Rao X, Wang J, Qiao Z
… +28 more, Hong L, Qiao M, Ni L, Song A, Deng Y, Zhao X, Meng J, Chen X, Zhou Y, Xue J, Chi Y, Wang X, Yu Z, Chen Q, Xu C, Tang S, Hu J, Xu M, Xu W, Zhang Z, Zhang Y, Xu Y, Jiang YZ, Wu J, Shen M, Guo X, Yu X, Chen FX
Breast cancer exhibits marked clinical heterogeneity and dynamic epigenetic reprogramming during tumor progression, yet current subtyping approaches fail to capture molecular changes associated with metastasis. Here, we...Breast cancer exhibits marked clinical heterogeneity and dynamic epigenetic reprogramming during tumor progression, yet current subtyping approaches fail to capture molecular changes associated with metastasis. Here, we establish a comprehensive biobank of patient-derived organoids (PDOs) from matched primary tumors, adjacent normal tissues, and lymph node metastases. Integrated genomic, transcriptomic, and epigenetic analyses demonstrate that these PDOs preserve tumor-specific molecular signatures and recapitulate epigenetic remodeling during disease evolution. Epigenetic profiling defines four distinct clusters, characterized by unique transcription factor (TF) networks, pathway activities, and therapeutic vulnerabilities not fully represented by conventional classifications. The lymph node metastasis cluster, predominantly comprising metastatic PDOs, displays extensive chromatin remodeling driven by metastasis-enriched TFs, whose depletion markedly impairs spontaneous metastasis in vivo. Together, these findings establish PDO-based epigenetic characterization as a platform for elucidating regulatory mechanisms underlying breast cancer progression and for advancing precision therapeutic strategies.
Zheng Z, Liu Y, Wang G
… +16 more, Li X, Peng S, Jia Z, Yue X, Fu Z, Zhao X, Han M, Yang Z, Tang C, Gao J, Kong Z, Chen C, Zhao K, Li T, Jiang X, Jing W
Autoimmune diseases involve the coordinated dysregulation of multiple types of immune cells, and single-cell targeted therapies often yield suboptimal results. Here, we developed chimeric antigen receptor (CAR)-engineere...Autoimmune diseases involve the coordinated dysregulation of multiple types of immune cells, and single-cell targeted therapies often yield suboptimal results. Here, we developed chimeric antigen receptor (CAR)-engineered follicular helper T (Tfh) cells capable of simultaneously suppressing T cells, B cells, and dendritic cells (DCs) to restore immune homeostasis in an autoimmune hepatitis (AIH) mouse model. Using amino acid-derived lipid nanoparticles, we deliver self-amplifying RNA encoding Forkhead box protein P3 (Foxp3) and a cytochrome P4502D6 (CYP2D6)-specific CAR to Tfh cells, conferring stable regulatory features and antigen-dependent suppressive activity. Engineered CAR-Tfh cells preferentially localize to the liver, recognize CYP2D6-expressing hepatocytes, and suppress pathogenic T cell and B cell responses. In AIH-II mouse models, CAR-Tfh cell generation restores a tolerogenic hepatic immune environment and ameliorates autoimmune liver injury. These findings establish in situ Tfh cell reprogramming as a modular approach to coordinately modulate multiple immune compartments, providing a potential therapeutic framework for AIH and related autoimmune diseases.
