Biology subjects

Spence, J.

Publications and source records attributed to Spence, J..

16 recordsLinked to original sources

bioRxiv2026

The Role of Meningeal Lymphatic Vessels and Perivascular Cerebrospinal Fluid Flow in Age-Related Processing Speed Decline

Meningeal lymphatic vessels (mLV) play essential roles in draining cerebrospinal fluid (CSF) into peripheral blood. The mLVs are hypothesized to be supportive structures to the glymphatic system, which is thought to remove metabolic byproducts from brain parenchyma and has been most directly studied in rodent models. Previous rodent studies have indicated a correlation between mLV function and cognitive performance, but this relationship in humans remains unexplored. Age-related declines in glymphatic system efficiency in humans and cognitive performance have been observed separately. This study investigates age- and sex-related differences in CSF production via choroid plexus volumes, mLV characteristics, and glymphatic system efficiency, overall elucidating the implication of cerebral lymphatic function on cognition. We recruited 26 healthy adults from Dallas-Fort Worth and acquired magnetic resonance images. mLVs along the sagittal sinus were visualized and segmented from T2-FLAIR images. The glymphatic system was evaluated by measuring diffusivity along the perivascular space. Choroid plexus volume and brain volume were estimated from T1-MPRAGE. Neuropsychological tests were conducted to assess cognitive function. Our findings indicate that glymphatic function diminishes with age, while mLV and choroid plexus volumes increase. Males displayed greater mLV volume than females, yet no sex differences were found in glymphatic function or choroid plexus volume. Notably, mLV volume increased as glymphatic function declined, independent of age. Moreover, a glymphatic-mLV latent variable significantly predicted processing speed, underscoring the influence of cerebral lymphatics on cognition. In conclusion, this study highlights a decline in glymphatic function with age, accompanied by increased mLV volumes and altered processing speed. These lymphatic system changes may underlie or contribute to the cognitive declines observed in healthy and pathological aging. Significance StatementThe glymphatic system and meningeal lymphatic vessels play crucial roles in removing brain cell waste. The relationship between these systems and their effect on human cognition, particularly processing speed, is unknown. We demonstrate that these systems change with advancing age. Variations in cerebral lymphatic function contribute to differences in processing speed independent of age, ultimately affecting higher-order cognitive function. The findings presented have implications for cognitive function in both healthy and diseased states.

neuroscience↗

bioRxiv2026

A robust human airway organoid platform enables scalable expansion and trajectory mapping of pulmonary neuroendocrine cells

Pulmonary neuroendocrine cells (PNECs) are rare chemosensory epithelial cells, facultative stem cells, and a cell-of-origin for neuroendocrine lung cancers, yet the mechanisms governing their differentiation and heterogeneity are poorly understood. Here we establish NEr-fAOs, a human fetal airway organoid platform that robustly enriches PNECs, and identify a cooperative requirement for dual GSK3 and NOTCH inhibition to drive directed PNEC differentiation. This strategy yields stable cultures with up to 60-fold expansion of PNECs whose transcriptomes closely match fetal and adult PNECs. In addition to PNEC-enrichment, NEr-fAOs retain diverse airway epithelial cell types, preserving epithelial complexity. Time-resolved single-cell transcriptomics maps PNEC trajectories in NEr-fAOs, resolving precursor and mature states. Comparative analyses further reveal a distal airway bias in NEr-fAOs and enrichment for lower-airway progenitors. NEr-fAOs thus provide a scalable, tractable platform to dissect human PNEC biology and distal airway progenitor hierarchies relevant to lung development, cancer, and disease.

developmental biology↗

bioRxiv2025

Limited generalizability of dynamic fMRI correlates of adolescent rumination

Rumination, or perseverative negative self-referential thinking, is a hallmark of depression. In adults, a dynamic resting-state fMRI model of trait rumination was recently identified through predictive modelling. In adolescents, a development period during which rumination and depression increase, the neurobiological correlates of ruminative thinking are less clear. In the current preregistered study, we examine dynamic connectivity correlates of self-reported rumination in the largest sample of adolescents to date (n = 443, containing clinical and non-clinical individuals). Notably, the adult model failed to generalize to our sample. In addition, linear models trained on default-mode network (DMN) connectivity, as well as whole-brain connectome models, failed to generalize to held-out data. In an exploratory random forest analysis, we found significant prediction performance of a model where increased variability between DMN-cerebellum, DMN-dorsal attention network, and DMN-DMN connections was nominally associated with higher rumination. However, the model did not generalize to an external sample with lower rumination scores and a distinct scanner protocol. Our findings illustrate the difficulty of characterizing the neurodevelopment of risk factors for depression.

