Biology subjects

Glass, I.

Publications and source records attributed to Glass, I..

At least 19 recordsLinked to original sources

bioRxiv2026

Membrane Tension Integrates Physical and Signaling Cues to Gate Cell Fate Transitions

Physical forces shape cell behavior, yet how they integrate with signaling to control fate and disease remains unclear. The alveolar epithelium is patterned by FGF signaling and mechanical stretch, but how these cues specify AT1 and AT2 cells is poorly understood. Here we show that cell membrane tension (CMT) is a conserved regulator of epithelial fate in mouse and human lungs. CMT drops before differentiation and is spatially patterned, defining where bipotent progenitors acquire AT1 or AT2 identity. Lower CMT enhances FGFR2 endocytosis and ERK signaling to drive AT2 differentiation and permits architectural remodeling that enables stretch-mediated YAP/TAZ nuclear entry for AT1 maturation. {beta}-catenin elevates CMT cell-intrinsically independent of its role in canonical WNT transcription, while embedding, osmotic compression, or fibroblast wrapping elevate CMT extrinsically. Combined intrinsic and extrinsic tension traps alveolar epithelial cells in a KRT8 transitional state seen in fibrotic lungs. Membrane tension thus integrates physical and molecular cues linking morphogenesis to fibrosis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=160 HEIGHT=200 SRC="FIGDIR/small/708749v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1a9c04forg.highwire.dtl.DTLVardef@190bee2org.highwire.dtl.DTLVardef@1e41664org.highwire.dtl.DTLVardef@17a3ec7_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefWe identify a conserved drop in cell membrane tension (CMT) that gates epithelial fate transitions across mouse and human lungs. In bipotent progenitors, reduced CMT promotes Alveolar Type 2 (AT2) fate via FGFR2 endocytosis and ERK signaling, as well as Alveolar Type 1 (AT1) fate by enabling architectural remodeling required for YAP/TAZ nuclear entry. We further show that intrinsic {beta}-catenin and extrinsic confinement cues, including mesenchymal contact, converge to elevate CMT, restricting differentiation and--in adult AT2s--inducing a KRT8 transitional state associated with fibrosis. HighlightsO_LICell membrane tension drops before differentiation and is required for AT1 and AT2 fate acquisition. C_LIO_LIReduced tension enhances FGFR2 endocytosis and ERK signaling to drive AT2 specification. C_LIO_LIReduced tension permits architectural remodeling and YAP/TAZ nuclear entry required for AT1 maturation. C_LIO_LIIntrinsic {beta}-catenin and extrinsic confinement elevate CMT to restrict differentiation and together strongly induce a KRT8 transitional state associated with fibrosis. C_LI

cell biology↗

bioRxiv2025

Human-mouse cross-species comparison identifies common and unique aspects of intestinal mesenchyme development

Using single-cell RNA sequencing (scRNA-seq) and histological approaches, we examine cross-species cellular identity, diversity and organization of mesenchymal (fibroblast) populations in the developing mouse and human intestines. In both species, we defined 7 fibroblast populations. Using cross-species integration and label transfer approaches we find that each mesenchymal cell subtype in the murine intestine is highly concordant to a cell type/state in the human intestine, and vice-versa, suggesting a strong conservation of mesenchymal cell types/states across species. Despite this conservation, we also observe that individual lineage-defining genes are not always shared and can be found in different mesenchymal populations. High resolution spatial analysis via fluorescent in situ hybridization (FISH) and immunofluorescence (IF) confirmed these findings and revealed that transcriptionally-defined sub-types of intestinal mesenchymal cells in mice and humans are organized within similar spatial domains.

