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Cell Press Sneak Peek is a public Mendeley user group that presents a preview of primary research papers under review in Cell Press journals.

Sneak Peek makes papers discoverable earlier in the publication process so authors can surface their research quickly and readers can build on their work.

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Cell Reports added 12 hours ago

PI3K- and PTEN-governed PIP2 and PIP3 equilibrium regulates the activation and function of B cells through Dock2 controlled growth of antigen receptor microclusters

The growth of B cell receptor (BCR) microclusters upon antigen stimulation is one of the most important events in B cell activation, however the underlying molecular mechanism unknown. Here, we systematically addressed this question through a combination of molecular imaging, genetic ablation, pharmacological inhibitor and mice model approaches. We showed that the earliest BCR signaling molecules, Lyn, Syk and PLCγ2 are required for B cells to initiate the growth of BCR microclusters. PI3K-mediated PIP3 production but not Akt and PDK1 activation was required for the sustained growth of the BCR microclusters. The PI3K counterpart signaling molecule, PTEN, potently inhibited the growth of the BCR microclusters, which was dependent on its membrane binding activities and on the lipid phosphatase but not protein phosphatase activity. Mechanistically, we showed that PIP3-dependent recruitment and activation of a unique guanine nucleotide exchange factor, Dock2, was required for the sustained growth of the BCR microclusters through the remodeling of the F-actin cytoskeleton. As a consequence, the formation of the antigen-induced B cell immunological synapse (IS) in Dock2 deficient B cells was drastically impaired. Moreover, Dock2 deficient B cells exhibited decreased Ca2+ influx. Physiologically, we found that mice with reduced expression of PTEN in B cells showed enhanced antibody responses and a spontaneous lupus-like autoimmune phenotype. Clinically, we showed that primary B cells from lupus patients exhibited more prominent BCR and PI3K microclusters than B cells from healthy controls. Thus, these results demonstrated the importance of PI3K- and PTEN-governed PIP2 and PIP3 equilibrium in regulating the dynamic growth of BCR microclusters during the initiation of B cell activation.

Status: Under Review

Neuron added a day ago

Compressed timeline of recent experience in monkey lPFC

Cognitive theories suggest that working memory maintains not only the identity of recently-presented stimuli but also a sense of the elapsed time since the stimuli presentation. Previous studies of the neural underpinnings of working memory have focused on sustained firing, which can account for maintenance of the stimulus identity, but not for representation of the elapsed time. We analyzed single-unit recordings from the macaque lateral prefrontal cortex (lPFC) during performance of a delayed-match-to-category task. The sample stimulus triggered a consistent sequence of neurons, each neuron in the sequence firing during a circumscribed period of time. The sequences initiated by different sample stimuli were distinct but overlapping, with the degree of overlap reflecting the visual similarity of the stimuli that caused the sequences. These sequences of neurons encoded both stimulus identity and the elapsed time. The temporal code became less precise as the sample stimulus receded into the past. These findings suggest that working memory is maintained as a compressed timeline, consistent with longstanding cognitive theories of human memory.

Status: Under Review

Cell added 2 days ago

Loss of Ataxin-1 Elevates BACE1 Expression and Impairs Axonal Targeting in the Cerebrum

Expansion of CAG trinucleotide repeats in the Ataxin-1 gene (ATXN1) causes spinocerebellar ataxia type 1 (SCA1), a neurodegenerative disease that impairs coordinated movement and cognitive functions. ATXN1 is associated with genetic risk for Alzheimer's disease (AD). Here, we show loss of Ataxin-1 potentiates AD pathogenesis. Specifically, knockout of Atxn1 in mice led to increased expression of β-secretase (BACE1) and elevated BACE1-mediated cleavage of the amyloid precursor protein (APP), selectively in AD-vulnerable brain regions. Ataxin-1 depletion exacerbated Aβ plaque deposition and gliosis in AD mice, and impaired hippocampal neurogenesis and axonal targeting. The SCA1-linked CAG repeat number was normal in AD patients. However, in SCA1 mice, aggregation of mutant Ataxin-1 led to BACE1 up-regulation and axon guidance defects in the hippocampal CA2 region. Together, these findings indicate that loss of Ataxin-1 potentiates Aβ pathology, and BACE1 elevation may represent a shared pathogenic mechanism underlying cognitive deficits in SCA1 and AD.

Status: Under Review

Neuron added 2 days ago

Homeostatic plasticity in the hippocampus facilitates memory extinction

Correlated activity in the hippocampus drives synaptic plasticity that is necessary for the recruitment of neuronal ensembles underlying fear memory. Sustained neural activity on the other hand can trigger homeostatic adaptations. However, whether homeostatic plasticity affects memory function remains unknown. Here, we induce cell autonomous homeostatic plasticity in CA1 pyramidal neurons and granule cells. High frequency spike trains applied for 10 min decreased the number of excitatory spine synapses and increased the number of inhibitory shaft synapses. This activity stopped dendritic spine formation via L-Type voltage dependent calcium channel activity and protein synthesis. Applied selectively to the ensemble of granule cells encoding a contextual fear memory, the spike trains impaired memory recall and facilitated extinction. Our results indicate that homeostatic plasticity triggered by neuronal firing alters the balance between excitation and inhibition to favor memory extinction.

Status: Under Review

Current Biology added 5 days ago

Intermittent stimulation of the Nucleus Basalis of Meynert improves working memory in adult monkeys.

