Biology subjects

Glass, I. A.

Publications and source records attributed to Glass, I. A..

18 recordsLinked to original sources

bioRxiv2026

Early-life human lymphopoiesis generates a distinct B-cell lineage

We characterize the first wave of human B-lymphopoiesis across gestation (n=42 donors) and identify a developmentally and functionally distinct B-cell lineage that shapes antibody specificity before birth. The earliest lymphoid progenitors engage an evolutionarily conserved genetic program enriched for imprinted genes associated with embryogenesis in mice and humans. These progenitors arise in the yolk sac and acquire Early B-cell Factor 1 (EBF1) in the embryonic liver, initiating B-lymphopoiesis before Hematopoietic Stem Cells emerge. Functionally, these early-life B-lymphoid progenitors (eBLPs; CD81hiTdT-IL3R+) respond to IL-3 to promote B-cell fate commitment and generate two waves of stereotyped public B-cell receptor (BCR) repertoires, shaping adaptive immunity at birth. The same molecular program and public BCRs are recapitulated during B-cell differentiation from pluripotent stem cells in vitro and after transplantation into humanized mice, where they generate antibody-secreting cells and SOX4+ B cells resembling infant lymphocytes. Developmental origin therefore intrinsically programs B-cell identity and antibody specificity.

immunology↗

bioRxiv2026

Prenatal cannabis exposure affects human fetal neurodevelopment: anintegrated multi-omics study

Prenatal cannabis use is on the rise, and observational studies suggest that such use results in neurodevelopmental deficits in the offspring. Because observational studies can be confounded by unaccounted factors, we studied the neurodevelopmental consequences, at the molecular level, of prenatal cannabis use. We applied an integrated multi-omics approach, combining transcriptomics and global proteomics, to first trimester (T1) and second trimester (T2) human fetal brains from pregnancies with and without documented maternal cannabis exposure and no use of drugs of abuse. Prenatal cannabis exposure produced minimal molecular effects in female T1 fetal brains but induced pronounced system-level disruption in male T2 fetal brains. These disrupted pathways have molecular signatures linked to neurodevelopmental and neuropsychiatric disorders, including autism spectrum disorder, schizophrenia-related pathology, and disorders of cortical connectivity, raising significant concerns of prenatal cannabis use.

neuroscience↗

bioRxiv2026

Phenotypic CRISPR screening identifies ZBTB10 as a novel regulator of human trophoblast differentiation

The human placenta is built by trophoblast cells that fuse together, secrete hormones, and invade the uterus, and defects in these processes contribute to pregnancy disorders such as preeclampsia. Because cell-cell fusion and hormone secretion are inherently non-cell-autonomous processes, their regulators have remained inaccessible to conventional pooled CRISPR screens. Here, we developed an arrayed CRISPR screen in fusogenic BeWo trophoblasts that simultaneously quantifies fusion and hCG secretion across 412 gene perturbations. The screen revealed that these two hallmark functions of trophoblast differentiation are genetically separable. We characterized the strongest novel hit, ZBTB10, in trophoblast stem cells, organoids, and placental tissue and find that ZBTB10 is an essential regulator of human trophoblast differentiation. ZBTB10 is required for invasive extravillous trophoblast differentiation and supports syncytiotrophoblast maturation, establishing it as a cross-lineage regulator that both activates and represses distinct trophoblast fate programs. Together, these findings provide a genetic platform and phenotypic dissection of how regulatory networks control human placental development.

cell biology↗

bioRxiv2026

Transcriptional Heterogeneity Reveals a Synaptic Gene Program in Developing and Adult Human Oligodendrocyte Precursor Cells