developmental biology↗

bioRxiv2025

Mapping mesenchymal diversity in the developing human intestine and organoids

The organization of diverse mesenchymal populations during human intestinal development is critical for tissue architecture and function yet remains poorly defined. To construct a comprehensive, tissue-scale map of the developing human small intestine, we leveraged single-cell RNA-sequencing data to build a custom Xenium spatial transcriptomics gene panel covering the diversity of cell types in the human intestine. Analysis was focused on the developing mesenchyme populations (also referred to as fibroblasts or stroma) given the lack of spatiotemporal information about these cell populations. We defined 5 broad mesenchymal populations occupying discrete anatomical locations within the lamina propria and submucosa - the subepithelial cells (SEC), lamina propria fibroblasts (LPF), submucosal fibroblasts (SMF), smooth muscle cells (SMC), and CXCL13+ fibroblasts. Our data reveal dynamic spatial remodeling of fibroblast communities during development and establish molecular markers to distinguish these populations. We leverage this high-resolution atlas to benchmark pluripotent stem cell-derived human intestinal organoids and to demonstrate how this foundational resource can be used to dissect intestinal stromal signaling in a spatial manner, with broad implications for modeling development, regeneration, and disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/665939v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@46299borg.highwire.dtl.DTLVardef@55a014org.highwire.dtl.DTLVardef@180a104org.highwire.dtl.DTLVardef@1cb42b2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA spatial atlas of fibroblast heterogeneity in the human intestine C_LIO_LIPopulations include subepithelial, submucosal, lamina propria, and CXCL13+ fibroblasts C_LIO_LIFibroblast position in the developing intestine is maintained into adulthood C_LIO_LIOrganoids largely recreate the spatial organization of the human intestine C_LI

developmental biology↗

bioRxiv2025

The mGluR5 Agonist, CHPG, Enhances Numbers of Differentiated Human Oligodendrocytes

Previous studies on adult mice indicate that the mGluR5 agonist 2-chloro-5-hydroxyphenyl glycine (CHPG), reduces cuprizone-elicited losses in myelin. This effect is partly mediated by CHPG binding to mGluR5 receptors on reactive astrocytes, triggering the release of brain derived neurotrophic factor (BDNF), which results in an increase in myelin, and alleviates behavioral deficits. However, it remains unclear whether CHPG has similar beneficial effects on human cells. To address this issue, we examined effects of CHPG on human cells using both human induced pluripotent stem cell (hiPSC)-derived oligodendrocytes and primary human fetal brain cells. Treatment of hiPSCs (30M, 5 days) or primary cells (30 M, 3 days) with CHPG increases the percent of MBP+O4+ mature oligodendrocytes relative to total O4+cells, without affecting survival. When effects of CHPG were evaluated on proliferating OPCs, effects on proliferation are observed. In contrast, when CHPG was evaluated in young oligodendrocytes, effects on proliferation were gone, suggesting that in this population CHPG is influencing differentiation. Interestingly, in contrast to observations in mice, mGluR5 expression in humans is localized on PDGFR+ oligodendrocyte precursor cells (OPCs) and O4+ immature oligodendrocytes, but not astrocytes. Moreover, using purified human OPC cultures, we show a direct effect of CHPG in enhanced differentiation. To identify potential cellular targets of CHPG in the adult human brain, we analyzed postmortem tissue from individuals with multiple sclerosis (MS) and healthy controls. In contrast to the hiPSCs or fetal cells, demyelinated white matter from MS patients showed elevated mGluR5 mRNA expression in astrocytes. Taken together, our findings suggest that CHPG enhances the differentiation of human OPCs during development through a mechanism distinct from that observed in adult cuprizone-treated mice. Moreover, astrocytes in MS pathology upregulate mGluR5, suggesting they may become responsive to CHPG under disease conditions.

neuroscience↗

bioRxiv2025

DIO3 coordinates photoreceptor development timing and fate stability in human retinal organoids