Dysfunction in the brain's cholinergic systems results in working memory and executive function impairments. The source of acetylcholine for the neocortex is the Nucleus Basalis of Meynert. We tested whether electrical activation of this nucleus would improve executive function in young adult monkeys. Continuous stimulation led to consistent performance impairments. In contrast, intermittent stimulation led to supranormal working memory performance. Optimal performance was achieved with delivery of 200 microsecond biphasic pulses at a frequency of 60 pulses per second, for 20 seconds every minute. Effects onset and offset within three minutes. Pharmacological experiments suggested both intermittent and continuous stimulation effects depended on cholinergic activation. Donepezil, a cholinesterase inhibitor, improved performance to supranormal levels in animals already impaired by continuous electrical stimulation. The same treatment did not impact performance while animals received intermittent stimulation. Administration of either nicotinic or muscarinic acetylcholine receptor antagonists prevented intermittent stimulation from altering performance. In the months after stimulation testing began, animal performance, measured in sessions without stimulation, improved. Over these months, the working memory delay at which animals achieved 80% correct performance increased three to five-fold. Our results show that cholinergic activation by deep brain stimulation enhances working memory performance and is a candidate treatment for losses in executive function in aging and Alzheimer's Disease.

Status: Under Review

Cell Metabolism added 5 days ago

Islet-derived eATP fuels autoreactive CD8+ cells and facilitates the onset of type 1 diabetes

Extracellular-ATP (eATP) activates T cells by engaging the P2X7R receptor. We discovered that 2 loss-of-function P2X7R mutations are protective toward type 1 diabetes (T1D) and we thus hypothesize that eATP/P2X7R signaling may be involved in an early step of T1D onset. We initially observed that in newly diagnosed T1D individuals, P2X7R is upregulated on CD8+ effector T cells as compared to controls. eATP is highly released by human/murine islets in vitro in high-glucose/inflammatory conditions and eATP upregulates in vitro P2X7R on CD8+ cells. P2X7R blockade with oATP reduces CD8+ cell-mediated autoimmune response in vitro and delays diabetes onset in NOD mice. CD8+ autoreactive T cell activation appeared highly dependent from eATP/P2X7R-mediated priming and our novel generated sP2X7R recombinant protein reduces CD8+ cell-related autoimmune response. eATP/P2X7R signaling facilitates the onset of autoimmune diabetes by fueling autoreactive CD8+ cells and is a novel targeted therapeutic for T1D.

Status: Under Review

Cell Reports added 6 days ago

Extensive homeostatic T cell phenotypic variation within the Collaborative Cross

The Collaborative Cross (CC) is a panel of reproducible recombinant inbred mouse strains with high levels of standing genetic variation, thereby affording unprecedented opportunity to perform experiments in a small animal model containing controlled genetic diversity while allowing for genetic replicates. Here, we advance the utility of this unique mouse resource for immunology research, as it allows for both examination and genetic dissection of mechanisms behind adaptive immune states in mice with distinct and defined genetic makeups. This approach is founded on quantitative trait locus mapping: identifying genetically variant genome regions associated with phenotypic variance in traits-of-interest. Furthermore, the CC can be utilized for mouse model development; distinct strains have unique immunophenotypes and immune properties, making them suitable for research on particular diseases and infections. Here, we describe variation in cellular immune phenotypes across F1 crosses of CC strains, and reveal novel quantitative trait loci responsible for several immune phenotypes.

Status: Under Review

Neuron added 6 days ago

Enhanced AMPA receptor trafficking mediates the anorexigenic effect of endogenous glucagon like peptide-1 in the paraventricular hypothalamus

Glucagon Like Peptide 1 (GLP-1) positive neurons in the hindbrain Nucleus Tractus Solitarius (NTS) send robust projections to the paraventricular nucleus of the hypothalamus (PVN), which is involved in the regulation of food intake. However, it is unclear whether this pathway is sufficient and necessary to control feeding behavior, or how the GLP-1 neurons affect synaptic function to modulate food intake. Here, we found that specific stimulation of GLP-1 afferent fibers within the PVN is sufficient to suppress food intake independent of glutamate release. GLP-1 receptor (GLP-1R) activation augments excitatory synaptic strength in PVN corticotropin-releasing hormone (CRH) neurons. Moreover, a protein kinase A (PKA) dependent signaling cascade is initiated by GLP-1R activation, which results in the phosphorylation of serine S845 of GluA1 AMPA receptors and subsequently promotes GluA1 trafficking to the plasma membrane. Finally, we show that postnatal depletion of GLP-1R in the PVN increases food intake and causes obesity. This study provides a comprehensive multi-level (circuit-, synaptic-, and molecular-) explanation of how food intake behavior and body weight are regulated by endogenous central GLP-1.

Status: Under Review

Cell Reports added 8 days ago

Phosphorylation of iRhom2 is essential for stimulated proteolytic shedding by the metalloprotease ADAM17/TACE

Cell surface metalloproteases coordinate signaling during development, tissue homeostasis and disease. TACE (TNFa Converting Enzyme), is the metalloprotease responsible for proteolytic release, ('shedding'), of membrane-tethered signaling molecules including the cytokine TNF, and activating ligands of the EGFR. A key step in TACE biogenesis involves its interaction with iRhom2, controlling TACE trafficking from the ER to the trans-Golgi network. Another important, but mechanistically unclear, feature of TACE biology is its ability to be rapidly stimulated on the cell surface, by numerous agents. Here we report a novel role for cell surface iRhom2 in TACE stimulation. Stimuli that provoke TACE shedding trigger iRhom2 phosphorylation within its cytoplasmic tail, dependent on MAP kinases. Blocking iRhom2 phosphorylation does not affect TACE trafficking, but impairs the shedding of TACE substrates, through defective proteolytic activity. Our data suggest that shedding stimuli utilize an 'inside out' signaling mechanism, transducing cytoplasmic signals through iRhom2, engaging TACE sheddase activity.

Status: Under Review

Cell Host & Microbe added 11 days ago

Three dimensional cartography of microbiome and metabolome data onto radiological images of the human lung

Our understanding of spatial variation of the chemical and microbial make-up of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge we developed a workflow, including the adaptation of a software, to enable the cartography of metabolomics and microbiome data onto a three dimensional (3D) organ reconstruction built off radiological images. Our methodology enabled for the first time visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, medications, and regiospecific metabolism of medications. Consequently, metabolomics data can now be understood in the context of microbial distributions in the lung. Our tool, which allows visualization of omics data on an organ in 3D and the browsable maps of the first 3D microbiome/metabolome reconstruction on a radiological image of a human lung are an interactive resource for the scientific community.