Mayama M, Whelan EC, Sato T
… +5 more, Stouffer DG, Leu AN, Strauss JF, Auchus RJ, Sasaki K
Cell Stem Cell
· 2026 Mar · PMID 41795428
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The adrenal cortex produces essential steroid hormones through a concentric zonal architecture, established by the centripetal transdifferentiation of subcapsular progenitors within a capsule-derived niche. To capture th...The adrenal cortex produces essential steroid hormones through a concentric zonal architecture, established by the centripetal transdifferentiation of subcapsular progenitors within a capsule-derived niche. To capture this complexity, we establish a human pluripotent stem cell-derived adrenal organoid system that faithfully recapitulates this process. RSPO3/WNT signaling from the capsule specifies definitive zone (DZ) progenitors from the adrenal primordium, which then differentiate into a cortisol-producing transitional zone and an androgen-producing fetal zone under the influence of RSPO3 and ACTH. Loss of NR0B1 impairs DZ specification and triggers direct adrenal primordium-to-fetal zone conversion, mirroring the mechanism of X-linked adrenal hypoplasia congenita. When DZ cells are encapsulated with capsule cells separately derived from pluripotent stem cells, they reconstitute zonation in vivo, forming ACTH-responsive tissue that produces both cortisol and androgens. This organoid platform offers a powerful tool to dissect human adrenal development and establishes a foundation for regenerative therapies targeting adrenal diseases.
Doludda B, Barde W, D'Egidio F
… +14 more, Fitzsimons CP, Frisén J, Gage FH, Jessberger S, Lazarov O, Lie DC, Lucassen PJ, de Lucia C, Salta E, Song H, Song J, Thuret S, Toda T, Kempermann G
Cell Stem Cell
· 2026 Mar · PMID 41795427
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The 38 currently registered clinical trials with the keyword "adult neurogenesis" indicate growing interest in new neurons as a target for intervention. Today, we have strong evidence that adult neurogenesis is involved...The 38 currently registered clinical trials with the keyword "adult neurogenesis" indicate growing interest in new neurons as a target for intervention. Today, we have strong evidence that adult neurogenesis is involved in hippocampal function and can contribute to brain functions in health and disease. Neurogenesis research can now ask new questions, such as (1) the identity of stem cells and their input integration for initiating neurogenesis, (2) the nature of the neurogenic niche and neurogenesis without stem cell activity, (3) the complex functionality beyond the hippocampus, and (4) evolutionary and computational theory, including neurogenic neural networks for artificial intelligence.
Twenty years have passed since the first demonstration of mouse induced pluripotent stem cells (iPSCs). What began as an unexpected observation in Kyoto quickly transformed stem cell biology and regenerative medicine wor...Twenty years have passed since the first demonstration of mouse induced pluripotent stem cells (iPSCs). What began as an unexpected observation in Kyoto quickly transformed stem cell biology and regenerative medicine worldwide. Over the past two decades, we have gained profound insights into the molecular mechanisms underlying cellular reprogramming and pluripotency. The technology has continued to evolve-becoming safer, more efficient, and more versatile. Today, iPSCs serve as a foundation for wide-ranging applications, from disease modeling and drug discovery to regenerative therapies and rejuvenation research. In this review, I reflect on the scientific journey of iPSCs, highlight key milestones in our understanding of reprogramming, and discuss the expanding clinical and societal impact of iPSCs.
In their recent Nature paper, Yuan et al. reconstruct patient-specific periportal architecture by assembling hepatocyte organoids with cholangiocytes and portal mesenchyme. Unlike previous attempts, these multicellular u...In their recent Nature paper, Yuan et al. reconstruct patient-specific periportal architecture by assembling hepatocyte organoids with cholangiocytes and portal mesenchyme. Unlike previous attempts, these multicellular units recapitulate much of the cell-cell interaction found in the adult human liver, providing a new sophisticated platform to understand liver biology.
Induced pluripotent stem cell (iPSC)-derived chimeric antigen receptor (CAR) natural killer (NK) cells are an emerging class of off-the-shelf cellular immunotherapy limited by short-term persistence. Wang et al. develop...Induced pluripotent stem cell (iPSC)-derived chimeric antigen receptor (CAR) natural killer (NK) cells are an emerging class of off-the-shelf cellular immunotherapy limited by short-term persistence. Wang et al. develop a platform for lineage-committed progenitor cell therapy to sustain in vivo CAR iNK cell lymphopoiesis and enhance tumor control.
