title: Transgenerational transcriptional heterogeneity from cytoplasmic chromatin

abstract: Transcriptional heterogeneity from plasticity of the epigenetic state of chromatin is thought to contribute to tumor evolution, metastasis, and drug resistance 1-3. However, the mechanisms leading to nongenetic cell-to-cell variation in gene expression remain poorly understood. Here we demonstrate that heritable transcriptional changes can result from the formation of micronuclei, aberrations of the nucleus that are common in cancer4,5. Micronuclei have fragile nuclear envelopes (NE) that are prone to spontaneous rupture, which exposes chromosomes to the cytoplasm and disrupts many nuclear activities 6,7. Using a combination of long-term live-cell imaging and same-cell, single-cell RNA sequencing (Look-Seq2), we identified significant reduction of gene expression in micronuclei, both before and after NE rupture. Furthermore, chromosomes in micronuclei fail to normally recover histone 3 lysine 27 acetylation, a critical step for the reestablishment of normal transcription after mitosis 8-10. These transcription and chromatin defects can persist into the next generation in a subset of cells, even after these chromosomes are incorporated into normal daughter nuclei. Moreover, persistent transcriptional repression is strongly associated with, and may be explained by, surprisingly long-lived DNA damage to these reincorporated chromosomes. Therefore, heritable alterations in transcription can originate from aberrations of nuclear architecture.


title: Canonical Wnt Signaling Induces Focal Adhesion and Integrin Beta-1 Endocytosis

abstract: During canonical Wnt signaling, the Lrp6 and Frizzled co-receptors bind to the Wnt growth factor and the complex is endocytosed and sequestered together with Glycogen Synthase Kinase 3 (GSK3), Dishevelled (Dvl), and Axin inside the intraluminal vesicles of late endosomes, known as multivesicular bodies (MVBs). Here we present experiments showing that Wnt causes the endocytosis of focal adhesion (FA) proteins and depletion of Integrin {beta} 1 (ITG{beta}1) from the cell surface. FAs and integrins link the cytoskeleton to the extracellular matrix. Wnt-induced endocytosis caused ITG{beta}1 depletion from the plasma membrane and was accompanied by striking changes in the actin cytoskeleton. In situ protease protection assays in cultured cells showed that ITG{beta}1 was sequestered within membrane-bounded organelles that corresponded to Wnt-induced MVBs containing GSK3 and FA-associated proteins. An in vivo model using Xenopus embryos dorsalized by Wnt8 mRNA showed that ITG{beta}1 depletion decreased Wnt signaling. The finding of a crosstalk between two mayor signaling pathways, canonical Wnt and focal adhesions, should be relevant to human cancer and cell biology.

category: cell biology


title: Functional interplay between arginyl-tRNA synthetases and arginyltransferase

abstract:
Protein arginylation, mediated by arginyltransferase ATE1, is a posttranslational modification of emerging biological importance that consists of transfer of the amino acid Arg to protein and peptide substrates. ATE1 utilizes charged tRNAArg as the donor of the arginyl group, which depends on the activity of Arg-tRNA synthetases (RARS) and is also utilized in translation. The mechanisms that regulate the functional balance between ATE1, RARS and translation are unknown. Here we addressed the functional interplay between these mechanisms using intracellular arginylation sensor in cell lines with overexpression or deletion of ATE1 and RARS isoforms. We find that arginylation levels depend on the physiological state of the cells but are not directly affected by translation activity or availability of RARS isoforms. However, displacement of RARS from the multi-synthetase complex leads to an increase in intracellular arginylation independently of RARS enzymatic activity. This effect is accompanied by ATE1s redistribution into the cytosol. Our results provide the first comprehensive analysis of the interdependence between translation, arginyl-tRNA synthesis, and arginylation.

Key PointsO_LIIntracellular arginylation depends on the physiological state of the cell, but does not compete with the translation machinery
C_LIO_LIA fraction of ATE1 binds directly to both long and short Arg-tRNA synthetases (RARS)
C_LIO_LIDisplacement of long RARS from the multi-tRNA synthetase complex increases cytosolic fraction and activity of ATE1
C_LI


title: Pericentrin is a Kinesin-1 Activator that Drives Centriole Motility

abstract: Centrosome positioning is essential for their function. Typically, centrosomes are transported to various cellular locations through the interaction of centrosome nucleated microtubules with motor proteins. However, it remains unknown how centrioles migrate in cellular contexts in which centrioles do not nucleate microtubules. Here, we demonstrate that during interphase inactive centrioles move directly along the non-centrosomal microtubule network as cargo for the motor protein Kinesin-1. We identify Pericentrin-Like-Protein (PLP) as a novel Kinesin-1 interacting molecule essential for centriole motility. PLP directly interacts with the cargo binding domain of Kinesin-1 and they comigrate on microtubules in vitro. Finally, we demonstrate that PLP-Kinesin-1 dependent transport is essential for centrosome asymmetry age-dependent centrosome inheritance in asymmetric stem cell division.


title: A molecular brake that modulates spliceosome pausing at detained introns contributes to neurodegeneration

abstract: Emerging evidence suggests that intron-detaining transcripts (IDTs) are a nucleus-detained and polyadenylated mRNA pool for cell to quickly and effectively respond to environmental stimuli and stress. However, the underlying mechanisms of detained intron (DI) splicing are still largely unknown. Here, we suggest that post-transcriptional DI splicing is paused at Bact state, an active spliceosome but not catalytically primed, which depends on SNIP1 (Smad Nuclear Interacting Protein 1) and RNPS1 (a serine-rich RNA binding protein) interaction. RNPS1 and Bact component preferentially dock at DIs and the RNPS1 docking is sufficient to trigger spliceosome pausing. Haploinsufficiency of Snip1 attenuates neurodegeneration and globally rescues IDT accumulation caused by a previously reported mutant U2 snRNA, a basal spliceosomal component. Snip1 conditional knockout in cerebellum decreases DI splicing efficiency and causes neurodegeneration. Therefore, we suggest that SNIP1 and RNPS1 form a molecular brake for the spliceosome pausing, and that its misregulation contributes to neurodegeneration.


title: Microscopic and ultramicroscopic anatomical characteristics of root nodules in Podocarpus macrophyllus during development

abstract:
To understand the morphological and structural characteristics of root nodules in Podocarpus macrophyllus and their development, this study prepared P. macrophyllus root nodule samples at the young, mature, and senescent stages. Optical microscopy and transmission electron microscopy (SEM) revealed that new nodules can be formed on roots and senescent nodules; new nodules formed on the roots are nearly spherical and have an internal structure similar to finite nodules; new nodules on senescent nodules are formed by extension and differentiation of the vascular cylinder of the original nodules; and these new nodules are nested at the base of the original nodules, which create growth space for new nodules by dissociating the cortical tissue; clusters of nodules are formed after extensive accumulation, and the growth pattern is similar to that of infinite nodules; the symbiotic bacteria of P. macrophyllus root nodules mainly invade from the epidermal intercellular space of the roots and migrate along the intercellular space of the nodule cortex; infected nodule cortex cells have a well-developed inner membrane system and enlarged and loose nuclei; and unique Frankia vesicles, and rhizobia cysts, and bacteriophages can all develop. Compared with common leguminous and nonleguminous plant nodules, P. macrophyllus root nodules are more complex in morphology, structure and composition. From the perspective of plant system evolution, the rhizobium nodules in leguminous angiosperms and Frankia nodules in nonleguminous angiosperms are most likely two branches derived from the nodules in gymnosperms, such as P. macrophyllus. The conclusions of this study can provide a theoretical basis for the developmental biology of P. macrophyllus root nodules and the evolutionary pattern of plant symbionts.