Human oligodendrocyte precursor cells (OPCs) arise early in gestation and expand broadly during cortical development, yet the extent of their heterogeneity remains poorly defined. Here, we isolated >2,300 highly pure OPCs from post-conceptional week (PCW) 17 human cortex using an optimized PDGFR-based immunopanning and performed single-cell RNA sequencing. Unsupervised clustering revealed four transcriptionally distinct embryonic OPC subsets, including a previously unrecognized population that expressed genes linked to synaptic development, synaptic signaling, and neuromodulation. This subset - designated embryonic synaptic OPCs (eSyn-OPCs) - comprised approximately 28.5% of all embryonic OPCs in the cortex and was characterized by robust expression of synapse-associated secreted factors (THBS2, WNT5A, WNT7A, PLAT, ACHE) and multiple neurotransmitter receptor subunits. Histological analyses across PCW 12-22 demonstrated that eSyn-OPCs first appear around PCW 15 and are enriched in proliferative germinal zones. Spatial transcriptomics confirmed their localization near neural stem and progenitor cells, suggesting proximal neuron-OPC communication during early cortical assembly. Purified eSyn-OPCs differentiated into mature oligodendrocytes in vitro, confirming their oligodendrocyte lineage identity. Reanalysis of adult human single-nucleus RNA-seq datasets uncovered a transcriptionally analogous OPC subset (adult synaptic OPCs, aSyn-OPCs), though with reduced representation of structural synaptic genes and neurotransmitter receptor diversity compared to eSyn-OPCs. Together, these results identify a synaptically specialized OPC population in both developing and adult human cortex and reveal that eSyn-OPCs possess unexpectedly rich synaptic signaling machinery. These findings suggest that human OPCs may participate directly in neuron-glia communication during early cortical development and raise the possibility of developmental stage-specific roles for eSyn-OPCs in shaping neural circuit formation.

neuroscience↗

bioRxiv2025

Lateral plate mesoderm directs human amnion and ventral skin organoid formation

Summary ParagraphEngineering organoids that faithfully replicate the intricate architecture and region-specific features of bodily organs and extraembryonic tissues remains a significant scientific challenge. Previously, we demonstrated that craniofacial skin organoids (cSkOs)--containing epidermis, dermis, and hair--could be generated by co-developing epidermal progenitors with cranial mesenchyme. Building on this approach, we precisely adjusted cellular composition and signaling environments to generate ventral skin organoids (vSkOs) with lateral plate mesoderm (LPM) progenitors, successfully recapitulating features of abdominal or groin skin. Modulating early BMP and FGF signaling redirected these vSkOs toward an extraembryonic fate, producing human amnion-like tissues, termed Amnioids. Like native human amnion, Amnioids rapidly expanded into large, avascular, hairless cysts, in sharp contrast to the primitive vasculature and abundant hair follicles of vSkOs. Single-cell RNA sequencing identified divergent molecular signatures and developmental trajectories, highlighting key roles for NOTCH, WNT, and YAP/Hippo signaling pathways. Functional studies further underscored mesenchymal-epithelial interactions and mechanical forces as critical regulators of epithelial expansion. Together, these models provide potent tools to investigate human development at the embryonic-extraembryonic interface, offering critical insights into congenital skin and amniotic disorders and opening new avenues for precision regenerative therapies.

developmental biology↗

bioRxiv2025

Multi-omic integration reveals dynamic changes in human placental metabolism across gestation

ObjectivesMetabolic demands of the developing conceptus are highly dynamic during pregnancy. While placental metabolism has been well described at term and in cell lines, changes in the placental metabolome during development remains understudied. We investigated the placental metabolome, metabolite trajectories, and altered pathways across trimesters in normal human pregnancy by integrating metabolomic and transcriptomic data. MethodsTargeted aqueous metabolomic profiling of 372 metabolites was conducted on placental biopsies from samples collected in the first (n=12), second (n=13), and third (n=11) trimesters of normal pregnancy using liquid chromatography-tandem mass spectrometry. Robust linear models identified differentially abundant metabolites across trimesters in models adjusted for fetal sex and total protein. We conducted pathway analysis using a human metabolic reconstruction. To further aid in biological interpretation, we leveraged publicly available transcriptomics data to conduct pathway-level multi-omic integration throughout gestation. ResultsSamples clustered by trimester in principal component analysis and we identified 5 metabolite trajectories. Out of 193 detectable metabolites, 149 (77%) differed by trimester (FDR<0.05). Using pathway-level multi-omic integration, pathways involved in extracellular transport, and pyruvate, amino acid, NAD, and membrane lipid metabolism are up-regulated in the second trimester compared to the first. In the late third trimester, pathways involved in amino acid metabolism, redox balance, mitochondrial transport, and biomolecule synthesis were down-regulated compared to second trimester. ConclusionsPlacental metabolite abundances change substantially across gestation and integration with metabolic gene expression provides insight into dynamic metabolic function during pregnancy. Observed pathway-level changes potentially reflect the metabolic response to invading maternal circulation in the first-to-second trimester transition, as well as changing maternal and fetal metabolic requirements. Differences observed at term may reflect placental senescence and preparation for parturition. These data can inform other molecular analyses of the placenta by providing enhanced resolution of metabolic changes across pregnancy.