Status: Under Review

Cell Host & Microbe added 11 days ago

BACTEROIDES FRAGILIS TOXIN COORDINATES A PRO-CARCINOGENIC INFLAMMATORY CASCADE VIA TARGETING OF COLONIC EPITHELIAL CELLS

Pro-carcinogenic bacteria have the potential to initiate and/or promote human colon cancer. However, the mechanism(s) by which a bacterium may trigger carcinogenesis remains unclear. Herein, we show Bacteroides fragilis toxin (BFT) secretion by the human pathobiont enterotoxigenic Bacteroides fragilis (ETBF) triggers in MinApc+/- mice a ETBF pro-carcinogenic inflammatory cascade requiring IL-17R, NF-κB, and Stat3 signaling in colonic epithelial cells (CEC). This signaling promotes the chemokine-dependent recruitment of pro-tumoral myeloid cells. Although necessary, Stat3 activation in CEC upon ETBF colonization is not sufficient to trigger colon tumorigenesis. Notably, IL-17-dependent NF-κB activation in CECs induces a proximal to distal mucosal gradient of C-X-C chemokines, including CXCL1 that mediates CXCR2-expressing polymorphonuclear immature myeloid cell recruitment with parallel onset of ETBF tumorigenesis in the distal colon, explaining the restricted localization of ETBF tumorigenesis. Inhibitors of pathway drivers linking specific microbial mediators to early colon tumorigenesis could disrupt a myeloid/epithelial pro-tumoral loop.

Status: Under Review

Current Biology added 12 days ago

Hof1 and Chs4 interact via F-BAR domain and Sel1-like repeats to control extracellular matrix deposition during cytokinesis in budding yeast

Localized extracellular matrix (ECM) remodeling, which mainly involves synthesis and breakdown of specific polysaccharides, is important for cytokinesis and cell separation in most, if not all, organisms [1-11]. This remodeling event is thought to stabilize the cleavage furrow and maintain cell shape. The remodeling requires exocytic delivery to and endocytic removal from the division site of synthetic and hydrolytic enzymes [12-20] that is spatiotemporally coordinated with a cytoskeletal structure pertaining to a kingdom of life, for example, the FtsZ ring in bacteria [21, 22], the phragmoplast in plants [23, 24], and the actomyosin ring (AMR) in fungi and animals [25-27]. While the cytoskeletal structures have been analyzed extensively in different systems, the ECM remodeling and its interplay with the cytoskeletal partner remains poorly understood. In the budding yeast Saccharomyces cerevisiae, the ECM remodeling refers to the collective activities of chitin synthase-II (CSII, Chs2)-mediated primary septum (PS) formation that closely follows AMR constriction, glucan synthase (Fks1 and Fks2) and chitin synthase-III (CSIII, the catalytic subunit Chs3 and its activator Chs4)-mediated secondary septum (SS) formation at both sides of the PS near or after the end of AMR constriction, and, finally, glucanase and endochitinase-mediated degradation of the PS and some SS, leading to cell separation [27, 28]. Surprisingly, both Chs2 and Chs3 are delivered to the division site at the onset of cytokinesis [14, 29, 30]. What keeps CSIII inactive until SS formation remains unknown. Here, we show that Hof1 [31-33], via its F-BAR domain [34], competes with Chs3 for binding to the Sel1-like repeats (SLR) of Chs4 and inhibits Chs3-mediated chitin synthesis during cytokinesis. In addition, Hof1 is required for the rapid accumulation as well as efficient endocytic removal of Chs4 at the division site. Thus, this study uncovers a dual mechanism by which Hof1 controls timely activation of Chs3 during cytokinesis, and defines a novel interaction and function between the conserved F-BAR domain and SLR that are otherwise known for their abilities to bind membrane lipids [35-37] and scaffold protein complex formation [38].

Status: Under Review

Cell Reports added 16 days ago

Local nucleation of microtubule bundles through tubulin concentration into a condensed tau phase

Non-centrosomal microtubule bundles play important roles in cellular organization and function. Although many diverse proteins are known that can bundle microtubules, biochemical mechanisms by which cells could locally control the nucleation and formation of microtubule bundles are understudied. Here, we demonstrate that concentration of tubulin into a condensed, liquid-like compartment composed of the unstructured neuronal protein tau is sufficient to nucleate microtubule bundles. We show that under conditions of macro-molecular crowding, tau forms liquid drops. Tubulin partitions into these drops, efficiently increasing tubulin concentration and driving the nucleation of microtubules. These growing microtubules form bundles enclosed in a liquid sheath of tau. Our data suggest that condensed tau compartments could promote the formation of microtubule bundles in neurons by acting as non-centrosomal microtubule nucleation centers and that liquid-like tau encapsulation could provide both stability and plasticity to long axonal microtubule bundles.

Status: Review Completed

Cell Systems added 18 days ago

C. elegans exhibits coordinated oscillation in gene expression during development

The advent of automated cell lineaging and the ability to track gene expression at single-cell resolution in vivo in C. elegans has yielded a dramatically more complete view into developmental processes. We present a novel meta-analysis of the EPIC single-cell-resolution gene expression dataset of Bao, Murray, Waterston et al., and show that a linear combination of the expression levels of the developmental genes in that dataset is strongly correlated with the wall-clock developmental age of the organism during early development, irrespective of the cell division rate of different cell lineages. We uncover a pattern of collective sinusoidal oscillation in gene expression, with multiple dominant sinusoidal frequencies, pointing to the existence of a global coordinated mechanism governing the timing of gene expression during development. We furthermore present a new method derived from Fisher's Discriminant Analysis that can be used to produce sinusoidal oscillations of any frequency and phase using just a linear weighting of the expression patterns of the genes in this dataset, strengthening the view that oscillatory timing mechanisms play an important role in development. The Fisher's Discriminant Analysis method also constitutes a generally useful tool for identifying the differential gene expression patterns that most strongly separate two distinct phenotypic or developmental traits.

