Deciphering interactions between tumor micro- and systemic immune macroenvironments is essential for developing more effective cancer diagnosis and therapeutic strategies. Here, we established a gel-liquid interface (GLI...Deciphering interactions between tumor micro- and systemic immune macroenvironments is essential for developing more effective cancer diagnosis and therapeutic strategies. Here, we established a gel-liquid interface (GLI) co-culture model of lung cancer organoids (LCOs) and paired peripheral-blood mononuclear cells (PBMCs), featuring enhanced interactions between immune cells and tumor organoids for optimized simulation of in vivo systemic anti-tumor immunity. By constructing a cohort of lung cancer patients, we demonstrated that the responses of GLI models under αPD1 treatment reflected the immunotherapy outcomes of the corresponding patients precisely. Furthermore, we dissected the various tumor immune processes mediated by PBMC-derived T cells within GLI models through functional multi-omics analyses, along with the characterization of circulating tumor-reactive T cells (GNLYCD44CD9) with effector memory-like phenotypes as a potential indicator of immunotherapy efficacy. Our findings indicate that the GLI co-culture model can be used to develop diagnostic strategies for precision immunotherapies, as well as understanding the underlying mechanisms.
Marketing approval for allogenic mesenchymal stromal cells (MSCs) by international regulatory jurisdictions including the US have been granted. Notwithstanding, the long-heralded clinical and commercial breakthrough for...Marketing approval for allogenic mesenchymal stromal cells (MSCs) by international regulatory jurisdictions including the US have been granted. Notwithstanding, the long-heralded clinical and commercial breakthrough for MSC products has never fully manifested. The withdrawal of an allogenic MSC product in Europe, based on inefficacious phase 3 results along with setbacks in industry-sponsored, advanced clinical trials of MSCs for COVID-19-related acute respiratory distress syndrome (ARDS) have dampened enthusiasm for MSC products. In this perspective, we highlight the hallmarks of MSC identity and potency, and how these can inform surrogate, sensitive critical quality attributes that correlate with clinical effectiveness in a variety of indications. We further highlight host-dependent pharmacological attributes of MSCs, which together with their critical quality attributes drive the observed clinical responses and thus impact the translational utility of MSCs. We provide a rational pathway to additional MSC regulatory approval and deployment for disorders with unmet medical needs.
We discuss how to diversify the reference iPSC line concept. We highlight workflows for generating diverse iPSC lines. We ask whether reference lines can act as inclusive sources of human diversity for use in benchmarkin...We discuss how to diversify the reference iPSC line concept. We highlight workflows for generating diverse iPSC lines. We ask whether reference lines can act as inclusive sources of human diversity for use in benchmarking controls for disease models or drug screens, or as clinical grade lines for cell therapies.
Recently, the US National Institutes of Health (NIH) announced an initiative to expand human-based research technologies and minimize animal use in research. Danilo Tagle, Director of the Office for Special Initiatives a...Recently, the US National Institutes of Health (NIH) announced an initiative to expand human-based research technologies and minimize animal use in research. Danilo Tagle, Director of the Office for Special Initiatives at the National Center for Advancing Translational Sciences, shares his perspective on the upcoming changes with Cell Stem Cell.
Recently in Med, Pinezich et al. present a therapeutic and diagnostic ("theranostic") cross-circulation platform that enables prolonged, real-time rehabilitation of injured donor lungs ex vivo. Their approach integrating...Recently in Med, Pinezich et al. present a therapeutic and diagnostic ("theranostic") cross-circulation platform that enables prolonged, real-time rehabilitation of injured donor lungs ex vivo. Their approach integrating systemic support, advanced diagnostics, and targeted therapies promises to expand the donor lung pool and transform lung transplantation with personalized organ care.
Cell Stem Cell
· 2025 Jun · PMID 40480206
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Parkinson's disease (PD), characterized by the selective loss of midbrain dopaminergic neurons (mDANs), is a promising target for cell replacement therapy. Two recent clinical trials published in Nature report the safety...Parkinson's disease (PD), characterized by the selective loss of midbrain dopaminergic neurons (mDANs), is a promising target for cell replacement therapy. Two recent clinical trials published in Nature report the safety and potential efficacy of human pluripotent stem cell-based approaches, representing a major milestone in regenerative medicine for PD.