neuroscience↗

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↗

bioRxiv2024

Endogenous FGFs drive ERK-dependent cell fate patterning in 2D human gastruloids

The role of FGF is the least understood of the morphogens driving mammalian gastrulation. Here we investigated the function of FGF in a stem cell model for human gastrulation known as a 2D gastruloid. We found a ring of FGF-dependent ERK activity that closely follows the emergence of primitive streak (PS)-like cells but expands further inward. We showed that this ERK activity pattern is required for PS-like differentiation and that loss of PS-like cells upon FGF receptor inhibition can be rescued by directly activating ERK. We further demonstrated that the ERK-ring depends on localized activation of basolaterally positioned FGF receptors (FGFR) by endogenous FGF gradients. We confirmed and extended previous studies in analyzing expression of FGF pathway components, showing FGFR1 is the main receptor, FGF2 is highly expressed across several cell types, and FGF4/17 are the main FGF ligands expressed in the PS-like cells, similar to the human and monkey embryo but different from the mouse. We found that knockdown of FGF4 greatly reduced PS-like differentiation while FGF17 knockdown primarily affected subsequent mesoderm differentiation. FGF8 expression was spatially displaced from PS-markers and FGF4 expression and peaked earlier, while knockdown led to an expansion in PS-like cells, suggesting FGF8 may counteract FGF4 to limit PS-like differentiation. Thus, we have identified a previously unknown role for FGF-dependent ERK signaling in 2D gastruloids and possibly the human embryo, driven by a mechanism where FGF4 and FGF17 signal through basally localized FGFR1 to induce PS-like cells and their derivatives, potentially restricted by FGF8.

developmental biology↗

bioRxiv2024

Multimodal Predictive Modeling: Scalable Imaging Informed Approaches to Predict Future Brain Health

BackgroundPredicting future brain health is a complex endeavor that often requires integrating diverse data sources. The neural patterns and interactions iden-tified through neuroimaging serve as the fundamental basis and early indica-tors that precede the manifestation of observable behaviors or psychological states. New MethodIn this work, we introduce a multimodal predictive modeling approach that leverages an imaging-informed methodology to gain insights into fu-ture behavioral outcomes. We employed three methodologies for evalua-tion: an assessment-only approach using support vector regression (SVR), a neuroimaging-only approach using random forest (RF), and an image-assisted method integrating the static functional network connectivity (sFNC) matrix from resting-state functional magnetic resonance imaging (rs-fMRI) alongside assessments. The image-assisted approach utilized a partially con-ditional variational autoencoder (PCVAE) to predict brain health constructs in future visits from the behavioral data alone. ResultsOur performance evaluation indicates that the image-assisted method ex-cels in handling conditional information to predict brain health constructs in subsequent visits and their longitudinal changes. These results suggest that during the training stage, the PCVAE model effectively captures relevant in-formation from neuroimaging data, thereby potentially improving accuracy in making future predictions using only assessment data. Comparison with Existing MethodsThe proposed image-assisted method outperforms traditional assessment-only and neuroimaging-only approaches by effectively integrating neuroimag-ing data with assessment factors, ConclusionThis study underscores the potential of neuroimaging-informed predictive modeling to advance our comprehension of the complex relationships between cognitive performance and neural connectivity. HighlightsO_LIMultifaceted perspective for studying longitudinal brain health changes. C_LIO_LIShowcases the versatility of methodologies through assessment-only, neuroimaging-only, and image-assisted predictive approaches. C_LIO_LIProvides predictive insights by revealing the neural patterns corresponding to alterations in behavior. C_LI Graphical Abstract

neuroscience↗

bioRxiv2024

Overcoming brain-derived therapeutic resistance in HER2+ breast cancer brain metastasis

