Cell Stem Cell

Airway epithelial homeostasis relies on multiple specialized cell types, with club cells playing central roles in maintaining epithelial integrity and regulating inflammation. Environmental insults such as allergens, viral infections, or pollutants preferentially damage club cells, impairing epithelial repair and contributing to pulmonary diseases. However, the functional properties of club cells remain incompletely defined, and tractable human models are lacking. Herein, we establish a robust platform to differentiate human pluripotent stem cells (hPSCs) into club cells exhibiting their hallmark secretory features, appropriate epithelial organization, and functional properties. Single-cell transcriptomic analyses and lineage trajectory inference revealed unexpected epithelial plasticity: hPSC-derived club cells give rise to multiciliated epithelial cells through a deuterosomal intermediate--a previously uncharacterized trajectory. Additionally, a distinct club cell subset exhibited transcriptional features indicative of neuroendocrine and goblet cell differentiation potential. This study uncovers club cell plasticity and establishes a hPSC-based platform for studying airway development, regeneration and disease modeling.

Post-traumatic osteoarthritis (PTOA) is a common long-term consequence of joint injury and a major cause of chronic pain and disability, yet no disease-modifying therapies are currently available. A central barrier to effective intervention is the persistence of maladaptive synovial inflammation, driven in part by macrophage-mediated signaling that sustains tissue degeneration and pain. Here, we developed a scalable, chemically defined platform to generate human induced pluripotent stem cell (iPSC)-derived anti-inflammatory macrophages (iMac-M2) as an off-the-shelf cell therapy designed to restore joint immune homeostasis after injury. These cells maintained a stable anti-inflammatory phenotype and function under osteoarthritis-relevant inflammatory conditions and suppressed inflammatory and catabolic responses in human joint cell co-culture systems. In a preclinical model of PTOA, intra-articular delivery of iMac-M2 after injury improved functional and structural outcomes while modulating synovial inflammatory and pain-associated transcriptional programs. Treatment was well tolerated, with no evidence of systemic immune activation or ectopic tissue formation. Together, these findings support iPSC-derived macrophage therapy as a clinically translatable immunomodulatory strategy to interrupt early inflammatory drivers of PTOA and preserve joint health following injury. One Sentence SummaryAn iPSC-derived macrophage therapy restores joint balance, protects cartilage, and relieves pain after traumatic joint injury.

The regulation of human hematopoietic stem cell (HSC) function through its native environment is virtually unknown. Cross-species chimeras, particularly humanized mice, are essential tools for investigating human HSC function in vivo. However, conventional models often require toxic conditioning that impairs niche and donor cell function, or simplify niche complexity. We utilize NSGW41 mice, which harbor a KIT receptor mutation, to achieve robust human leukocyte engraftment without prior treatment. We demonstrate that KIT-proficient human HSCs possess a clear advantage, effectively outcompeting endogenous murine stem cells and progenitors to establish stable, multilineage human hematopoiesis. Crucially, the murine niche undergoes significant plastic adaptation in response to humanization. We identify that mesenchymal stromal cells (MSCs) expand and undergo a transcriptional shift, transitioning from a mixed adipo- or osteo-primed state toward predominantly Lepr+ adipo-primed HSC-supporting cells. This adaptation is vital; the depletion of Lepr+ MSCs or the targeted deletion of Stem Cell Factor (SCF) from these cells leads to the mobilization or loss of human HSC engraftment, respectively. These findings provide compelling evidence for functional cross-species niche-HSC communication, identifying Lepr+MSCs as primary regulators of human HSC maintenance in xenotransplantation models. By mapping this molecular dialogue, our work establishes a physiological in vivo platform to study human HSC biology and evaluate niche-targeted therapeutic interventions to improve transplantation outcomes.