The intestinal secretory lineage is thought to comprise four distinct cell types derived from one Atoh1 progenitor, but the mechanisms that distinguish Paneth and goblet cells are unclear. Bhattacharya et al. argue that...The intestinal secretory lineage is thought to comprise four distinct cell types derived from one Atoh1 progenitor, but the mechanisms that distinguish Paneth and goblet cells are unclear. Bhattacharya et al. argue that these cells are instead phenotypic manifestations of a common terminal Atoh1 cell, actively shaped by niche-derived signals.
In this issue, Chadarevian et al. showed that engraftment of human iPSC-derived microglia (iMG) engineered to express secreted neprilysin (sNEP) under the plaque-responsive CD9 promoter reduces amyloid burden, neuronal d...In this issue, Chadarevian et al. showed that engraftment of human iPSC-derived microglia (iMG) engineered to express secreted neprilysin (sNEP) under the plaque-responsive CD9 promoter reduces amyloid burden, neuronal damage, and inflammation in an Alzheimer's disease (AD) mouse model. These findings establish a cell-based strategy to treat neurological diseases.
Embryo-like models derived from stem cells have emerged as powerful tools to study early development. In this issue, Lodewijk et al. demonstrate that activating just two enhancers via CRISPR activation (CRISPRa) in mouse...Embryo-like models derived from stem cells have emerged as powerful tools to study early development. In this issue, Lodewijk et al. demonstrate that activating just two enhancers via CRISPR activation (CRISPRa) in mouse embryonic stem cells (ESCs) can drive self-organization into structured embryo-like models, offering a genome-driven approach in stem cell and developmental biology.
Chimeric antigen receptor (CAR) T cell therapies in solid tumors have been limited by on-target, off-tumor toxicity, antigen heterogeneity, and an inability to simultaneously overcome multiple diverse resistance mechanis...Chimeric antigen receptor (CAR) T cell therapies in solid tumors have been limited by on-target, off-tumor toxicity, antigen heterogeneity, and an inability to simultaneously overcome multiple diverse resistance mechanisms within the tumor microenvironment that attenuate anti-tumor activity. Here, we describe an induced pluripotent stem cell (iPSC)-derived CAR T cell that combines a human epidermal growth factor receptor 2 (HER2)-targeting CAR-differentially recognizing tumor from normal cells and enabling detection of both truncated and misfolded HER2-with multiplex editing designed to address and overcome obstacles to maximize efficacy in solid tumor indications. The iPSC-derived, HER2-directed CAR T cells maintained potent HER2-specific anti-tumor activity in both in vitro and in vivo settings, with limited cytolytic targeting of HER2+ normal targets. Combination with therapeutic antibodies enabled comprehensive multi-antigen targeting through both the CAR and a high-affinity, non-cleavable CD16a Fc receptor. Additionally, specific engineering of interleukin (IL)-7R-fusion, transforming growth factor β (TGF-β)-IL-18R, and CXCR2 enabled sustained persistence, resistance to TGF-β-mediated suppression, and specific migration to the tumor.
Zhang J, Gu Y, Tong L
… +28 more, Feng B, Dong S, Shao Q, Chen Y, Tu H, Wang Z, Wang Y, Li X, Yu H, Lin Z, Wang X, Li Z, Ai Z, Xiang Y, Jiang Z, Jin Z, Li Z, Chen Y, Shen Z, Huang C, Liu J, Liu J, Xu P, Yu Y, Xia P, Liang H, Huang H, Chen D
Primordial germ cells (PGCs) are specified early during embryogenesis and establish the germ cell lineage for transmitting genetic and epigenetic information from parents to offspring. However, whether N-methyladenosine...Primordial germ cells (PGCs) are specified early during embryogenesis and establish the germ cell lineage for transmitting genetic and epigenetic information from parents to offspring. However, whether N-methyladenosine (mA)-mediated epigenetic regulation is involved in the specification of PGCs remains elusive. In this study, we report that a knockout of mA writers or overexpression of mA erasers leads to an increased percentage of human PGC-like cells (hPGCLCs) induced from embryonic stem cells using a 3D aggregate system. We identify the mA reader IGF2BP1 as the key factor for restricting hPGCLC fate induction by stabilizing OTX2 mRNAs in an mA-dependent manner. In turn, OTX2 protein suppresses the function of TFAP2C via histone variant MacroH2A.1 during germ cell lineage specification. We also observe a similar role of Igf2bp1 in zebrafish in the induction of PGC fate. In summary, we identify an mA-IGF2BP1-OTX2-MacroH2A.1-TFAP2C signaling axis that restricts the specification of human germ cell fate.
