Biology subjects

Tsai, Y.-H.

Publications and source records attributed to Tsai, Y.-H..

At least 19 recordsLinked to original sources

bioRxiv2026

Diverse Intestinal Injuries Drive Heterogeneous Transcriptional Responses and Limited Reactivation of Developmental Gene Programs in Human Enteroids

The murine intestine reactivates developmental gene programs following various forms of damage in vivo and in vitro; however, injury response mechanisms used by the human intestine remain unclear. Using adult human small intestinal epithelium-only organoids ("enteroids"), we characterized the early response to eight injury conditions and injury-associated signaling pathways (P53, PGE2, YAP, TGFB) to interrogate whether human developmental genes were activated. P53 activation and decreased proliferation were common features across treatments. Most (7/8) injuries did not activate human development genes. Butyrate is a notable exception given it inhibited P53 and promoted a human developmental transcriptional signature. We observe that P53 induces a human adult gene signature while TGFB and YAP promote a developmental signature. Together our data characterizes various transcriptional responses to injury, supports injury-associated signaling pathways as regulators of human adult and developmental genes, and highlights how our data can be mined to predict injury-specific interventions for epithelial protection.

cell biology↗

bioRxiv2026

Suspension-Based Human Esophagoids Recapitulate WNT2B-Dependent Regulation of Esophageal Basal Progenitors

Background & AimsThe human esophagus undergoes a tightly regulated developmental program, transitioning from a simple columnar epithelium in early development to a mature stratified squamous tissue essential for adult barrier function. Here, we constructed a developmental cell atlas spanning early development to adulthood and leveraged it to generate physiologically relevant in vitro models. MethodsWe utilized single-cell RNA sequencing and spatial multiplex proteomics of human esophageal tissue from early development through adulthood. We established a feeder-supported 2D culture system and a Matrigel-free, suspension-based 3D esophagoid model in a 96-well format. To interrogate WNT2B function, we analyzed patient tissue harboring WNT2B loss-of-function mutations and performed WNT inhibition in esophagoids. ResultsSequencing profiling identified stage-specific epithelial populations: multiciliated and GPC3 basal cells were unique to early development; KRT14 basal and CRNN luminal cells were adult-specific; and COL17A1, LY6D, and KRT4 populations were shared across stages. Spatially organized WNT2B, KIT, and VWC2 mesenchymal subtypes were identified. The 2D system preserved both epithelial and mesenchymal compartments with transcriptional fidelity. Esophagoids exhibited basal-to-luminal stratification, mesenchymal compartmentalization, and required stromal interactions for formation. WNT2B repressed self-renewal of TP63 basal progenitors and inhibited proliferation, confirmed by pharmacologic inhibition of WNT in the in vitro esophagoids. ConclusionsWe present a stage-resolved atlas of human esophageal development and a scalable esophagoid platform recapitulating esophageal architecture. WNT2B regulates progenitor dynamics by restraining basal cell self-renewal. Esophagoids provide a physiologically relevant system for modeling esophageal development and disease. Visual Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/733451v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1af5743org.highwire.dtl.DTLVardef@8a061dorg.highwire.dtl.DTLVardef@1975c3forg.highwire.dtl.DTLVardef@292ce9_HPS_FORMAT_FIGEXP M_FIG C_FIG Key Findings and ImplicationsO_LIDevelopmental Atlas: The study presents a comprehensive transcriptional and structural atlas of the human esophageal epithelium, identifying conserved and stage-specific epithelial populations from early development to adulthood. Notably, stage-specific gene expression of multiciliated and GPC3 basal cells were unique to early development, while KRT14 basal and CRNN luminal cells were adult specific, with COL17A1+ (basal), LY6D+ (epibasal), and KRT4+ (middle), shared at all stages. C_LIO_LIMesenchymal Diversity: Spatial and transcriptional profiling revealed distinct mesenchymal subtypes, including WNT2B, KIT, and VWC2 populations, which are spatially organized and contribute to epithelial-mesenchymal signaling. These findings reinforce the role of stromal-epithelial interactions in esophageal development. C_LIO_LI2D Esophagus Cell Culture System: A feeder-supported 2D cell culture system was developed that retains both epithelial and mesenchymal populations, preserving transcriptional fidelity and enabling long-term expansion for mechanistic studies. C_LIO_LI3D Esophagoid Model: A suspension-based 3D organoid system was optimized using a 96-well format, enabling high-throughput generation of esophagoids with robust epithelial stratification and mesenchymal compartmentalization. These organoids recapitulate key features of the human esophagus, including basal-to-luminal organization, and require stromal interactions for formation. C_LIO_LIFunctional Role of WNT2B in esophagus development: Both in vivo and in vitro analyses demonstrated that WNT2B regulates epithelial progenitor dynamics and tissue architecture by repressing self-renewal of basally localized TP63+ cells and inhibiting proliferation. Loss-of-function models and WNT pathway modulation confirmed its role in epithelial-mesenchymal crosstalk and organoid integrity. C_LI

