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Moore, D.

Publications and source records attributed to Moore, D..

At least 19 recordsLinked to original sources

Cornealia: automated collective order analysis reveals density-dependent reorganization of donor corneal endothelium

The corneal endothelium is a non-regenerative monolayer whose health determines transplant success, yet donor tissue is assessed only by single-cell metrics that ignore how the monolayer is organized collectively. A physics-based spring constant K, derived from the radial distribution function of cell positions, captures this collective order but has remained limited to semi-manual studies without physical interpretation. Here we present Cornealia, an automated pipeline for collective-order and intercellular-force analysis. In cultured endothelial cells, collective order declines with passaging and is higher under growth-factor conditions that preserve N-cadherin junctions, differences invisible to cell density and hexagonality. Across 2,177 donor cornea images from two cohorts, collective order, distinct from classical metrics, responds most to mechanical perturbation: corneas with endothelial cell density above 2,400 cells/mm^2 mostly gain order, whereas less dense ones lose it, on one curve shared by both cohorts. Reconstructed intercellular forces track these changes. This switch lies within the minimum donor densities used by eye banks, suggesting a mechanical basis for these clinical thresholds and establishing collective order as an automatable measure of endothelial quality.

bioinformatics↗

MitoSAM-dependent lipoylation controls postnatal heart development via metabolic remodeling

The neonatal heart undergoes a rapid metabolic transition from fetal glycolysis to oxidative phosphorylation, requiring coordinated metabolic remodeling. Mechanisms driving this transition remain unclear. Here, we demonstrate that sufficient mitochondrial S-adenosylmethionine (mitoSAM), imported via the solute carrier Slc25a26, is essential for this shift by sustaining the lipoylation of 2-oxoacid dehydrogenases, critical for TCA cycle activation. Proteomic and metabolomic profiling revealed that reduced mitoSAM availability impaired lipoylation, blocking TCA cycle function and restricting nucleotide synthesis, while mitochondrial gene expression and respiratory capacity remained largely intact. In vivo EdU labeling showed persistent cardiomyocyte proliferation imposing further strain on nucleotide pools. Supplementation with medium-chain triglycerides during the suckling-to-weaning transition restored metabolic function and normalized cardiac growth and morphology. Our data reveal a critical developmental window in which mitoSAM-dependent lipoylation ensures heart maturation.

biochemistry↗

Phase response curve and RNA-sequencing demonstrate spiders' sensitivity to light and pinpoint candidate light-responsive genes

Spiders can maintain a wide range of free-running periods while still being entrained to a 24-hour day. To investigate the underlying mechanism of this entrainment, we constructed the phase-response curve (PRC) for the orb weaver, Metazygia wittfeldae, by subjecting the spiders to one-hour light pulses at various times throughout the circadian day. The resulting type 0 PRC showed high amplitude (> 6 hour) phase advance and delays when the light pulse was applied during circadian time (CT) 16-18, with a break point of advances to delays at CT 17. We then investigated the genetic mechanism of the phase response to light by splitting M. wittfeldae adult females entrained to 12 hours light:12 hours dark (LD 12:12) into two groups. One group received a 1-hour light pulse 5 hours after lights off (CT17), and one group did not. We then sacrificed spiders for RNA isolations 1 and 10 hours after the light pulse. We identified numerous genes that were downregulated by the light pulse 1 hour after the pulse relative to no pulse group. Intriguingly, many of these genes had a flipped pattern of expression 9 hours later - the pulse group had higher expression than the no pulse group. This pattern is consistent with the shifted phase of locomotor activity expected after the light pulse application. We also identified clock gene homologs in M. wittfeldae that had distinct expression patterns from other arthropods.

animal behavior and cognition↗

Gut microbiota as a modulator of circadian neural development in the honey bee model.