Status: Review Completed

Current Biology added 18 days ago

The phospho-caveolin-1 scaffolding domain dampens force fluctuations in focal adhesions to drive cancer cell migration

Caveolin-1 (Cav1), a major Src kinase substrate phosphorylated on tyrosine-14 (Y14), contains the highly-conserved membrane-proximal caveolin scaffolding domain (CSD; amino acids 82-101). Here we show, using CSD mutants (F92A/V94A) and membrane-permeable CSD competing peptides, that Src kinase-dependent pY14Cav1 regulation of focal adhesion protein stabilization, focal adhesion tension and cancer cell migration is CSD-dependent. Quantitative proteomic analysis of Cav1-GST (1-101 amino acids) pulldowns showed 6-fold increased binding of vinculin and, to a lesser extent, α-actinin, talin and filamin, to phosphomimetic Cav1Y14D relative to non-phosphorylatable Cav1Y14F. Consistently, pY14Cav1 enhanced CSD-dependent vinculin tension in focal adhesions, dampening force fluctuation and synchronously stabilizing cellular focal adhesions in a high-tension mode, paralleling effects of actin stabilization. By promoting focal adhesion traction, functional interaction between Cav1 Y14 phosphorylation and the CSD shifts the molecular clutch linking adhesions and the actin cytoskeleton to high gear, and thereby drives cancer cell migration.

Status: Under Review

Cell Systems added 18 days ago

ROSE: a deep learning based framework for predicting ribosome stalling

We present a deep learning based framework, called ROSE, to accurately predict ribosome stalling events in translation elongation from coding sequences based on high-throughput ribosome profiling data. Our validation results demonstrate the superior performance of ROSE over conventional prediction models. ROSE provides an effective index to estimate the likelihood of translational pausing at codon resolution and understand diverse putative regulatory factors of ribosome stalling. Also, the ribosome stalling landscape computed by ROSE can recover the functional interplay between ribosome stalling and cotranslational events in protein biogenesis, including protein targeting by the signal recognition particle (SRP) and protein secondary structure formation.

Status: Review Completed

Cell added 18 days ago

Sensitive, non-destructive detection and analysis of neoantigen-specific T cell populations from tumors and blood

Tumor neoantigens are fragments of mutated proteins that contain the mutation, and can be presented by major histocompatibility complex molecules on tumor cells, where they are surveyed by T cells. The rapid and sensitive identification of neoantigen-specific T cell populations from tumor tissues or blood has proven challenging. A microchip platform for the non-destructive identification of neoantigen-specific CD8+ T cells is described. The method utilizes a library of neoantigen/MHC tetramers linked to a magnetic nanoparticle via a DNA barcode. The neoantigen-specificity of the T cells is determined by decoding the barcode through sequential fluorescent microscopy reads. The captured T cells may be further characterized for function, or via matching the neoantigen-specificity with the T cell receptor gene. Tumor infiltrating lymphocytes and non-expanded peripheral blood mononuclear cells collected from melanoma patients at various time points across an anti-PD1 therapy regimen are shown to contain overlapping neoantigen-specific T cell populations.

Status: Under Review

Cell Reports added 21 days ago

High‐Throughput Drug Screening identifies Pazopanib and Clofilium tosylate as promising treatments For malignant rhabdoid tumors

The poor prognosis of rhabdoid tumors (RT) justifies the search for new therapies. By a high‐throughput drug screening and subsequent in vitro confirmation of selected drugs, we identified as good SMARCB1‐dependent therapeutic candidates, broad inhibitors of tyrosine kinase receptors (RTK) such as pazopanib, and the potassium channel inhibitor clofilium tosylate (CfT). Their combination significantly induced RT apoptotic cell death in vitro. A human phospho‐kinase antibody array revealed PDGFRα/β and FGFR2 as pazopanib targets, while these genes were the most highly expressed RTK in our primary tumor data set. Of note, combined genetic inhibition of at least two RTK was only partially able to recapitulate the effect of pazopanib, emphasizing the requirement of broad inhibition. We then showed that pazopanib treatment reduced tumor growth in vivo while its combination with CfT could at least recapitulate the efficiency of conventional chemotherapy. Altogether, these results may influence future clinical trials for RT.

Status: Under Review

Cell Stem Cell added 21 days ago

Latrophilin 2 specifies cardiac lineage commitment and heart development

Identifying lineage‐specific markers is pivotal for understanding developmental processes and developing cell therapies. We report a new cardiac‐specific cell surface marker, latrophilin 2 (LPHN2), expressed specifically by cardiac progenitor cells (CPCs) and cardiomyocytes (CMCs) during mouse and human pluripotent stem cells (PSCs) differentiation in vitro and exclusively in the heart during mouse embryonic development. Lphn2 knockout in mice is embryonically lethal owing to severe heart, but not vascular, defects. PSCderived LPHN2+ cells differentiated into CMCs and regenerated the myocardium when transplanted into the infarcted heart, unlike LPHN2‐ cells. Transplanted LPHN2+ cells improved left‐ventricle systolic function and reduced infarct size. Molecular pathway analysis showed that CDK5 was a key downstream molecule of LPHN2 that interacted in parallel with Src and induced P38MAPK phosphorylation, subsequently activating cardiac‐related gene transcription. These findings provide a valuable tool for isolating cardiomyogenic progenitors and CMCs from PSCs and shed light on heart development and regeneration.