systems biology↗

bioRxiv2025

Clinical Interventions and Inflammatory Signaling Shape the Transcriptional and Cellular Architecture of the Early Postnatal Lung

The early postnatal period in human development is characterized by extensive remodeling of the distal lung to support gas exchange, but this critical period remains poorly understood. Here, we constructed a comprehensive cellular atlas of the early postnatal human lung (0 to 2 years) using single-nucleus RNA sequencing of histologically normal specimens from 23 individuals. Our analysis identified two previously unknown and mutually exclusive transcriptional states of alveolar type 2 (AT2) cells, one defined by upregulation of genes involved in lipid metabolism and identified by unique expression of FMO5, and the other defined by upregulation of inflammatory response genes and identified by unique expression of CFTR. Using spatial transcriptomics, we discovered that AT2 cell states reside in specific niches and interact with distinct alveolar fibroblast subtypes. Clinical data and organoid experiments further suggest that the environment dictates which state prevails as the pro-inflammatory/pro-regenerative signals TNF- and IL-1{beta} promoted the CFTR+ state in vitro, while patients treated with the anti-inflammatory drug dexamethasone (Dex) had more abundant FMO5+ AT2 cells, and Dex induced the FMO5+ state in vitro. These observations link inflammatory signaling and anti-inflammatory clinical interventions to shifts in transcriptional state of the alveolar epithelium. We benchmarked two neonatal lung diseases, bronchopulmonary dysplasia and pulmonary interstitial glycogenosis, revealing a profound disruption in the balance of AT2 states, a broad arrest of postnatal cellular development, and impaired cellular maturation. Our work uncovers a fundamental new understanding of early postnatal human lung biology, linking pro- and anti-inflammatory signaling to AT2 transcriptional phenotypes and providing a new framework for understanding lung disease.

developmental biology↗

bioRxiv2025

The Impact of Delayed Evacuation on the Quality of Human Fetal Tissue

BackgroundDigoxin and other agents are frequently administered to arrest fetal circulation before the evacuation of human fetal tissue (HFT) in pregnancy terminations to address concerns about fetal viability. However, the impact of delayed evacuation on HFT quality remains unknown. Analyzing HFT is critical for diagnosing pregnancies affected by fetal abnormalities and for driving progress in biomedical research. ObjectiveThis study aims to assess the effects of delayed evacuation following fetal circulation cessation on the quality of HFT for both diagnostic and research purposes. Study DesignHFT samples were collected from second-trimester dilation and evacuation (D&E) procedures, with and without agent injection approximately 24 hours prior, as per standard care protocols. We assessed multiple parameters relevant to diagnostics and research, including: 1) cell morphology, 2) cell proliferation, 3) apoptosis, 4) cell viability in culture, and 5) nucleic acid quality. To simulate in utero conditions and determine the timeline for tissue degradation, we incubated brain tissue obtained from D&E without induced demise at 37{degrees}C for up to 18 hours. ResultsWe analyzed 18 HFT samples from D&E procedures performed 19-25 hours after digoxin or potassium chloride (KCl) injection and compared them to 26 HFT samples from immediate evacuations without prior injection. Induced fetal demise resulted in 1) disrupted cell morphology, 2) decreased cell proliferation, 3) increased apoptosis, 4) reduced cell viability in culture, and 5) lower RNA quality. Despite these findings, all samples yielded DNA of sufficient quality for polymerase chain reaction (PCR). ConclusionD&E procedures performed after fetal demise induced by digoxin or KCl lead to decreased HFT quality, limiting its diagnostic and research potential beyond gross tissue evaluation and DNA extraction. Limiting the time between fetal circulation arrest and evacuation may improve HFT quality for clinical and research applications.

pathology↗

bioRxiv2025

Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia

Accumulating evidence links pediatric cancers to prenatal transformation events, yet the influence of the developmental stage on oncogenesis remains elusive. We investigated how hematopoietic stem cell developmental stages affect leukemic transformation, disease progression, and therapy response using a novel, humanized model of NUP98::NSD1-driven pediatric acute myeloid leukemia, that is particularly aggressive with WT1 co-mutations. Fetal-derived hematopoietic stem cells readily transform into leukemia, and WT1 mutations further enhance stemness and alter lineage hierarchy. In contrast, stem cells from later developmental stages become progressively resistant to transformation. Single-cell analyses revealed that fetal-origin leukemia stem cells exhibit greater quiescence and reliance on oxidative phosphorylation than their postnatal counterparts. These differences drive distinct therapeutic responses, despite identical oncogenic mutations. In patients, onco-fetal transcriptional programs correlate with worse outcomes. By targeting key vulnerabilities of fetal-origin leukemia cells, we identified combination therapies that significantly reduce aggressiveness, highlighting the critical role of ontogeny in pediatric cancer treatment.