HighlightsWe discuss from the perspective of cell developmental biology, the rhizobium nodules in leguminous angiosperms and Frankia nodules in nonleguminous angiosperms are most likely two branches derived from the nodules in gymnosperms, such as Podocarpus macrophyllus.

category: developmental biology


title: Differential Requirement of DICER1 Activity during Development of Mitral and Tricuspid Valves

abstract:
Mitral and tricuspid valves are essential for unidirectional blood flow in the heart. They are derived from similar cell sources, and yet congenital dysplasia affecting both valves is clinically rare, suggesting the presence of differential regulatory mechanisms underlying their development. We specifically inactivated Dicer1 in the endocardium during cardiogenesis, and unexpectedly found that Dicer1-deletion caused congenital mitral valve stenosis and regurgitation, while it had no impact on other valves. We showed that hyperplastic mitral valves were caused by abnormal condensation and extracellular matrix (ECM) remodeling. Our single-cell RNA Sequencing analysis revealed impaired maturation of mesenchymal cells and abnormal expression of ECM genes in mutant mitral valves. Furthermore, expression of a set of miRNAs that target ECM genes was significantly lower in tricuspid valves compared to mitral valves, consistent with the idea that the miRNAs are differentially required for mitral and tricuspid valve development. Our study thus reveals miRNA-mediated gene regulation as a novel molecular mechanism that differentially regulates mitral and tricuspid valve development, thereby enhancing our understanding of the non-association of inborn mitral and tricuspid dysplasia observed clinically.

Summary statementAlthough mitral and tricuspid heart valves are both derived from same cell sources in the atrioventricular region through similar initiation and remodeling processes, congenital dysplasia simultaneously affecting both valves is clinically uncommon. We show that DICER1 activity is only essential for mitral valve development whereas it is dispensable for other valves. Our study thus reveals miRNA-mediated gene regulation as a novel molecular mechanism that is differentially required to regulate mitral and tricuspid valve development, thereby enhancing our understanding of the non-association of inborn mitral and tricuspid dysplasia observed clinically.


title: Ontogenetic Color Switching in Lizards as a by-Product of Guanine Cell Development

abstract: Many animals undergo dramatic changes in colour during development1,2. Changes in predation risk during ontogeny are associated with spectacular switches in defensive colours, typically involving the replacement of skin or the production of new pigment cells3. Ontogenetic colour systems are ideal models for understanding the evolution and formation mechanisms of animal colour which remain largely enigmatic2. We show that defensive colour switching in lizards arises by reorganization of a single photonic system, as an incidental by-product of chromatophore maturation. The defensive blue tail colour of hatchling A. beershebensis lizards is produced by light scattering from premature guanine crystals in underdeveloped iridophore cells. Camouflaged adult tail colours emerge upon reorganization of the guanine crystals into a photonic reflector during chromatophore maturation. The substituent guanine crystals form by the attachment of individual nanoscopic plates, which coalesce during growth to form single crystals. Our results show that the blue colour of hatchlings is a fortuitous, but necessary, precursor to the development of adult colour. Striking functional colours in animals can thus arise not as distinct evolutionary innovations but via exploitation of the timing of naturally occurring changes in chromatophore cell development.


title: Developmental origins of cell heterogeneity in the human lung

abstract: The lung contains numerous specialized cell-types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a first comprehensive topographic atlas of early human lung development. We report 83 cell states, several spatially-resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated scRNA-Seq and spatial transcriptomics into a web-based, open platform for interactive exploration. To illustrate the utility of our approach we show distinct states of secretory and neuroendocrine cells, largely overlapping with the programs activated either during lung fibrosis or small cell lung cancer progression. We define the origin of uncharacterized airway fibroblasts associated with airway smooth muscle in bronchovascular bundles, and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.


title: Structural basis of ion - substrate coupling in the Na+-dependent dicarboxylate transporter VcINDY

abstract: The Na+-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na+ gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen induced-fit mechanism. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPinb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDYs induced-fit mechanism is a result of the sodium-dependent formation of the substrate binding site.

category: biophysics


title: How many bits of information can be transferred between residues in a protein and how fast?

abstract: Time resolved Raman and infrared spectroscopy experiments show the basic features of information transfer between residues in proteins. Here, we present the theoretical basis of information transfer using a simple elastic net model and recently developed entropy transfer concept in proteins. Mutual information between two residues is a measure of communication in proteins which shows the maximum amount of information that may be transferred between two residues. However, it does not explain the actual amount of transfer nor the transfer rate of information between residues. For this, dynamic equations of the system are needed. We used the Schreiber theory of information transfer and the Gaussian network Model of proteins, together with the solution of the Langevin equation, to quantify allosteric information transfer. Results of the model are in perfect agreement with ultraviolet resonance Raman measurements. Analysis of the allosteric protein Human NAD-dependent isocitrate dehydrogenase shows that a multitude of paths contribute collectively to information transfer. While the peak values of information transferred are small relative to information content of residues, considering the estimated transfer rates, which are in the order of megabits per second, sustained transfer during the activity time-span of proteins may be significant.


title: Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

abstract:
The most commonly occurring intrinsically disordered proteins (IDPs) are polyampholytes, which are defined by the duality of low net charge per residue and high fractions of charged residues. Recent experiments have uncovered nuances regarding sequence-ensemble relationships of model polyampholytic IDPs. These include differences in conformational preferences for sequences with lysine vs. arginine, and the suggestion that well-mixed sequences form a range of conformations, including globules, conformations with ensemble averages that are reminiscent of ideal chains, or self-avoiding walks. Here, we explain these observations by analyzing results from atomistic simulations. We find that polyampholytic IDPs generally sample two distinct stable states, namely globules and self-avoiding walks. Globules are favored by electrostatic attractions between oppositely charged residues, whereas self-avoiding walks are favored by favorable free energies of hydration of charged residues. We find sequence-specific temperatures of bistability at which globules and self-avoiding walks can coexist. At these temperatures, ensemble averages over coexisting states give rise to statistics that resemble ideal chains without there being an actual counterbalancing of intra-chain and chain-solvent interactions. At equivalent temperatures, arginine-rich sequences tilt the preference toward globular conformations whereas lysine-rich sequences tilt the preference toward self-avoiding walks. We also identify differences between aspartate and glutamate containing sequences, whereby the shorter aspartate sidechain engenders preferences for metastable, necklace-like conformations. Finally, although segregation of oppositely charged residues within the linear sequence maintains the overall two-state behavior, compact states are highly favored by such systems.

Significance StatementIntrinsically disordered regions (IDRs) of proteins, when tethered to folded domains, function either as flexible tails or as linkers between domains. Most IDRs are polyampholytes that comprise a mixture of oppositely charged residues. Recent measurements of tethered polyampholytes showed that tendency of arginine- and lysine-rich sequences to behave very differently from one another. Using computer simulations, we show that these differences are determined by differences in free energies of hydration, steric volumes, and other considerations. Further, the interplay between electrostatic attractions and favorable free energies of hydration creates distinct stable states for polyampholytic IDRs. These findings have implications for switch-like transitions and the regulation of effective concentrations of interaction motifs by IDRs.


title: Strand-switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA

abstract: G-rich sequences found at multiple sites throughout all genomes may form secondary structures called G-quadruplexes (G4), which act as roadblocks for molecular motors. Among the enzymes thought to process these structures, the Pif1 DNA helicase is considered as an archetypical G4-resolvase and its absence has been linked to G4-related genomic instabilities in yeast. Here we developed a single-molecule assay to observe Pif1 opening a DNA duplex and resolving the G4 in real time. In support of former enzymological studies, we show that the helicase reduces the lifetime of G4 from hours to seconds. However, we observe that in presence of a G4, Pif1 exhibits a strong strand switching behavior, which can lead to Pif1 escaping G4 resolution, depending on the structural context surrounding the substrate. This behavior is also detected in presence of other roadblocks (LNA or RNA). We propose that the efficiency of Pif1 to remove a roadblock (G4 or other) is affected by its strand switching behavior and depends on the context surrounding the obstacle. We discuss how this switching behavior may explain several aspects of Pif1 substrate preference and affect its activity as a G4 resolvase in vivo.