Brain metastasis of HER2+ breast cancer occurs in about 50% of all women with metastatic HER2+ breast cancer and confers poor prognosis for patients. Despite effective HER2-targeted treatments of peripheral HER2+ breast cancer with Trastuzumab +/-HER2 inhibitors, limited brain permeability renders these treatments inefficient for HER2+ breast cancer brain metastasis (BCBM). The scarcity of suitable patient-derived in-vivo models for HER2+ BCBM has compromised the study of molecular mechanisms that promote growth and therapeutic resistance in brain metastasis. We have generated and characterized new HER2+ BCBM cells (BCBM94) isolated from a patient HER2+ brain metastasis. Repeated hematogenic xenografting of BCBM94 consistently generated BCBM in mice. The clinically used receptor tyrosine kinase inhibitor (RTKi) Lapatinib blocked phosphorylation of all ErbB1-4 receptors and induced the intrinsic apoptosis pathway in BCBM94. Neuregulin-1 (NRG1), a ligand for ErbB3 and ErbB4 that is abundantly expressed in the brain, was able to rescue Lapatinib-induced apoptosis and clonogenic ability in BCBM94 and in HER2+ BT474. ErbB3 was essential to mediate the NRG1-induced survival pathway that involved PI3K-AKT signalling and the phosphorylation of BAD at serine 136 to prevent apoptosis. High throughput RTKi screening identified the brain penetrable Poziotinib as highly potent compound to reduce cell viability in HER2+ BCBM in the presence of NRG1. Successful in-vivo ablation of BCBM94- and BT474-derived HER2+ brain tumors was achieved upon two weeks of treatment with Poziotinib. MRI revealed BCBM remission upon poziotinib, but not with Lapatinib treatment. In conclusion, we have established a new patient-derived HER2+ BCBM in-vivo model and identified Poziotinib as highly efficacious RTKi with excellent brain penetrability that abrogated HER2+ BCBM brain tumors in our mouse models.

cancer biology↗

bioRxiv2022

Human neutrophils direct epithelial cell extrusion to enhance intestinal epithelial host defense during Salmonella infection

Infection of the human gut by Salmonella enterica Typhimurium (STM) results in a localized inflammatory disease that is not mimicked in murine infections. To determine mechanisms by which neutrophils, as early responders to bacterial challenge, direct inflammatory programming of human intestinal epithelium, we established a multi-component human intestinal organoid (HIO) model of STM infection. HIOs were micro-injected with STM and then seeded with primary human polymorphonuclear leukocytes (PMN-HIOs), specifically neutrophils and analyzed for bacterial growth and host cell survival. Surprisingly, PMNs did not affect luminal colonization of Salmonella, but their presence reduced intraepithelial bacterial burden. Adding PMNs to infected HIOs resulted in substantial accumulation of shed intestinal epithelial cells that could be blocked by Caspase-1 or Caspase-3 inhibition. Cleaved Caspase-3 was present in epithelial cells, but expression of the inflammasome adaptor, ASC, was only detected in PMNs. Caspase inhibition also increased bacterial burden in the epithelium of the PMN-HIO, suggesting PMNs enhance activation of cell death pathways in human intestinal epithelial cells as a protective response to infection. These data support a critical function for neutrophils beyond their antimicrobial role whereby they amplify cell death and extrusion of epithelial cells from the Salmonella-infected intestinal monolayer. Significance statementNeutrophils are early responders to Salmonella intestinal infection, but how they influence infection progression and outcome is unknown. Here we use a co-culture model of human intestinal organoids and human primary neutrophils to study the contribution of human neutrophils to Salmonella infection of the intestinal epithelium. We found that neutrophils markedly enhanced epithelial defenses, including enhancing cell extrusion to reduce intraepithelial burden of Salmonella and association with the epithelium, rather than directly killing Salmonella in the HIO lumen. These findings reveal a novel role for neutrophils in the gut beyond killing invading pathogens and illuminate how neutrophils can reprogram cells in the gut environment to enhance antimicrobial defenses.

microbiology↗

bioRxiv2020

THE INFLUENCE OF PRE-SUPPLEMENTARY MOTOR AREA TARGETED HIGH-DEFINITION TRANSCRANIAL DIRECT CURRENT STIMULATION ON INHIBITORY CONTROL

