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Kim, S.

Publications and source records attributed to Kim, S..

At least 541 records · Page 30Linked to original sources
bioRxiv2020

Acyclovir Improves the Efficacy of Chemoradiation in Nasopharyngeal Cancer Containing the Epstein Barr Virus Genome

Nasopharyngeal carcinoma (NPC) is a malignancy endemic to East Asia and is caused by Epstein-Barr Virus (EBV)-mediated cancerous transformation of epithelial cells. The standard of care treatment for NPC involves radiation and chemotherapy. While treatment outcomes continue to improve, up to 50% of patients can be expected to recur by five years, and additional innovative treatment options are needed. We posit that a potential way to do this is by targeting the underlying cause of malignant transformation, namely EBV. One method by which EBV escapes immune surveillance is by undergoing latent phase replication, during which EBV expression of immunogenic proteins is reduced. However, chemoradiation is known to drive conversion of EBV from a latent to a lytic phase. This creates an opportunity for the targeting of EBV-infected cells utilizing anti-viral drugs. Indeed, we found that combining acyclovir with cisplatin and radiation significantly decreases the viability of the EBV-infected C666-1 cell line. Western blot quantification revealed a resultant increase of thymidine kinase (TK) and apoptosis-inducing mediators, cleaved PARP (cPARP) and phosphorylated ERK (pERK). These studies suggest that the addition of anti-viral drugs to frontline chemoradiation may improve outcomes in patients treated for EBV-related NPC and future in vivo and clinical studies are needed.

cancer biology↗
bioRxiv2020

The Polyadenosine RNA Binding Protein ZC3H14 is Required in Mice for Proper Dendritic Spine Density

ZC3H14 (Zinc finger CysCysCysHis domain-containing protein 14), an evolutionarily conserved member of a class of tandem zinc finger (CCCH) polyadenosine (polyA) RNA binding proteins, is associated with a form of heritable, nonsyndromic autosomal recessive intellectual disability. Previous studies of a loss of function mouse model, Zc3h14{Delta}ex13/{Delta}ex13, provide evidence that ZC3H14 is essential for proper brain function, specifically for working memory. To expand on these findings, we analyzed the dendritic spines of hippocampal neurons from Zc3h14{Delta}ex13/{Delta}ex13 mice. These studies reveal that loss of ZC3H14 does not affect dendritic spine density in either CA1 pyramidal neurons or dentate gyrus granule cells in the hippocampus. However, overexpression of ZC3H14 in cultured hippocampal neurons increases the overall density of spines. We next performed biochemical analyses of synaptosomes prepared from whole wild-type and Zc3h14{Delta}ex13/{Delta}ex13 mouse brains to determine if there are changes in steady state levels of postsynaptic proteins upon the loss of ZC3H14. We found that ZC3H14 is present within synaptosomes and that a crucial postsynaptic protein, CaMKII, is significantly increased in these synaptosomal fractions upon loss of ZC3H14. Together, these results demonstrate that ZC3H14 localizes to synapses, that its levels influence dendritic spine morphology, and that its loss dysregulates synaptic CaMKII levels, suggesting a potential role for ZC3H14 in synaptic function and plasticity.

neuroscience↗
bioRxiv2020

Social isolation impairs the prefrontal- nucleus accumbens circuit subserving social recognition in mice

The medial prefrontal cortex (mPFC) plays important roles in social behaviors, but it is not clear how early social experiences affect the mPFC and its subcortical circuit. We report that mice singly housed for 8 weeks immediately after weaning (SH mice) show a deficit in social recognition, even after 4 weeks of re-socialization. In SH mice, prefrontal infralimbic (IL) neurons projecting to the shell region of nucleus accumbens (NAcSh) showed decreased excitability compared to normally group housed (GH) mice. Furthermore, NAcSh-projecting IL neurons were activated when the mice encountered a familiar conspecific, which was not shown in SH mice. Chemogenetic inhibition of NAcSh-projecting IL neurons in normal mice selectively impaired social recognition without affecting social interaction, whereas activation of these neurons reversed social recognition deficit in SH mice. Therefore, mPFC IL-NAcSh projection is a novel brain circuit affected by early social experience; its activation is required for the social recognition.

