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Elliott, D.

Publications and source records attributed to Elliott, D..

15 recordsLinked to original sources

Alpha Protein Kinase 3 Gene Therapy Restores Heart Function in Mouse and Human Models of Cardiomyopathy

Truncating variants in the Alpha Kinase 3 (ALPK3) gene have recently emerged as an important cause of genetic cardiomyopathy globally and here we demonstrate the efficacy and safety of a viral-based gene replacement therapy for ALPK3. Given the loss-of-function nature of these variants, we reasoned that a gene replacement approach would improve heart function in this patient population. We demonstrate that the delivery of full length ALPK3 via adeno-associated virus could restore contractile function in human cardiac organoids and in vivo mouse models carrying clinically relevant mutations in ALPK3. The role of disrupted proteostasis networks in multiple forms of genetic cardiomyopathy suggest that delivery this novel AAV-ALPK3 may provide functional benefit outside of cardiomyopathy induced by ALPK3. Titin truncating variants (TTNtv) are the most common cause of dilated cardiomyopathy, and interestingly also contributes to the M-Band protein quality control network coordinated by ALPK3. Notably, in human cardiac organoids carrying a TTNtv we observed that the ALPK3 gene therapy could completely restore contractile deficits. This opens the exciting prospect for indication expansion of AAV-ALPK3 into other forms of cardiomyopathy that currently have no therapeutic options.

physiology↗

Application of spatial transcriptomics across organoids: a high-resolution spatial whole-transcriptome benchmarking dataset

Stem cell-derived organoids hold promise to model tissue-specific disease. To enable this, it is crucial to assess how transcriptional signatures, cellular organisation and composition of organoids compare to in vivo counterparts. However, technologies which elucidate regional molecular identity, like spatial transcriptomics, have been challenging to apply to organoids. This study presents the first systematic profiling of multiple stem cell derived organoid models (brain, heart muscle, heart valve, kidney, lung, cartilage, and haematopoietic) with Stereo-seq, a full transcriptome, spatial transcriptomics assay using on-chip in situ RNA capture at subcellular resolution. It describes optimisation of this assay to characterise organoids, use of multiple organoid samples on a single chip, assess differences in RNA capture efficiency compared to reference tissues and its limitations. This study introduces a bespoke analysis method that partitions samples into regions and further characterises them. These findings inform future works to characterise organoids using spatial transcriptomics, providing insights in optimising RNA capture of multiple organoids across a chip and novel methods for regional analysis.

bioinformatics↗

Pharmacological Activation of NO-Sensitive Guanylyl Cyclase Ameliorates Obesity-Induced Arterial Stiffness

ObjectiveArterial stiffness, or loss of elastic compliance in large arteries, is an independent precursor of cardiovascular disease (CVD)1 and dementia2. Akin to anti-hypertensive and lipid-lowering drugs, arterial de-stiffening therapies could be beneficial at decreasing CVD risk. We previously discovered that enhanced cytoskeletal actin polymerization in vascular smooth muscle cells (VSMCs) contributes to increased arterial stiffness3. In aortas and VSMCs, we previously found that decreased NO-sensitive guanylyl cyclase (NO-GC), the NO receptor which synthesizes cGMP, caused downregulation of cGMP-dependent protein kinase I (cGKI) and of its target vasodilator-stimulated phosphoprotein (pVASPS239), leading to increased cytoskeletal actin polymerization3. In the current study, we tested whether activating NO-GC with an NO-GC activator (cinaciguat) modulates pVASPS239 and cytoskeletal actin polymerization in VSMCs, thereby preventing obesity-induced arterial stiffness. Approach & ResultsCinaciguat administration (5 mg/kg) to high fat, high sucrose diet (HFHS)-fed mice, our established model of arterial stiffness4, (1) decreased pulse wave velocity, the in vivo index of arterial stiffness, without affecting blood pressure, (2) increased aortic pVASPS239 levels, and (3) decreased the ratio of filamentous (F) to globular (G) actin, compared to vehicle administration. In cultured VSMCs, cinaciguat (10 mol/L) increased pVASPS239 levels and decreased the F/G actin ratio at baseline and after stimulation with the cytokine tumor necrosis factor (TNF), used to mimic the inflammatory milieu of HFHS aortas. These effects were abrogated in aortas and VSMCs from mice with smooth muscle-specific cGKI deletion (cGKISMKO), while being mimicked by a cell-permeable cGMP analog (8-Br-cGMP, 1 mol/L), which also decreased VSMC stiffness in vitro. ConclusionsCollectively, our data strongly support the notion that pharmacological NO-GC activation would be beneficial in decreasing obesity-associated arterial stiffness by decreasing VSMC cytoskeletal actin hyper-polymerization. If translated to humans, NO-GC activators could become a viable approach to clinically treat arterial stiffness, which remains an unmet medical need.