title: Human endothelial cells display a rapid and fluid flow dependent tensional stress increase in response to tumor necrosis factor-α

abstract: As endothelial cells form the inner layer of blood vessels they display the first barrier to interstitial tissues, which results in a crucial role for inflammation. On the global, systemic level an important element of the complex process controlling the inflammatory response is the release of the cytokine tumor necrosis factor- (TNF-). While other pro-inflammatory agents like thrombin or histamine are known to induce acute but transient changes in endothelial cells which have been well studied biologically as well as mechanically, TNF- is primarily known for its sustained effects on permeability and leukocyte recruitment. These functions are associated with transcriptional changes that take place on the timescale of hours and days. Here we show that already 4 minutes after the addition of TNF- onto monolayers of human umbilical vein endothelial cells, a striking rise in mechanical substrate traction force and internal monolayer tension can be recorded. As expected, the traction forces act primarily at the boundary of the monolayer. While the traction forces increase monotonically during the initial cellular response, we find that the internal monolayer tension displays a rapid peak that can be abolished when applying a shear flow to the cells. The increased internal monolayer tension may provide a mechanical signal for the cells to prepare for the recruitment of leukocytes, additionally to the well studied biochemical response.


title: cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach

abstract: The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Nuclear-encoded LHCPs are synthesized in the cytoplasm then imported into the chloroplast. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54, a 54 kDa subunit homologous to the universally conserved GTPase in cytosolic SRP pathways. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. However, the high flexibility and structural dynamics of cpSRP43 is yet unexplained by current crystal structures of cpSRP43. This is due, in part, to the fact that free full length cpSRP43 is so flexible that it is unable to crystalize. In this study, we explore the structural stability of cpSRP43 under different conditions using various biophysical techniques and find that this protein is concurrently highly stable and flexible. This conclusion is interesting considering that stable proteins typically possess a non-dynamic structure. Molecular dynamics (MD) simulations which correlated with data from biophysical experimentation were used to explain the basis of the extraordinary stability of cpSRP43. This combination of biophysical data and microsecond-level MD simulations allows us to obtain a detailed perspective of the conformational landscape of these proteins.


title: Augmentation of extracellular ATP synergizes with chemotherapy in triple negative breast cancer

abstract:
IntroductionBreast cancer affects two million women worldwide every year and is the most common cause of cancer-related death among women. The triple-negative breast cancer (TNBC) sub-type is associated with an especially poor prognosis because currently available therapies, fail to induce long-lasting responses. Therefore, there is an urgent need to develop novel therapies that result in durable responses. One universal characteristic of the tumor microenvironment is a markedly elevated concentration of extracellular adenosine triphosphate (eATP). Chemotherapy exposure results in further increases in eATP through its release into the extracellular space of cancer cells via P2RX channels. eATP levels are reduced by eATPases. Given that high concentrations of eATP are cytotoxic, we hypothesized that augmenting the release of eATP through P2RX channels and inhibiting extracellular ATPases would sensitize TNBC cells to chemotherapy.

MethodsTNBC cell lines MDA-MB 231, Hs 578t and MDA-MB 468 and non-tumorigenic immortalized mammary epithelial MCF-10A cells were treated with increasing concentrations the chemotherapeutic agent paclitaxel in the presence of eATPase inhibitors, specific agonists or antagonists of P2RXs with cell viability and eATP content being measured. Additionally, the mRNA, protein and cell surface expressions of the purinergic receptors P2RX4 and P2RX7 were evaluated in all examined cell lines via qRT-PCR, western blot, and flow cytometry analyses, respectively.

ResultsIn the present study, we observed dose-dependent declines in cell viability and increases in eATP in paclitaxel-treated TNBC cell lines in the presence of inhibitors of eATPases. These effects were reversed by specific antagonists of P2RXs. Similar results were observed with P2RX activators. All examined cell lines expressed both P2RX4 and P2RX7 at the mRNA, protein and cell surface levels.

ConclusionThese results reveal that eATP modulates the chemotherapeutic response in TNBC cell lines which could be exploited to enhance the efficacy of chemotherapy regimens for TNBC.

category: cancer biology


title: Practical and Thermodynamic Constraints on Electromicrobially-Accelerated CO2 Mineralization

abstract: By the end of the century tens of gigatonnes of CO2 will need to be removed from the atmosphere every year to maintain global temperatures. Natural weathering of ultramafic rocks and subsequent mineralization reactions can convert atmospheric CO2 into ultra-stable carbonates. But, while natural weathering will eventually draw down all excess CO2, this process will need hundreds of thousands of years to do it. The CO2 mineralization process could be accelerated by weathering ultramafic rocks with biodegradable lixiviants like organic acids. But, in this article we show that if these lixiviants are produced from cellulosic biomass, the demand created by CO2 mineralization could monopolize the worlds supply of biomass even if CO2 mineralization performance is high. In this article we demonstrate that electromicrobial production technologies (EMP) that combine renewable electricity and microbial metabolism could produce lixiviants for as little as $200 to $400 per tonne at solar electricity prices achievable within the decade. Furthermore, this allows the lixiviants needed to sequester a tonne of CO2 to be produced for less than $100, even with modest CO2 mineralization performance.

category: synthetic biology


title: Signal denoising through topographic modularity of neural circuits

abstract: Information from the sensory periphery is conveyed to the cortex via structured projection pathways that spatially segregate stimulus features, providing a robust and efficient encoding strategy. Beyond sensory encoding, this prominent anatomical feature extends throughout the neocortex. However, the extent to which it influences cortical processing is unclear. In this study, we combine cortical circuit modeling with network theory to demonstrate that the sharpness of topographic projections acts as a bifurcation parameter, controlling the macroscopic dynamics and representational precision across a modular network. By shifting the balance of excitation and inhibition, topographic modularity gradually increases task performance and improves the signal-to-noise ratio across the system. We show that this is a robust and generic structural feature that enables a broad range of behaviorally-relevant operating regimes, and provide an in-depth theoretical analysis unravelling the dynamical principles underlying the mechanism.

category: neuroscience


title: Spinal cord homeostatic plasticity gates mechanical allodynia in chronic pain

abstract: Central sensitization caused by disinhibition of spinal cord circuits is a key mechanism of mechanical allodynia in neuropathic pain. Despite intense efforts, the molecular mechanisms that drive disinhibition and induce allodynia after peripheral nerve injury remain unclear. Using the spared-nerve injury (SNI) model of allodynia, we here demonstrate that SNI induces disinhibition of spinal nociceptive circuits by triggering homeostatic synaptic plasticity. Specifically, SNI-triggered homeostatic plasticity suppresses the inhibitory outputs of parvalbumin-positive (PV+) interneurons that form synapses on both primary afferent terminals and excitatory interneurons, causing hyperactivation of the nociceptive pathway. Using genetic manipulations, we identified the retinoic acid receptor RAR as the key mediator of the homeostatic synaptic plasticity underlying this synaptic disinhibition. Deletion of RAR in PV+ neurons blocked SNI-induced spinal disinhibition, central sensitization, and allodynia. Moreover, deletion of RAR in spinal PV+ neurons or application of an RAR antagonist in the spinal cord prevented the development of SNI-induced mechanical allodynia. Together, our results reveal a molecular mechanism of neuropathic pain whereby homeostatic plasticity causes the mis-direction of tactile information flow to ascending nociceptive pathways following peripheral nerve injury.