The mechanisms governing the generation of neuronal subtypes at distinct times and proportions during human retinal development are poorly understood. While thyroid hormone (TH) signaling specifies cone photoreceptor subtypes, how this regulation changes over time remains unclear. To address this question, we studied the expression and function of type 3 iodothyronine deiodinase (DIO3), an enzyme that degrades TH, in human retinal organoids. We show that DIO3 is a master regulator of human photoreceptor developmental timing and cell fate stability. DIO3 is highly expressed in retinal progenitor cells (RPCs) and decreases as these cells asynchronously differentiate into neurons, progressively reducing TH degradation and increasing TH signaling. DIO3 mutant organoids display precocious development of S cones, L/M cones, and rods, increased photoreceptor (PR) density, and adoption of L/M cone fate characteristics by S cones and rods. Our multiomics and chimeric organoid experiments show that cell autonomous and non-autonomous mechanisms locally coordinate and maintain DIO3 expression and TH signaling levels among cells. Computational modeling reveals a mechanism that couples TH levels and fate specification, providing robustness to photoreceptor development as compared to a probabilistic, cell-intrinsic mechanism. Based on our findings, we propose an hourglass hypothesis, in which the proportion of progenitors to neurons decreases over time to relieve TH degradation, which triggers development of PR subtypes at specific times. Our study identifies how local regulation of thyroid hormone signaling influences neural cell fate specification, which may be a consideration for designing regenerative therapies.

developmental biology↗

bioRxiv2024

The Human Neural Cell Atlas of Zika Infection in developing human brain tissue: viralpathogenesis, innate immunity, and lineage reprogramming

Zika virus (ZIKV) infection during pregnancy can lead to fetal brain infection and developmental anomalies collectively known as congenital Zika syndrome (CZS). To define the molecular features underlying CZS in a relevant human cell model, we evaluated ZIKV infection and neurodevelopment in primary fetal brain explants and induced pluripotent stem cell-derived mixed neural cultures at single cell resolution. We identified astrocytes as key innate immune sentinel cells detecting ZIKV and producing IFN-{beta}. In contrast, neural progenitor cells displayed impaired innate immunity and supported high levels of viral replication. ZIKV infection of neurons suppressed differentiation and synaptic signaling networks and programmed a molecular switch from neurogenesis to astrogliogenesis. We identified a universal ZIKV-driven cellular stress response linked to intrinsic apoptosis and regulated by IFN-{beta}. These findings reveal how innate immune signaling intersects with ZIKV-driven perturbations in cellular function to influence CZS outcomes including neuron developmental dysfunction and apoptotic cell death.

immunology↗

bioRxiv2024

Multi-omics identification of extracellular components of the fetal monkey and human neocortex.

During development, precursor cells are continuously and intimately interacting with their extracellular environment, which guides their ability to generate functional tissues and organs. Much is known about the development of the neocortex in mammals. This information has largely been derived from histological analyses, heterochronic cell transplants, and genetic manipulations in mice, and to a lesser extent from transcriptomic and histological analyses in humans. However, these approaches have not led to a characterization of the extracellular composition of the developing neocortex in any species. Here, using a combination of single-cell transcriptomic analyses from published datasets, and our proteomics and immunohistofluorescence analyses, we provide a more comprehensive and unbiased picture of the early developing fetal neocortex in humans and non-human primates. Our findings provide a starting point for further hypothesis-driven studies on structural and signaling components in the developing cortex that had previously not been identified.

neuroscience↗

bioRxiv2024

Ciliary marginal zone of the developing human retina maintains retinal progenitor cells until late gestational stages

Non-mammalian vertebrates maintain a proliferative stem cell population at the far periphery of their retina called the ciliary marginal zone (CMZ), which gives rise to all retinal cell types and contributes to retinal regeneration upon injury. Humans do not maintain a proliferative CMZ into adulthood; however, it is not known how long in development this region continues to generate new neurons. Here, we identify a population of cells in the far peripheral retina of the fetal human that continues to proliferate long after the rest of the retina is quiescent. Single cell RNA-sequencing and EdU tracing at late time points in development reveal that this region has features of the non-mammalian CMZ, including the capacity to produce both early and late born cell types at late developmental stages, and a longer cell cycle than more centrally located retinal progenitor cells (RPCs). Moreover, while more central RPCs exit the cell cycle with the addition of a TGF{beta}-inhibitor, we show that early RPCs within the CMZ do not. These findings define the late stages of neurogenesis in human retinal development, and present a unique model system to study the fetal CMZ in humans.

developmental biology↗

bioRxiv2023

A Spatiotemporal and Machine-Learning Platform Accelerates the Manufacturing of hPSC-derived Esophageal Mucosa