Sirenko M, Lee S, Sun Z
… +32 more, Chaligne R, Loghavi S, Asimomitis G, Brierley CK, Bernard E, Cai SF, Myers RM, Nadorp B, Sango J, Lallo M, Levine MF, Domenico D, Arango Ossa JE, Medina-Martinez JS, Menghrajani K, Lasry A, Mims AS, Desai H, Laganson A, Famulare C, Patel M, Lozanski G, Bolton KL, Viny AD, Roshal M, Levine RL, Papapetrou EP, Stein EM, Landau DA, Eisfeld AK, Aifantis I, Papaemmanuil E
Cell Stem Cell
· 2025 Jul · PMID 40409258
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Isocitrate dehydrogenase 1/2 (IDH) mutations are early initiating events in acute myeloid leukemia (AML). The complex clonal architecture and cellular heterogeneity in IDH-mutant AML underlies the heterogeneous clinical...Isocitrate dehydrogenase 1/2 (IDH) mutations are early initiating events in acute myeloid leukemia (AML). The complex clonal architecture and cellular heterogeneity in IDH-mutant AML underlies the heterogeneous clinical presentation and outcomes. Integrating single-cell genotyping and transcriptomics, we demonstrate a stem-like and inflammatory phenotype of IDH-mutant AML and identify clone-specific programs associated with NPM1, NRAS, and SRSF2 co-mutations. Furthermore, these clones had distinct responses to treatment with combination IDH inhibitors and chemotherapy, including elimination, reconstitution of myeloid differentiation, or retention within progenitor populations. At relapse after IDH inhibitor monotherapy, we identify upregulated stemness, inflammation, mitochondrial metabolism, and anti-apoptotic factors, as well as downregulated major histocompatibility complex (MHC) class II antigen presentation. At the pre-leukemic stage, we observe upregulation of IDH2-associated pathways, including inflammation. We deliver a detailed phenotyping of IDH-mutant AML and a framework for dissecting contributions of recurrently mutated genes in AML at diagnosis and following therapy, with implications for precision medicine.
Yuan WC, Earl AS, Ma S
… +13 more, Alcedo K, Russell JO, Duarte FM, Chu YT, Chang PC, Chen HY, Chi HH, Zhu Q, Rodriguez-Fraticelli AE, Patel SH, Lee YR, Buenrostro JD, Camargo FD
Cell Stem Cell
· 2025 Jun · PMID 40403721
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Hepatocytes can reprogram into biliary epithelial cells (BECs) during liver injury, but the underlying epigenetic mechanisms remain poorly understood. Here, we define the chromatin dynamics of this process using single-c...Hepatocytes can reprogram into biliary epithelial cells (BECs) during liver injury, but the underlying epigenetic mechanisms remain poorly understood. Here, we define the chromatin dynamics of this process using single-cell ATAC-seq and identify YAP/TEAD activation as a key driver of chromatin remodeling. An in vivo CRISPR screen highlights the histone acetyltransferase HBO1 as a critical barrier to reprogramming. HBO1 is recruited by YAP to target loci, where it promotes histone H3 lysine 14 acetylation (H3K14ac) and engages the chromatin reader zinc-finger MYND-type containing 8 (ZMYND8) to suppress YAP/TEAD-driven transcription. Loss of HBO1 accelerates chromatin remodeling, enhances YAP binding, and enables a more complete hepatocyte-to-BEC transition. Our findings position HBO1 as an epigenetic brake that restrains YAP-mediated reprogramming, suggesting that targeting HBO1 may enhance hepatocyte plasticity for liver regeneration.