neuroscience↗
bioRxiv2020

High-throughput phenotypic characterization of zebrafish CRISPR mutants of DNA repair genes

A systematic knowledge of the roles of DNA repair genes at the level of the organism has been limited due to the lack of appropriate experimental techniques. Here, we generated zebrafish loss-of-function mutants for 32 DNA repair and replication genes through multiplexed CRISPR/Cas9-mediated mutagenesis. High-throughput phenotypic characterization of our mutant collection revealed that three genes (atad5a, ddb1, pcna) are essential for proper embryonic development and hematopoiesis; seven genes (apex1, atrip, ino80, mre11a, shfm1, telo2, wrn) are required for growth and development during juvenile stage and six genes (blm, brca2, fanci, rad51, rad54l, rtel1) play critical roles in sex development. Furthermore, mutation in six genes (atad5a, brca2, polk, rad51, shfm1, xrcc1) displayed hypersensitivity to DNA damage agents. Further characterization of atad5a-/- mutants demonstrate that Atad5a is required for normal brain development and hematopoiesis. Our zebrafish mutant collection provides a unique resource for understanding of the roles of DNA repair genes at the organismal level.

developmental biology↗
bioRxiv2020

Combined analysis of the time-resolved transcriptome and proteome of the pathogenicity-activated plant pathogen Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) is a plant pathogen responsible for causing bacterial blight in rice. The immediate alterations in Xoo upon initial contact with rice are essential for pathogenesis. We studied time-resolved genome-wide gene expression in pathogenicity-activated Xoo cells at the transcriptome and proteome levels. The early response genes of Xoo include genes related to cell motility, inorganic ion transport, and effectors. The alteration of gene expression is initiated as early as few minutes after the initial interaction and changes with time. The time-resolved comparison of the transcriptome and proteome shows the differences between transcriptional and translational expression peaks in many genes, although the overall expression pattern of mRNAs and proteins is conserved. The discrepancy suggests an important role of translational regulation in Xoo at the early stages of pathogenesis. The gene expression analysis using time-resolved transcriptome and proteome provides unprecedented valuable information regarding Xoo pathogenesis.

plant biology↗
bioRxiv2020

The organization and developmental establishment ofcortical interneuron presynaptic circuits

Sensory and cognitive functions are processed in discrete cortical areas and depend upon the integration of long range cortical and subcortical inputs. PV and SST inhibitory interneurons (cINs) gate these inputs and failure to do so properly is implicated in many neurodevelopmental disorders. The logic by which these interneuron populations are integrated into cortical circuits and how these vary across sensory versus associative cortical areas is unknown. To answer this question, we began by surveying the breadth of afferents impinging upon PV and SST cINs within distinct cortical areas. We found that presynaptic inputs to both cIN populations are similar and primarily dictated by their areal location. By contrast, the timing of when they receive these afferents is cell-type specific. In sensory regions, both SST and PV cINs initially receive thalamocortical first order inputs. While by adulthood PV cINs remain heavily skewed towards first order inputs, SST cINs receive an equal balance of first and higher order thalamic afferents. Remarkably, while perturbations to sensory experience affect PV cIN thalamocortical connectivity, SST cIN connectivity is disrupted in a model of fragile X syndrome (Fmr1 loss of function) but not a model of ASD (Shank3B loss of function). Altogether, these data provide a comprehensive map of cIN afferents within different functional cortical areas and reveal the region-specific logic by which PV and SST cIN circuits are established.