title: Vascular topology is acutely impacted by experimental febrile status epilepticus

abstract: Febrile status epilepticus (FSE) is an important risk factor for temporal lobe epilepsy and early identification is vital. In a rat model of FSE, we identified an acute novel MRI signal in the basolateral amygdala (BLA) at 2 hours post FSE that predicted epilepsy in adulthood. This signal remains incompletely understood and hypothesized that it might derive from changes to vascular topology. Experimental FSE was induced in rat pups and compared to normothermic littermate controls. We examined cerebral vascular topology at 2 hours, using a novel vessel painting and analysis protocol. Blood vessel density of the cortical vasculature was significantly reduced in FSE rats, and this effect was lateralized, as reported for the MRI signal. The middle cerebral artery (MCA) exhibited abnormal topology in FSE pups but not in controls. In the BLA, significant vessel junction reductions and decreased vessel diameter were observed, together with a strong trend for reduced vessel length. In summary, FSE results in acute vascular topological changes in the cortex and BLA that may underlie the acute MRI signal that predicts progression to future epilepsy. The altered vasculature may be amenable to intervention treatments to potentially reduce the probability of progression to epilepsy following FSE.


title: Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts

abstract:
G protein-coupled receptors (GPCRs) enable cells to sense environmental cues and are indispensable for coordinating vital processes including quorum sensing, proliferation, and sexual reproduction. GPCRs comprise the largest class of cell surface receptors in eukaryotes, and for more than three decades the pheromone-induced mating pathway in bakers yeast Saccharomyces cerevisiae has served as a model for studying heterologous GPCRs (hGPCRs). Here we report transcriptome profiles following mating pathway activation in native and hGPCR-signaling yeast, and use a model-guided approach to correlate gene expression to morphological changes. From this we demonstrate mating between haploid cells armed with hGPCRs and endogenous biosynthesis of their cognate ligands. Furthermore, we devise a ligand-free screening strategy for hGPCR compatibility with the yeast mating pathway and enable hGPCR-signaling in the probiotic yeast Saccharomyces boulardii. Combined, our findings enable new means to study mating, hGPCR-signaling, and cell-cell communication in a model eukaryote and yeast probiotics.

One-sentence summaryEnabling sensing in probiotic yeast and synthetic yeast mating with human and fungal G protein-coupled receptors.


title: Ionophore-stimulation promotes re-organization of the invasion machinery of Toxoplasma gondii

abstract: Host cell invasion by intracellular, eukaryotic parasites, like the many important species within the phylum Api-complexa, is a remarkable and active process involving the coordinated action of many apical organelles and other structures. To date, capturing how these various structures interact during invasion has been difficult to observe in detail. Here, we used cryogenic electron tomography to generate images of the apical complex of Toxoplasma gondii tachyzoites under conditions that mimic resting parasites and those primed to invade through addition of a calcium ionophore. Using AI-based image-processing we were able to annotate 48 tomograms to identify and extract densities of the relevant subcellular organelles and accurately analyze features in 3D. We describe an interaction between an anteriorly located apical vesicle and a rhoptry tip that occurs only in the ionophore-stimulated parasites and that is associated with dramatic changes in the vesicles shape in what appears to be a stalled fusion event. We also present information to support the presumption that this vesicle originates from the well-described vesicles that parallel the intraconoidal microtubules and that the latter two structures are linked by a novel tether. Lastly, we show that a previously described rosette is found associated with more than just the anterior-most apical vesicle, indicating that multiple such vesicles are primed to enable rhoptry secretion.


title: Novel modification of Luminex assay for characterization of extracellular vesicle populations in biofluids.

abstract: Most approaches to extracellular vesicle (EV) characterization focus on EV size or density. However, such approaches provide few clues regarding EV origin, molecular composition, and function. New methods to characterize the EV surface proteins may aid our understanding of their origin, physiological roles, and biomarker potential. Recently developed immunoassays for intact EVs based on ELISA, NanoView, SIMOA and MesoScale platforms are highly sensitive, but have limited multiplexing capabilities, whereas MACSPlex FACS enables the detection of multiple EV surface proteins, but requires significant quantities of purified EVs, which limits its adoption. Here, we describe a novel Luminex-based immunoassay, which combines multiplexing capabilities with high sensitivity and, importantly, bypasses the enrichment and purification steps that require larger sample volumes. We demonstrate the methods specificity for detecting EV surface proteins using multiple EV depletion techniques, EVs of specific cellular origin isolated from culture media, and by co-localization with established EV surface markers. Using this novel approach, we elucidate differences in the tetraspanin profiles of the EVs carrying erythrocyte and neuron markers. Using size exclusion chromatography, we show that plasma EVs of putative neuronal and tissue macrophage origin are eluted in fractions distinct from those derived from erythrocytes, or from their respective cultured cells. In conclusion, our novel multiplexed assay differentiates between EVs from erythrocytes, macrophages, and neurons, and offers a new means for capture, classification, and profiling of EVs from diverse sources.


title: Amniotic fluid stem cell extracellular vesicles promote fetal lung branching and cell differentiation in experimental congenital diaphragmatic hernia

abstract:
Pulmonary hypoplasia secondary to congenital diaphragmatic hernia (CDH) is characterized by impaired branching morphogenesis and differentiation. We have previously demonstrated that administration of extracellular vesicles derived from rat amniotic fluid stem cells (AFSC-EVs) rescues development of hypoplastic lungs at the pseudoglandular and alveolar stages in rodent models of CDH. Herein, we tested whether AFSC-EVs exert their regenerative effects at the canalicular and saccular stages, as these are translationally relevant for clinical intervention. To induce fetal pulmonary hypoplasia, we gavaged rat dams with nitrofen at embryonic day 9.5 and demonstrated that nitrofen-exposed lungs had impaired branching morphogenesis, dysregulated signaling pathways relevant to lung development (FGF10/FGFR2, ROBO/SLIT, Ephrin, Neuropilin 1, {beta}-catenin) and impaired epithelial and mesenchymal cell marker expression at both stages. AFSC-EVs administered to nitrofen-exposed lung explants rescued airspace density and increased the expression levels of key factors responsible for branching morphogenesis. Moreover, AFSC-EVs rescued the expression of alveolar type 1 and 2 cell markers at both canalicular and saccular stages, and restored markers of club, ciliated epithelial, and pulmonary neuroendocrine cells at the saccular stage. AFSC-EV treated lungs also had restored markers of lipofibroblasts and PDGFRA+ cells to control levels at both stages. EV tracking showed uptake of AFSC-EV RNA cargo throughout the fetal lung and an mRNA-miRNA network analysis identified that several miRNAs responsible for regulating lung development processes were contained in the AFSC-EV cargo. These findings suggest that AFSC-EV based therapies hold potential for restoring fetal lung growth and maturation in babies with pulmonary hypoplasia secondary to CDH.

Graphical abstractBabies with congenital diaphragmatic hernia have hypoplastic lungs characterized by impaired branching morphogenesis and undifferentiated epithelium and mesenchyme. The authors demonstrate that amniotic fluid stem cell extracellular vesicles (AFSC-EVs) administered to rat hypoplastic fetal lungs restore branching and exert regenerative effects on epithelial and mesenchymal cells, partly through miRNA cargo transfer. AFSC-EV beneficial effects were obtained at translationally relevant timepoints.