Luo T, Liu C, Cheng T
… +16 more, Zhao GQ, Huang Y, Luan JY, Guo J, Liu X, Wang YF, Dong Y, Xiao Y, He E, Sun RZ, Chen X, Chen J, Ma J, Megason S, Ji J, Xu PF
Precise dorsal-ventral (D-V) patterning of the neural tube (NT) is essential for the development and function of the central nervous system. However, existing models for studying NT D-V patterning and related human disea...Precise dorsal-ventral (D-V) patterning of the neural tube (NT) is essential for the development and function of the central nervous system. However, existing models for studying NT D-V patterning and related human diseases remain inadequate. Here, we present organizers derived from pluripotent stem cell aggregate fusion ("ORDER"), a method that establishes opposing BMP and SHH gradients within neural ectodermal cell aggregates. Using this approach, we generated NT organoids with ordered D-V patterning from both zebrafish and human pluripotent stem cells (hPSCs). Single-cell transcriptomic analysis revealed that the synthetic human NT organoids (hNTOs) closely resemble the human embryonic spinal cord at Carnegie stage 12 (CS12) and exhibit greater similarity to human NT than to mouse models. Furthermore, using the hNTO model, we demonstrated the critical role of WNT signaling in regulating intermediate progenitors, modeled TCTN2-related D-V patterning defects, and identified a rescue strategy.
Sobecki M, Chen J, Krzywinska E
… +29 more, Nagarajan S, Fan Z, Nelius E, Monné Rodriguez JM, Seehusen F, Hussein A, Moschini G, Hajam EY, Kiran R, Gotthardt D, Debbache J, Badoual C, Sato T, Isagawa T, Takeda N, Tanchot C, Tartour E, Weber A, Werner S, Loffing J, Sommer L, Sexl V, Münz C, Feghali-Bostwick C, Pachera E, Distler O, Snedeker J, Jamora C, Stockmann C
Shi M, Crouse B, Sundaram N
… +13 more, Pode Shakked N, Thorner K, King NM, Dutta P, Ester L, Zhang W, Govindarajah V, Kopan R, Cebrian C, Mayhew CN, Helmrath MA, Bonventre JV, McCracken KW
Cell Stem Cell
· 2025 Jul · PMID 40345193
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Kidneys maintain homeostasis through an array of parallel nephrons, which fuse during development to a system of collecting ducts (CDs), establishing the essential luminal pathway for excretion of metabolic waste. Human...Kidneys maintain homeostasis through an array of parallel nephrons, which fuse during development to a system of collecting ducts (CDs), establishing the essential luminal pathway for excretion of metabolic waste. Human kidney organoids derived from pluripotent stem cells (human pluripotent stem cells [hPSCs]) generate nephrons that lack CDs and terminate as blind-ended tubules, limiting their functional potential. Here, we describe a developmentally inspired hPSC differentiation system that addresses this deficiency through assembly of induced nephrogenic mesenchyme with ureteric bud (UB) progenitors, leading to a CD network functionally integrated in kidney organoids through fusion with the distal tubule. The nephron fusion occurs stereotypically and is regulated by proximal-distal nephron patterning, which can be modulated through temporal manipulation of developmental pathways. This work provides a platform for interrogating the principles and mechanisms underlying nephron-UB fusion and a framework for engineering unobstructed nephrons with collecting systems, an important step toward de novo generation of functional kidney tissue.