cancer biology↗

bioRxiv2024

A spatially-resolved blueprint of the developing human lung reveals a basal cell population regulated by a WNT-driven niche

Organs are composed of diverse cell types that change across space and time during development. To interrogate this diversity, we micro-dissected developing human lungs along the proximal-distal axis during the late pseudoglandular stage and generated an integrated analysis of single-nucleus sequencing and spatial transcriptomics, creating a cellularly-resolved atlas of the lung. These rich datasets revealed positional niches and cellular heterogeneity along the proximal-distal axis, including the identification of a unique population of TP63+ basal cells, the primary stem cell of the airway, marked by expression of LGR5 and LGR6. Analysis of the LGR5+ basal cell niche and functional experiments with primary organoid models suggest a tonic level of WNT pathway activity in LGR5+ basal cells that is potentiated by mesenchyme-derived R-SPONDIN. We found that basal cell self-renewal is enhanced by WNT activity, suggesting that the WNT pathway plays a previously unappreciated but critical role in airway stem cell maintenance during human development. These results enhance our fundamental understanding of the positional and cellular heterogeneity in the developing human lungs and begin to reveal unique niches that maintain homeostasis throughout the lung.

developmental biology↗

bioRxiv2023

Lipid nanoparticle-mediated delivery of mRNA into the mouse and human retina and other ocular tissues.

Structured Abstract PurposeLipid nanoparticles (LNPs) show promise in their ability to introduce mRNA to drive protein expression in specific cell types of the mammalian eye. Here, we examined the ability of mRNA encapsulated in lipid nanoparticles (LNPs) with two distinct formulations to drive gene expression in mouse and human retina and other ocular tissues. MethodsWe introduced mRNA carrying LNPs into two biological systems. Intravitreal injections were tested to deliver LNPs into the mouse eye. Human retinal pigment epithelium (RPE) and retinal explants were used to assess mRNA expression in human tissue. We analyzed specificity of expression using histology, immunofluorescence, and imaging. ResultsIn mice, mRNAs encoding GFP and ciliary neurotrophic factor (CNTF) were specifically expressed by Muller glia and retinal pigment epithelium (RPE). Acute inflammatory changes measured by microglia distribution (Iba-1) or interleukin-6 (IL-6) expression were not observed 6 hours post-injection. Human RPE also expressed high levels of GFP. Human retinal explants expressed GFP in cells with apical and basal processes consistent with Muller glia and in perivascular cells consistent with macrophages. ConclusionsWe demonstrated the ability to reliably transfect subpopulations of retinal cells in mice eye tissues in vivo and in human ocular tissues. Of significance, intravitreal injections were sufficient to transfect the RPE in mice. To our knowledge we demonstrate delivery of mRNA using LNPs in human ocular tissues for the first time. Translational RelevanceOcular gene-replacement therapies using non-viral vector methods are of interest as alternatives to adeno-associated virus (AAV) vectors. Our studies show that mRNA LNP delivery can be used to transfect retinal cells in both mouse and human tissues without inducing significant inflammation. This promising methodology could be used to transfect retinal cell lines, tissue explants, mice, or potentially as gene-replacement therapy in a clinical setting in the future.

molecular biology↗

bioRxiv2023

A transient dermal niche and dual epidermal programs underlie sweat gland development

Eccrine glands are mammalian skin appendages indispensable for human thermoregulation. Like all skin-derived appendages, eccrine glands form from multipotent progenitors in the basal skin epidermis. It remains unclear how epidermal progenitors progressively specialize to specifically form eccrine glands, precluding efforts to regenerate these vital organs. Herein, we applied single nucleus transcriptomics to compare the expression content of wildtype, eccrine-forming mouse skin to that of mice harboring a skin-specific disruption of Engrailed 1 (En1), a transcription factor that promotes the formation of eccrine glands in both humans and mice. We identify two concurrent epidermal transcriptomes in the earliest eccrine anlagen: a predominant transcriptome that is shared with hair follicles, and a vastly underrepresented transcriptome that is En1-dependent and eccrine-specific. We demonstrate that differentiation of the eccrine anlage requires the induction of a transient and transcriptionally unique dermal niche that forms around each developing gland in humans and mice. Our study defines the transcriptional determinants underlying eccrine identity in the epidermis and uncovers the dermal niche required for eccrine developmental progression. By identifying these defining components of the eccrine developmental program, our findings set the stage for directed efforts to regenerate eccrine glands for comprehensive skin repair.