Maimets et al. reveal that appropriate tissue shape is required during maturation of the intestinal epithelium from the fetal to adult state, and this transition is mediated by the mechanotransduction protein-YAP. The in...Maimets et al. reveal that appropriate tissue shape is required during maturation of the intestinal epithelium from the fetal to adult state, and this transition is mediated by the mechanotransduction protein-YAP. The introduced method transforms fetal cells into mature, functional cells in vitro, unachievable by traditional three-dimensional cultures.
Intestinal homeostasis and regeneration rely on intestinal stem cells (ISCs). Li et al. identified neuronal vasoactive intestinal peptide (VIP) as a brake on ISCs through VIPR1 to limit regeneration. In Nature Immunology...Intestinal homeostasis and regeneration rely on intestinal stem cells (ISCs). Li et al. identified neuronal vasoactive intestinal peptide (VIP) as a brake on ISCs through VIPR1 to limit regeneration. In Nature Immunology, Jakob et al. and Pirzgalska et al. further showed that VIP-VIPR1 signaling restrains secretory lineage expansion and balances immune responses..
Ruiz JG, Oliva AA, Ramdas KN
… +22 more, Javier J, Rosen J, Perry R, Blanco A, Ylisastigui P, Walston J, Arai H, Volpi E, Newman AB, Varnado B, McClain-Moss L, Naioti E, Mehranfard D, Gincel D, Wang C, Mintzer MJ, Danisi J, Green GA, Botbyl J, Zainul Z, Rash BG, Hare JM
Cell Stem Cell
· 2026 Mar · PMID 41747733
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Frailty, a syndrome that decreases healthspan in older individuals, lacks effective therapies. We conducted a randomized, dose-finding clinical trial to test whether human bone marrow-derived allogeneic mesenchymal stem...Frailty, a syndrome that decreases healthspan in older individuals, lacks effective therapies. We conducted a randomized, dose-finding clinical trial to test whether human bone marrow-derived allogeneic mesenchymal stem cells (MSCs; laromestrocel) improve physical functioning and patient self-reported outcomes in ambulatory individuals with frailty (ClinicalTrials.gov #NCT03169231; N = 148). Laromestrocel infusion results in clinically meaningful, dose- and time-dependent increases in the 6-min walk test (6MWT; primary endpoint) compared with placebo: 63.4 m (95% confidence interval [CI]: 17.1-109.6 m; p = 0.0077) at month 9 and 41.3 m (95% CI: -2.4-84.9 m; p = 0.0635) at month 6. Increased 6MWT distance correlates with PROMIS Physical Function score, and increasing doses of laromestrocel are associated with decreases in soluble (degraded) tyrosine kinase with immunoglobulin and epidermal growth factor homology domains (TIE2), the cognate receptor for the angiopoietins, identifying a potential biomarker of laromestrocel responsiveness. These findings identify a stem cell therapy approach for the management of patients with hypomobility and other features of aging frailty.
Wang Z, Zhang L, Huang D
… +18 more, Xia C, Weng Q, Lin Y, Liu Y, Liu Z, Yi R, Zhang F, Zhao Y, Wu J, Qi H, Liu L, Shen Y, Chen Y, Zhu Y, Wang T, Zhang M, Hu F, Wang J
Reducing relapse rates post-chemotherapy remains a major challenge for improving cancer therapy. Here, we developed a pluripotent stem cell-derived induced natural killer (NK) lineage-committed progenitor (iNKP) cell the...Reducing relapse rates post-chemotherapy remains a major challenge for improving cancer therapy. Here, we developed a pluripotent stem cell-derived induced natural killer (NK) lineage-committed progenitor (iNKP) cell therapy in leukemia models. We generated abundant iNKP cells via an organoid culture system. The iNKP cells, engineered to express C-X-C motif chemokine receptor 4 (CXCR4) and chimeric antigen receptors (CARs), efficiently migrated to the bone marrow and generated CAR-iNK cells, which persisted in multiple organs and peripheral blood for over 80 days. Notably, CAR-iNKP cell infusion precisely protected animals from tumor challenges. Furthermore, a single low-dose infusion of CAR-iNKP cells following conventional chemotherapy reduced minimal residual disease and significantly prevented cancer relapse in human CD19 B-ALL and CD7 T-ALL tumor-bearing animals. CAR-iNKP cell treatment addresses the limitations of traditional CAR-NK cell infusion and offers a new strategy for future application in human cancer therapy.