developmental 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

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

A morphological comparison of the caudal rami of the superior temporal sulcus in humans, chimpanzees, and other great apes

For centuries, anatomists have charted the folding patterns of the sulci of the cerebral cortex in primates. Improvements in neuroimaging technologies over the past decades have led to advancements in understanding of the sulcal organization of the human cerebral cortex, yet comparisons to chimpanzees, one of humans closest extant phylogenetic relatives, remain to be performed in many regions, such as superior temporal cortex. For example, while several posterior branches, or rami, of the superior temporal sulcus (STS) have been identified in great apes since the late 1800s, no study has yet to comprehensively identify and quantitatively compare these rami across species. To fill this gap in knowledge, in the present study, we defined the three caudal branches of the STS (cSTS) in 72 human and 29 chimpanzee brains (202 total hemispheres) and then extracted and compared the morphological (depth and surface area) properties of these sulci. We report three main findings. First, modern methods replicate classic findings that three rami of the posterior STS are unique to the hominid lineage (i.e., humans and great apes). Second, normalizing for brain size, the cSTS rami were relatively deeper in chimpanzees compared to humans. Third, the cSTS branches were relatively larger in surface area in humans compared to chimpanzees. Finally, we share probabilistic predictions of the cSTS to guide the identification of these sulci in future studies. Altogether, these findings bridge the gap between historic qualitative observations and modern quantitative measurements in a part of the brain that has expanded substantially throughout evolution and that is involved in human-specific aspects of cognition.

neuroscience↗

bioRxiv2025

Tryptophan and IFN-γ Differentially Modulate Cellular Uptake, Intracellular Trafficking, and Gene Expression of Messenger RNA-Loaded Lipid Nanoparticles in Dendritic Cells

Lipid nanoparticle (LNP)-mediated mRNA delivery has emerged as a powerful platform for both immunostimulatory and immunomodulatory applications. However, the influence of local immunometabolic cues on the intracellular fate and translational efficiency of mRNA-LNPs remains poorly understood. In this study, we investigated how interferon-gamma (IFN-{gamma}), a potent inducer of indoleamine 2,3-dioxygenase 1 (IDO1), and tryptophan (Trp) deprivation independently and combinatorially affect mRNA-LNP function in DC2.4 dendritic cells. These two cues are canonical drivers of immunoregulatory microenvironments, particularly those that favor tolerogenic dendritic cell programming and the induction of regulatory T cells. Using dual-reporter mRNA constructs and high-resolution confocal imaging, we show that IFN-{gamma} stimulation reduces total cellular mRNA uptake and lysosomal accumulation without affecting translation efficiency and endosomal escape efficiency. Whereas Trp deprivation also reduces the overall cellular uptake of mRNA-LNPs, it also significantly impairs protein synthesis from mRNA-LNPs and modestly reduces endosomal escape, despite having minimal impact on lysosomal mRNA levels. Spatial compartmentalization analysis revealed that IFN-{gamma} and Trp limitation disrupt distinct steps in the delivery-translation cascade, acting independently but additively to suppress the ultimate protein translation from mRNA-LNPs in DC2.4 dendritic cells. These findings highlight the importance of considering local metabolic and cytokine contexts when deploying mRNA-LNPs for immunological applications. Our work provides mechanistic insights into how immunoregulatory environments impair the delivery and translation of mRNA-LNPs, suggesting strategies to tune delivery outcomes for tolerogenic purposes.

biochemistry↗

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↗

bioRxiv2024

Lateral frontoparietal functional connectivity based on individual sulcal morphology