developmental biology↗

bioRxiv2023

MerTK mediates the immunologically silent uptake of alpha-synuclein fibrils by human microglia

MerTK is a receptor tyrosine kinase that mediates the immunologically silent phagocytic uptake of diverse types of cellular debris. Highly expressed on the surface of microglial cell, MerTK is of importance in brain development, homeostasis, plasticity, and disease. Yet, involvement of this receptor in the clearance of protein aggregates that accumulate with aging and in neurodegenerative diseases has yet to be defined. The current study explored the function of MerTK in the microglial uptake of alpha-synuclein fibrils which play a causative role in the pathobiology of synucleinopathies. Using human primary and induced pluripotent stem cell-derived microglia, the MerTK- dependence of alpha-synuclein fibril internalization was investigated in vitro. Relevance of this pathway to synucleinopathies was assessed by analyzing MerTK expression in patient-derived cells and tissues. Pharmacological inhibition of MerTK and siRNA-mediated MERTK knockdown both caused a decreased rate of alpha-synuclein fibril internalization by human microglia. Consistent with the immunologically silent nature of MerTK-mediated phagocytosis, alpha-synuclein fibril internalization did not induce secretion of pro-inflammatory cytokines from microglia. In addition, burden analysis in two independent patient cohorts revealed a significant association between rare functionally deleterious MERTK variants and Parkinsons disease in one of the cohorts (p = 0.002). Accordingly, MERTK expression was significantly upregulated in nigral microglia from Parkinsons disease/Lewy body dementia patients compared to those from non-neurological control donors in a single-nuclei RNA-sequencing dataset (p = 5.08x10-21), and MerTK protein expression positively correlated with alpha-synuclein level in human cortex lysates (p = 0.0029). Taken together, our findings define a novel role for MerTK in mediating the uptake of alpha-synuclein aggregates by human microglia, with possible involvement in limiting alpha-synuclein spread in synucleinopathies such as Parkinsons disease.

cell biology↗

bioRxiv2022

Human iPSC Derived Enamel Organoid Guided by Single-Cell Atlas of Human Tooth Development

Tooth enamel secreted by ameloblasts is the hardest material in the human body, acting as a shield protecting the teeth. However, the enamel is gradually damaged or partially lost in over 90% of adults and cannot be regenerated due to a lack of ameloblasts in erupted teeth. Here we use sci-RNA-seq to establish a spatiotemporal single-cell atlas for the developing human tooth and identify regulatory mechanisms controlling the differentiation process of human ameloblasts. We reveal key signaling pathways involved between the support cells and ameloblasts during fetal development and recapitulate those findings in a novel human ameloblast in vitro differentiation from iPSCs. We furthermore develop a mineralizing enamel organ-like 3D organoid system. These studies pave the way for future regenerative dentistry and therapies toward genetic diseases affecting enamel formation.

developmental biology↗

bioRxiv2021

Cellular resolution anatomical and molecular atlases for prenatal human brains

Increasing interest in studies of prenatal human brain development, particularly using new single-cell genomics and anatomical technologies to create cell atlases, creates a strong need for accurate and detailed anatomical reference atlases. In this study, we present two cellular-resolution digital anatomical atlases for prenatal human brain at post-conceptional weeks (PCW) 15 and 21. Both atlases were annotated on sequential Nissl-stained sections covering brain-wide structures on the basis of combined analysis of cytoarchitecture, acetylcholinesterase staining and an extensive marker gene expression dataset. This high information content dataset allowed reliable and accurate demarcation of developing cortical and subcortical structures and their subdivisions. Furthermore, using the anatomical atlases as a guide, spatial expression of 37 and 5 genes from the brains respectively at PCW 15 and 21 was annotated, illustrating reliable marker genes for many developing brain structures. Finally, the present study uncovered several novel developmental features, such as the lack of an outer subventricular zone in the hippocampal formation and entorhinal cortex, and the apparent extension of both cortical (excitatory) and subcortical (inhibitory) progenitors into the prenatal olfactory bulb. These comprehensive atlases provide useful tools for visualization, targeting, imaging and interpretation of brain structures of prenatal human brain, and for guiding and interpreting the next generation of cell census and connectome studies.