Status: Under Review

Cell Reports added 21 days ago

Histone deacetylase AtSRT1 coordinates metabolic flux and stress-response in Arabidopsis

How plant metabolic flux impacts gene expression to optimize plant growth and response to stress remains largely unknown. Here we show that Arabidopsis NAD+-dependent histone deacetylase AtSRT1 negatively regulates plant tolerance to stress and glycolysis, but stimulates mitochondrial respiration rate. AtSRT1 interacts with Arabidopsis cMyc-Binding Protein-1 (AtMBP-1), a transcriptional repressor produced by alternative translation of the cytosolic glycolytic enolase gene LOS2/ENO2. AtSRT1 is associated with chromatin of AtMBP-1 targets LOS2/ENO2 and STZ/ZAT10 (both are master stress regulatory genes), reduces H3K9ac from the loci, and represses transcription of the genes. Over-expression of both AtSRT1 and AtMBP-1 had synergistic effects on glycolytic gene expression and enzyme activity and mitochondrial respiration. In addition, AtSRT1 could remove lysine acetylation from AtMBP-1 protein and thereby enhance its stability in vivo. The results indicate that AtSRT1 has a function to coordinate primary metabolism and stress-response by both epigenetic regulation and modulating transcriptional activity of AtMBP-1.

Status: Review Completed

Cell Reports added 21 days ago

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during trophectoderm and inner cell mass specification

The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and an outer functional epithelium called trophectoderm (TE). The lineage specific transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4) by inhibiting OCT4 from promoting its own expression. However its downstream network in the developing early embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify components of the CDX2-regulated network in vivo. To identify genes likely to be regulated by CDX2 directly, we performed CDX2 ChIP-Seq on trophoblast stem (TS) cells, derived from the TE. In addition, we examined the dynamics of gene expression changes using an inducible CDX2 embryonic stem (ES) cell system, so that we could predict which CDX2-bound genes are activated or repressed by CDX2 binding. By integrating these data with observations of chromatin modifications, we were able to identify novel regulatory elements that are likely to repress gene expression in a lineage-specific manner. Interestingly, we found CDX2 binding sites within regulatory elements of key pluripotent genes such as Pou5f1 and Nanog, pointing to the existence of a novel mechanism by which CDX2 maintains repression of OCT4 in trophoblast. Our study proposes a general mechanism in regulating lineage segregation during mammalian development.

Status: Review Completed

Cell Chemical Biology added 22 days ago

EDHS-206, an exquisitely selective inhibitor of TAK1, targets pro survival TNFα-dependent signaling, inducing apoptosis in rheumatoid arthritis and breast cancer models.

Tumor necrosis factor alpha (TNFα) administration has shown limited therapeutic utility in cancer and inflammatory disorders due to dose-limiting side effects. We propose an alternative approach to targeting TNFα-mediated diseases by selectively inducing the TNFα apoptotic response in TNFα-rich microenvironments. TAK1 acts as a key mediator between survival and cell death in TNFα signaling. We report a novel potent and exquisitely selective TAK1 inhibitor (EDHS-206, IC50 9.5nM) that induces apoptosis in a TNFα-dependent manner in models of metastatic breast cancer and rheumatoid arthritis. Co-crystallization studies demonstrated that EDHS-206 inhibits the kinase in a DFG-in conformation. Kinetic analysis of EDHS-206-TAK1 interactions revealed a substrate-like intermolecular autophosphorylation mechanism for TAK1 activation, during which EDHS-206 delays the proceedings of the rate-limiting step. EDHS-206 represents an attractive starting point for the development of a novel generation of inhibitors that greatly sensitize cells to TNFα-induced cell death, potentially broadening the therapeutic efficacy of TNFα.

Status: Under Review

Structure added 23 days ago

Structural and functional characterization of a cross-reactive dengue virus neutralizing antibody that recognizes a cryptic epitope

Understanding the molecular basis of the neutralizing antibody response to dengue virus (DENV) is an essential component in the design and development of effective vaccines and immunotherapeutics. We previously identified a number of cross-reactive neutralizing antibodies isolated from mice immunized with domain III (DIII) of the dengue envelope (E) protein. ¬¬Here we present the structure of one such antibody, 3E31, in complex with DIII derived from DENV-4. Co-crystallization revealed 3E31 recognises a conserved, cryptic epitope on DIII that is not available in any of the known conformations of E on the dengue virion. This finding was further validated by functional assays, which revealed that virion binding and neutralization is temperature-sensitive. We observed that 3E31 inhibits E-mediated membrane fusion, suggesting that the antibody is able to neutralize virus through binding an as yet uncharacterized intermediate conformation of DENV E and sterically block trimer formation and the fusion process. Finally, we assessed the capacity of 3E31 for antibody-dependent enhancement (ADE) of infection, and showed that, unlike cross-reactive fusion peptide-specific antibodies, 3E31 does not promote infectious virus entry at sub-neutralizing concentrations. Our results highlight the 3E31 epitope on the E protein DIII as a promising target for immunotherapeutics or vaccine design.

Status: Under Review

Neuron added 25 days ago

Memory trace superimposition impairs recall in a mouse model of AD

Learning and memory processes depend on the hippocampus and are impaired in Alzheimer's disease (AD). Active neuronal ensembles form an engram by encoding information during learning. Their reactivation is required for memory recall. However, it remains unresolved whether the engram in CA1 principal neurons is impaired under AD-like conditions. We used two-photon in vivo imaging to visualize the expression of the immediate early gene c-fos within CA1 neurons during contextual fear conditioning and retrieval. Surprisingly, we identified engrams in wild-type mice and in the mouse model of AD indicating intact memory formation. However, under AD-like conditions engrams were superimposed by a high number of newly recruited fosGFP+ neurons during memory recall. This superimposition resembled the network configuration of wild-type mice exposed to a novel context. Artificial superimposition of the memory trace during recall in wild-type mice was sufficient to induce memory impairment. Thus, we propose superimposition of the CA1 memory trace as a mechanism for memory impairment in a mouse model of AD.