neuroscience↗
bioRxiv2020

Advanced Retinal Imaging and Ocular Parameters of the Rhesus Macaque Eye

PurposeTo determine the normal ocular biometric and perform advanced retinal imaging and functional assessment of a non-human primate used commonly in scientific research, the rhesus macaque. MethodsWe performed ocular phenotyping on rhesus macaques at the California National Primate Research Center. This consisted of anterior and posterior segment eye examination by ophthalmologists, advanced retinal imaging, and functional retinal electrophysiology. ResultsFull eye exams were performed on 142 animals consisting of pupillary light reflex, tonometry, external exam and photography, anterior slit lamp examination, and posterior segment examination by indirect ophthalmoscopy. Ages of the rhesus macaques ranged from 0.7 to 29 years (mean=16.4 years, stdev=7.5 years). Anterior segment measurements such as intraocular pressure (n=142), corneal thickness (n=84), lens thickness (n=114), and axial length (n=114) were acquired. Advanced retinal imaging in the form of fundus photography (n=78), optical coherence tomography (n=60), and quantitative autofluorescence (n=44) were obtained. Electroretinography (n=75) was used to assay retinal function. Quantitative analyses of macular structure, retinal layer segmentation, and rod and cone photoreceptor electrical responses are reported. Quantitative assessments were made and variations between genders and age groups were analyzed to compare with established sex and age-related changes in human eyes. ConclusionsThe rhesus macaque has ocular structure and function very similar to that of the human eye. Age-related ocular changes between rhesus and humans are similar. In particular, macular structure and function are very similar to humans making this species particularly useful for the study of macular biology and development of therapies for inherited and age-related macular degenerations as well as cone photoreceptor disorders.

physiology↗
bioRxiv2020

Plant NLR targets P-type ATPase for executing plasma membrane depolarization leading to calcium influx and cell death

Hypersensitive response (HR) is a robust immune response mediated by plant nucleotide-binding and leucine-rich repeat receptor (NLR). However, the early molecular event linking NLR to cell death is obscure. Here we demonstrate that NLR targets plasma membrane H+-ATPases (PMA) generating electrochemical potential across the membrane. CCA309, an autoactive N-terminal domain of pepper coiled-coil NLR (CNL), associates with PMAs and its autoactivity is affected by silencing or overexpression of PMA. CCA309-induced extracellular alkalization accompanied with membrane depolarization is followed by calcium influx and cell death. CCA309 interacts with C-terminal regulatory domain of PMA and 14-3-3 negatively affects CCA309-induced cell death. Moreover, pharmacological experiments with fusicoccin, an irreversible PMA activator, confirmed that CC- and CNL-mediated cell death occurred through inhibiting PMA. We propose PMAs as the primary target of plasma membrane-associated CNL to disrupt electrochemical homeostasis leading to HR cell death.

plant biology↗
bioRxiv2020

A simplified cell-based assay to identify coronavirus 3CL protease inhibitors

We describe a mammalian cell-based assay capable of identifying coronavirus 3CL protease (3CLpro) inhibitors without requiring the use of live virus. By enabling the facile testing of compounds across a range of coronavirus 3CLpro enzymes, including the one from SARS-CoV-2, we are able to quickly identify compounds with broad or narrow spectra of activity. We further demonstrate the utility of our approach by performing a curated compound screen along with structure-activity profiling of a series of small molecules to identify compounds with antiviral activity. Throughout these studies, we observed concordance between data emerging from this assay and from live virus assays. By democratizing the testing of 3CL inhibitors to enable screening in the majority of laboratories rather than the few with extensive biosafety infrastructure, we hope to expedite the search for coronavirus 3CL protease inhibitors, to address the current epidemic and future ones that will inevitably arise.

microbiology↗
bioRxiv2020

Imaging meningeal inflammation in CNS autoimmunity identifies a therapeutic role for BTK inhibition