Human pluripotent stem cell-derived tissue engineering offers great promise in designer cell-based personalized therapeutics. To harness such potential, a broader approach requires a deeper understanding of tissue-level interactions. We previously developed a manufacturing system for the ectoderm-derived skin epithelium for cell replacement therapy. However, it remains challenging to manufacture the endoderm-derived esophageal epithelium, despite both possessing similar stratified structure. Here we employ single cell and spatial technologies to generate a spatiotemporal multi-omics cell atlas for human esophageal development. We illuminate the cellular diversity, dynamics and signal communications for the developing esophageal epithelium and stroma. Using the machine-learning based Manatee, we prioritize the combinations of candidate human developmental signals for in vitro derivation of esophageal basal cells. Functional validation of the Manatee predictions leads to a clinically-compatible system for manufacturing human esophageal mucosa. Our approach creates a versatile platform to accelerate human tissue manufacturing for future cell replacement therapies to treat human genetic defects and wounds.

developmental biology↗

bioRxiv2023

Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA, PDK3, MAB21L1, and RB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four omes to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.

genetics↗

bioRxiv2023

Developmental adaptation of rod photoreceptor number via photoreception in melanopsin (OPN4) retinal ganglion cells

Photoreception, a form of sensory experience, is essential for normal development of the mammalian visual system. Detecting photons during development is a prerequisite for visual system function - from visions first synapse at the cone pedicle and maturation of retinal vascular networks, to transcriptional establishment and maturation of cell types within the visual cortex. Consistent with this theme, we find that the lighting environment regulates developmental rod photoreceptor apoptosis via OPN4-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs). Using a combination of genetics, sensory environment manipulations, and computational approaches, we establish a molecular pathway in which light-dependent glutamate release from ipRGCs is detected via a transiently expressed kainate receptor (GRIK3) in immature rods localized to the inner retina. Communication between ipRGCs and nascent inner retinal rods appears to be mediated by unusual hybrid neurites projecting from ipRGCs that sense light before eye-opening. These structures, previously referred to as outer retinal dendrites (ORDs), span the ipRGC-immature rod distance over the first postnatal week and contain the machinery for sensory detection (melanopsin, OPN4) and axonal/anterograde neurotransmitter release (Synaptophysin, and VGLUT2). Histological and computational assessment of human mid-gestation development reveal conservation of several hallmarks of an ipRGC-to-immature rod pathway, including displaced immature rods, transient GRIK3 expression in the rod lineage, and the presence of ipRGCs with putative neurites projecting deep into the developing retina. Thus, this analysis defines a retinal retrograde signaling pathway that links the sensory environment to immature rods via ipRGC photoreceptors, allowing the visual system to adapt to distinct lighting environments priory to eye-opening.

neuroscience↗

bioRxiv2023

Multimodal analysis of neuronal maturation in the developing primate prefrontal cortex

The prefrontal cortex (PFC) is critical for myriad high-cognitive functions and is associated with several neuropsychiatric disorders. Here, using Patch-seq and single-nucleus multiomic analyses, we identified genes and regulatory networks governing the maturation of distinct neuronal populations in the PFC of rhesus macaque. We discovered that specific electrophysiological properties exhibited distinct maturational kinetics and identified key genes underlying these properties. We unveiled that RAPGEF4 is important for the maturation of resting membrane potential and inward sodium current in both macaque and human. We demonstrated that knockdown of CHD8, a high-confidence autism risk gene, in human and macaque organotypic slices led to impaired maturation, via downregulation of key genes, including RAPGEF4. Restoring the expression of RAPGEF4 rescued the proper electrophysiological maturation of CHD8-deficient neurons. Our study revealed regulators of neuronal maturation during a critical period of PFC development in primates and implicated such regulators in molecular processes underlying autism.

neuroscience↗

bioRxiv2023

Opposing roles for TGFbeta and BMP-signaling during nascent alveolar differentiation in the developing human lung

Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in repair after injury. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development. Using lung explant and organoid models, we identified opposing effects of TGF{beta}- and BMP-signaling, where inhibition of TGF{beta}- and activation of BMP-signaling in the context of high WNT- and FGF-signaling efficiently differentiated early lung progenitors into AT2-like cells in vitro. AT2-like cells differentiated in this manner exhibit surfactant processing and secretion capabilities, and long-term commitment to a mature AT2 phenotype when expanded in media optimized for primary AT2 culture. Comparing AT2-like cells differentiated with TGF{beta}-inhibition and BMP-activation to alternative differentiation approaches revealed improved specificity to the AT2 lineage and reduced off-target cell types. These findings reveal opposing roles for TGF{beta}- and BMP-signaling in AT2 differentiation and provide a new strategy to generate a therapeutically relevant cell type in vitro.

developmental biology↗

bioRxiv2023

APOE-NOTCH Axis Governs Elastogenesis During Human Cardiac Valve Remodeling

BackgroundValve remodeling is a complex process involving extracellular matrix organization, development of trilaminar structures, and physical elongation of valve leaflets. However, the cellular and molecular mechanisms regulating valve remodeling and their roles in congenital valve disorders remain poorly understood. MethodsSemilunar valves and atrioventricular valves from healthy and age-matched human fetal hearts with pulmonary stenosis (PS) were collected. Single-Cell RNA-sequencing (scRNA-seq) was performed to determine the transcriptomic landscape of multiple valvular cell subtypes in valve remodeling and disease. Spatial localization of newly-identified cell subtypes was determined via immunofluorescence and RNA in situ hybridization. The molecular mechanisms mediating valve development was investigated utilizing primary human fetal heart valve interstitial cells (VICs) and endothelial cells (VECs). ResultsscRNA-seq analysis of healthy human fetal valves identified a novel APOE+ elastin-producing VIC subtype (Elastin-VICs) spatially located underneath VECs sensing the unidirectional flow. Knockdown of APOE in fetal VICs resulted in significant elastogenesis defects. In pulmonary valve with PS, we observed decreased expression of APOE and other genes regulating elastogenesis such as EMILIN1 and LOXL1, as well as elastin fragmentation. These findings suggested the crucial role of APOE in regulating elastogenesis during valve remodeling. Furthermore, cell-cell interaction analysis revealed that JAG1 from unidirectional VECs activates NOTCH signaling in Elastin-VICs through NOTCH3. In vitro Jag1 treatment in VICs increased elastogenesis, while similar observations were found in VICs co-cultured with VECs in the presence of unidirectional flow. Notably, we found that the JAG1-NOTCH3 signaling pair was drastically reduced in the PS valves. Lastly, we demonstrated that APOE is indispensable for JAG1-induced NOTCH activation in VICs, reinforcing the presence of a synergistic intrinsic and external regulatory network involving APOE and NOTCH signaling that is responsible for regulating elastogenesis during human valve remodeling. ConclusionscRNA-seq analysis of human fetal valves identified a novel Elastin-VIC subpopulation, and revealed mechanism of intrinsic APOE and external NOTCH signaling in regulating elastogenesis during cardiac valve remodeling. These mechanisms may contribute to deciphering the pathogenesis of elastin malformation in congenital valve diseases. Clinical Perspective What Is New?O_LIHigh-resolution single-cell transcriptome atlas generated from healthy human fetal heart valves and valves affected by pulmonary stenosis during the early phase of valve remodeling prior to birth. C_LIO_LIA unique subset of valve interstitial cells (VICs) that produce elastin (Elastin-VICs) was identified. C_LIO_LIElastin-VICs specifically located underneath the valve endothelial cells (VECs) sensing unidirectional flow, and played a crucial role in elastin maturation via the expression of APOE. C_LIO_LIElastin-VICs communicated with adjacent VECs via the JAG1-NOTCH signaling, facilitating elastin formation and valve remodeling. C_LI What Are the Clinical Implications?O_LIElastin-VICs from patient valvular tissues with Pulmonary Stenosis exhibit decreased APOE-NOTCH signaling and elastin fragmentation. C_LIO_LIDirect targeting of APOE and NOTCH signaling could be a novel approach to promote elastin fiber formation and valve remodeling in patients with valvular defects. C_LI