Zhu M, Yuan J, Meng Q
… +22 more, Yu J, Xu X, Xu M, Ren X, Hu Y, Wei G, Jia Z, Yuan G, Zang L, Liu S, Yang Y, Zheng Y, Wang J, Cong T, Xie W, Lan X, Cong L, Ma T, Ding S, Guo W, Zhang X, Li Y
Although CRISPR-Cas9 holds therapeutic promise, broader application demands an understanding of complications in vast non-coding regions. We found that CRISPR-Cas9 can cause premature differentiation of neural stem cells...Although CRISPR-Cas9 holds therapeutic promise, broader application demands an understanding of complications in vast non-coding regions. We found that CRISPR-Cas9 can cause premature differentiation of neural stem cells in vivo and mouse embryonic stem cells in vitro, even when cleavage occurred at distant sites tens of kilobases away from the nearest regulatory elements. To investigate this, we employed an integrated assay for transposase-accessible chromatin (ATAC)/RNA sequencing (AR-seq) approach and identified editing-induced chromatin accessibility changes, with their scale varying by cell type. Cells with stemness are most affected, experiencing perturbations that extend over a hundred kilobases. Furthermore, even local DNA perturbations can disrupt CTCF- and condensate-associated chromatin architecture, causing distal transcriptional rewiring and, ultimately, loss of stemness identity. To minimize chromatin perturbations and preserve cell identity, we refined gene-editing strategies, including distance-aware sgRNA design, pharmacological attenuation of DNA resection, and alternative editing systems. This work paves the way for the safer and broader application of genome-editing technologies.
Shen Y, Benlabiod C, Watson E
… +22 more, Gurashi K, Fower A, Rodriguez-Romera A, Reyat JS, Adnan-Awad S, Hargreaves R, Kemble S, Smith CG, Croft AP, Oppermann U, Welsh A, Murphy L, Murphy E, Moetazedian A, Jooss N, Wong ZC, Rayes J, Mead AJ, Roy A, Gooding S, Psaila B, Khan AO
Cell Stem Cell
· 2026 Mar · PMID 41734765
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The bone marrow is the primary site of blood and immune cell production in postnatal life. Current human models do not capture lympho-myeloid hematopoiesis and the stromal diversity needed for lifelong blood and immune m...The bone marrow is the primary site of blood and immune cell production in postnatal life. Current human models do not capture lympho-myeloid hematopoiesis and the stromal diversity needed for lifelong blood and immune maintenance. Here, we introduce comBO (combined bone and lympho-myeloid bone marrow organoid), a scalable induced pluripotent stem cell (iPSC)-derived system that generates osteolineage, vascular, lymphoid, and myeloid compartments within a single organoid. Developed under physioxia in granular microgel scaffolds, comBOs improve scalability and reproducibility and sustain long-term lympho-myeloid potential in serial organoid re-seeding assays. Incorporating healthy or malignant donor cells produces "chimeroids" that model physiological and pathological states. Using multiple myeloma as an exemplar, comBOs recapitulate niche remodeling and identify macrophage inhibitory factor (MIF) signaling as a disease driver. MIF inhibition reduces inflammation and myeloma proliferation, highlighting its therapeutic potential. comBOs offer a physiologically faithful bone marrow platform for disease modeling and therapeutic discovery in translational hematology and immunology.