Leptomeningeal inflammation in multiple sclerosis is associated with worse clinical outcomes and greater cortical pathology. Despite progress in identification of this process in multiple sclerosis patients using post-contrast FLAIR imaging, early trials attempting to target meningeal inflammation have been unsuccessful. There is a lack of appropriate model systems to screen potential therapeutic agents targeting meningeal inflammation. We utilized ultra-high field (11.7 Tesla) MRI to perform post-contrast FLAIR imaging in SJL/J mice with experimental autoimmune encephalomyelitis induced using immunization with proteolipid protein peptide (PLP139-151) and complete Freunds adjuvant. Imaging was performed in both a cross-sectional and longitudinal fashion at time-points ranging from 2 to 14 weeks post-immunization. Following imaging, we euthanized animals and collected tissue for pathological evaluation, which identified dense cellular infiltrates corresponding to areas of contrast-enhancement involving the leptomeninges. These areas of meningeal inflammation contained B cells (B220+), T cells (CD3+) and myeloid cells (Mac2+). We also noted features consistent with tertiary lymphoid tissue within these areas - presence of peripheral node addressin (PNAd) positive structures, CXCL13 producing cells and FDC-M1+ follicular dendritic cells. In the cortex adjacent to areas of meningeal inflammation we identified astrocytosis, microgliosis, demyelination and evidence of axonal stress/damage. Since areas of meningeal contrast enhancement persisted over several weeks in longitudinal experiments, we utilized this model to test the effects of a therapeutic intervention on established meningeal inflammation. We randomized mice with evidence of meningeal contrast enhancement on MRI scans performed at 6 weeks post-immunization, to treatment with either vehicle or evobrutinib (a Brutons tyrosine kinase inhibitor) for a period of 4 weeks. These mice underwent serial imaging and we examined the effect of treatment on the areas of meningeal contrast enhancement and noted a significant reduction in the evobrutinib group compared to vehicle (30% reduction versus 5% increase; P = 0.003). We utilized ultra-high field MRI imaging to identify areas of meningeal inflammation and to track them over time in SJL/J mice with experimental autoimmune encephalomyelitis and then utilized this model to identify Brutons tyrosine kinase inhibition as a novel therapeutic approach to target meningeal inflammation. The results of this study provide support for future studies in multiple sclerosis patients with imaging evidence of meningeal inflammation.

neuroscience↗
bioRxiv2020

LoVIS-Seq reveals clonal dynamics of human-HSPC in humanized mice and vector integration bias

BackgroundCurrent understanding of hematopoiesis is largely derived from mouse models that are physiologically distant from humans. Humanized mice provide the most physiologically relevant small animal model to study human diseases, most notably preclinical gene-therapy studies. However, the clonal repopulation dynamics of human hematopoietic stem and progenitor cells (HSPC) in these animal models is only partially understood. Using a new clonal tracking methodology designed for small sample volumes, we aim to reveal the underlying clonal dynamics of human cell repopulation in a mouse environment. MethodsHumanized BLT (bone marrow-liver-thymus) mice were generated by transplanting lentiviral vector transduced human fetal liver HSPC (FL-HSPC) in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice implanted with a piece of human fetal thymus. We developed a methodology to track vector integration sites (VIS) in a mere 25{micro}l of mouse blood for longitudinal and quantitative clonal analysis of human HSPC repopulation in mouse environment. We explored transcriptional and epigenetic features of human HSPC for possible VIS bias. Results897 HSPC clones were longitudinally tracked in BLT mice--providing a first-ever demonstration of clonal dynamics and competitive expansion of therapeutic and control vector-modified human cell populations simultaneously repopulating in the same humanized mice. The polyclonal repopulation stabilized at 19 weeks post-transplant and the contribution of the largest clone doubled within 4 weeks. Moreover, 550 ([~]60%) clones persisted over 6 weeks and were highly shared between different organs. The normal clonal profiles confirmed the safety of our gene therapy vectors. Multi-omics analysis of human FL-HSPC revealed that 54% of vector integrations in repopulating clones occurred within {+/-}1kb of H3K36me3-enriched regions. ConclusionsHuman repopulation in mice is polyclonal and stabilizes more rapidly than that previously observed in humans. VIS preference for H3K36me3 has no apparent negative effects on HSPC repopulation. Our study provides a methodology to longitudinally track clonal repopulation in small animal models extensively used for stem cell and gene-therapy research and with lentiviral vectors designed for clinical applications. Results of this study provide a framework for understanding the clonal behavior of human HPSC repopulating in a mouse environment, critical for translating results from humanized mice models to the human settings.

