes that limit the expansion of mutation-driven clones that could reduce host fitness (e.g. greatest for U2AF1 mutations), with such pressures waning at post-reproductive ages.

Mechanisms of aging are present in the aetiology of human age-related diseases. Indeed, hallmarks of ageing can partially explain disease co-occurrence in humans. There is marked inequality in health during aging. Obesity and social deprivation both increase the incidence of diseases associated with specific aging hallmarks. These findings support the geroscience hypothesis, that human health during aging could be improved by targeting mechanisms of aging with drugs. We have been investigating two potentially geroprotective drugs, rapamycin and trametinib, and find that they are especially geroprotective in combination, in both Drosophila and mice. The mechanisms at work warrant more detailed study.

Cellular senescence is characterized by a stable arrest of the cell cycle in response to diverse stressors, serving as a crucial tumor-suppressive mechanism. Yet, it has become increasingly clear that senescent cells are not merely passive bystanders. Through the senescence-associated secretory phenotype (SASP), they release a wide array of pro-inflammatory mediators that can fuel chronic inflammation and tissue dysfunction. While senolytic agents that selectively eliminate senescent cells have gained attention as potential therapeutics, their indiscriminate use risks disrupting the beneficial roles of senescent cells in tissue repair and homeostasis. To achieve safer interventions, it is essential to understand and target the upstream triggers of senescence rather than focusing solely on their removal. In this presentation, I will discuss our recent work identifying microbial factors as pivotal contributors to the onset of cellular senescence, highlighting their implications for aging biology and therapeutic development.

Cellular senescence is a stress response that enforces stable cell-cycle arrest, classically known for its role in tumour suppression but also implicated in ageing. Recent studies have expanded its functions to embryonic development and tissue regeneration. Our work and others have shown that senescence promotes cellular plasticity and facilitates in vivo reprogramming, suggesting a general principle by which it can support tissue repair.

In this talk, I will discuss our recent efforts to dissect the interplay between senescence and cellular reprogramming. We found that overexpression of reprogramming factors modifies senescence features, with implications for both tissue rejuvenation and ageing. I will also present our work on the physiological induction of senescence during postpartum mammary gland involution. Using genetic and pharmacological approaches, we demonstrate that p16-dependent senescence supports tissue remodeling but simultaneously enhances tumour-initiating cell plasticity, thereby promoting postpartum breast cancer (PPBC). This work establishes a critical link between physiological senescence and tumour progression, providing new insights into how senescence contributes to cancer in an age- and context-dependent manner.

Together, these studies underscore the importance of understanding senescence regulation across physiological and pathological settings.

Aging of the immune system is accompanied by stereotyped changes in adaptive and innate immune function that leads to a chronic, sterile inflammation known as "inflammaging." More specifically, recent profiling of aged immune compartments has demonstrated the emergence of tissue resident lymphocytes characterized by markers of exhaustion, concurrent with the accumulation of pro-inflammatory macrophages. Studies of inflammaging have primarily focused on cell-autonomous changes in the various immune compartments with age, but little is known about how alteration in the tissue microenvironment drives inflammaging. In this talk, we will present a structural basis for immune aging in the lung, highlighting a novel role for aging fibroblasts as orchestrators of the inflammaging phenotype. Utilizing mouse genetic models, single cell RNA sequencing, and spatial transcriptomics, we will present evidence that age-related changes in fibroblasts lead to remodelling of the immune architecture and inflammaging in the lung. Furthermore, fibroblast-intrinsic activation of age-related pathway can alter the inflammatory setpoint and increase susceptibility to lung diseases associated with advanced age. Our data suggest that age-related alteration in the immune cell niche drives aging of the immune compartment that takes up residence in peripheral tissues.

The adult endothelium is generally considered quiescent, based on autoradiographic studies conducted primarily on aorta or inferior vena cava (IVC). However, whether this quiescence extends to the broader vascular network-including arterioles, venules and especially capillaries-and the identity of resident progenitor cells supporting turnover in these regions remain unknown. Here, we systematically investigated endothelial cell (EC) turnover across adult organs using an Endo-dual reporter mouse model, revealing heterogeneous turnover dynamics among different vascular beds. While the aorta and IVC exhibit overall quiescence, we observe that capillaries consistently display more active physiological turnover than arterioles and venules across most organs. We further identified the transcription factor Lhx6 as enriched in quiescent ECs. Lhx6 is expressed in a subset of venous and capillary ECs (1-6% of all ECs) across multiple organs, but is absent from arterial or lymphatic ECs. These Lhx6 cells contribute substantially to the maintenance of venous and capillary ECs during homeostasis, but do not contribute to arterial or lymphatic endothelium. Mechanistically, Lhx6 maintains endothelial viability through the Rspo3-Wnt pathway. Functionally, Lhx6+ cells dominantly (>90%) contribute to angiogenesis in tissue regeneration and lung cancer models. Our findings indicate that major endothelial compartments are maintained by independent resident progenitor pools. Lhx6+ ECs represent a lineage-restricted progenitor population supporting venous-capillary homeostasis and pathological angiogenesis.