Status: Review Completed

Cell Reports added 25 days ago

Suppression of NF-κB activation in basal keratinocytes via cell autonomous and non-autonomous functions of microRNA-223

MicroRNA-223, a principally myeloid-specific anti-inflammatory microRNA, is dysregulated in numerous inflammatory conditions. Here we report that miR-223 deficient zebrafish displayed augmented neutrophilic inflammation, which was due primarily to elevated activation of the canonical NF-κB pathway. Cul1a/b, Traf6 and Tab1 were identified as direct targets of miR-223. Unexpectedly, the NF-κB over-activation was restricted to the basal epithelial cells, a squamous layer between the basal membrane and the apical epithelium. MiR-223 was detected in both apical and basal epithelium besides phagocytes. Not only phagocytes, but also epithelial cells were involved in miR-223 mediated regulation of neutrophil wound response and NF-κB activation. In addition, miR-223 was expressed in human bronchial epithelial cells and directly down-regulated NF-κB signaling components in human. Together, our data demonstrated a direct connection of miR-223 and the canonical NF-κB pathway, providing a mechanistically understanding of the multifaceted role of miR-223 and highlighted the previously overlooked relevance of epithelial cells.

Status: Under Review

Cell Host & Microbe added a month ago

Collaboration between two distinct Rab small GTPase trafficking circuits to mediate bacterial clearance from the bladder epithelium

Rab small GTPases are central organizers of numerous intracellular events, including immune defense against infections. Here, we describe collaboration between two distinct Rab protein-orchestrated trafficking circuits in bladder epithelial cells (BECs) in abolishing intracellular Uropathogenic E.coli (UPEC) infections. We found that both RAB11a and RAB27b and their associated trafficking circuitry were simultaneously involved in clearing intracellular UPEC from BECs. While RAB11a recruited its effector, Rab11FIP3 and a downstream motor protein Dynein, RAB27b mobilized its effectors, MyRIP and MyosinVIIa to mediate bacterial expulsion. We further observed that this collaboration is coordinated by the deposition of exocyst complex on the cytosolic surface of bacteria containing vesicles (BCVs), an event triggered by Toll-like Receptor (TLR) 4. Both RAB11a and RAB27b were found to be specifically recruited by the exorcist components SEC6/SEC15. These observations reveal the capacity of the cell autonomous defense system to mobilize and coalesce multiple subcellular trafficking circuitry to clear infections.

Status: Under Review

Cell added a month ago

Chemical metagenomics of an anti-HIV compound from uncultivated symbionts

Microbial symbionts in humans, animals, and plants are unparalleled sources of compounds for drug discovery. However, methods are needed to access natural biodiversity and make it amenable to pharmaceutical and biotechnological development. Here, we employ a novel approach marrying traditional natural products chemistry with modern metagenomics and synthetic biology in Escherichia coli to discover, synthesize, and analogue divamides, anti-HIV molecules from rare coral reef animals. We demonstrate that divamides are produced by Prochloron symbiotic bacteria, which have eluded cultivation for >40 years. This represents a new paradigm of direct compound discovery from a true symbiotic relationship. We show that the divamides arise from a diversity-generating biosynthetic pathway, which was exploited to generate derivatives for mechanism of action studies. The synthesis of closely related, yet functionally distinct compounds by a single biosynthetic pathway provides the first direct evidence supporting the "speculative metabolism" hypothesis of chemical diversity.

Status: Under Review

Cell added a month ago

The eukaryotic CO2-concentrating organelle is liquid-like and exhibits dynamic reorganization

Approximately 30-40% of global CO2 fixation occurs inside a poorly understood non-membrane-bound organelle called the pyrenoid, which is found in the chloroplasts of most eukaryotic algae. The pyrenoid matrix, which is densely packed with the CO2-fixing enzyme Rubisco, is thought to be crystalline. Here, we show that the pyrenoid matrix of the unicellular green alga Chlamydomonas reinhardtii is not crystalline, but behaves as a liquid that dissolves and condenses during cell division. Furthermore, we show that the pyrenoid is inherited both by fission and de novo assembly. A simple model inspired by this system predicts the existence of a "magic number" effect that influences phase separation in liquid-like organelles. This view of the pyrenoid matrix as a phase-separated compartment provides a new paradigm for understanding its structure, biogenesis, and regulation. More broadly, our findings expand our understanding of the fundamental principles that govern the architecture and inheritance of liquid-like organelles.

Status: Review Completed

Neuron added a month ago

Decoding the Influence of Anticipatory States on Visual Perception in the Presence of Temporal Distractors

While it has long been recognised that anticipatory states amplify early EEG responses to visual targets in humans, it remains unclear how such modulations relate to the actual content of the neural representation. Using multivariate orientation decoding of high temporal-resolution EEG recordings, we demonstrate that anticipation also increases the amount of stimulus-identity information contained in these early brain responses. Furthermore, this approach enabled us to characterize the influence of temporally adjacent distractors on target identity decoding, revealing that anticipation did not just attenuate distractor interference on target representations but, instead, delayed it. Enhanced target decoding and distractor resilience were further predicted by the attenuation of posterior 8-14 Hz alpha oscillations. The findings offer several novel insights into how anticipatory states prioritise relevant sensory input in time, and they highlight the potential of non-invasive multivariate electrophysiology to track cognitive influences on perception in tasks with rapidly changing displays.

Status: Under Review

Cell Host & Microbe added a month ago

Deciphering the origin and evolution of hepatitis B viruses

Hepatitis B viruses constitute the family Hepadnaviridae, enveloped viruses with reverse-transcribed DNA genomes. An outstanding feature is their streamlined genome organization with extensive gene overlap. Remarkably, the ~1,100 bp long open reading frame (ORF) coding for the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of hepatitis B viruses including genome replication via protein-primed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction revealed that both virus families separated more than 400 million years ago before the rise of tetrapods. We show that hepatitis B viruses are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo leading to a major transition in viral life-style, followed by co-evolution with their hosts over geologic eras.