Disruption in gut microbiota during the early postnatal period can disrupt normal neural development and result in long-term behavioral alterations1. Similar to other neural systems, the circadian clock mechanism continues to mature after birth2, yet how microbial disturbances in the early period influence the onset of circadian rhythms and the development of central clock mechanisms remains poorly understood. Here we studied whether early-life gut dysbiosis affects the ontogeny of behavioral circadian rhythms and the maturation of clock neurons using the honey bee (Apis mellifera), a model organism that shares features of postnatal development of behavioral circadian rhythm and clock system3-5 with humans6. Our findings demonstrate that antibiotic-treated and gnotobiotic-reared bees display reduced rhythmicity compared to controls. These treatments also impair the development of the circadian pacemaker, marked by fewer Pigment-Dispersing Factor (PDF)-expressing neurons. Additionally, antibiotic exposure increased the expression of the Insulin-like Growth Factor Binding Protein Acid Labile Subunit (IGFALS) in early ages, which stabilizes the IGF-1/27, a hormone important for neurodevelopmental processes42. Together, these results identify gut microbiota as a modulator of circadian development. Our work provides an understanding of how early-life microbial disruptions influence the development of circadian rhythms, providing information that may extend to other animals, including humans.

neuroscience↗

De novo heterozygous variants in EHMT2 genocopy Kleefstra syndrome via loss of G9a methyltransferase activity

EHMT1 and EHMT2 genes encode human euchromatin histone lysine methyltransferase 1 and 2 (EHMT1 alias GLP; EHMT2 alias G9a) that form heteromeric GLP/G9a complexes with essential roles in epigenetic regulation of gene expression. While EHMT1 haploinsufficiency has been established as the cause of Kleefstra syndrome 1, the pathogenesis of G9a dysfunction in human disease remains largely unknown. We identified seven de novo EHMT2 variants in patients with clinical presentation, episignatures, histone modifications and transcriptomic profiles similar to those of Kleefstra syndrome 1. In vitro studies revealed that these variants encode for structurally stable G9a proteins that are catalytically incompetent due to aberrant interactions either with histone H3 tail or with S-adenosylmethionine. Heterozygous mice carrying a patient-derived variant exhibited growth retardation, facial/skull dysmorphia and aberrant behavior. Here we report pathogenic EHMT2 variants that likely exert dominant-negative effect on GLP/G9a complexes and thus genocopy the EHMT1 haploinsufficiency via a distinct molecular mechanism, defining an autosomal dominant EHMT2-related Kleefstra syndrome.

genetics↗

Nutrient-Sensing Nuclear Receptor PPARα Controls Liver Proteostasis

Peroxisome proliferator-activated receptor alpha (PPAR) is a nuclear receptor that orchestrates metabolic adaptation to fasting by regulating hepatic lipid and glucose metabolism. While these functions are well established, its role in protein homeostasis, another energy-intensive process, has remained unclear. Here, we performed multi-omics analyses in wild-type and PPAR knockout mice treated with the PPAR agonist fenofibrate to define its broader role in proteostasis. Interestingly, chronic PPAR activation suppressed hepatic secretory pathways, reducing secretome gene expression and circulating serum proteins, and downregulated genes involved in endoplasmic reticulum (ER) translocation, glycosylation, folding, and trafficking. Concurrently, PPAR activation enhanced proteasome activity, which was associated with selective induction of proteasome 26S subunit non-ATPase (PSMD) family members. In addition, hepatic protein synthesis was strongly attenuated. This was associated with an increase in the inhibitory phosphorylation of the eukaryotic translation initiation factor 2 (eIF2), that in turn was linked to disrupted iron homeostasis. Together, these findings identify PPAR as a regulator of proteostasis, suppressing protein synthesis and secretion while promoting protein degradation pathways. Beyond its canonical role in lipid and glucose metabolism, we conclude that PPAR exerts an additional energy-conserving function by coordinating proteostasis, expanding our understanding of its systemic metabolic role.

physiology↗

Integrated histopathologic modeling of detailed tumor subtypes and actionable biomarkers