bioinformatics↗

bioRxiv2023

A Trisomy 21 Lung Cell Atlas

Trisomy 21 (T21), resulting in Down Syndrome (DS), is the most prevalent chromosomal abnormality worldwide. While pulmonary disease is a major cause of morbidity and mortality in DS, the ontogeny of pulmonary complications remains poorly understood. We recently demonstrated that T21 lung anomalies, including airway branching and vascular lymphatic abnormalities, are initiated in utero. Here, we aimed to describe molecular changes at the single cell level in prenatal T21 lungs. Our results demonstrate differences in the proportion of cell populations and detail changes in gene expression at the time of initiation of histopathological abnormalities. Notably, we identify shifts in the distribution of alveolar epithelial progenitors, widespread induction of key extracellular matrix molecules in mesenchymal cells and hyper-activation of IFN signaling in endothelial cells. This single cell atlas of T21 lungs greatly expands our understanding of antecedents to pulmonary complications and should facilitate efforts to mitigate respiratory disease in DS.

developmental biology↗

bioRxiv2023

Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A

ObjectivesTranscript sequencing of patient derived samples has been shown to improve the diagnostic yield for solving cases of likely Mendelian disorders, yet the added benefit of full-length long-read transcript sequencing is largely unexplored. MethodsWe applied short-read and full-length isoform cDNA sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis. ResultsWe identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts a branch point critical for intron 6 spicing. Full-length long-read isoform cDNA sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates five distinct altered splicing transcripts. All five altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 protein levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A). DiscussionThis case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.

genetics↗

bioRxiv2022

Distinct airway progenitor cells drive epithelial heterogeneity in the developing human lung

Recent advances using single cell genomic approaches have identified new epithelial cell types and uncovered cellular heterogeneity in the murine and human lung (1). Here, using scRNA-seq and microscopy we identify and describe a secretory-like cell that is enriched in the small airways of the developing human lung and identified by the unique co-expression of SCGB3A2/SFTPB/CFTR. To place these cells in the hierarchy of airway development, we apply a single cell barcode-based lineage tracing method track the fate of SCGB3A2/SFTPB/CFTR cells during airway organoid differentiation in vitro (2). Lineage tracing revealed that these cells have distinct developmental potential from basal cells, giving rise predominantly to pulmonary neuroendocrine cells (PNECs) and a subset of multiciliated cells distinguished by high C6 and low MUC16 expression. We conclude that SCGB3A2/SFTPB/CFTR cells act as a progenitor cell contributing to the cellular diversity and heterogeneity in the developing human airway. SIGNIFICANCE STATEMENTThe current study identifies a novel secretory cell type that is present predominantly in the small airway of the developing human lung. These secretory cells are defined by co-expression of SCGB3A2/SFTPB/CFTR, and functional studies show that this cell gives rise to pulmonary neuroendocrine cells and a sub-population of multiciliated cells, thereby leading to cellular heterogeneity.

developmental biology↗

bioRxiv2022

A Development-Inspired Niche for Homeostatic Human Mini-Intestines

Epithelial organoids derived from intestinal tissue, also referred to as mini-intestines or mini-guts, recapitulate many aspects of the organ in vitro and can be used for biological discovery, personalized medicine, and drug development. Murine intestinal organoids represent a homeostatic system that balances stem cell maintenance within a crypt-like compartment and differentiation within a villus-like compartment1-3. However, this homeostatic balance and spatial organization has not been achieved with human intestinal organoids4. Here, we leverage single cell RNA-seq data (scRNA-seq) and high-resolution imaging to interrogate the developing human intestinal stem cell niche. We identified an EGF-family member, EPIREGULIN (EREG), as uniquely expressed in the developing crypt, and found that EREG can take the place of EGF as an in vitro niche factor. Unlike EGF, which leads to growth of thin-walled cystic organoids, EREG-organoids are spatially resolved into budded and proliferative crypt domains and a differentiated villus-like central lumen. Transcriptomics and epigenomics showed that EREG-organoids are globally similar to the native intestine while EGF-organoids have an altered chromatin landscape, downregulate the master intestinal transcription factor CDX25,6, and ectopically express stomach genes.

developmental biology↗