Rejuvenating aging human skin is a major therapeutic goal, but objective, quantitative measures of intrinsic aging are limited. We performed a cross-sectional histological study of UV-protected buttock and abdominal skin in adults spanning multiple decades of life to identify features that reliably track age. Epidermal thickness measured between rete ridges was unchanged, but rete ridge size declined linearly with age: ridges became shorter and thinner in both sites, though rete ridge number decreased only in the abdomen. Consistent with these structural changes, proliferative cells (Ki67+) per ridge and expression of integrin {beta}4 (ITGB4), a putative stem-cell marker, were reduced in aged skin. We combined these biomarkers into a predictive model that estimated skin age more accurately than any single marker. To test whether the model detects longitudinal change, we analyzed aged abdominal skin before and after xenografting onto young or aged mice, a procedure previously reported to rejuvenate human skin in young but not aged recipient mice. Both individual biomarkers and the imaging model indicated rejuvenation regardless of host age; however, notably, engraftment efficiency was lower in aged hosts, with surviving grafts showing younger histological phenotypes. These results provide quantitative criteria for assessing intrinsic skin aging and suggest that the process of engraftment itself is sufficient to induce rejuvenation-like changes.

The developmental program governing meibomian gland (MG) morphogenesis and proliferation remains poorly understood, largely due to the lack of physiologically relevant model systems. Here, we established a novel high-fidelity, three-dimensional organoids model derived from mouse meibomian gland (mMGO) epithelium. Transcriptomic and phenotypic analyses demonstrated that mMGOs faithfully recapitulate postnatal gland development in vivo, including dynamic transcription program, branching morphogenesis, lineage differentiation, and functional lipid accumulation. Leveraging this model, we identified the Hippo-YAP pathway as a pivotal regulator of MG epithelial proliferation and homeostasis for the first time. YAP inhibition severely impaired organoids growth, while pharmacological inhibition of Hippo pathway with XMU-MP-1 enhanced proliferation and progenitor clonogenicity. Crucially, in inflammation-induced atrophic organoids, XMU-MP-1 treatment rescued YAP nuclear localization and stimulated regrowth and functional restoration. Our study provided new mechanistic insights and a robust organoids platform for MG development research, and nominated targeted Hippo pathway inhibition as a promising strategy to reverse glandular atrophy in meibomian gland dysfunction.

Tumor-associated macrophages (TAM) exert essential functions during the immune response to cancer. However, investigations of TAM within a native human tumor microenvironment (TME) have been impeded by a lack of appropriate model systems. Here, patient-derived organoids (PDO) from air-liquid interface (ALI)-grown tumor fragments, containing a human TME that encompassed stroma and immune subsets, robustly preserved TAM that were maintained by endogenous CSF-1 and appropriately responded to polarization signals. Antibody blockade of the CD47 regulatory checkpoint in organoids stimulated phagocytosis and remodeled TAM cytokine secretion profiles that were confirmed in anti-CD47 phase I trial patients. Amongst PDO histologies screened, anti-CD47 tumor killing was notable in clear cell renal cell carcinoma (ccRCC) which was associated with increased TAM infiltration. PDO contained diverse previously described TAM subsets; however, anti-CD47 reprogrammed organoid TAM toward an immunosuppressive SPP1+ phenotype, highlighting a negative feedback mechanism. Our findings uncover a resistance circuit engaged by macrophage checkpoint blockade and position ALI PDO as a robust translational platform for dissecting human macrophage biology and informing precision immunotherapy.

Investigation of gene regulatory programs underlying corneal epithelial cell specification and homeostasis is essential for understanding how the cornea maintains vision. Here, we describe the use of true single-cell resolution spatial transcriptomics (ST), enriched with full-tissue single-cell RNAseq (SC), to improve spatial resolution and enhance cell cluster size up to 65-fold and per-cell transcriptomic depth up to 17-fold. This enabled cell type specification across the full differentiation trajectory from limbal stem cells (LSC) to superficial corneal epithelium and identification of an activated signature (Atf3, Zfp36, Gsta4 and Dapl1) marking differentiation-primed states across multiple cell types, including a major activated intermediate epithelium (AIE) population. Validation using ST data from murine corneas at different postnatal ages and multiple human SC datasets confirms a large AIE population, which spatial localization and transcriptomic profiling suggest is an active intermediate state distinct from quiescent wing cells. Sub-clustering further revealed early (Sox9, Hes1), proliferative (Mki67, Top2a) and mature (Ccdn1, Dapl1) transient amplifying cell subpopulations and four LSC subpopulations, including putative active (Atf3, Socs3, Zfp36), quiescent (Gpha2, Ifitm3, Cd63) and Apoe-specific. Direct ST-to-SC comparison revealed enhanced axonal processes and genes (Sema3f, Sema 4d, Pax6) and cell-cell adhesion and cell-matrix markers (Itgb4, Tns4, Tjp3) in ST data, suggesting cell dissociation from tissue in SC masks epithelial innervation, adhesion and barrier functions. Our findings identify and localize key transcriptional programs in situ, prompting a re-evaluation of epithelial states in scRNA-seq data.