molecular biology↗
bioRxiv2020

A New Paradigm of Developing Therapeutics to Infectious Diseases by Combining Insights from Nature and Engineering

Broad host-spectrum antibiotics not only kill pathogens, but also beneficial commensal bacteria of the host microbiome that play crucial roles for health. In Nature, bacteria kill other bacteria much more selectively than antibiotics do. Because there is metabolic cost involved in producing molecules to inhibit others, evolution endowed bacteria with bacteriocins to kill those who are similar enough to compete for the same niche, while leaving more distantly related bacteria, intact. The presence of such narrow host-spectrum antibacterial molecules suggests that by engineering and reprogramming what is found in nature, it may be possible to develop highly effective yet selective therapeutics to infectious diseases, either as purified drugs, or as live bacterial therapeutics. Here, I propose a new paradigm of developing highly selective therapeutics by combining insights from Nature and engineering and applied this against foodborne pathogens, one of the most common causes of bacterial infections for humans.

bioengineering↗
bioRxiv2020

Decoding Multivoxel Representations of Affective Scenes in Retinotopic Visual Cortex

The perception of opportunities and threats in complex scenes represents one of the main functions of the human visual system. In the laboratory, its neurophysiological basis is often studied by having observers view pictures varying in affective content. This body of work has consistently shown that viewing emotionally engaging, compared to neutral, pictures (1) heightens blood flow in limbic structures and frontoparietal cortex, as well as in anterior ventral and dorsal visual cortex, and (2) prompts an increase in the late positive event-related potential (LPP), a scalp-recorded and time-sensitive index of engagement within the network of aforementioned neural structures. The role of retinotopic visual cortex in this process has, however, been contentious, with competing theoretical notions predicting the presence versus absence of emotion-specific signals in retinotopic visual areas. The present study used multimodal neuroimaging and machine learning to address this question by examining the large-scale neural representations of affective pictures. Recording EEG and fMRI simultaneously while observers viewed pleasant, unpleasant, and neutral affective pictures, and applying multivariate pattern analysis to single-trial BOLD activities in retinotopic visual cortex, we identified three robust findings: First, unpleasant-versus-neutral decoding accuracy, as well as pleasant-versus-neutral decoding accuracy, were well above chance level in all retinotopic visual areas, including primary visual cortex. Second, the decoding accuracy in ventral visual cortex, but not in early visual cortex or dorsal visual cortex, was significantly correlated with LPP amplitude. Third, effective connectivity from amygdala to ventral visual cortex predicted unpleasant-versus-neutral decoding accuracy, and effective connectivity from ventral frontal cortex to ventral visual cortex predicted pleasant-versus-neutral decoding accuracy. These results suggest that affective pictures evoked valence-specific multivoxel neural representations in retinotopic visual cortex and that these multivoxel representations were influenced by reentry signals from limbic and frontal brain regions.

neuroscience↗
bioRxiv2020

Identifying genes and cell types with dynamic alternative polyadenylation in multi-cluster single-cell transcriptomics data