pharmacology and toxicology↗

Maturation of human cardiac organoids are required for disease modelling and drug discovery

Cardiac maturation is an important developmental phase culminating in profound biological and functional changes to adapt to the high demand environment after birth1,2. Maturation of human pluripotent stem cell-derived human cardiac organoids (hCO) to more closely resemble human heart tissue is critical for understanding disease pathology. Herein, we profile human heart maturation in vivo3 to identify key signalling pathways that drive maturation in hCOs4,5. Transient activation of both the 5 AMP-activated kinase (AMPK) and estrogen-related receptor (ERR) promoted hCO maturation by mimicking the increased functional demands of post-natal development. hCOs cultured under these directed maturation (DM) conditions (DM-hCOs) display robust transcriptional maturation including increased expression of mature sarcomeric and oxidative phosphorylation genes resulting in enhanced metabolic capacity. DM-hCOs have functionally mature properties such as sarcoplasmic reticulum-dependent calcium handling, accurate responses to drug treatments perturbing the excitation-coupling process and ability to detect ectopy CASQ2 and RYR2 mutants. Importantly, DM- hCOs permit modelling of complex human disease processes such as desmoplakin (DSP) cardiomyopathy, which is driven by multiple cell types. Subsequently, we deploy DM-hCOs to demonstrate that bromodomain extra-terminal inhibitor INCB054329 rescues the DSP phenotype. Together, this study demonstrates that recapitulating in vivo development promotes advanced maturation enabling disease modelling and the identification of a therapeutic strategy for DSP- cardiomyopathy.

bioengineering↗

Actin Polymerization Status Regulates Tendon Homeostasis through Myocardin-Related Transcription Factor-A

The actin cytoskeleton is a potent regulator of tenocyte homeostasis. However, the mechanisms by which actin regulates tendon homeostasis are not entirely known. This study examined the regulation of tenocyte molecule expression by actin polymerization via the globular (G-) actin-binding transcription factor, myocardin-related transcription factor-a (MRTF). We determined that decreasing the proportion of G-actin in tenocytes by treatment with TGF{beta}1 increases nuclear MRTF. These alterations in actin polymerization and MRTF localization coincided with favorable alterations to tenocyte gene expression. In contrast, latrunculin A increases the proportion of G-actin in tenocytes and reduces nuclear MRTF, causing cells to acquire a tendinosis-like phenotype. To parse out the effects of F-actin depolymerization from regulation by MRTF, we treated tenocytes with cytochalasin D. Similar to latrunculin A treatment, exposure of cells to cytochalasin D increases the proportion of G-actin in tenocytes. However, unlike latrunculin A treatment, cytochalasin D increases nuclear MRTF. Compared to latrunculin A treatment, cytochalasin D led to opposing effects on the expression of a subset of genes. The differential regulation of genes by latrunculin A and cytochalasin D suggests that actin signals through MRTF to regulate a specific subset of genes. By targeting the deactivation of MRTF through the inhibitor CCG1423, we verify that MRTF regulates Type I Collagen, Tenascin C, Scleraxis, and -smooth muscle actin in tenocytes. Actin polymerization status is a potent regulator of tenocyte homeostasis through the modulation of several downstream pathways, including MRTF. Understanding the regulation of tenocyte homeostasis by actin may lead to new therapeutic interventions against tendinopathies, such as tendinosis.

cell biology↗

The Diversified Astrocyte Developmental Programs are Modulated by Primary Ciliary Signaling