A salient neuroanatomical feature of the human brain is its pronounced cortical folding, and there is mounting evidence that sulcal morphology is relevant to functional brain architecture and cognition. However, our understanding of the relationships between sulcal anatomy, brain activity, and behavior is still in its infancy. We previously found the depth of three small, shallow sulci in lateral prefrontal cortex (LPFC) was linked to reasoning performance in childhood and adolescence (Voorhies et al., 2021). These findings beg the question: what is the linking mechanism between sulcal morphology and cognition? To shed light on this question, we investigated functional connectivity among sulci in LPFC and lateral parietal cortex (LPC). We leveraged manual parcellations (21 sulci/hemisphere, total of 1806) and functional magnetic resonance (fMRI) data from a reasoning task from 43 participants aged 7-18 years (20 female). We conducted clustering and classification analyses of individual- level functional connectivity among sulci. Broadly, we found that 1) the connectivity patterns of individual sulci could be differentiated - and more accurately than rotated sulcal labels equated for size and shape; 2) sulcal connectivity did not consistently correspond with that of probabilistic labels or large-scale networks; 3) sulci clustered together into groups with similar patterns, not dictated by spatial proximity; and 4) across individuals, greater depth was associated with higher network centrality for several sulci under investigation. These results highlight that functional connectivity can be meaningfully anchored to individual sulcal anatomy, and demonstrate that functional network centrality can vary as a function of sulcal depth. Significance StatementA salient, and behaviorally relevant, feature of the human brain is its pronounced cortical folding. However, the links between sulcal anatomy and brain function are still poorly understood - particularly for small, shallow, individually variable sulci in association cortices. Here, focusing on individually defined sulci in lateral prefrontal and parietal regions, we offer a novel, anatomically informed approach to defining functional connectomes. Further, we demonstrate, for the first time, a link between functional network centrality and sulcal morphology.

neuroscience↗

bioRxiv2023

Activation of Store-Operated Calcium Entry and Mitochondiral Respiration by Enterovirus 71 Is Essential for Viral Replication

Enterovirus (EV) infections disrupt cellular calcium (Ca2+) homeostasis. The EV protein 2B is localized to the endoplasmic reticulum (ER) and causes depletion of ER Ca2+ stores. This depletion coincides with a substantial increase in cytosolic Ca2+ levels driven by extracellular Ca2+ influx. However, the precise mechanism underlying this influx remains elusive. In the present study, we demonstrated that EV71 infections induce store-operated Ca2+ entry (SOCE) by activating the Ca2+ sensor stromal interaction molecule 1 (STIM1), which subsequently interacts with Orai1, a plasma membrane (PM) Ca2+ channel. This finding was supported by confocal imaging, which revealed that STIM1, typically localized in the ER, becomes active and colocalizes with Orai1 at the PM in EV71-infected cells. Pharmacological inhibition of the STIM1-Orai1 interaction and knockdown of either STIM1 or Orai1 significantly reduced virus-induced cytosolic Ca2+ levels and viral replication. Global transcriptome analysis revealed that differentially expressed genes are primarily associated with the mitochondrial electron transport chain (ETC) upon SOCE activation, contributing to enhanced ATP generation and oxygen consumption. This increase in mitochondrial Ca2+ levels is correlated with the mid-stage of virus infection. Furthermore, we demonstrated that high levels of mitochondrial Ca2+ influx led to apoptotic cell death favoring viral release at the late stage of virus infection. Finally, SOCE-dependent EV replication was observed in a mouse intestinal organoid culture, a more physiologically relevant cell system. Our results provide valuable insights into the mechanism through which EV infections induce SOCE-mediated spatial and temporal control of Ca2+ signaling, substantially affecting the virus life cycle. IMPORTANCEHost cell Ca2+ signals play crucial roles in various steps of virus life cycles, including entry, replication, and exit. EV requires increased cytosolic Ca2+ levels for efficient replication, but the precise mechanisms underlying the association between Ca2+ levels and EV replication remain elusive. Using EV71 as a model virus, we demonstrated that EV71 infection elevated cytosolic Ca2+ levels through store-operated Ca2+ entry activation and progressive Ca2+ mobilization to mitochondria. This led to the upregulation of electron transport chain activity, which is essential for efficient virus replication and apoptotic cell death, facilitating viral release during the mid and late stages of the infectious cycle, respectively. These findings substantially enhance the understanding of how EVs co-opt host cell mechanisms to promote their own life cycle. STIM1 and Orai1 may be novel targets for broad-spectrum host-directed therapeutics against EVs and other viruses that employ similar replication mechanisms.