Alternative polyadenylation (APA) causes shortening or lengthening of the 3-untranslated region (3-UTR) of genes across multiple cell types. Bioinformatic tools have been developed to identify genes that are affected by APA (APA genes) in single-cell RNA-Seq (scRNA-Seq) data. However, they suffer from low power, and they cannot identify APA genes specific to each cell type (cell-type-specific APA) when multiple cell types are analyzed. To address these limitations, we developed scMAPA that systematically integrates two novel steps. First, scMAPA quantifies 3-UTR long and short isoforms without requiring assumptions on the read density shape of input data. Second, scMAPA estimates the significance of the APA genes for each cell type while controlling confounders. In the analyses on our novel simulation data and human peripheral blood mono cellular data, scMAPA showed enhanced power in identifying APA genes. Further, in mouse brain data, scMAPA identifies cell-type-specific APA genes, improving interpretability for the cell-type-specific function of APA. We further showed that this improved interpretability helps to understand a novel role of APA on the interaction between neurons and blood vessels, which is critical to maintaining the operational condition of brains. With high sensitivity and interpretability, scMAPA shed novel insights into the function of dynamic APA in complex tissues. Key PointsO_LIWe developed a bioinformatic tool, scMAPA, that identifies dynamic APA across multiple cell types and a novel simulation pipeline to assess performance of such tools in APA calling. C_LIO_LIIn simulation data of various scenarios from our novel simulation pipeline, scMAPA achieves sensitivity with a minimal loss of specificity. C_LIO_LIIn human peripheral blood monocellular data, scMAPA identifies APA genes accurately and robustly, finding unique associations of APA with hematological processes. C_LIO_LIscMAPA identifies APA genes specific to each cell type in mouse brain data while controlling confounders that sheds novel insights into the complex molecular processes. C_LI

bioinformatics↗
bioRxiv2020

Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction

The current COVID-19 pandemic has led to a devastating impact across the world. SARS-CoV-2 (the virus causing COVID-19) is known to use receptor-binding domain (RBD) at viral surface spike (S) protein to interact with the angiotensin-converting enzyme 2 (ACE2) receptor expressed on many human cell types. The RBD-ACE2 interaction is a crucial step to mediate the host cell entry of SARS-CoV-2. Recent studies indicate that the ACE2 interaction with the SARS-CoV-2 S protein has higher affinity than its binding with the structurally identical S protein of SARS-CoV-1, the virus causing the 2002-2004 SARS outbreak. However, the biophysical mechanism behind such binding affinity difference is unclear. This study utilizes a combined single-molecule force spectroscopy and steered molecular dynamics (SMD) simulation approach to quantify the specific interactions between CoV-2 or CoV-1 RBD and ACE2. Depending on the loading rates, the unbinding forces between CoV-2 RBD and ACE2 range from 70 to 110 pN, and are 30-50% higher than those of CoV-1 RBD and ACE2 under similar loading rates. SMD results indicate that CoV-2 RBD interacts with the N-linked glycan on Asn90 of ACE2. This interaction is mostly absent in the CoV-1 RBD-ACE2 complex. During the SMD simulations, the extra RBD-N-glycan interaction contributes to a greater force and prolonged interaction lifetime. The observation is confirmed by our experimental force spectroscopy study. After the removal of N-linked glycans on ACE2, its mechanical binding strength with CoV-2 RBD decreases to a similar level of the CoV-1 RBD-ACE2 interaction. Together, the study uncovers the mechanism behind the difference in ACE2 binding between SARS-CoV-2 and SARS-CoV-1, and could aid in the development of new strategies to block SARS-CoV-2 entry. STATEMENT OF SIGNIFICANCEThis study utilizes a combined single-molecule force spectroscopy and steered molecular dynamics simulation approach to quantify the specific interactions between SARS-CoV-2 or SARS-CoV-1 receptor-binding domain and human ACE2. The study reveals the mechanism behind the difference in ACE2 binding between SARS-CoV-2 and SARS-CoV-1, and could aid in the development of new strategies to block SARS-CoV-2 entry.