Status: Under Review

Cell Reports added a month ago

Positive regulation of interleukin-1 beta bioactivity by physiological ROS-mediated Cysteine S-glutathionylation

Reactive oxygen species (ROS)-induced Cysteine S-glutathionylation is an important posttranslational modification (PTM) that controls a wide range of intracellular protein activities. However, whether physiological ROS can modulate the function of extracellular components via S-glutathionylation remains elusive. Here using a screening approach, we identified ROS-mediated cysteine S-glutathionylation on several extracellular cytokines. Glutathionylation positively regulated IL-1β bioactivity via the highly conserved Cys-188 residue by preventing its ROS-induced irreversible oxidation, including sulfinic acid and sulfonic acid formation, and the subsequent deactivation ex vivo and in an in vivo system of irradiation-induced bone marrow (BM) injury. Glutaredoxin 1 (Grx1), an enzyme that catalyzes deglutathionylation, was present and active in the extracellular space in serum and the BM, physiologically regulating IL-1β glutathionylation and bioactivity. Collectively, we identify cysteine S-glutathionylation as a novel cytokine regulatory mechanism that could be a therapeutic target in the treatment of various infectious and inflammatory diseases.

Status: Review Completed

Cell Reports added a month ago

The Tgf-β/Bmp co-receptor Endoglin is a key component of the molecular oscillator that regulates the hair follicle cycle

The hair follicle is a biological oscillator that sequentially alternates phases of growth, regression and rest. The cyclic activity of this oscillator is driven by a stem cell population regulated by nurse cells and located in the hair follilcle bulge region. As a whole, this morpho-functional structure constitutes a suitable model to study the dynamics of the stem cell niches that actually maintain homeostatic and regeneration processes during development and in adult tissues. In the hair follicle, the activation of the stem cell niche and subsequent entry into the growing phase is mainly regulated by Wnt/β-catenin signalling, while regression and resting phases are mainly regulated by Tgf-β/Bmp/Smad activity. A major question still unresolved is the nature of the molecular switch that dictates the transition between both signalling pathways during the hair follicle growth cycle. Here we have focused on the role of Endoglin (Eng), a key co-receptor for members of the Tgf-β/Bmp family of growth factors. Using a haploinsufficient mouse model we have demonstrated that Eng is required for the stimulation of the hair follicle stem cell niche and to maintain a correct follicle cycling pattern. We further report that β-catenin binds to the Eng promoter depending on Bmp signalling. Moreover, β-catenin interacts with Smad4 in a Bmp/Eng dependent context and both proteins act synergistically to activate Eng promoter transcription. These observations point to the existence of a growth/rest switching mechanism in the hair follicle that is based on an Eng-dependent feedback crosstalk between Wnt/β-catenin and Bmp/Smad signals.

Status: Review Completed

Cell Reports added a month ago

Preventing HIV infection by binding LEDGF with an intracellular antibody that mimics HIV integrase

Preventing the protein-protein interaction of the cellular chromatin binding protein LEDGF and HIV integrase is an important strategy for alternative anti-viral treatment for AIDS. While potent small molecules capable of performing this function have been difficult to develop, intracellular antibody fragments can readily be designed to perform with high affinity binding in vivo. We have isolated a single VH domain that binds to LEDGF and blocks the binding of HIV integrase to LEDGF. The crystal structure of the LEDGF-VH complex reveals a remarkably similar region of the binding for the single domain antibody fragment and HIV integrase on LEDGF as a mimic of integrase. In cell assays, the intracellular domain antibody inhibits virus capsid p24 protein production after HIV virus infection into CD4-expressing target T cells. Therefore, blocking the HIV interaction surface of cellular LEDGF with the potent antibody fragment macromolecule is a way to prevent HIV spread in infected patients. This antibody fragment is available for intracellular vaccination approaches in combating HIV-based disease by inhibiting retroviral incorporation into the genome of infected cells in HIV-positive patients.

Status: Review Completed

Cell Systems added a month ago

Joker de Bruijn: sequence libraries to cover all k-mers using joker characters

Sequence libraries that cover all k-mers enable universal and unbiased measurements of binding to both oligonucleotides and peptides. For these measurements, it is desirable to search the largest possible library of k-mers, as this increases the information content of any returned motif and the ability to predict function in vivo. However, while the number of k-mers required grows exponentially in k, space on all experimental platforms is limited. The optimal solution makes use of a de Bruijn sequence, which covers all k-mers in the most compact manner but still requires the explicit occurrence of all k-mers within the sequence. Here, we introduce a novel advance to shrink k-mer library sizes further by using joker characters, which represent all characters in the alphabet simultaneously. In this work, we consider the practical problem of generating a minimum-length sequence that covers each k-mer at least p times with the caveat that at most one or two joker characters occur in each k-mer, thereby limiting the potential degeneracy that joker characters could introduce. We present the first algorithmic solution to this problem, JokerCAKE (Joker Covering All K-mErs). By running our algorithm on a range of parameters and alphabets, we show that JokerCAKE produces sequences that are very close to the theoretical lower bound. Moreover, through comparison with data from hundreds of DNA-protein binding experiments and direct comparison between experimental results obtained for both standard de Bruijn k-mer sequences and joker de Bruijn k-mer sequences, we establish that accurate binding scores can be inferred for high-affinity k-mers using JokerCAKE libraries.