Accurate cancer subtyping with accompanying molecular characterization is critical for precision oncology. While machine learning approaches have been applied to both digital pathology and cancer genomics, previous work has been limited in sample size and has typically aggregated granular cancer subtypes into coarse groupings, likely obfuscating informative molecular and prognostic associations and phenotypic variation of more detailed tumor subtypes. Accordingly, we collated 378,123 hematoxylin and eosin (H&E)-stained whole-slide images (WSIs) with matched targeted DNA clinical sequencing results and OncoTree detailed cancer subtypes from a real-world cohort of 71,142 patients. Using this scaled, granular dataset and a cancer subtype knowledge graph, we developed Mosaic: a family of calibrated machine learning models using H&E WSI embeddings to classify tumors and identify molecular phenotypes across 163 detailed subtypes. The cancer subtyping module (Aeon) achieved an area under the receiver operating characteristic curve (AUROC) of 0.992 overall, with 161/163 subtypes reaching an AUROC [≥] 0.90 and improved performance over a state-of-the-art genomics-based classifier. The genomic inference module (Paladin) achieved an AUROC [≥] 0.80 for 167 pairs of detailed subtypes and genomic targets. We further used the learned histopathologic representations to i) identify key associations of the histopathologic embeddings with clinical biomarkers; ii) identify unsupervised sub-clusters of tumors with genomic determinants of tumor phenotype; iii) specify granular diagnoses for cancers of unknown primary, evaluated by genomic associations and expected clinical outcome distributions; iv) annotate functional significance for variants of uncertain significance (VUS); and v) identify cases that mimic the phenotypic effect of known DNA variants on H&E in the absence of detectable DNA alterations. Taken together, this work advances our understanding of phenotypic variation of granular tumor subtypes, their relevance to enhanced diagnostics, and their potential utility in risk stratification with multimodal machine learning in cancer.

cancer biology↗

A structure-guided antibody detects SOD1 oligomers in diverse ALS genotypes.

Antibodies offer versatility as diagnostic and therapeutic tools to target specific protein epitopes. However, the transient nature of intermediate protein conformations, such as that of amyloid oligomers, poses a challenge for antibody development. We use a structure-guided approach to generate a monoclonal antibody against oligomers of Superoxide Dismutase 1 (SOD1). Mutations in SOD1 are linked to a subset of familial Amyotrophic Lateral Sclerosis (fALS), a fatal neurodegenerative disease. Based on the corkscrew-like features of non-native SOD1 oligomers previously determined, we generate an antibody specific to SOD1 oligomers. We show that the antibody, CSAb detects SOD1 oligomers, not fibrils or native SOD1, and alleviates the cytotoxic effects of SOD1 oligomers in a cell culture model of primary motor neurons. Immunohistochemical analyses of human ALS subjects show CSAb reactivity in both neuronal and non-neuronal cells. Finally, we provide evidence that CSAb reactive SOD1 oligomers are present in non-SOD1 linked fALS and sporadic ALS subjects. Together, our study provides a new probe against SOD1 oligomers and suggests that cytotoxic SOD1 oligomers are prevalent in diverse ALS genotypes.

neuroscience↗

The KRAB-Zinc Finger protein ZKSCAN3 represses enhancers via embedded retrotransposons

Gene cis-regulatory sequences are increasingly recognised as containing "domesticated" transposable elements that impact their function. The KRAB Zinc Finger Protein (KZFP) family of transcription factors is typically associated with transposable element silencing through establishment of heterochromatin. Here, using acute protein depletion in embryonic stem cells, we reveal that the KZFP ZKSCAN3 represses enhancer activity through targeting enhancer-embedded retrotransposons and that ZKSCAN3-mediated repression does not rely on the induction of heterochromatin. ZKSCAN3, which exhibits strong genetic association with the neurodevelopmental disorder schizophrenia, operates during neural differentiation and is necessary for proper cell specification and expression of genes that regulate axon guidance, neuronal motility and pathfinding. These findings define ZKSCAN3 as an enhancer regulator and uncover a heterochromatin-independent KZFP. Additionally, they exemplify how a KZFP epigenetically regulates enhancers in a native setting and highlight how transposable elements and their KZFP binders have shaped gene expression networks.

molecular biology↗

The mitochondrial methylation potential gates mitoribosome assembly

S-adenosylmethionine (SAM) is crucial for cellular processes, primarily serving as the principal methyl group donor of the cell and playing a key role in gene regulation and translation on the ribosome. Inside mitochondria, SAM-dependent methylations occur at several steps of gene expression, but their role and significance remain unclear. Using direct long-read RNA sequencing on mouse tissue and mouse embryonic fibroblasts, we demonstrate that the mitochondrial ribosomal gene cluster is not efficiently processed without mitochondrial SAM. This results in the accumulation of unprocessed ribosomal RNA precursors. Protein profiling of ribosome fractions revealed that these precursors are associated with processing and ribosome assembly factors, indicating stalling at an early stage. Structural analysis of the mitochondrial ribosome by cryogenic electron microscopy revealed that mitochondrial SAM is required during peptidyl transferase centre formation and mitochondrial ribosome assembly. Our data thus identify a critical role for methylation at two steps during mitochondrial gene expression.