Stem cell-derived embryo models could greatly facilitate our understanding of embryonic development. Although human and monkey embryo models have reached early gastrulation stage, the development of robust models beyond this time remains to be accomplished. Using an optimized three-dimensional (3D) suspension culture system, we have successfully advanced the in vitro culture of stem cell-derived monkey blastoid to day 25 (D25). Morphological and histological analyses showed that these monkey embryoids underwent gastrulation and largely recapitulated key developmental events of the late gastrulation stage observed in vivo, with the appearance of neural plate, hematopoietic system, allantois, primitive gut, primordial germ cells, yolk sac structures, and progenitors of other organs, excluding trophoblast derivatives. Single-cell transcriptomic analyses revealed that the lineage composition and differentiation trajectories of cells in these monkey embryoids were similar to those found in natural embryos during gastrulation. Thus, this primate stem cell-derived embryo model provides a valuable platform for dissecting the mechanisms of primate embryonic development from blastocyst to late gastrulation stage.

Recent advances in adult tissue stem cell–based organoid technology have transformed our ability to model human development, regeneration, and disease. Organoids can faithfully reproduce tissue architecture, genetic context, and regenerative dynamics, yet reconstituting authentic tissue functions remains a major challenge. This limitation stems from current culture systems that rely heavily on proliferative signals, often inducing epigenetic drift or metaplastic conversion that erodes native identity. Using primary human hepatocytes, we identified divergent regenerative programs in which YAP activation triggers metaplasia, while STAT3 signaling preserves lineage fidelity by counteracting this process. Building on this principle, we established a new culture system incorporating STAT3 activators that supports long-term propagation of functional hepatocytes with robust metabolic activity. Similar regenerative logic has been applied to other epithelial organoids, revealing shared mechanisms that balance proliferation and identity maintenance.

In this symposium, I will discuss how decoding regenerative mechanisms enables the design of next-generation organoid systems that better emulate human tissue function. I will also highlight our efforts to translate these insights into regenerative therapies for the intestine and liver. Together, these studies illustrate how fundamental understanding of regeneration can bridge organoid biology with clinical applications in tissue repair and disease modeling.

Cellular senescence, a stress response program characterized by stable cell cycle arrest and a proinflammatory secretome, is a key hallmark of the aging process. While in younger organisms senescent cells are effectively cleared by the immune system; in the elderly they accumulate in tissues and are thought to contribute to aging pathobiology. Yet how do they build up and how do they contribute to aging remains unclear. Two key limitations that have held the field back in answering these questions have been the lack of: 1) surface markers to isolate and characterize senescent cells from aged tissues and 2) specific somatic approaches to target them without the need to breed and age for years genetically engineered mouse models (GEMMs) or employ unspecific chemical approaches. In a departure from these strategies we develop cell-based senolytic therapies based on chimeric antigen receptor (CAR) T cells. Harnessing them, we here explore the profile and characteristics of senescent cells that accumulate during physiological aging and their functional impact on aging phenotypes. In addition, we explore the preventive and therapeutic potential of immune-based cell therapies for age-related pathologies.

Hematopoietic stem cells (HSCs) exhibit remarkable heterogeneity in self-renewal, lineage potential, and response to aging. Over two decades of our work have revealed how this diversity evolves into functional decline and how it may be reversed through molecular reprogramming.

In Sudo et al. (J. Exp. Med., 2000), we first defined age-associated characteristics of murine HSCs, showing that aged HSCs accumulate but display reduced lymphoid potential, impaired homing, and myeloid-biased differentiation. Extending this, Morita et al. (J. Exp. Med., 2010) demonstrated that even within the most primitive HSC compartment, distinct subpopulations exist—ranging from myeloid-biased to balanced and lymphoid-biased HSCs—each with unique self-renewal and reconstitution kinetics. This work established a functional hierarchy within HSCs, revealing that lymphoid-biased HSCs possess limited self-renewal and diminished erythroid–megakaryocytic potential.