microbiology↗

bioRxiv2023

Coordinated differentiation of human intestinal organoids with functional enteric neurons and vasculature

Human intestinal organoids (HIOs) derived from human pluripotent stem cells co-differentiate both epithelial and mesenchymal lineages in vitro but lack important cell types such as neurons, endothelial cells, and smooth muscle. Here, we report an in vitro method to derive HIOs with epithelium, mesenchyme, enteric neuroglial populations, endothelial cells, and organized smooth muscle in a single differentiation, without the need for co-culture. When transplanted into a murine host, these populations expand and organize to support organoid maturation and function. Functional experiments demonstrate enteric nervous system function, with HIOs undergoing peristaltic-like contractions, suggesting the development of a functional neuromuscular unit. HIOs also form functional vasculature, demonstrated in vitro using microfluidic devices to introduce vascular-like flow, and in vivo following transplantation, where HIO endothelial cells anastomose with host vasculature. Collectively, we report an in vitro model of the human gut that simultaneously co-differentiates epithelial, stromal, endothelial, neural, and organized muscle populations.

bioengineering↗

bioRxiv2023

YAP and TAZ differentially regulate postnatal cortical progenitor proliferation and astrocyte differentiation

WW domain-containing transcription regulator 1 (TAZ) and Yes-associated protein (YAP) are transcriptional co-activators traditionally studied together as a part of the Hippo pathway and best known for their roles in stem cell proliferation and differentiation. Despite their similarities, TAZ and YAP can exert divergent cellular effects by differentially interacting with other signaling pathways that regulate stem cell maintenance or differentiation. In the developing central nervous system, In this study, we show that TAZ regulates astrocytic differentiation and maturation of postnatal neural stem and progenitor cells (NPCs), and that TAZ mediates some but not all of the effects of bone morphogenetic protein (BMP) signaling on astrocytic development. By contrast, TAZ and YAP both mediate effects on NPC fate of {beta}1-integrin and integrin-linked kinase (ILK) signaling, and these effects are dependent on extracellular matrix (ECM) cues. These findings demonstrate that TAZ and YAP perform divergent functions in the regulation of astrocyte differentiation, where YAP regulates cell cycle states of astrocytic progenitors and TAZ regulates differentiation and maturation from astrocytic progenitors into astrocytes. Summary StatementAstrocytes are accounts for nearly half of the cells in the central nervous system, where they perform a diverse array of physiological functions. During development, astrocytes are primarily generated after neuronal differentiation in a stepwise manner from multiple glial committed progenitor subtypes. How gliogenic progenitors maintain proliferative properties versus differentiate into astrocytes is not fully understood. This work aims to elucidate how environmental signals utilizes molecularly similar intracellular components to achieve distinct developmental outcomes. In addition, many of the cell types that are involved in glial development are also present in brain tumors including glioblastoma. Knowledge on mechanisms regulating proliferation and differentiation of glial progenitors will provide insights into differences and similarities between normal and malignant cells.

neuroscience↗

bioRxiv2023

Updating the sulcal landscape of the human lateral parieto-occipital junction provides anatomical, functional, and cognitive insights

Recent work has uncovered relationships between evolutionarily new small and shallow cerebral indentations, or sulci, and human behavior. Yet, this relationship remains unexplored in the lateral parietal cortex (LPC) and the lateral parieto-occipital junction (LPOJ). After defining thousands of sulci in a young adult cohort, we revised the previous LPC/LPOJ sulcal landscape to include four previously overlooked, small, shallow, and variable sulci. One of these sulci (ventral supralateral occipital sulcus, slocs-v) is present in nearly every hemisphere and is morphologically, architecturally, and functionally dissociable from neighboring sulci. A data-driven, model-based approach, relating sulcal depth to behavior, further revealed that the morphology of only a subset of LPC/LPOJ sulci, including the slocs-v, is related to performance on a spatial orientation task. Our findings build on classic neuroanatomical theories and identify new neuroanatomical targets for future "precision imaging" studies exploring the relationship among brain structure, brain function, and cognitive abilities in individual participants.

neuroscience↗

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↗

bioRxiv2022

Enhanced expression of 4-Cl-IAA and 6-Cl-IAA by touch stimulus for rapid and differential growths of the Madeira vine