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title: SLC38A2 provides proline to fulfil unique synthetic demands arising during osteoblast differentiation and bone formation.

abstract: Cellular differentiation is associated with the acquisition of a unique protein signature which is essential to attain the ultimate cellular function and activity of the differentiated cell. This is predicted to result in unique biosynthetic demands that arise during differentiation. Using a bioinformatic approach, we discovered osteoblast differentiation is associated with increased demand for the amino acid proline. When compared to other differentiated cells, osteoblast-associated proteins including RUNX2, OSX, OCN and COL1A1 are significantly enriched in proline. Using a genetic and metabolomic approach, we demonstrate that the neutral amino acid transporter SLC38A2 acts cell autonomously to provide proline to facilitate the efficient synthesis of proline-rich osteoblast proteins. Genetic ablation of SLC38A2 in osteoblasts limits both osteoblast differentiation and bone formation in mice. Mechanistically, proline is primarily incorporated into nascent protein with little metabolism observed. Collectively, these data highlight a requirement for proline in fulfilling the unique biosynthetic requirements that arise during osteoblast differentiation and bone formation.


title: Heritable and climatic sources of variation in juvenile tree growth in an Austrian common garden experiment of Central European Norway spruce populations

abstract: We leveraged publicly available data on juvenile tree height of 299 Central European Norway spruce populations grown in a common garden experiment across 24 diverse trial locations in Austria and weather data from the trial locations and population provenances to parse the heritable and climatic components of juvenile tree height variation. Principal component analysis of geospatial and weather variables demonstrated high interannual variation among trial environments, largely driven by differences in precipitation, and separation of population provenances based on altitude, temperature, and snowfall. Tree height was highly heritable and modeling the covariance between populations and trial environments based on climatic data led to more stable estimation of heritability and population x environment variance. Climatic similarity among population provenances was highly predictive of population x environment estimates for tree height.

category: ecology


title: Automation of tree-ring detection and measurements using deep learning

abstract:
O_LIWe present an implementable neural network-based automated detection and measurement of tree-ring boundaries from coniferous species.
C_LIO_LIWe trained our Mask R-CNN extensively on over 8,000 manually annotated rings. We assessed the performance of the trained model from our core processing pipeline on real world data.
C_LIO_LIThe CNN performed well, recognizing over 99% of ring boundaries (precision) and a recall value of 95% when tested on real world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were a 99% match with human measurements of the same samples.
C_LIO_LIOur CNN is readily deployable through a Docker container and requires only basic command line skills. Application outputs include editable annotations which facilitate the efficient generation of ring-width measurements from tree-ring samples, an important source of environmental data.
C_LI


title: The heritability of BMI varies across the range of BMI: a heritability curve analysis in a twin cohort

abstract: The heritability of traits such as body mass index (BMI), a measure of obesity, is generally estimated using family, twin, and increasingly by molecular genetic approaches. These studies generally assume that genetic effects are uniform across all trait values, yet there is emerging evidence that this may not always be the case. This paper analyzes twin data using a recently developed measure of heritability called the heritability curve. Under the assumption that trait values in twin pairs are governed by a flexible Gaussian mixture distribution, heritability curves may vary across trait values. The data consist of repeated measures of BMI on 1506 monozygotic (MZ) and 2843 like-sexed dizygotic (DZ) adult twin pairs, gathered from multiple surveys in older Finnish Twin Cohorts. The heritability curve and BMI value-specific MZ and DZ pairwise correlations were estimated, and these varied across the range of BMI. MZ correlations were highest at BMI values from 21 to 24, with a stronger decrease for women than for men at higher values. Models with additive and dominance effects fit best at low and high BMI values, while models with additive genetic and common environmental effects fit best in the normal range of BMI. Thus, we demonstrate that twin and molecular genetic studies need to consider how genetic effects vary across trait values. Such variation may reconcile findings of traits with high heritabilities and major differences in mean values between countries or over time.

category: genetics


title: Limb, joint and pelvic kinematic control in the quail coping with step perturbations

abstract:
Small cursorial birds display remarkable walking skills and can negotiate complex and unstructured terrains with ease. The neuromechanical control strategies necessary to adapt to these challenging terrains are still not well understood. Here, we analyzed the 2D- and 3D pelvic and leg kinematic strategies employed by the common quail to negotiate visible step-up and step-down perturbations of 1 cm, 2.5 cm, and 5 cm. We used biplanar fluoroscopy to accurately describe joint positions in three dimensions and performed semi-automatic landmark localization using deep learning.

Quails negotiated vertical perturbations without major problems and rapidly regained steady-state locomotion. When coping with step-up perturbations, the quail mostly adapted the trailing limb to permit the leading leg to step on the elevated substrate in a similar way as it did during level locomotion. When the quail negotiated step-down perturbations, both legs showed significant adaptations. For small and moderate perturbations (not inducing aerial running) the quail kept the function of the distal joints (i.e., their kinematic pattern) largely unchanged during uneven locomotion, and most changes occurred in proximal joints. The hip regulated leg length, while the distal joints maintained the spring-damped limb patterns. However, to negotiate the largest visible step perturbations, more dramatic kinematic alterations were observed. For these large perturbations, all joints contributed to leg lengthening/ shortening in the trailing leg and both the trailing and leading legs stepped more vertically and less abducted. This indicates a shift from a dynamic walking program to strategies that are focused on maximizing safety.

category: animal behavior and cognition


title: Peak Space Motion Artifact Cancellation Applied to Textile Electrode Waist Electrocardiograms Recording During Outdoors Walking and Jogging

abstract:
BackgroundObtaining reliable rate heart estimates from waist based electrocardiograms (ECGs) poses a very challenging problem due to the presence of extreme motion artifacts. The literature reveals few, if any, attempts to apply motion artifact cancellation methods to waist based ECGs. This paper describes a new methodology for ameliorating the effects of motion artifacts in ECGs by specifically targeting ECG peaks for elimination that are determined to be correlated with accelerometer peaks. This peak space cancellation is applied to real world waist based ECGs.

Algorithm SummaryThe methodology includes successive applications of a previously described pattern-based heart beat detection scheme (Temporal Pattern Search, or "TEPS"). In the first application, TEPS is applied to accelerometer signals recorded contemporaneously with ECG signals to identify high-quality accelerometer peak sequences (SA) indicative of quasi-periodic motion likely to impair identification of peaks in a corresponding ECG signal. The process then performs ECG peak detection and locates the closest in time ECG peak to each peak in an SA. The differences in time between ECG and SA peaks are clustered. If the number of elements in a cluster of peaks in an SA exceeds a threshold, the ECG peaks in that cluster are removed from further processing. After this peak removal process, further QRS detection proceeds according to TEPS.

ExperimentThe above procedure was applied to data from real world experiments involving four sessions of walking and jogging on a dirt road for approximately 20-25 minutes. A compression shirt with textile electrodes served as the ground truth recording. A textile electrode based chest strap was worn around the waist to generate a single channel signal upon which to test peak space cancellation/TEPS.

ResultsBoth walking and jogging heart rates were generally well tracked. In the four recordings, the percentage of segments within 10 beats/minute of reference was 96%, 99%, 92% and 96%. The percentage of segments within 5 beats/minute of reference was 86%, 90%, 82% and 78%. There was very good agreement between the RR intervals associated with the reference and waist recordings. For acceptable quality segments, the root mean square sum of successive RR interval differences (RMSSD) was calculated for both the reference and waist recordings. Next, the difference between waist and reference RMSSDs was calculated ({Delta}RMSSD). The mean {Delta}RMSSD (over acceptable segments) was 4.6 m, 5.2 ms, 5.2 ms and 6.6 ms for the four recordings. Given that only one waist ECG channel was available, and that the strap used for the waist recording was not tailored for that purpose, the proposed methodology shows promise for waist based sinus rhythm QRS detection.