Precise orchestration of stem and progenitor cells is essential for tissue homeostasis and regeneration but becomes dysregulated during aging. Despite the known markers, the age-related dynamics of esophageal epithelial cell lineages remain unclear. Using single-cell single cell transcriptomics, we analyzed human esophageal epithelia across different age groups. We identified two stem cell populations: quiescent (qeSCs) and proliferative (peSCs) esophageal stem cells. qeSCs from young donors showed higher WNT10A expression and Wnt signaling activity. Analysis of cell lineage trajectories combined with cell plastic potentials showed stronger connectivity between peSCs and differentiated cells in younger tissues, indicating more efficient and rapid epithelial turnover and homeostatic maintenance. Cell-cell interaction analysis further demonstrated that NOTCH signaling is more prominent within peSCs and qeSCs in younger esophagi, whereas in older tissues, NOTCH activity is preferentially retained in differentiated cells. Additionally, the inflammatory signaling, Interleukin-1 pathway, is more active in younger esophagi but is largely restricted to differentiated cells. Our findings suggest that age-related decline in esophageal homeostasis is primarily driven by impaired differentiation dynamics rather than by alterations in stem cell self-renewal capacity.

Stem cell renewal and crypt survival are tightly controlled processes critical for gut repair. Defining key regulators of intestinal healing is critical for the development of new epithelial-targeted therapies. We previously showed that the nuclear receptor LRH-1 (NR5A2) maintains intestinal epithelial health and protects against inflammatory damage. Here, using lineage tracing and selective LRH-1 knockout in the Atoh1+ secretory lineage we show LRH-1 is vital for intestinal stem cell (ISC) regeneration in complementary in vivo and ex vivo injury-recovery models. Transcriptomic profiling and pathway analysis reveal downregulation of ER stress and unfolded protein response (UPR) programs. Using a new in vivo model to ascertain how LRH-1 directly impacts intestinal cell responses, we identify key ER stress response genes Ire1 and Xbp1 as potential LRH-1 targets. Together our results uncover a novel mechanism whereby LRH-1 sustains the IRE1-XBP1 arm of the UPR to support injury-induced dedifferentiation and ISC regeneration. Our findings highlight LRH-1 as a promising therapeutic target for restoring epithelial integrity in inflammatory intestinal disorders.

Reversible drug-tolerant persister states are emerging as key drivers of limited therapeutic durability, offering a complementary non-genetic perspective distinct from traditional models of acquired resistance. This is of particular interest in lung adenocarcinoma where EGFR tyrosine kinase inhibitors (TKIs) elicit dramatic responses, yet residual surviving cells persist and ultimately seed relapse. To define mechanisms that enable survival during this earliest residual-disease phase, we focused on the drug-tolerant persister population that remains after EGFR TKI exposure and can later give rise to outgrowth. Initial observations of elevated transcript levels of PRKCA, which encodes PKC, in established TKI-resistant models, together with markedly delayed tumor relapse following PKC suppression in vivo, nominated PKC as a candidate regulator of the persister-to-relapse transition. Genetic ablation of PRKCA or its inhibition with enzastaurin reduced residual survival and outgrowth after TKI exposure, indicating that PKC functions as an early dependency of drug-tolerant persisters rather than as a general mediator of acquired resistance. Mechanistically, PKC was required for persister-associated EMT, migratory capacity, and robust induction of ALDH1A1, the latter constraining oxidative stress and enhancing persister survival. Functionally, PKC was specifically necessary for survival of a rare, pre-existing CD44High stem-like subpopulation that exhibited marked plasticity and ultimately seeded persistence. Together, these data identify a PKC-dependent EMT/stemness/ROS pathway as a critical survival program in EGFR TKI-tolerant persister cells and support therapeutic strategies aimed at eliminating residual disease to prolong clinical responses.