Astrocyte diversity is greatly influenced by local environmental modulation. Here, we report that the vast majority of brain astrocytes across the entire brain possess a singular primary cilium, a specialized signaling antenna localized to cell soma. Comparative single-cell transcriptomics reveals that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Independent of canonical Shh signaling, primary cilia are important regulators for astrocyte morphology and intracellular signaling balance. Dendritic spine analysis and transcriptomics reveal that perturbation of astrocytic cilia leads to disruption of neuronal development and global intercellular connectomes in the brain. Ultimately, mice with primary ciliary deficient astrocytes show behavioral deficits in sensorimotor function, sociability, learning and memory. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain.

neuroscience↗

Affinity purification-mass spectrometry and single fiber physiology/proteomics reveals mechanistic insights of C18ORF25

C18ORF25 was recently shown to be phosphorylated at S67 by AMP-activated protein kinase (AMPK) in skeletal muscle following acute exercise in humans. Phosphorylation was shown to improve ex vivo skeletal muscle contractile function in mice but our understanding of the molecular mechanisms is incomplete. Here, we profiled the interactome of C18ORF25 in mouse myotubes using affinity purification coupled to mass spectrometry. This analysis included an investigation of AMPK-dependent and S67-dependent protein:protein interactions. Several nucleocytoplasmic and contractile-associated proteins were identified, and revealed a subset of GTPases that associate with C18ORF25 in an AMPK- and S67 phosphorylation-dependent manner. We confirmed that C18ORF25 is localised to the nucleus and the contractile apparatus in skeletal muscle. Mice lacking C18Orf25 display defects in calcium handling specifically in fast-twitch muscle fibers. To investigate these mechanisms, we developed an integrated single fiber physiology and single fiber proteomic platform. The approach enabled detailed assessment of various steps in the excitation-contraction (EC) pathway including SR calcium handling and force generation followed by paired single fiber proteomic analysis. This enabled us to identify >700 protein:phenotype associations and 36 fiber-type specific differences following loss of C18Orf25. Taken together, our data provide unique insights into the function of C18ORF25 and its role in skeletal muscle physiology.

physiology↗

An anciently diverged family of RNA binding proteins maintain correct splicing of ultra-long exons through cryptic splice site repression.

We previously showed that the germ cell specific nuclear protein RBMXL2 represses cryptic splicing patterns during meiosis and is required for male fertility. RBMXL2 evolved from the X-linked RBMX gene, which is silenced during meiosis due to sex chromosome inactivation. It has been unknown whether RBMXL2 provides a direct replacement for RBMX in meiosis, or whether RBMXL2 evolved to deal with the transcriptionally permissive environment of meiosis. Here we find that RBMX primarily operates as a splicing repressor in somatic cells, and specifically regulates a distinct class of exons that exceed the median human exon size. RBMX protein-RNA interactions are enriched within ultra-long exons, particularly within genes involved in genome stability, and repress the selection of cryptic splice sites that would compromise gene function. These similarities in overall function suggested that RBMXL2 might replace the function of RBMX during meiosis. To test this prediction we carried out inducible expression of RBMXL2 and the more distantly related RBMY protein in somatic cells, finding each could rescue aberrant patterns of RNA processing caused by RBMX depletion. The C-terminal disordered domain of RBMXL2 is sufficient to rescue proper splicing control after RBMX depletion. Our data indicate that RBMX and RBMXL2 have parallel roles in somatic tissues and the germline that must have been conserved for at least 200 million years of mammalian evolution. We propose RBMX family proteins are particularly important for the splicing inclusion of some ultra-long exons with increased intrinsic susceptibility to cryptic splice site selection.

molecular biology↗

Acute repair of meniscus root tear partially restores joint displacements as measured with MRI and loading in a porcine knee

The meniscus serves important load-bearing functions and protects the underlying articular cartilage. Unfortunately, meniscus tears are common and impair the ability of the meniscus to distribute loads, greatly increasing the risk for developing osteoarthritis. Therefore, surgical repair of the meniscus is a frequently performed procedure; however, this repair does not always prevent osteoarthritis. This is hypothesized to be due to altered joint loading post injury and repair, where the functional deficit of the meniscus prevents it from performing its role of distributing forces. However, many studies of meniscus function required opening the joint, which alters kinematics. The objective of this study was to use novel MRI methods to image the intact joint under axial load and measure the acute meniscus and femur displacements in an intact joint, after a meniscus root tear, and after suture repair in the porcine knee, a frequently used in vivo model. We found that anterior root tear led to large meniscus and femur displacements under physiological axial loading, and that suture anchor repair reduced these displacements, but did not fully restore intact joint kinematics. After tear and repair, the anterior region of the meniscus moved posteriorly and medially as it was forced out of the joint space under loading, while the posterior region had small displacements as the posterior attachment acted as a hinge about which the meniscus rotated in the axial plane. This technique can be applied to evaluate the effect of knee injuries and to develop improved repair strategies to restore joint kinematics.