category: bioengineering


title: Computational Prediction of Heteromeric Protein Complex Disassembly Order with Hybrid Monte Carlo/Molecular Dynamics Simulation

abstract: The physicochemical entity of biological phenomenon in the cell is a network of biochemical reactions and the activity of such a network is regulated by multimeric protein complexes. Mass spectroscopy (MS) experiments and multimeric protein docking simulations based on structural bioinformatics techniques have revealed the molecular-level stoichiometry and static configuration of subcomplexes in their bound forms, then revealing the subcomplex populations and formation orders. Meanwhile, these methodologies are not designed to straightforwardly examine temporal dynamics of multimeric protein assembly and disassembly, essential physicochemical properties to understand functional expression mechanisms of proteins in the biological environment. To address the problem, we had developed an atomistic simulation in the framework of the hybrid Monte Carlo/Molecular Dynamics (hMC/MD) method and succeeded in observing disassembly of homomeric pentamer of the serum amyloid P component protein in experimentally consistent order. In this study, we improved the hMC/MD method to examine disassembly processes of the tryptophan synthase tetramer, a paradigmatic heteromeric protein complex in MS studies. We employed the likelihood-based selection scheme to determine a dissociation-prone subunit pair at each hMC/MD simulation cycle and achieved highly reliable predictions of the disassembly orders with the success rate over 0.9 without a priori knowledge of the MS experiments and structural bioinformatics simulations. We similarly succeeded in reliable predictions for the other three tetrameric protein complexes. These achievements indicate the potential availability of our hMC/MD approach as the general purpose methodology to obtain microscopic and physicochemical insights into multimeric protein complex formation.


title: Viscoelastic properties of suspended cells measured with shear flow deformation cytometry

abstract: Numerous cell functions are accompanied by phenotypic changes in viscoelastic properties, and measuring them can help elucidate higher-level cellular functions in health and disease. We present a high-throughput, simple and low-cost microfluidic method for quantitatively measuring the elastic (storage) and viscous (loss) modulus of individual cells. Cells are suspended in a high-viscosity fluid and are pumped with high pressure through a 5.8 cm long and 200 {micro}m wide microfluidic channel. The fluid shear stress induces large, near ellipsoidal cell deformations. In addition, the flow profile in the channel causes the cells to rotate in a tank-treading manner. From the cell deformation and tank treading frequency, we extract the frequency-dependent viscoelastic cell properties based on a theoretical framework developed by R. Roscoe1 that describes the deformation of a viscoelastic sphere in a viscous fluid under steady laminar flow. We confirm the accuracy of the method using atomic force microscopy-calibrated polyacrylamide beads and cells. Our measurements demonstrate that suspended cells exhibit power-law, soft glassy rheological behavior that is cell cycle-dependent and mediated by the physical interplay between the actin filament and intermediate filament networks.


title: MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas

abstract: Combining multiple therapeutic strategies in NRAS/BRAF mutant melanoma - namely MEK/BRAF kinase inhibitors, immune checkpoint inhibitors, and targeted immunotherapies - may offer an improved survival benefit by overcoming limitations associated with any individual therapy. Still, optimal combination, order, and timing of administration remains under investigation. Here, we measure how MEK inhibition alters anti-tumor immunity by utilizing quantitative immunopeptidomics to profile changes the peptide MHC (pMHC) repertoire. These data reveal a collection of tumor antigens whose presentation levels are selectively augmented following therapy, including several epitopes present at over 1000 copies-per-cell. We leveraged the tunable abundance of MEKi-modulated antigens by targeting 4 epitopes with pMHC-specific T cell engagers and antibody drug conjugates, enhancing cell killing in tumor cells following MEK inhibition. These results highlight drug treatment as a means to enhance immunotherapy efficacy by targeting specific upregulated pMHCs and provide a methodological framework for identifying, quantifying, and therapeutically targeting additional epitopes of interest.


title: Elevated FAM84B promotes cell proliferation via interacting with NPM1 in esophageal squamous cell carcinoma

abstract: Family with sequence similarity 84, member B (FAM84B) is a significant copy number amplification gene in the 8q24.21 locus identified by our previous WGS study in esophageal squamous cell carcinoma (ESCC). However, its clinical relevance and potential mechanisms have been elusive. Here, we performed the association analyses between FAM84BAmp and clinicopathological features using our dataset with 507 ESCC samples. The results indicated that, compared with the FAM84Bnon-Amp patients, the FAM84BAmp patients showed a more aggressive and a worse prognosis. Significant correlation was discovered between the expression level of FAM84B and FAM84BAmp in ESCC cohort. Furthermore, we found that the forced expression change of FAM84B can influence ESCC cell proliferation and cell cycle status, which is probably mediated by NPM1. A direct interaction between FAM84B and the C-terminal (189-294aa) of NPM1 was identified, which increased the NPM1 nuclear expression. Over-expression of NPM1 could inhibit the CDKN2A protein expression, which might affect the ESCC cell cycle. Our results indicate FAM84B CNA may be a potential diagnostic and therapeutic biomarker in ESCC, meanwhile, reveal a novel mechanism of FAM84B that it promotes tumorigenesis via interacting with NPM1 and suppressing CDKN2A.


title: 40 new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds.

abstract: Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur-bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most detailed morphological assessment of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds.

category: paleontology


title: Magnetic Stimulation Allows Focal Activation of the Mouse Cochlea

abstract: Cochlear implants (CIs) strive to restore hearing to those with severe to profound hearing loss by artificially stimulating the auditory nerve. While most CI users can understand speech in a quiet environment, hearing that utilizes complex neural coding (e.g., appreciating music) has proved elusive, probably because of the inability of CIs to create narrow regions of spectral activation. Several novel approaches have recently shown promise for improving spatial selectivity, but substantial design differences from conventional CIs will necessitate much additional safety testing before clinical viability is established. Outside the cochlea, magnetic stimulation from small coils (micro-coils) has been shown to confine activation more narrowly than that from conventional micro-electrodes, raising the possibility that coil-based stimulation of the cochlea could improve the spectral resolution of CIs. To explore this, we delivered magnetic stimulation from micro-coils to multiple locations of the cochlea and measured the spread of activation utilizing a multi-electrode array inserted into the inferior colliculus; responses to magnetic stimulation were compared to analogous experiments with conventional micro-electrodes as well as to the responses to auditory monotones. Encouragingly, the extent of activation with micro-coils was [~]60% narrower than that from electric stimulation and largely similar to the spread arising from acoustic stimulation. The dynamic range of coils was more than three times larger than that of electrodes, further supporting a smaller spread of activation. While much additional testing is required, these results support the notion that coil-based CIs can produce a larger number of independent spectral channels and may therefore improve functional performance. Further, because coil-based devices are structurally similar to existing CIs, fewer impediments to clinical translational are likely to arise.


title: Astrogliosis mapping in individual brains using multidimensional MRI

abstract: There are currently no noninvasive imaging methods available for astrogliosis mapping in the central nervous system despite its essential role in the response to injury, disease, and infection. We have developed a machine learning-based multidimensional MRI framework that provides a signature of astrogliosis, distinguishing it from normative brain at the individual level. We investigated ex vivo cortical tissue specimen derived from subjects who sustained blast induced injuries, which resulted in scar-border forming astrogliosis without being accompanied by other types of neuropathology. By performing a combined postmortem radiology and histopathology correlation study we found that astrogliosis induces microstructural changes that are robustly detected using our framework, resulting in MRI neuropathology maps that are significantly and strongly correlated with co-registered histological images of increased glial fibrillary a cidic protein deposition. The demonstrated high spatial sensitivity in detecting reactive astrocytes at the individual level has great potential to significantly impact neuroimaging studies in diseases, injury, repair, and aging.


title: Failed remyelination of the non-human primate optic nerve leads to axon degeneration, retinal damages and visual dysfunction.

abstract:
White matter disorders of the CNS such as MS, lead to failure of nerve conduction and long-lasting neurological disabilities affecting a variety of sensory and motor systems including vision. While most disease-modifying therapies target the immune and inflammatory response, the promotion of remyelination has become a new therapeutic avenue, to prevent neuronal degeneration and promote recovery. Most of these strategies are developed in short-lived rodent models of demyelination, which spontaneously repair and do not reflect the size, organization, and biology of the human CNS. Thus, well-defined non-human primate models are required to efficiently advance therapeutic approaches for patients. Here, we followed the consequence of long-term toxin-induced demyelination of the macaque optic nerve on remyelination and axon preservation, as well as its impact on visual functions. Findings from oculo-motor behavior, ophthalmic examination, electrophysiology, and retinal imaging indicate visual impairment involving the optic nerve and retina. These visual dysfunctions fully correlated at the anatomical level, with sustained optic nerve demyelination, axonal degeneration, and alterations of the inner retinal layers. This non-human primate model of chronic optic nerve demyelination associated with axonal degeneration and visual dysfunction, recapitulates several key features of MS lesions and should be instrumental in providing the missing link to translate emerging repair pro-myelinating/neuroprotective therapies to the clinic for myelin disorders such as MS.