biophysics↗
bioRxiv2020

Intrinsic excitability mechanisms of neuronal ensemble formation

Neuronal ensembles are coactive groups of cortical neurons, found in spontaneous and evoked activity, that can mediate perception and behavior. To understand the mechanisms that lead to the formation of ensembles, we co-activated optogenetically and electrically layer 2/3 pyramidal neurons in brain slices from mouse visual cortex, in animals from both sexes, replicating in vitro an optogenetic protocol to generate ensembles in vivo. Using whole-cell and perforated patch-clamp pair recordings we find that, after optogenetic or electrical stimulation, coactivated neurons increase their correlation in spontaneous activity, a hallmark of ensemble formation. Coactivated neurons showed small biphasic changes in presynaptic plasticity, with an initial depression followed by a potentiation after a recovery period. Unexpectedly, optogenetic and electrical stimulation-induced significant increases in frequency and amplitude of spontaneous EPSPs, even after single-cell stimulation. In addition, we observed strong and persistent increases in neuronal excitability after stimulation, with increases in membrane resistance and reduction in spike threshold. A pharmacological agent that blocks changes in membrane resistance can revert this effect. These significant increases in excitability may partly explain the observed biphasic synaptic plasticity. We propose that cell-intrinsic changes in excitability are involved in the formation of neuronal ensembles. We propose an "iceberg" model, by which increased neuronal excitability makes subthreshold connections suprathreshold, enhancing the effect of already existing synapses, and generating a new neuronal ensemble. Significance StatementWe investigated the synaptic and cellular mechanisms underlying the formation of neuronal ensembles, i.e., spontaneously coactive groups of neurons. Using in vitro electrophysiology and optogenetic in slices of mouse neocortex we replicated a protocol that generates ensembles in vivo. After optogenetic and electrical stimulation, we observed biphasic synaptic plasticity and, unexpectedly, major increases in excitability, input resistance, and reductions in firing threshold. The increased excitability can explain the observed synaptic plasticity. Our results reveal a major role for intrinsic excitability in the establishment of neuronal ensembles.

neuroscience↗
bioRxiv2020

Endocardial/endothelial angiocrines regulate cardiomyocyte development and maturation and induce features of ventricular non-compaction

Non-compaction cardiomyopathy is a devastating genetic disease caused by insufficient consolidation of ventricular wall muscle that can result in inadequate cardiac performance. Despite being the third most common cardiomyopathy, the mechanisms underlying the disease, including the cell types involved, are poorly understood. We have previously shown that endothelial cell-specific deletion of the chromatin remodeler gene Ino80 results in defective coronary vessel development that leads to ventricular noncompaction in embryonic mouse hearts. Here, we used single-cell RNA-sequencing to characterize endothelial and endocardial defects in Ino80-deficient hearts. We observed a pathological endocardial cell population in the non-compacted hearts, and identified multiple dysregulated angiocrine factors that dramatically affected cardiomyocyte behavior. We identified Col15A1 as a coronary vessel-secreted angiocrine factor, downregulated by Ino80-deficiency, that functioned to promote cardiomyocyte proliferation. Furthermore, mutant endocardial and endothelial cells (ECs) upregulated expression of secreted factors, such as Tgfbi, Igfbp3, Isg15, and Adm, which decreased cardiomyocyte proliferation and increased maturation. These findings support a model where coronary ECs normally promote myocardial compaction through secreted factors, but that endocardial and ECs can secrete factors that contribute to non-compaction under pathological conditions.

developmental biology↗
bioRxiv2020

ClpAP proteolysis does not require rotation of the ClpA unfoldase relative to ClpP

AAA+ proteases, which perform regulated protein degradation in all kingdoms of life, consist of a hexameric AAA+ unfoldase/translocase in complex with a self-compartmentalized peptidase. Based on asymmetric features of cryo-EM structures and a sequential hand-over-hand model of substrate translocation, recent publications have proposed that the AAA+ unfoldases ClpA and ClpX must rotate with respect to their partner peptidase ClpP to allow function. Here, we test this model by covalently crosslinking ClpA to ClpP to prevent rotation. We find that crosslinked ClpAP omplexes unfold, translocate, and degrade protein substrates, albeit modestly slower han uncrosslinked enzyme controls. Rotation of ClpA with respect to ClpP therefore is ot required for ClpAP protease activity, although some flexibility in how the AAA+ ring ocks on ClpP may be necessary for optimal function.

biochemistry↗