Intestinal stem cells (ISCs) drive epithelial renewal and regeneration, yet how neural cues shape ISC behavior remains unclear. Here, we identify a neuronal checkpoint that directly restrains ISC regenerative output duri...Intestinal stem cells (ISCs) drive epithelial renewal and regeneration, yet how neural cues shape ISC behavior remains unclear. Here, we identify a neuronal checkpoint that directly restrains ISC regenerative output during injury. We show that vasoactive intestinal peptide (VIP)-producing enteric neurons directly signal to ISCs through the epithelial receptor VIP receptor 1 (VIPR1). In steady state, VIP-VIPR1 signaling restrains ISC hyperproliferation by engaging an extracellular signal-regulated kinase (ERK)-Notum-Wnt/β-catenin inhibitory axis. During colitis, VIPergic neurons expand within the ulcerated regions and amplify this pathway, thereby suppressing ISC-driven regeneration and exacerbating epithelial injury. Selective deletion of Vipr1 in the epithelium or in ISCs releases this neuronal brake, restores early regenerative activity, and markedly alleviates colitis. The ISC-suppressive function of VIP-VIPR1 signaling is conserved in human intestinal models. Together, these findings define VIPR1 as an ISC-intrinsic neuronal checkpoint that restricts ISC-driven epithelial regeneration and highlight epithelial VIPR1 blockade as a potential strategy to enhance mucosal regeneration in colitis.
Yang F, Pavon N, Matsubara T
… +5 more, Sebastian R, Martinez-Martin B, Pak C, Sun Y, Kim DH
Cell Stem Cell
· 2026 Mar · PMID 41734763
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Positional patterning during human brain development is orchestrated through highly coordinated interplays of locally produced inductive signals. Although animal models have elucidated general signaling pathways during e...Positional patterning during human brain development is orchestrated through highly coordinated interplays of locally produced inductive signals. Although animal models have elucidated general signaling pathways during early neurodevelopment, individual morphogens' effects underlying the proper human brain regionalization remain unclear. Current technologies are limited in generating stable, well-confined gradients in neural organoids for robust regionalization. Here, we report a Matrigel-free passive diffusion-based morphogen gradient generator (PdMG) that reliably established a steep exogenous spatial morphogen gradient in human neural organoids. We further established dorsal-ventral forebrain, rostral-caudal fore-midbrain-like, and rostral-caudal fore-hindbrain-like patterning by applying Sonic hedgehog/Wingless/int1 (WNT) inhibitor, WNT, and retinoic acid gradients, respectively. Spatial transcriptomics analysis revealed robust regionalization in early-stage patterned organoids, as well as active neurogenesis and γ-aminobutyric acid (GABAergic) interneuron migrations in late-stage patterned organoids. Together, this study provides a framework for modeling the spatial-temporal morphogen dynamics that regulate key cell fate specifications and axis formations using patterned neural organoid models.
Uenaka T, Napole A, Saha AD
… +24 more, Sun D, Singavarapu A, Calzada E, Chen J, Erlebach L, McQuade A, Ramos DM, Rigamonti A, Salazar L, Samelson AJ, Sedov K, Welsh NJ, Wild K, Wu Q, Arenas E, Bassett AR, Kampmann M, Kronenberg-Versteeg D, Merkle FT, Schüle B, Thompson LM, Skarnes WC, Ward ME, Wernig M
Transgenes are often silenced upon differentiation of pluripotent stem cells using conventional expression systems. Here, we developed the TK4 PiggyBac vector to conduct a comparative analysis to evaluate the impact of v...Transgenes are often silenced upon differentiation of pluripotent stem cells using conventional expression systems. Here, we developed the TK4 PiggyBac vector to conduct a comparative analysis to evaluate the impact of various promoters, transcriptional regulatory elements, insulators, and genomic integration sites on transgene silencing during neuronal differentiation. Our findings reveal that specific combinations of CAG and Ubc promoters with the Woodchuck hepatitis virus post-transcriptional regulatory element (WPRE) can prevent transgene silencing during differentiation, whereas chromatin insulators have less impact on sustained expression. Three novel safe harbor loci, distant from known genes, as well as the citrate lyase beta-like (CLYBL) locus, similarly support the prevention of transgene silencing. Remarkably, the TK4 vector showed complete resistance to silencing across various neuronal and microglial differentiation protocols, as independently confirmed by seven laboratories. This construct will be highly useful for assays requiring stable transgene expression during differentiation and holds potential for broad applications in various research fields.