molecular biology↗

Immunization with Plant-based Vaccine Expressing Toxoplasma gondii SAG1 Fused to Plant HSP90 Elicits Protective Immune Response in Lambs

Toxoplasma gondii is a protozoan parasite causing toxoplasmosis, a principal concern for public health and livestock industries. Effective vaccination strategies are crucial for controlling toxoplasmosis, particularly in the lamb, which are significant reservoirs of T. gondii. In addition, ovine toxoplasmosis also causes economic losses due to abortions and reproductive complications. In this study, we evaluated two immunization strategies to elucidate the immune protective potential of SAG1 fused to the plant Hsp90 adjuvant against experimental toxoplasmosis in lambs. We performed an oral administration of AtHsp81.2-SAG1HC-infiltrated fresh leaves homogenate (Plant Vaccine) and a subcutaneous administration of recombinant NbHsp90.3-SAG1HC produced in Escherichia coli (Recombinant Vaccine). Our results showed that only the Recombinant Vaccine significantly increased anti-rSAG1 total IgG values. In addition, only lambs immunized with the Plant Vaccine showed a significant increase in IFN-{gamma} serum levels after the experimental infection (evaluated 8 days post-challenge). On the other hand, we also observed a statistically significant decrease in histopathological lesions (injury score) in challenged vaccinated lambs compared to challenged but not vaccinated animals (vehicle and control groups). Finally, to evaluate T. gondii infection, we choose the chimera rGra4-Gra7 as an acute phase protein marker. All lambs from the control and vehicle groups showed higher rates of serological reactivity than lambs from the vaccinated groups, concurrently with increased severity of lesions. These results suggest that both the plant-based and recombinant vaccines are promising candidates for controlling T. gondii infection in lambs, with potential benefits for enhancing public health and animal welfare.

molecular biology↗

Assessment of the Genetic Diversity of Atlantic Bottlenose Dolphin (Tursiops truncatus) Strandings in the Mississippi Sound (USA)

The common bottlenose dolphin (Tursiops truncatus) is a key marine mammal species in the northern Gulf of Mexico, playing an essential role as a top predator. This study focuses on the genetic diversity and population structure of bottlenose dolphins stranded in the Mississippi Sound from 2010 to 2021. A total of 511 tissue samples (muscle, liver, lung, kidney, and brain) were collected from stranded dolphins, and mitochondrial DNA (mtDNA) was extracted for analysis. Using high-throughput sequencing methods, 417 samples were successfully amplified and sequenced, producing 386 complete mitogenomes. Genetic diversity metrics, such as nucleotide and haplotype diversity, were calculated, and population structure was inferred for both mitochondrial control region (mtCR) and whole mitogenome sequences. Using the whole mitogenome, the study identified four genetically distinct populations within the Mississippi Sound, demonstrating regional variation in dolphin populations. Notably, some individuals likely originated from populations outside the sampled area. The use of whole mitogenomes allowed for improved resolution of genetic diversity and population differentiation compared to previous studies using partial mtDNA sequences. These findings provide critical insights into the genetic structure of bottlenose dolphins in the region and highlight the value of using stranded animals for population genetic studies.

genomics↗

ATG9 vesicles are a subtype of intracellular nanovesicle

Cells are filled with thousands of vesicles, which mediate protein transport and ensure homeostasis of the endomembrane system. Distinguishing these vesicles functionally and molecularly represents a major challenge. Intracellular nanovesicles (INVs) are a large class of transport vesicles that likely comprises of multiple subtypes. Here, we define the INV proteome and find that it is molecularly heterogeneous, and enriched for transmembrane cargo molecules including integrins, transporters, and ATG9A, a lipid scramblase associated with autophagy. ATG9A is known to reside in ATG9 vesicles: small vesicles that contribute to autophagosome formation. Using in-cell vesicle capture assays we found that ATG9A, as well as other ATG9 vesicle cargos, were in INVs. Quantitative analysis showed that virtually all ATG9 vesicles are INVs, but that only [~]20% of INVs are ATG9 vesicles, suggesting that ATG9 vesicles are in fact a subtype of INV, which we term ATG9A-flavor INVs. Finally, we show that perturbing ATG9A-flavor INVs impaired the autophagy response induced by starvation.