The specific contribution of tissue-resident macrophages (TRMs) to pancreatic ductal adenocarcinoma (PDAC) progression remains unclear. Here, we found that a high abundance of TRM-derived tumor-associated macrophages (TRM-TAMs) is an independent indicator of poor prognosis in patients with PDAC. To elucidate the underlying mechanism, we established an advanced organoid platform (iMac-FPCO), which incorporates macrophages derived from human induced pluripotent stem cells to reflect the differentiation process of TRMs. Single-cell transcriptomic analysis revealed this model recapitulates the transcriptional identity of TRM-TAMs in patient tissue. We demonstrated that TRM-TAMs drive cancer cell proliferation, while maintaining chemoresistance, and identified TRM-derived insulin-like growth factor 1 (IGF1) as the critical mediator. This result provides a rationale for why previous trials targeting IGF1 receptor (IGF1R) failed to improve survival in unselected patient populations. We hypothesize that stratifying patients by TRM-TAM abundance could help identify a responsive subgroup, thereby reviving IGF1R-targeted therapy as a viable treatment for PDAC.

Glioblastoma (GBM) is a devastating primary brain tumor with remarkable inter- and intra-tumoral heterogeneity. GBM cells assume a spectrum of neurodevelopmental-like phenotypes and co-opt normal neurophysiological processes, which include synaptic integration with their neuronal microenvironment. This is mediated by neuron-tumor synapses (NTS) that predominantly involve glutamatergic receptors, which drive calcium elevations that promote tumor proliferation and invasion. The exact relationship between synaptic signaling and tumor cell fate specification, however, remains largely unexplored. Here, we develop and leverage a synapse-optimized human organoid tumor transplantation (so-HOTT) model of GBM to decipher how glutamatergic signaling impacts GBM lineage trajectories. so-HOTT preserves patient tumor heterogeneity, features excitatory NTS, and enables clonal lineage tracing of tumor cells after NTS perturbations. Genetic and pharmacological inhibition of AMPA and kainate receptors in so-HOTT shifts tumor cell composition from neuronal fates toward progenitor-proximal astrocytic/mesenchymal states. This occurs through the attenuation of calcium signaling and reduced plasticity of malignant radial glia (RG)-like progenitors, a previously unrecognized target of NTS. Through the integration of inputs from the neuronal microenvironment into glutamatergic signaling, progenitor populations modulate their transcriptional programs and cell fate, ultimately shaping GBM tumor heterogeneity. Targeting synaptic input may thus constrain the heterogeneity that fuels GBM adaptation and therapeutic escape.

Chronic inflammation and aging skew hematopoiesis toward myelopoiesis at the expense of lymphoid output. We screened type 2 and anti-inflammatory cytokines to identify extrinsic signals capable of restoring lymphoid lineage commitment in hematopoietic stem and progenitor cells (HSPCs). Interleukin-4 (IL-4) specifically inhibited inflammation-induced myelopoiesis and shifted multipotent progenitor (MPP) differentiation toward the lymphoid lineage. IL-4 activated a STAT6-dependent transcriptional program in MPPs, increasing expression of lymphoid-specific genes. Mechanistically, the receptor tyrosine kinase FLT3, highly expressed in MPPs, interacted with IL-4R to facilitate STAT6 activation. In vivo, IL-4 reversed inflammation-induced hematopoietic imbalance and accelerated lymphoid recovery. In aged mice, IL-4 administration shifted the MPP composition toward lymphoid bias and restored B and T lymphocyte output. Long-term IL-4 treatment of aged mice improved immune, metabolic, physical, and cognitive functions; these rejuvenating effects were recapitulated by transplantation of IL-4-treated HSPCs. Promoting IL-4 signaling on MPPs may enable correcting hematopoietic dysregulation in inflammatory and aging-related conditions.