Madeira vine (MV) grows 30 times faster after encountering a support. In vivo x-ray diffraction made on live MV stems revel the appearance of crystallized IAA (C10H9NO2), 4-Cl-IAA (C10H8ClNO2) and 6-Cl-IAA (C10H8ClNO2) in the stems. Small angle neutron scattering spectra of the IAA extracted from MVs stem reveal a progressive increase in the size of crystallized IAA transported downward from the apex of the shoots. High resolution X-ray diffractions made on the extracted IAA reveal significantly larger amounts of 4-Cl-IAA and 6-Cl-IAA in the climbing MVs than in the swaying around MVs. The gas chromatography-mass spectrometry spectra reveal the production of 9% more IAA and 90% more 4-Cl-IAA+6-Cl-IAA at the apexes of climbing MVs than swaying MVs. More 4-Cl-IAA+6-Cl-IAA were transported to the contact-free side than to the contact side of the vine. In vivo neutron tomography of naturally climbing MVs reveals a substantially higher H+ concentration in the contact-free parts than in the contact parts. The absorption spectra also reveal more expansin in the contact-free parts than in the contact parts. These results provide a view, at the molecular level, of what triggers the faster and differential growths in MVs in response to touching a support.

plant biology↗

bioRxiv2022

Stable iPSC-derived NKX2-1+ Lung Bud Tip Progenitor Organoids Give Rise to Airway and Alveolar Cell Types

Bud tip progenitors (BTPs) in the developing lung give rise to all epithelial cell types found in the airways and alveoli. The current work aimed to develop an iPSC organoid model enriched with stable NKX2-1+ BTP-like cells. Building on prior work, we optimized a directed differentiation paradigm to generate spheroids with robust NKX2-1 expression. Spheroids were expanded into organoids that possessed NKX2-1+/CPM+ BTP-like cells, which increased in number over time. Single cell RNA-sequencing analysis revealed a high degree of transcriptional similarity between induced BTPs (iBTPs) and in vivo BTPs. Using FACS, iBTPs can be purified and expanded as induced bud tip organoids (iBTO), which maintain an enriched population of bud tip progenitors. When iBTOs are directed to differentiate into airway or alveolar cell types using well-established methods, they give rise to organoids composed of organized airway or alveolar epithelium, respectively. Collectively, iBTOs are transcriptionally and functionally similar to in vivo BTPs, providing an important model to study human lung development and differentiation. SUMMARY STATEMENTiPSC-derived lung bud tip progenitors emerge in organoid culture, can be isolated and expanded, are transcriptionally similar to primary bud tip progenitors, and can differentiate into airway or alveolar organoids.

developmental biology↗

bioRxiv2021

In vitro models of the human esophagus reveal ancestrally diverse response to injury

European Americans (EA) are more susceptible to esophageal tissue damage and inflammation when exposed to gastric acid and bile acid reflux and have a higher incidence of esophageal adenocarcinoma when compared to African Americans (AA). Population studies have implicated specific genes for these differences; however, the underlying cause for these differences is not well understood. We describe a robust long-term culture system to grow primary human esophagus in vitro, use single cell RNA sequencing to compare primary human biopsies to their in vitro counterparts, identify known and new molecular markers of basal cell types, and demonstrate that in vivo cellular heterogeneity is maintained in vitro. We further developed an ancestrally diverse biobank and a high-content, image based, screening assay to interrogate bile-acid injury response. These results demonstrated that AA esophageal cells responded significantly differently than EA-derived cells, mirroring clinical findings, having important implications for addressing disparities in early drug development pipelines.

cell biology↗

bioRxiv2021

R-SPONDIN2+ Mesenchymal Cells Form the Bud Tip Progenitor Niche During Human Lung Development

Mammalian respiratory system development is regulated by complex reciprocal signaling events that take place between epithelial cells and the surrounding mesenchymal cells; however, mesenchymal heterogeneity and function in the developing human lung is poorly understood. We interrogated single cell RNA sequencing data from multiple human lung specimens and identified a mesenchymal cell population present during development that is highly enriched for expression of the WNT agonist R-SPONDIN2 (RSPO2), and we found that adjacent epithelial bud tip progenitors are enriched for the RSPO2 receptor LGR5. By carrying out functional experiments using organoid models, lung explant cultures, and FACS-isolated RSPO2+ mesenchyme, we show that RSPO2 is a critical niche cue that potentiates WNT signaling in human lung progenitors to maintain their multipotency.

developmental biology↗