Yuan Y, Wang X, Yan X
… +21 more, He N, Lu X, Yang J, Xie X, Yuan H, Chen N, Liu Y, Ren H, Zhang R, Cui L, Ren P, Lin S, Cheng S, Yang X, Guo Y, Li R, Yan T, Guo J, Xiao Z, Wei Y, Yu L
The Carnegie stage 9 (CS9) embryo is a pivotal phase signifying the conclusion of gastrulation and the onset of early organogenesis, crucial for initiating major organ system development. Utilizing spatial transcriptomic...The Carnegie stage 9 (CS9) embryo is a pivotal phase signifying the conclusion of gastrulation and the onset of early organogenesis, crucial for initiating major organ system development. Utilizing spatial transcriptomics, we analyzed an intact CS9 human embryo in a spatially detailed manner. Through the examination of 75 transverse cryosections, we digitally reconstructed a 3D model, allowing us to identify diverse cell types, including those from brain and spine regions, the primitive gut tube, distinct somite formation stages, somatic mesoderm, splanchnic mesoderm, etc. Notably, we observed two distinct trajectories of hindbrain development, pinpointed the isthmic organizer at the midbrain-hindbrain boundary, delineated the bi-layered structure of neuromesodermal progenitor (NMP) cells, and described the early aorta formation and primordial germ cells (PGCs) presence in the aorta-gonad-mesonephros (AGM) region. This study provides key insights into the transcriptomic and spatial intricacies shaping the human body plan.
Scuderi S, Kang TY, Jourdon A
… +10 more, Nelson A, Yang L, Wu F, Anderson GM, Mariani J, Tomasini L, Sarangi V, Abyzov A, Levchenko A, Vaccarino FM
Cell Stem Cell
· 2025 Jun · PMID 40315847
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The repertoire of neurons and their progenitors depends on their location along the antero-posterior and dorso-ventral axes of the neural tube. To model these axes, we designed the Dual Orthogonal-Morphogen Assisted Patt...The repertoire of neurons and their progenitors depends on their location along the antero-posterior and dorso-ventral axes of the neural tube. To model these axes, we designed the Dual Orthogonal-Morphogen Assisted Patterning System (Duo-MAPS) diffusion device to expose spheres of induced pluripotent stem cells (iPSCs) to concomitant orthogonal gradients of a posteriorizing and a ventralizing morphogen, activating WNT and SHH signaling, respectively. Comparison with single-cell transcriptomes from the fetal human brain revealed that Duo-MAPS-patterned organoids generated an extensive diversity of neuronal lineages from the forebrain, midbrain, and hindbrain. WNT and SHH crosstalk translated into early patterns of gene expression programs associated with the generation of specific brain lineages with distinct functional networks. Human iPSC lines showed substantial interindividual and line-to-line variations in their response to morphogens, highlighting that genetic and epigenetic variations may influence regional specification. Morphogen gradients promise to be a key approach to model the brain in its entirety.
Sun Y, Ikeuchi Y, Guo F
… +3 more, Hyun I, Ming GL, Fu J
Cell Stem Cell
· 2025 May · PMID 40315834
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Neural organoids have been utilized to recapitulate different aspects of the developing nervous system. While hailed as promising experimental tools for studying human neural development and neuropathology, current neura...Neural organoids have been utilized to recapitulate different aspects of the developing nervous system. While hailed as promising experimental tools for studying human neural development and neuropathology, current neural organoids do not fully recapitulate the anatomy or microcircuitry-level functionality of the developing brain, spinal cord, or peripheral nervous system. In this review, we discuss emerging bioengineering approaches that control morphogen signals and biophysical microenvironments, which have improved the efficiency, fidelity, and utility of neural organoids. Furthermore, advancements in bioengineered tools have facilitated more sophisticated analyses of neural organoid functions and applications, including improved neural-bioelectronic interfaces and organoid-based information processing. Emerging bioethical issues associated with advanced neural organoids are also discussed. Future opportunities of neural organoid research lie in enhancing their fidelity, maturity, and complexity and expanding their applications in a scalable manner.
Financial dispositions against unapproved stem cell interventions have grown significantly, with successful class-action lawsuits, malpractice claims, and collaborative prosecutions between government agencies. In additi...Financial dispositions against unapproved stem cell interventions have grown significantly, with successful class-action lawsuits, malpractice claims, and collaborative prosecutions between government agencies. In addition to improved dispositions, federal circuit courts have given unanimous affirmation to the FDA's regulatory authority over stem cell interventions, establishing critical precedents for oversight.