AO_SCPLOWBSTRACTC_SCPLOWThe neural underpinnings of inhibitory control, an executive cognitive control function, has been a topic of interest for several decades due to both its clinical significance and the maturation of cognitive science disciplines. Behavioral, imaging, and electrophysiological studies suggest that the pre-supplementary motor area (preSMA) serves as a primary hub in a network of regions engaged in inhibition. High-definition transcranial direct current stimulation (HD-tDCS) allows us to modulate neural function to assess cortical contribution to cognitive functioning. The present study targeted HD-tDCS modulation of preSMA to affect inhibition. Participants were randomly assigned to receive 20 min of Sham, Anodal, or Cathodal stimulation prior to completing a semantically cued go/nogo task while electroencephalography (EEG) data were recorded. Both anodal and cathodal stimulation improved inhibitory performance as measured by faster reaction times and increased (greater negative) N2 event-related potentials (ERPs). In contrast, the Sham group did not show such changes. We did not find support for the anodal/cathodal dichotomy for HD neural stimulation. These findings constitute an early investigation into role of the preSMA in inhibitory control and in exploring application of HD-tDCS to the preSMA in order to improve inhibitory control.

neuroscience↗

bioRxiv2020

Differentiation of human intestinal organoids with endogenous vascular endothelial cells

Human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) generated using directed differentiation lack some cellular populations found in the native organ, including vasculature. Using single cell RNA sequencing (scRNAseq), we have identified a transient population of endothelial cells (ECs) present early in HIO differentiation that are lost over time in culture. Here, we have developed a method to enhance co-differentiation and maintenance of ECs within HIOs (vHIOs). Given that ECs are known to possess organ specific gene expression, morphology and function, we used bulk RNAseq and scRNAseq to interrogate the developing human intestine, lung, and kidney in order to identify organ-enriched EC-gene signatures in these organ systems. By comparing organ-specific gene signatures along with markers validated by fluorescent in situ hybridization to HIO ECs, we find that HIO ECs grown in vitro share the highest similarity with native intestinal ECs relative to kidney and lung. Together, these data show that HIOs can co-differentiate a native EC population that are properly patterned with an intestine-specific EC transcriptional signature in vitro.

developmental biology↗

bioRxiv2019

Identification of selection and inhibition components in a go/nogo task from EEG spectra using a machine learning model

AO_SCPLOWBSTRACTC_SCPLOWPrior Go/NoGo studies have localized specific regions and EEG spectra for which traditional approaches have distinguished between Go and NoGo conditions. A more detailed characterization of the spatial distribution and timing of the synchronization of frequency bands would contribute substantially to the clarification of neural mechanisms that underlie performance of the Go/NoGo task. The present study used a machine learning approach to learn the features that distinguish between ERSPs involved in selection and inhibition in a Go/NoGo task. A neural network classifier was used to predict task conditions for each subject to characterize ERSPs associated with Go versus NoGo trials. The final model accurately identified individual task conditions at an overall rate of 92%, estimated by 5-fold cross-validation. The detailed accounting of EEG time-frequency patterns localized to brain sources (i.e., thalamus, preSMA, orbitofrontal cortex, and superior parietal cortex) provides elaboration on previous findings from fMRI and EEG studies and more information about EEG power changes in multiple frequency bands (i.e., primarily theta power increase, alpha decreases, and beta increases and decreases) within these regions underlying the selection and inhibition processes engaged in the Go and NoGo trials. This extends previous findings, providing more information about neural mechanisms underlying selection and inhibition processes engaged in the Go and NoGo trials, respectively, and may offer insight into therapeutic uses of neuromodulation in neural dysfunction.

neuroscience↗

bioRxiv2018

Organoid single-cell profiling identifies a transcriptional signature of glomerular disease

Podocyte injury is central to many forms of kidney disease, but transcriptional signatures reflecting podocyte injury and compensation mechanisms are challenging to analyze in vivo. Human kidney organoids derived from pluripotent stem cells (PSCs), a new model for disease and regeneration, present an opportunity to explore the transcriptional plasticity of podocytes. Here, transcriptional profiling of over 12,000 single cells from human PSC-derived kidney organoid cultures was used to identify robust and reproducible cell-lineage gene expression signatures shared with developing human kidneys based on trajectory analysis. Surprisingly, the gene expression signature characteristic of developing glomerular epithelial cells was also observed in glomerular tissue from a kidney disease cohort. This signature correlated with proteinuria and inverse eGFR, and was confirmed in an independent podocytopathy cohort. Three genes in particular were further identified as critical components of the glomerular disease signature. We conclude that cells in human PSC-derived kidney organoids reliably recapitulate the developmental transcriptional program of podocytes and other cell lineages in the human kidney, and that the early transcriptional profile seen in developing podocytes is reactivated in glomerular disease. Our findings demonstrate an innovative approach to identifying novel molecular programs involved in the pathogenesis of glomerulopathies.