The accelerating biodiversity crisis, compounded by emerging infectious diseases like African swine fever (ASF), necessitate innovative conservation and disease management. ASF susceptibility varies wildly across species, from near-100% mortality in Asian suids to asymptomatic carriage in African forest species. We report the first successful derivation of integration-free induced pluripotent stem cells (iPSCs) from four phylogenetically distinct species: wild boar (Sus scrofa), Bornean bearded pig (Sus barbatus), Babirusa (Babyrousa babyrussa), and Red river hog (Potamochoerus porcus). Using Sendai virus-mediated reprogramming, we achieved efficiencies between 0.003% and 0.26%. These iPSCs were successfully differentiated into CD14CD11b monocytes - the primary target cells for the ASF virus - establishing a renewable, comparative research platform. This system enables host-pathogen studies previously hindered by ethical and logistical constraints of wildlife sampling. Beyond disease research, these iPSC lines serve as vital genetic repositories for endangered suids. Our methodology provides a replicable framework for extending stem cell technology to other conservation-priority taxa, demonstrating how high-tech cellular tools can advance both fundamental research and biodiversity preservation against emerging pathogen threats.

Chronic fibrotic disorders like idiopathic pulmonary fibrosis (IPF) are characterized by aberrant alveolar regeneration and severely limited treatment options. Identification of the mechanisms driving aberrant epithelial repair can lead to new viable therapeutic targets. Using integrated single nucleus ATAC- and RNA-sequencing on human lungs and an in vitro model of dysplastic repair, we identify two distinct regenerative trajectories for alveolar type 2 (AT2) cells: a resolvable euplastic repair trajectory and a persistent, non-resolving dysplastic repair trajectory. The latter is governed by a spatially restricted ITGB6/TGF{beta}1/SMAD3 signaling axis in fibrotic regions of IPF lungs and in murine lungs characterized by chronic epithelial remodeling. Mechanistically, SMAD3 directly regulates dysplastic transitional cell (DTC) markers, including KRT17 and Stratifin. We show that TGF{beta}1 signaling promotes a physical interaction between KRT17 and Stratifin at the leading edge of migrating DTCs in vitro and in vivo, which is essential for their migratory capacity. These findings collectively define the molecular regulation of AT2-driven dysplastic regeneration and identify TGF{beta}1-induced KRT17-Stratifin axis as a central driver of pathological epithelial remodeling in chronic fibrosis, which can be targeted therapeutically to tilt the balance in favor of euplastic regeneration.

Neural stem cells (NSCs) persist in the mammalian brain after development, but their potential for replacing neural populations lost in brain damage is dramatically restricted. Quiescence, or the ability to transition in and out of the cell cycle is a hallmark of adult NSCs. It deepens as the organism ages and is regarded as a strategy to protect the reservoirs of NSC for the long term. Deciphering the molecular code of dormancy is a major interest in cellular and molecular biology of ageing and in regenerative medicine since it has important implications for potentially manipulating NSCs to improve tissular homeostasis. In this work we have identified the mitotic kinase Polo like kinase 1 (Plk1) as a novel intrinsic regulator of the dynamic transition between NSC quiescence and activation in adult neurogenic niches. Using quantitative phosphoproteomics to pinpoint mechanistical mediators of the role of Plk1, we have identified the quiescence/activation molecular switch formed by E3 ubiquitin ligase Huwe1 and its target, the transcription factor Ascl1/Mash1, as novel effectors of Plk1 in NSCs. We discover that Plk1 restrains the accumulation of Ascl1/Mash1 by acting upstream of Huwe1, providing a direct molecular connection between completion of the cell cycle and the re-establishment of a low activation state following NSC division, which supports the concept that quiescence is an actively maintained state. Moreover we demonstrate that pharmacological inhibition of Plk1 is sufficient to enhance adult neurogenesis in vivo, identifying Plk1 as a viable target to acutely boost endogenous stem cell activation.

Neural stem cells (NSCs) sustain lifelong neurogenesis through the tight regulation of quiescence, self-renewal and differentiation. Quiescent NSCs (qNSCs) exist in distinct substates, ranging from deep to shallow quiescence, yet the mechanisms governing these transitions remain unclear. In long-term self-renewing NSCs of the adult zebrafish pallium, we show that mTORC1 activity is specifically enriched during a prolonged quiescence phase in which NSCs acquire activation competence. Functional perturbations, analyzed in situ and using single-cell RNA sequencing, reveal that mTORC1 regulates cell progression during this phase, concomitantly ensuring the correct tempo for NSC transition towards activation and the preservation of stemness. These findings challenge the classical view of mTORC1 as a simple regulator of proliferation and identify it as a key regulator of NSC quiescence heterogeneity and dynamics under physiological conditions. By coordinating stemness maintenance with activation competence, mTORC1 emerges as a central player balancing long-term NSC preservation with neurogenic output in the adult brain.