cell biology↗

Frontal Cortex Hyperactivation and Gamma Desynchrony in Fragile X Syndrome: Correlates of Auditory Hypersensitivity

Fragile X syndrome (FXS) is an X-linked disorder that often leads to intellectual disability, anxiety, and sensory hypersensitivity. While sound sensitivity (hyperacusis) is a distressing symptom in FXS, its neural basis is not well understood. It is postulated that hyperacusis may stem from temporal lobe hyperexcitability or dysregulation in top-down modulation. Studying the neural mechanisms underlying sound sensitivity in FXS using scalp electroencephalography (EEG) is challenging because the temporal and frontal regions have overlapping neural projections that are difficult to differentiate. To overcome this challenge, we conducted EEG source analysis on a group of 36 individuals with FXS and 39 matched healthy controls. Our goal was to characterize the spatial and temporal properties of the response to an auditory chirp stimulus. Our results showed that males with FXS exhibit excessive activation in the frontal cortex in response to the stimulus onset, which may reflect changes in top-down modulation of auditory processing. Additionally, during the chirp stimulus, individuals with FXS demonstrated a reduction in typical gamma phase synchrony, along with an increase in asynchronous gamma power, across multiple regions, most strongly in temporal cortex. Consistent with these findings, we observed a decrease in the signal-to-noise ratio, estimated by the ratio of synchronous to asynchronous gamma activity, in individuals with FXS. Furthermore, this ratio was highly correlated with performance in an auditory attention task. Compared to controls, males with FXS demonstrated elevated bidirectional frontotemporal information flow at chirp onset. The evidence indicates that both temporal lobe hyperexcitability and disruptions in top-down regulation play a role in auditory sensitivity disturbances in FXS. These findings have the potential to guide the development of therapeutic targets and back-translation strategies.

neuroscience↗

Single-nucleus and spatial landscape of the sub-ventricular zone in human glioblastoma

The sub-ventricular zone (SVZ) is the most well-characterized neurogenic area in the mammalian brain. We previously showed that in 65% of patients with glioblastoma (GBM), the SVZ is a reservoir of cancer stem-like cells that contribute to treatment resistance and emergence of recurrence. Here, we built a single-nucleus RNA-sequencing-based microenvironment landscape of the tumor mass (T_Mass) and the SVZ (T_SVZ) of 15 GBM patients and 2 histologically normal SVZ (N_SVZ) samples as controls. We identified a mesenchymal signature in the T_SVZ of GBM patients: tumor cells from the T_SVZ relied on the ZEB1 regulatory network, whereas tumor cells in the T_Mass relied on the TEAD1 regulatory network. Moreover, the T_SVZ microenvironment was predominantly characterized by tumor-supportive microglia, which spatially co-exist and establish heterotypic interactions with tumor cells. Lastly, differential gene expression analyses, predictions of ligand-receptor and incoming/outgoing interactions, and functional assays revealed that the IL-1{beta}/IL-1RAcP and Wnt-5a/Frizzled-3 pathways are therapeutic targets in the T_SVZ microenvironment. Our data provide insights into the biology of the SVZ in GBM patients and identify specific targets of this microenvironment.

cancer biology↗

Focused Ultrasound Blood-Brain Barrier Opening Arrests the Growth and Formation of Cerebral Cavernous Malformations