Significance StatementPromotion of remyelination has become a new therapeutic avenue, to prevent neuronal degeneration and promote recovery in white matter diseases such as MS. To date most of these strategies are developed in short-lived rodent models of demyelination, which spontaneously repair. Well-defined non-human primate models closer to man would allow to efficiently advance therapeutic approaches. Here we present a non-human primate model of optic nerve demyelination that recapitulates several features of MS lesions. The model leads to failed remyelination, associated with progressive axonal degeneration and visual dysfunction, thus providing the missing link to translate emerging pre-clinical therapies to the clinic for myelin disorders such as MS.


title: Influence of data sampling methods on the representation of neural spiking activity in vivo

abstract: In vivo single-unit recordings distinguish the basal spiking properties of neurons in different experimental settings and disease states. Here, we examined over 300 spike trains recorded from Purkinje cells and cerebellar nuclei neurons to test whether data sampling approaches influence the extraction of rich descriptors of firing properties. Our analyses included neurons recorded in awake and anesthetized control mice, as well as disease models of ataxia, dystonia, and tremor. We find that recording duration circumscribes overall representations of firing rate and pattern. Notably, shorter recording durations skew estimates for global firing rate variability towards lower values. We also find that only some populations of neurons in the same mouse are more similar to each other than to neurons recorded in different mice. These data reveal that recording duration and approach are primary considerations when interpreting task-independent single-neuron firing properties. If not accounted for, group differences may be concealed or exaggerated.


title: Single-nucleus RNA-seq of normal-appearing brain regions in relapsing-remitting vs. secondary progressive multiple sclerosis

abstract: Multiple sclerosis (MS) is an immune-mediated demyelinating disease that alters central nervous system (CNS) functions. Relapsing-remitting MS (RRMS) is the most common form, which can transform into secondary-progressive MS (SPMS) that is associated with progressive neurodegeneration. Single-nucleus RNA sequencing (snRNA-seq) of MS lesions identified disease-related transcriptomic alterations; however, their relationship to non-lesioned MS brain regions has not been reported and which could identify prodromal or other disease susceptibility signatures. Here, snRNA-seq was used to generate high-quality RRMS vs. SPMS datasets of 33,197 nuclei from 8 normal-appearing MS brains, which revealed divergent cell type-specific changes. Notably, SPMS brains downregulated astrocytic sphingosine kinases (SPHK1/2) - the enzymes required to phosphorylate and activate the MS drug, fingolimod. This reduction was modeled with astrocyte-specific Sphk1/2 null mice in which fingolimod lost activity, supporting functionality of observed transcriptomic changes. These data provide an initial resource for studies of single cells from non-lesioned RRMS and SPMS brains.


title: Identification of Mfn2-S249 as a Phosphoregulatory Switch of Mitochondrial Fusion Dynamics

abstract: Mitochondrial remodeling is a fundamental process underlying cellular respiration and metabolism. Here we report TAK1 as a direct regulator of mitochondrial fusion. TAK1 is activated by a variety of mitogenic factors, cytokines and environmental stimuli, which we find induces rapid fragmentation through Mfn2 inactivation. TAK1 phosphorylates Mfn2 at Ser249, which inhibits the binding of GTP required for Mfn trans-dimerization and mitochondrial membrane fusion. Accordingly, expression of Mfn2-S249 phosphomimetics (Mfn2-E/D) constitutively promote fission whereas alanine mutant (Mfn2-A) yields hyperfused mitochondria and increased bioenergetics in cells. In mice, Mfn2-E knock-in yields embryonic lethality in homozygotes whereas heterozygotes are viable but exhibit increased visceral fat accumulation despite normal body weight and cognitive/motor functions compared to wildtype and Mfn2-A mice. Mature white adipocytes isolated from mutant mice reveal cell-autonomous TAK1-related effects on mitochondrial remodeling and lipid metabolism. These results identify Mfn2-S249 as a dynamic phosphoregulatory switch of mitochondrial fusion during development and energy homeostasis.


title: Global monitoring of soil animal communities using a common methodology

abstract: Here we introduce the Soil BON Foodweb Team, a cross-continental collaborative network that aims to monitor soil animal communities and food webs using consistent methodology at a global scale. Soil animals support vital soil processes via soil structure modification, direct consumption of dead organic matter, and interactions with microbial and plant communities. Soil animal effects on ecosystem functions have been demonstrated by correlative analyses as well as in laboratory and field experiments, but these studies typically focus on selected animal groups or species at one or few sites with limited variation in environmental conditions. The lack of comprehensive harmonised large-scale soil animal community data including microfauna, mesofauna, and macrofauna, in conjunction with related soil functions, limits our understanding of biological interactions in soil communities and how these interactions affect ecosystem functioning. To provide such data, the Soil BON Foodweb Team invites researchers worldwide to use a common methodology to address six long-term goals: (1) to collect globally representative harmonised data on soil micro-, meso-, and macrofauna communities; (2) to describe key environmental drivers of soil animal communities and food webs; (3) to assess the efficiency of conservation approaches for the protection of soil animal communities; (4) to describe soil food webs and their association with soil functioning globally; (5) to establish a global research network for soil biodiversity monitoring and collaborative projects in related topics; (6) to reinforce local collaboration networks and expertise and support capacity building for soil animal research around the world. In this paper, we describe the vision of the global research network and the common sampling protocol to assess soil animal communities and advocate for the use of standard methodologies across observational and experimental soil animal studies. We will use this protocol to conduct soil animal assessments and reconstruct soil food webs on the sites included in the global soil biodiversity monitoring network, Soil BON, allowing us to assess linkages among soil biodiversity, vegetation, soil physico-chemical properties, and ecosystem functions. In the present paper, we call for researchers especially from countries and ecoregions that remain underrepresented in the majority of soil biodiversity assessments to join us. Together we will be able to provide science-based evidence to support soil biodiversity conservation and functioning of terrestrial ecosystems.


title: Detection of bifenthrin, bifenazate, etoxazole resistance in Tetranychus urticae collected from mint fields and hop yards using targeted sequencing and TaqMan approaches

abstract: Tetranychus urticae (Koch) is an economically important pest of many agricultural commodities in the Pacific Northwest. Multiple miticides are currently registered for control including abamectin, bifenazate, bifenthrin, and extoxazole. However, populations of Tetranychus urticae have developed miticide resistance through multiple mechanisms, in many different growing regions. Producers of agricultural commodities where Tetranychus urticae infestations are problematic rely on integrated pest management tools to determine optimal control methods. Within this species multiple single nucleotide polymorphisms have been documented in different genes which are associated with miticide resistance phenotypes. The detection of these mutations through TaqMan qPCR has been suggested as a practical, quick, and reliable tool to inform agricultural producers of miticide resistance phenotypes present within their fields and have potential utility for making appropriate miticide application and integrated pest management decisions. Within this investigation we examined the use of a TaqMan qPCR-based approach to determine miticide resistance genotypes in field-collected populations of Tetranychus urticae from mint fields and hop yards in the Pacific Northwest of the United States and confirmed the results with a multiplex targeted sequencing. The results suggest the TaqMan approach accurately genotypes Tetranychus urticae populations collected from agricultural fields. The interpretation of the results, however, provide additional challenges for integrated pest management practitioners, including making miticide application recommendations where populations of Tetranychus urticae are a mix of resistant and wildtype individuals.