neuroscience↗

bioRxiv2020

An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine

Human intestinal organoids (HIOs) generated from pluripotent stem cells provide extraordinary opportunities to explore development and disease. Here, we generate a single-cell transcriptome reference atlas from HIOs and from multiple developing human organs to quantify the specificity of HIO cell fate acquisition, and to explore alternative fates. We identify epithelium-mesenchyme interactions, transcriptional regulators involved in cell fate specification, and stem cell maturation features in the primary tissue that are recapitulated in HIOs. We use an HIO time course to reconstruct the molecular dynamics of intestinal stem cell emergence, as well as the specification of multiple mesenchyme subtypes. We find that the intestinal master regulator CDX2 correlates with distinct phases of epithelial and mesenchymal development, and CDX2 deletion perturbs the differentiation of both intestinal epithelium and mesenchyme. Collectively our data provides a comprehensive and quantitative assessment of HIO development, and illuminates the molecular machinery underlying endodermal and mesodermal cell fate specification.

developmental biology↗

bioRxiv2020

Spatial and single-cell transcriptional landscape of human cerebellar development

ABSTRACTCerebellar development and function require precise regulation of molecular and cellular programs to coordinate motor functions and integrate network signals required for cognition and emotional regulation. However, molecular understanding of human cerebellar development is limited. Here, we combined spatially resolved and single-cell transcriptomics to systematically map the molecular, cellular, and spatial composition of early and mid-gestational human cerebellum. This enabled us to transcriptionally profile major cell types and examine the dynamics of gene expression within cell types and lineages across development. The resulting ‘Developmental Cell Atlas of the Human Cerebellum’ demonstrates that the molecular organization of the cerebellar anlage reflects cytoarchitecturally distinct regions and developmentally transient cell types that are insufficiently captured in bulk transcriptional profiles. By mapping disease genes onto cell types, we implicate the dysregulation of specific cerebellar cell types, especially Purkinje cells, in pediatric and adult neurological disorders. These data provide a critical resource for understanding human cerebellar development with implications for the cellular basis of cerebellar diseases.Competing Interest StatementA.B.R, C.R., and G.Se. are shareholders of Split Bioscience.View Full Text

developmental biology↗

bioRxiv2018

Basal stem cell fate specification is mediated by SMAD signaling in the developing human lung

Basal stem cells (basal cells), located in the bronchi and trachea of the human lung epithelium, play a critical role in normal airway homeostasis and repair, and have been implicated in the development of diseases such as cancer1-4. Additionally, basal-like cells contribute to alveolar regeneration and fibrosis following severe injury5-8. However, the developmental origin of basal cells in humans is unclear. Previous work has shown that specialized progenitor cells exist at the tips of epithelial tubes during lung branching morphogenesis, and in mice, give rise to all alveolar and airway lineages9,10. These bud tip progenitor cells have also been described in the developing human lung11-13, but the mechanisms controlling bud tip differentiation into specific cell lineages, including basal cells, are unknown. Here, we interrogated the bud tip-to-basal cell transition using human tissue specimens, bud tip progenitor organoid cultures11, and single-cell transcriptomics. We used single-cell mRNA sequencing (scRNAseq) of developing human lung specimens from 15-21 weeks gestation to identify molecular signatures and cell states in the developing human airway epithelium. We then inferred differentiation trajectories during bud tip-to-airway differentiation, which revealed a previously undescribed transitional cell state ( hub progenitors) and implicated SMAD signaling as a regulator of the bud tip-to-basal cell transition. We used bud tip progenitor organoids to show that TGFT1 and BMP4 mediated SMAD signaling robustly induced the transition into functional basal-like cells, and these in vitro-derived basal cells exhibited clonal expansion, self-renewal and multilineage differentiation. This work provides a framework for deducing and validating key regulators of cell fate decisions using single cell transcriptomics and human organoid models. Further, the identification of SMAD signaling as a critical regulator of newly born basal cells in the lung may have implications for regenerative medicine, basal cell development in other organs, and understanding basal cell misregulation in disease.

developmental biology↗