BACKGROUNDCerebral cavernous malformations (CCM) are vascular lesions within the central nervous system, consisting of dilated and hemorrhage-prone capillaries. CCMs can cause debilitating neurological symptoms, and surgical excision or stereotactic radiosurgery are the only current treatment options. Meanwhile, transient blood-brain barrier opening (BBBO) with focused ultrasound (FUS) and microbubbles is now understood to exert potentially beneficial bioeffects, such as stimulation of neurogenesis and clearance of amyloid-{beta}. Here, we tested whether FUS BBBO could be deployed therapeutically to control CCM formation and progression in a clinically-representative murine model. METHODSCCMs were induced in mice by postnatal, endothelial-specific Krit1 ablation. FUS was applied for BBBO with fixed peak-negative pressures (PNPs; 0.2-0.6 MPa) or passive cavitation detection-modulated PNPs. Magnetic resonance imaging (MRI) was used to target FUS treatments, evaluate safety, and measure longitudinal changes in CCM growth after BBBO. RESULTSFUS BBBO elicited gadolinium accumulation primarily at the perilesional boundaries of CCMs, rather than lesion cores. Passive cavitation detection and gadolinium contrast enhancement were comparable in CCM and wild-type mice, indicating that Krit1 ablation does not confer differential sensitivity to FUS BBBO. Acutely, CCMs exposed to FUS BBBO remained structurally stable, with no signs of hemorrhage. Longitudinal MRI revealed that FUS BBBO halted the growth of 94% of CCMs treated in the study. At 1 month, FUS BBBO-treated lesions lost, on average, 9% of their pre-sonication volume. In contrast, non-sonicated control lesions grew to 670% of their initial volume. Lesion control with FUS BBBO was accompanied by a marked reduction in the area and mesenchymal appearance of Krit mutant endothelium. Strikingly, in mice receiving multiple BBBO treatments with fixed PNPs, de novo CCM formation was significantly reduced by 81%. Mock treatment plans on MRIs of patients with surgically inaccessible lesions revealed their lesions are amenable to FUS BBBO with current clinical technology. CONCLUSIONSOur results establish FUS BBBO as a novel, non-invasive modality that can safely arrest murine CCM growth and prevent their de novo formation. As an incisionless, MR image-guided therapy with the ability to target eloquent brain locations, FUS BBBO offers an unparalleled potential to revolutionize the therapeutic experience and enhance the accessibility of treatments for CCM patients.

bioengineering↗

Deciphering the diversity and sequence of extracellular matrix and cellular spatial patterns in lung adenocarcinoma using topological data analysis

Extracellular matrix (ECM) organization influences cancer development and progression. It modulates the invasion of cancer cells and can hinder the access of immune cells to cancer cells. Effective quantification of ECM architecture and its relationship to the position of different cell types is, therefore, important when investigating the role of ECM in cancer development. Using topological data analysis (TDA), particularly persistent homology and Dowker persistent homology, we develop a novel analysis pipeline for quantifying ECM architecture, spatial patterns of cell positions, and the spatial relationships between distinct constituents of the tumour microenvironment. We apply the pipeline to 44 surgical specimens of lung adenocarcinoma from the lung TRACERx study stained with picrosirius red and haematoxylin. We show that persistent homology effectively encodes the architectural features of the tumour microenvironment. Inference using pseudo-time analysis and spatial mapping to centimetre scale tissues suggests a gradual and progressive route of change in ECM architecture, with two different end states. Dowker persistent homology enables the analysis of spatial relationship between any pair of constituents of the tumour microenvironment, such as ECM, cancer cells, and leukocytes. We use Dowker persistent homology to quantify the spatial segregation of cancer and immune cells over different length scales. A combined analysis of both topological and non-topological features of the tumour microenvironment indicates that progressive changes in the ECM are linked to increased immune exclusion and reduced oxidative metabolism.

cancer biology↗

Vitamin B2 enables peroxisome proliferator-activated receptor α regulation of fasting glucose availability

Flavin adenine dinucleotide (FAD) interacts with flavoproteins to mediate oxidation-reduction reactions required for cellular energy demands. Not surprisingly, mutations that alter FAD binding to flavoproteins cause rare inborn errors of metabolism (IEMs) that disrupt liver function and render fasting intolerance, hepatic steatosis, and lipodystrophy. In our study, depleting FAD pools in mice with a vitamin B2 deficient diet (B2D) caused phenotypes associated with organic acidemias and other IEMs, including reduced body weight, hypoglycemia, and fatty liver disease. Integrated discovery approaches revealed B2D tempered fasting activation of target genes for the nuclear receptor PPAR, including those required for gluconeogenesis. Treatment with the PPAR agonist fenofibrate activated the integrated stress response and refilled amino acid substrates to rescue fasting glucose availability and overcome B2D phenotypes. Overall, these findings reveal PPAR governs metabolic responses to FAD availability and nominate its pharmacologic activation as strategies for organic acidemias.

physiology↗