Yamamoto et al. (Cell Stem Cell, 2018) further dissected the aged HSC compartment through large-scale single-cell transplantation, identifying clonal expansion of myeloid-restricted progenitors and the presence of "latent" HSCs that regain multipotency only upon secondary transplantation. Most recently, Igarashi et al. (in revision) discovered that activation of a fetal-like regulatory program can restore youthful properties in aged HSCs, enhancing their regenerative and engraftment capacity without genetic alteration.

Together, these studies define the continuum of HSC aging—from hierarchical diversification to clonal restriction and eventual rejuvenation—and provide a framework for developing strategies to restore hematopoietic balance and regenerative capacity in aging and disease.

Spinal cord injury (SCI) is a devastating neurological condition with no established regenerative treatment. To address this challenge, our group has pursued stem cell–based strategies for over 25 years, progressing from fetal neural stem/progenitor cell (NS/PC) studies to induced pluripotent stem cell (iPSC)-derived NS/PC transplantation. Preclinical work in rodents and non-human primates demonstrated functional recovery, with graft-derived neuronal activity, synaptic integration, and remyelination identified as key mechanisms of action. In collaboration with CiRA, we established rigorous safety and quality control pipelines, enabling the world’s first first-in-human clinical trial of iPSC-derived NS/PC transplantation for subacute complete SCI (AIS A, 2–4 weeks post-injury). Four participants underwent transplantation of two million cells each into the lesion epicenter, followed by one year of observation. The trial met its primary endpoint of safety: no tumorigenesis was detected on MRI, and no serious adverse events were attributable to the cells. Importantly, two patients showed neurological improvement (AIS A→C and A→D), and the median motor score gain was 13 points at 52 weeks—exceeding historical registry outcomes (4–7 points), suggesting significant efficacy of iPSC-derived NS/PC transplantation.

Building on this milestone, we are preparing a physician-led trial for chronic incomplete SCI, a more prevalent yet refractory condition. In preclinical studies, spinal cord–type gliogenic iPSC-derived NSCs differentiated into neurons and oligodendrocytes, promoted axonal regeneration, and improved locomotor recovery. The upcoming trial, scheduled for 2026, will combine transplantation with advanced neurorehabilitation, including robotic assistive technologies such as the Hybrid Assistive Limb (HAL). By optimizing graft type, ameliorating the hostile chronic environment, and integrating rehabilitation, we aim to overcome barriers specific to chronic SCI.

Together, these efforts represent not only an expansion of clinical indications but also a critical step toward scalable, regulatory-approved regenerative therapies for neurological disorders.

A comprehensive recording of cell lineage histories and dynamic molecular programs during mammalian development remains a fundamental goal in developmental biology. Here, we present DeepTrack, a mouse model that integrates in vivo lineage tracing with single-cell multi-omics to simultaneously profile clonal fates, transcriptomic states, and chromatin accessibility. Using DeepTrack, we uncovered early fate priming within epiblast clones and mapped their divergent contributions to germ layers, fetal organs, and specific tissue regions. Embryo-wide multi-omic lineage tracing at single-cell resolution revealed fate commitment in neuromesodermal progenitors (NMPs) and identified transcriptional and epigenetic programs governing fate decisions. Integrating lineage with multi-omic profiles enabled inference of fate-associated gene-regulatory networks and identified the transcription factor Cdx2 as a key regulator of mesodermal specification in NMPs. Genetic perturbation of Cdx2 in chimeric embryos impaired paraxial mesoderm differentiation. Together, DeepTrack provides a versatile framework for decoding multimodal regulation of cell fate across diverse developmental contexts.

In mice, the repressive histone mark H3K27me3 undergoes both region-specific inheritance and erasure during the parental-to-embryonic transition, with the underlying mechanisms poorly understood. Here, we show that PRC2, which catalyzes H3K27me3, binds both classic Polycomb targets and noncanonical H3K27me3 domains in growing oocytes but dissociates from chromatin in fully grown oocytes. After fertilization, PRC2 rebinds noncanonical H3K27me3 domains before relocating to Polycomb targets in blastocysts. Interestingly, the binding and activity of PRC2 are restricted by a maternal inhibitory factor, EZH inhibitory protein (EZHIP), which co-binds with PRC2. Upon knockout of Ezhip, hyperactive PRC2 promiscuously deposits H3K27me3 genome-wide. This overwrites H3K27me3 memories at noncanonical imprinted genes and paradoxically causes derepression of H3K27me3 targets, defective X chromosome inactivation, and diluted chromatin PRC2. H3K27me3 restoration at Polycomb targets after implantation is also attenuated, accompanied by sub-lethality. These data unveil principles of epigenetic inheritance that both insufficient and excessive heterochromatic marks cause loss of epigenetic memories and repression.