bioengineering↗

Destabilization of F-actin by Mechanical Stress Deprivation or Tpm3.1 Inhibition Promotes a Pathological Phenotype in Tendon Cells

The actin cytoskeleton is a central mediator between mechanical force and cellular phenotype. In tendon, it is speculated that mechanical stress deprivation regulates gene expression by filamentous (F-) actin destabilization. However, the molecular mechanisms that stabilize tenocyte F-actin networks remain unclear. Tropomyosins (Tpms) are master regulators of F-actin networks. There are over 40 mammalian Tpm isoforms, with each isoform having the unique capability to stabilize F-actin sub-populations. Thus, the specific Tpm(s) expressed by a cell defines overall F-actin organization. Here, we investigated F-actin destabilization by stress deprivation of tendon and tested the hypothesis that stress fiber-associated Tpm(s) stabilize tenocyte F-actin to regulate cellular phenotype. Stress deprivation of mouse tail tendon fascicles downregulated tenocyte genes (collagen-I, tenascin-C, scleraxis, -smooth muscle actin) and upregulated matrix metalloproteinase-3. Concomitant with mRNA modulation were increases in DNAse-I/Phallodin (G/F-actin) staining, confirming F-actin destabilization by tendon stress deprivation. To investigate the molecular regulation of F-actin stabilization, we first identified the Tpms expressed by mouse tendons. Tendon cells from different origins (tail, Achilles, plantaris) express three isoforms in common: Tpm1.6, 3.1, and 4.2. We examined the function of Tpm3.1 since we previously determined that it stabilizes F-actin stress fibers in lens epithelial cells. Tpm3.1 associated with F-actin stress fibers in native and primary tendon cells. Inhibition of Tpm3.1 depolymerized F-actin, leading to decreases in tenogenic expression, increases in chondrogenic expression, and enhancement of protease expression. These expression changes by Tpm3.1 inhibition are consistent with tendinosis progression. A further understanding of F-actin stability in musculoskeletal cells could lead to new therapeutic interventions to prevent alterations in cellular phenotype during disease progression.

cell biology↗

Prediction of DNA from context using neural networks

One way to better understand the structure in DNA is by learning to predict the sequence. Here, we train a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model is a neural network that obtains an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, we show that the neural network is significantly better than any of the alternative models by a large margin. We report on where the accuracy is obtained, observing first that the performance appears to be uniform over the chromosomes. The models perform best in repetitive sequences, as expected, although they are far from random performance in the more difficult coding sections, the proportions being ~ 70:40%. Exploring further the sources of the accuracy, Fourier transforming the predictions reveals weak but clear periodic signals. In the human genome the characteristic periods hint at connections to nucleosome positioning. To understand this we find similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before. On other large genomes similarly high accuracy is found, while lower predictive accuracy is observed on smaller genomes. Only in mouse did we see periodic signals in the same range as in human, though weaker and of different type. Interestingly, applying a model trained on the mouse genome to the human genome results in a performance far below that of the human model, except in the difficult coding regions. Despite the clear outcomes of the likelihood ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures.

bioinformatics↗

A de novo paradigm for male infertility

IntroductionDe novo mutations (DNMs) are known to play a prominent role in sporadic disorders with reduced fitness1. We hypothesize that DNMs play an important role in male infertility and explain a significant fraction of the genetic causes of this understudied disorder. To test this hypothesis, we performed trio-based exome-sequencing in a unique cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare protein altering DNMs were classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of Loss-of-Function (LoF) DNMs in LoF-intolerant genes (p-value=1.00x10-5) as well as predicted pathogenic missense DNMs in missense-intolerant genes (p-value=5.01x10-4). One DNM gene identified, RBM5, is an essential regulator of male germ cell pre-mRNA splicing2. In a follow-up study, 5 rare pathogenic missense mutations affecting this gene were observed in a cohort of 2,279 infertile patients, with no such mutations found in a cohort of 5,784 fertile men (p-value=0.009). Our results provide the first evidence for the role of DNMs in severe male infertility and point to many new candidate genes affecting fertility.