Maimets M, Nikolaev M, Lövkvist C
… +14 more, Bertillot F, Larsen HL, Bressan RB, Georgantzoglou A, Gjorevski N, Filidou E, Zøylner M, Hansen SL, Baattrup AM, Banjac I, Guiu J, Wickström SA, Lutolf MP, Jensen KB
Cell Stem Cell
· 2026 Mar · PMID 41687611
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During morphogenesis, the intestine undergoes significant structural remodeling, transitioning from a simple tube of immature epithelium into a complex crypt-villus architecture housing mature cell types. However, the re...During morphogenesis, the intestine undergoes significant structural remodeling, transitioning from a simple tube of immature epithelium into a complex crypt-villus architecture housing mature cell types. However, the relationship between these structural changes and epithelial maturation has remained enigmatic. Using engineered scaffolds that replicate crypt-like geometries, we establish a robust platform for guiding the morphogenesis and differentiation of fetal intestinal cells into mature engineered tissues that mimic their in vivo counterparts. Mechanistically, tissue maturation is driven by cell crowding, leading to reduced YAP1 activation. Modulating YAP signaling in both engineered tissues and the developing mouse intestine alters epithelial lineage specification. These findings uncover a geometry-dependent mechanism that links tissue architecture to cell fate transitions. Our work provides a platform for modeling aspects of intestinal development and offers insights for refining stem cell differentiation protocols and regenerative strategies for intestinal disorders.
Cao S, Yu S, Li D
… +19 more, Ye J, Yang X, Li C, Wang X, Mai Y, Qin Y, Wu J, He J, Zhou C, Liu H, Zhao B, Shu X, Wu C, Chen R, Chan W, Pan G, Chen J, Liu J, Pei D
Sleep disturbances are associated with pathogenesis of numerous chronic disorders, including chronic gastrointestinal diseases. However, the mechanism that transmits sleep disturbance-induced aberrant neural signaling fr...Sleep disturbances are associated with pathogenesis of numerous chronic disorders, including chronic gastrointestinal diseases. However, the mechanism that transmits sleep disturbance-induced aberrant neural signaling from the brain to the gut remains elusive. We show that acute sleep deprivation (SD) impairs intestinal stem cell (ISC) function, leading to shortening of crypt-villus architecture and Paneth cell loss. We identified the dorsal motor nucleus of vagus (DMV) as the SD-sensitive central nervous system center that transmits sleep effects to the gut. SD aberrantly activates DMV neurons, driving excessive acetylcholine release from the vagus nerve into the gut. Acetylcholine triggers 5-hydroxytryptamine (5-HT) release by enterochromaffin cells and suppresses its reuptake via muscarinic receptors, thereby causing a spike in 5-HT levels. Elevated 5-HT induces excessive oxidative stress in ISCs through its receptor HTR4, promoting gut pathologies. Overall, we reveal an SD-responsive neural circuit that controls ISCs and identify therapeutic strategies for mitigating SD-related gut diseases.
Clinical success of in vitro maturation (IVM) for fertility treatment is currently limited by the lack of a reliable source of ovarian support cells (OSCs) to nurture oocytes. Kramme et al. develop "Fertilo," a scalable,...Clinical success of in vitro maturation (IVM) for fertility treatment is currently limited by the lack of a reliable source of ovarian support cells (OSCs) to nurture oocytes. Kramme et al. develop "Fertilo," a scalable, clinical-grade hiPSC-derived OSC product that significantly enhances oocyte maturation and improves clinical reproductive outcomes..