Status: Review Completed

Cell Host & Microbe added a month ago

Evolutionary analysis provides insight into the origin and adaptation of HCV

Using a selection‐informed evolutionary model we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago and that the oldest genotypes are endemic to Asia. Equine hepacivirus, HCV most closely related virus, originated around 1100 CE. These time estimates are not consistent with the possibility that HCV derives from a cross‐species transmission from horses and suggest a single zoonotic event with subsequent spread and diversification in human populations. Herein evolutionary analysis also support a role for hepaciviruses as drivers of CD81 evolution in Chiroptera and Glires, implicating these mammals as the HCV reservoirs. We describe a number of biologically‐important sites in the major HCV genotypes that have been positively selected and indicate that drug resistance‐associated variants are significantly enriched at positively selected sites. These results shed light on the origin of HCV and provide a catalog of candidate genetic modulators of HCV phenotypic diversity.

Status: Review Completed

Cell Reports added a month ago

Identification of a second conserved polybasic domain in septin 9 involved in microtubule-dependent Golgi assembly

Septins belong to a family of GTP-binding proteins that bind to phosphoinositides (PIs) by a polybasic domain (PB1). We reported that the deletion of PB1 in septin 9 markedly reduced, its binding to PIs and its assembly. Here, using homology modelling, we reveal the presence of another polybasic domain (PB2) conserved among the different human septins. PB1 and PB2 from two distinct molecules form an extended basic cluster in the NC interface of the filament. Importantly binding of septin 9 to PIs through PB1 and PB2 is required for recruitment of microtubules to Golgi stacks and their assembly. Knockdown of septin 9 recapitulates these effects and affects nucleus/centrosomal positioning and protein secretion. Thus septin 9 could be considered as a crucial regulator of events require for membrane trafficking and organelle morphology.

Status: Review Completed

Cell Reports added a month ago

Association with Uncertainty Monitoring, Not Value Comparison in Ventromedial Prefrontal Cortex during Value-Based Decisions

Value comparison is the key process of value-based decision-making. Dorsal anterior cingulate cortex (dACC) and ventromedial prefrontal cortex (vmPFC) have been suggested to be critically involved in value comparison, as their activities are correlated with the absolute value difference (AVD) of options. However, value-based decision-making is usually accompanied by uncertainty with the decisions; consequently, the metacognitive process of uncertainty monitoring is automatically elicited. We found that the vmPFC activity associated with AVD might be caused by negative regulation from dACC and its association network, which were indeed correlated with decision uncertainty (DUC), involved in uncertainty monitoring. Instead, we found that intra-parietal sulcus (IPS) and medial orbitofrontal cortex (mOFC) were associated with signed option value difference (OVD), suggesting involvement in value comparison. Thus, our findings suggest that the activities of dACC and vmPFC, as well as their association networks, correlating with AVD, may be irrelevant to value comparison, but associated with decision uncertainty monitoring.

Status: Review Completed

Cell added a month ago

DNA polymerase β mediates robust base lesion repair in mammalian mitochondria

Mitochondrial genome integrity is fundamental to mammalian cell viability. Yet, mitochondrial DNA is constantly under attack from oxygen radicals released during ATP production. DNA repair is important in removing oxidatively-induced base lesions in mitochondrial DNA, but the presence of a robust base excision repair system has remained unclear. Therefore, we addressed the questions of the presence and repair role of DNA polymerase β (pol β) in mitochondria of mammalian cells. Pol β was localized to mitochondria by electron microscopic immunogold staining and biochemical experiments. Extracts from mitochondria exhibited a strong base excision repair activity that was dependent on pol β. Mitochondria in pol β-deficient mouse fibroblasts exhibited altered morphology by electron microscopy and were deficient in energy metabolism. These results indicate mammalian mitochondria have a robust base lesion repair system.

Status: Review Completed

Cell Reports added a month ago

Redefining the Ca2+-Apoptosis Link Reveals a Widespread Vulnerability of Cancer Cells

Intracellular Ca2+ dynamics determine cell fate and when mitochondrial Ca2+ homeostasis is compromised, different pathological conditions can occur, depending on the cell type involved. It this context, mitochondrial Ca2+ overload was regarded as detrimental and this paradigm has provided tangible opportunities for rational therapies. Here, we demonstrated that sustained mitochondrial Ca2+ overload is not effective in inducing cell-death against all odds. This stimulus requires concomitant inhibition of autophagy to counteract its prosurvival action, thereby allowing mitochondrial depolarization and release of Cytochrome C. Using xenograft mouse models, cell line-based studies, and ex-vivo tumor models from clinical specimens, we showed that only a dual-targeting strategy based on mitochondrial Ca2+ overload and autophagy inhibition induced by drugs in clinical evaluation, synergically sensitizes many cancer cell types to various chemotherapies. Collectively, these findings challenge a crucial paradigm in cell-death and open up new avenues for treatment of patient with cancer or diseases associated with mitochondrial Ca2+-defects.

Status: Review Completed

Cell Reports added a month ago

Mer‐Mediated Efferocytosis Tempers Arthritis by Preventing Secondary Necrotic Neutrophil Spilling in the Knee Joint

Rheumatoid arthritis is characterized by an inflammatory response in synovial joints, showing a predominant influx of neutrophils. A key mediator of the resolution of inflammation and the uptake of apoptotic cells, or efferocytosis, is the receptor tyrosine kinase Mer. Overexpression of the Mer ligand Pros1 resulted in reduced production of inflammatory mediators by macrophages and synovial cells of arthritic mice, diminished joint pathology, reduced numbers of cleaved Caspase 3-positive apoptotic cells and secondary necrotic neutrophils. Conversely, inhibiting Mer-mediated efferocytosis by either antibodies or Mertk gene ablation resulted in aggravation of arthritis, as evidenced by increased inflammation and tissue destruction. Additionally, Mer-inhibited mice had increased numbers of apoptotic cells in their joints, and higher serum levels of IL-16C, a cytokine released by secondary necrotic neutrophils. Together, these results demonstrate that Mer locally plays an exceptional protective role in joint disease by enhancing resolution of arthritis-associated inflammation.

Status: Under Review