genetics↗

Hierarchical stem cell topography splits growth and homeostatic functions in the fish gill

While lower vertebrates contain adult stem cells (aSCs) that maintain homeostasis and drive unexhaustive organismal growth, mammalian aSCs display mainly the homeostatic function. Understanding aSC-driven growth is of paramount importance to promote organ regeneration and prevent tumor formation in mammals. Here we present a clonal approach to address common or dedicated populations of aSCs for homeostasis and growth. Our functional assays on medaka gills demonstrate the existence of separate homeostatic and growth aSCs, which are clonal but differ in their topology. While homeostatic aSCs are fixed, embedded in the tissue, growth aSCs locate at the expanding peripheral zone. Modifications in tissue architecture can convert the homeostatic zone into a growth zone, indicating a leading role for the physical niche defining stem cell output. We hypothesize that physical niches are main players to restrict aSCs to a homeostatic function in animals with a fixed adult size.

developmental biology↗

Multi-scale Loading and Damage Mechanisms of Rat Tail, Plantaris, and Achilles Tendons

Tendinopathy, degeneration of tendon that leads to pain and dysfunction, is common in both sports and occupational settings, but multi-scale mechanisms for tendinopathy are still unknown. We recently showed that micro-scale sliding (shear) is responsible for both load transfer and damage mechanisms in rat tail tendon; however, rat tail tendon is a specialized non-load bearing tendon, and thus the load transfer and damage mechanisms are still unknown for load-bearing tendons. The objective of this study was to investigate the load transfer and damage mechanisms of load-bearing tendons using rat plantaris and Achilles tendons. We demonstrated that the micro-scale sliding is a key component for both mechanisms in plantaris tendon, similar to tail tendon. Namely, the micro-scale sliding was correlated with applied strain, demonstrating that load was transferred via micro-scale sliding in the plantaris and tail tendons. In addition, while the micro-scale strain fully recovered, the micro-scale sliding was non-recoverable and strain-dependent, and correlated with a tissue-scale mechanical parameters. When the applied strain was normalized, the % magnitudes of non-recoverable sliding was similar between the plantaris and tail tendons. Achilles tendon demonstrated some of the mechanical responses observed in plantaris and tail tendons, yet the results were inconclusive due to its complex structure. Statement of Clinical Significance: Understanding the mechanisms responsible for the pathogenesis and progression of tendinopathy can improve prevention and rehabilitation strategies and guide therapies and design of engineered constructs.

biophysics↗

A direct glia-to-neuron natural transdifferentiation ensures nimble sensory-motor coordination of male mating behaviour

The coordinated execution of innate, stereotyped sexual behaviours, such as courtship and mating, requires sexually dimorphic sensory-motor circuits that are genetically specified during development (reviewed in [1-3]). Studies in the nematode Caenorhabditis elegans, in which the development and function of neural circuits can be interrogated with single cell resolution, have revealed two general developmental mechanisms underlying sexual dimorphism in the nervous system. The first involves the acquisition of sexually dimorphic features in sex-shared neurons during sexual maturation, which include changes in terminal gene expression, such as odorant receptors, neurotransmitters and synaptic regulators [4-10]. The second mechanism involves the generation of sex-specific neurons [11-13]. This requires sex-specific cell death [14]or neurogenesis events resulting from extensive sex differences in the cell division patterns and neurodevelopmental programmes of post-embryonic cell lineages (reviewed in [3]). Here we identify a third, novel way to generate sexual dimorphism in the nervous system. We find that during sexual maturation (L4 stage), a class of sex-shared glial cells acquires sexually dimorphic function by undergoing a direct glia-to-neuron transdifferentiation that results in the production of male-specific neurons. This plasticity is regulated cell-intrinsically by the sex-determination pathway. These previously unnoticed neurons, which we term PHDs, are putative proprioceptors that regulate male locomotion during specific steps of mating. One of these steps is a novel readjustment movement performed when intromission becomes difficult to achieve. Our results reveal sex-specific direct transdifferentiation as a novel mechanism for generating sex-specific neurons and also show the importance of proprioceptive feedback during the complex steps of mating for successful reproduction.

neuroscience↗