systems biology↗

bioRxiv2018

Tissue-specific BMAL1 cistromes reveal that enhancer-enhancer interactions regulate rhythmic transcription

AbtsractThe mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of thousands of genes. Consistent with the various biological functions under clock control, rhythmic gene expression is tissue-specific despite an identical clockwork mechanism in every cell. Here we show that BMAL1 DNA binding is largely tissue-specific, due to differences in chromatin accessibility between tissues and co-binding of tissue-specific transcription factors. Our results also indicate that BMAL1 ability to drive tissue-specific rhythmic transcription not only relies on the activity of BMAL1 cis-regulatory elements (CREs), but also on the activity of neighboring CREs. Characterization of the physical interactions between BMAL1 CREs and other CREs in the mouse liver reveals that interactions are quite stable, and that BMAL1 controls rhythmic transcription by regulating the activity of other CREs. This supports that much of BMAL1 target gene transcription depends on BMAL1 capacity to rhythmically regulate a network of enhancers.

genetics↗

bioRxiv2018

Single-cell analysis of progenitor cell dynamics and lineage specification of the human fetal kidney

The mammalian kidney develops through repetitive and reciprocal interactions between the ureteric bud and the metanephric mesenchyme to give rise to the entire collecting system and the nephrons, respectively. Most of our knowledge of the developmental regulators driving this process has been gained from the study of gene expression and functional genetics in mice and other animal models. In order to shed light on human kidney development, we have used singlecell transcriptomics to characterize gene expression in different cell population, and to study individual cell dynamics and lineage trajectories during development. Single cell transcriptome analyses of 3,865 cells identified 17 clusters of specific cell types as defined by their gene expression profile, including markers of ureteric bud tip- and metanephric mesenchyme-specific progenitors, as well as their intermediate and differentiated lineages including the mature collecting ducts, the renal vesicle and comma- and s-shaped bodies, immature and mature podocytes, proximal tubules, loops of Henle and distal tubules. Other lineages identified include mesangium and cortical and medullary interstitium, endothelial and immune cells as well as hematopoietic cells. Novel markers for these cell types were revealed in the analysis as well as components of key signaling pathways driving renal development in animal models. Altogether, we provide a comprehensive and dynamic gene expression array of the human developing kidney at the single-cell level.

developmental biology↗

bioRxiv2017

Authentic Enzyme Intermediates Captured "on-the-fly" by Mix-and-Inject Serial Crystallography

Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Here, we demonstrate a general method for capturing enzyme catalysis in-action by mix-and-inject serial crystallography. Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis -lactamase with the 3rd generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation on the millisecond to second time scales including the crossover from transition state kinetics to steady-state kinetics.\n\nSynopsisAn enzymatically catalyzed reaction is initiated by diffusion based mixing of substrate and followed at runtime by time-resolved serial crystallography using a free electron laser.

biophysics↗

bioRxiv2017

Integrated growth factor signaling promotes lung epithelial progenitor cell expansion and maintenance in mice and humans

The bud tip epithelium of the branching mouse and human lung contains multipotent progenitors that are able to self-renew and give rise to all mature lung epithelial cell types. The current study aimed to understand the developmental signaling cues that regulate bud tip progenitor cells in the human fetal lung, which are present during branching morphogenesis, and to use this information to induce a bud tip progenitor-like population from human pluripotent stem cells (hPSCs) in vitro. We identified that FGF7, CHIR-99021 and RA maintained isolated human fetal lung epithelial bud tip progenitor cells in an undifferentiated state in vitro, and led to the induction of a 3-dimensional lung-like epithelium from hPSCs. 3-dimensional hPSC-derived lung tissue was initially patterned, with airway-like interior domains and bud tip-like progenitor domains at the periphery. Epithelial bud tip-like domains could be isolated, expanded and maintained as a nearly homogeneous population by serial passaging. Comparisons between human fetal lung epithelial bud tip cells and hPSC-derived bud tip-like cells were carried out using immunostaining, in situ hybridization and transcriptome-wide analysis, and revealed that in vitro derived tissue was highly similar to native lung. hPSC-derived epithelial bud tip-like structures survived in vitro for over 16 weeks, could be easily frozen and thawed and maintained multi-lineage potential. Furthermore, hPSC-derived epithelial bud tip progenitors successfully engrafted in the proximal airways of injured immunocompromised NSG mouse lungs, where they persisted for up to 6 weeks and gave rise to several lung epithelial lineages.

developmental biology↗