Patients with non-small cell lung cancer (NSCLC) carrying activating EGFR mutations typically respond favorably to third-generation EGFR tyrosine kinase inhibitors (TKIs) such as osimertinib. Nevertheless, resistance almost inevitably emerges, ultimately limiting the durability of these treatments. We investigated non-genomic mechanisms enabling drug-tolerant persister cells to survive EGFR inhibition, likely co-opting compensatory HER3 activation, whose underlying mechanisms remain unclear. Using a combination of immortalized and patient-derived cellular models, together with single-cell RNA sequencing, we demonstrate that activation of EGFR/HER3 axis constitutes an early adaptive response to TKI exposure enriched in pulmonary alveolar type I and type II cancer cells. This response is driven by neuregulin-1 (NRG1), produced by stromal cells and by cancer cells undergoing NE-like/EMT dedifferentiation. Importantly, in vivo studies demonstrated that combining EGFR inhibition and NRG1 neutralization by monoclonal antibody successfully eradicated tumors. Together, these findings point to a therapeutic strategy to overcome TKI resistance in NSCLC through targeting HER3 signalling, its interplay with EGFR, and tumor microenvironment-derived cues.

The ability to generate functional B cells from human pluripotent stem cells (hPSCs) would open new opportunities to develop novel B cell-based therapies to treat a range of human diseases and disorders. Towards this goal, we established a protocol that promotes the efficient development of B lineage cells from definitive hematopoietic progenitors generated from different hPSC lines. Flow cytometric and multi-omic scRNA-seq analyses revealed that B cell development from hPSCs transitions through the well-established pro-B, pre-B and naive B cell stages, accurately recapitulating B lymphopoiesis in the human adult bone marrow. Importantly, the naive B cells generated with this approach could be induced to mature into plasma cells that secrete antibodies and undergo class switching. Analyses of signaling pathways that regulate B lymphopoiesis in these cultures uncovered a potent inhibitory effect of IL-7 on functional IgH rearrangement, resulting in the development of abnormal cells that failed to undergo pre-B cell maturation. Finally, analysis of the different hPSC-derived hematopoietic programs revealed that both definitive and yolk sac progenitors display B cell potential, indicating that there are distinct developmental sources of human B lineage cells. Taken together, these findings demonstrate the efficient generation of B cells from hPSCs and, in doing so, provide a system for further investigating the earliest stages of human B lymphopoiesis and a source of appropriately staged plasma cells for future therapeutic applications.

Islet transplantation can restore glycemic control in type 1 diabetes, yet the heterogeneity of patient immune responses and transplant outcomes motivates the need for technologies to monitor the graft. Since transplanted islets are not readily accessible for biopsy due to their diffuse engraftment within the liver, clinical monitoring relies on measurements such as islet mass, blood glucose, and C-peptide levels, which are lagging indicators that change only after substantial graft injury. Here, we developed a minimally invasive synthetic immunological niche (IN) that captures graft-associated immune responses through serial subcutaneous biopsy. We evaluated the IN across murine syngeneic, allogeneic, and autoimmune islet transplant models, including CD40/CD154 costimulatory blockade with anti-CD40L. In syngeneic versus allogeneic recipients, IN identified immune populations and transcriptomic signatures that mirrored the graft and distinguished healthy from rejecting grafts. In anti-CD40L treated allografts, IN revealed innate macrophage- and dendritic cell-associated programs linked to graft acceptance versus rejection, whereas IN from untreated allografts showed stronger adaptive immune signatures. Longitudinal IN profiling further detected progressive inflammatory activation in accepted allografts, indicating persistent subclinical risk. Finally, in an autoimmune allograft model treated with anti-CD40L plus rapamycin, IN identified a 13-gene signature that separated early from late rejection trajectories and distinguished autoimmune-from alloimmune-associated rejection programs. Overall, these findings establish IN as a surrogate tissue for minimally invasive monitoring of islet graft and early detection of rejection-associated immune dysregulation. One Sentence SummaryAn engineered immunological niche captures distinct immune signatures of allo- and auto-mediated islet transplant rejection