title: Consideration of genetic variation and evolutionary history in future conservation of Indian one-horned rhinoceros (Rhinoceros unicornis)

abstract: The extant members of the Eurasian rhino species have experienced severe population and range declines through a combination of natural and anthropogenic factors since Pleistocene. The one-horned rhino is the only Asian species recovered from such strong population decline but most of their fragmented populations in India and Nepal are reaching carrying capacity. Implementation of any future reintroduction-based conservation efforts would greatly benefit from currently unavailable detailed genetic assessments and evolutionary history of these populations. We sequenced wild one-horned rhino mitogenome from all the extant populations (n=16 individuals) for the first time, identified the polymorphic sites and assessed genetic variation (2531bp mtDNA, n=111 individuals) across India. Results showed 30 unique rhino haplotypes distributed as three distinct genetic clades (Fst value 0.68-1) corresponding to the states of Assam (n=28 haplotypes), West Bengal and Uttar Pradesh (both monomorphic). Phylogenetic analyses suggest earlier coalescence of Assam ([~]0.5 Mya) followed by parallel divergence of West Bengal and Uttar Pradesh/Nepal ([~]0.06-0.05Mya), supported by the paleobiogeographic history of the Indian subcontinent. Combined together, we propose recognising three  Evolutionary Significant Units (ESUs) of Indian rhino. As recent assessments suggest further genetic isolations of Indian rhinos at local scales, future management efforts should focus on identifying genetically variable founder animals and consider periodic supplementation events while planning future rhino reintroduction programs in India. Such well-informed, multidisciplinary approach is the only way to ensure evolutionary, ecological and demographic stability of the species across its range.


title: Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe species studied in any evolutionary investigation generally constitute a very small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has been rarely studied and is thus poorly understood. In this study, we use mathematical analysis and simulations to examine the robustness of species tree methods based on a multispecies coalescent model under gene flow sourcing from an extant or ghost lineage. We found that very low levels of extant or ghost introgression can result in anomalous gene trees (AGTs) on three-taxon rooted trees if accompanied by strong incomplete lineage sorting (ILS). In contrast, even massive introgression, with more than half of the recipient genome descending from the donor lineage, may not necessarily lead to AGTs. In cases involving an ingroup lineage (defined as one that diverged no earlier than the most basal species under investigation) acting as the donor of introgression, the time of root divergence among the investigated species was either underestimated or remained unaffected, but for the cases of outgroup ghost lineages acting as donors, the divergence time was generally overestimated. Under many conditions of ingroup introgression, the stronger the ILS was, the higher was the accuracy of estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

category: evolutionary biology


title: Divergence and introgression among the virilis group of Drosophila

abstract: Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains around a dozen species that are geographically widespread and show varying levels of pre-zygotic and post-zygotic isolation. Here, we utilize de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and much more recent gene flow between closely-related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and may be related to the evolution of sexual isolation. We suggest that gene flow between closely-related species has potentially had an impact on lineage-specific adaptation and the evolution of reproductive barriers. Our results show how ancient and recent introgression confuse phylogenetic reconstruction, and suggest that shared variation can facilitate adaptation and speciation.


title: TEX13B is important for germ cell development and male fertility

abstract: The recent epidemiological studies suggest that nearly one out of every 7 reproductive age couples face problem to conceive a child after trying for at least one year. Impaired fertility of the male partner is causative in approximately 50% of the infertile couples. However, the etiologies of large proportion of male infertility are still unclear. Our unpublished exome sequencing data identified several novel genes including TEX13B, which motivated us to further explore the role of TEX13B in male infertility in large infertile case control cohort. Hence in this study, we have examined the role of TEX13B in male infertility by whole gene sequencing 628 infertile and 427 control men and have demonstrated the functional role of Tex13b in spermatogonia GC1spg (GC1) cells. We identified 2 variants on TEX13B which are tightly associated with male infertility. TEX13B gene exclusively expressed in germ cells, but its molecular functions in germ cells are still unknown. Hence, we demonstrated the functional importance of Tex13b in GC1 cell line by genomic manipulation via CRISPR-Cas9 and mass spectrometry-based whole cell proteomics. The gene knock out in GC1 cell line clearly shows that Tex13b play an important role in germ cell growth and morphology. We demonstrate that Tex13b knockout or conditional overexpression in GC1 cells reprograms the metabolic status from an oxidative phosphorylation to glycolysis state and vice versa. In conclusion, our study clearly showed the importance of Tex13b in germ cells development and Its association with male infertility.


title: House sparrows do not exhibit a preference for the scent of potential partners with different MHC-I allele numbers and genetic distances

abstract: MHC genes play a fundamental role in immune recognition of pathogens and parasites. Therefore, females may increase offspring heterozygosity and genetic diversity by selecting MHC genetically compatible or heterozygous males. In birds, several studies suggest that MHC genes play a role in mate choice, and recent evidence suggest that olfaction may play a role in such discrimination. Previous studies indicated that house sparrow females with low allelic diversity prefer males with higher diversity in MHC-I alleles. Here, we directly explored whether both house sparrow females and males could estimate by scent the number in MHC amino acid and functional variants as well as the level of MHC-I similarity or dissimilarity of potential partners. Our results show that neither females nor males exhibit a preference related to the number of MHC-I amino acid variants or functional variants or in relation to MHC amino acid or functional similarity of potential partners, suggesting that MHC-I is not detected through olfaction. Further studies are needed to understand the mechanisms responsible for MHC-I based mate discrimination in birds.


title: Rational design yields molecular insights on leaf binding of the anchor peptide Macaque Histatin

abstract: 1In times of a constantly growing world population and increasing demand for food, sustainable agriculture is crucial. To reduce the amount of applied nutrients, herbicides, and fungicides, the rainfastness of plant protection agents is of pivotal importance. As a result of protective agent wash-off, plant protection is lost, and soils and groundwater are severely polluted. To date, rainfastness of plant protection products is achieved by adding polymeric adjuvants to the agrochemicals. However, polymeric adjuvants will be regarded as microplastics in the future, and environmentally friendly alternatives are needed. Anchor peptides (APs) are promising biobased and biodegradable adhesion promoters. While the adhesion of anchor peptides to artificial surfaces, such as polymers, has already been investigated in theory and experimentally, exploiting the adhesion to biological surfaces remains challenging. The complex nature and composition of biological surfaces such as plant leaf and fruit surfaces complicate the generation of accurate models. Here, we present the first detailed three-layered atomistic model of the surface of apple leaves and use it to compute free energy profiles of the adhesion and desorption of APs to and from that surface. Our model is validated by a novel fluorescence-based MTP assay that mimicks these complex processes and allows quantifying them. For the AP Macaque Histatin, we demonstrate that aromatic and positively charged amino acids are essential for binding to the waxy apple leaf surface. The established protocols should generally be applicable for tailoring the binding properties of APs to biological interfaces.


title: Magnetic Temporal Interference for Noninvasive Focal Brain Stimulation

abstract: Non-invasive stimulation of deep brain regions has been a major goal for neuroscience and neuromodulation in the past three decades. Transcranial magnetic stimulation (TMS), for instance, cannot target deep regions in the brain without activating the overlying tissues and has a poor spatial resolution. In this manuscript, we propose a new concept that relies on the temporal interference of two high-frequency magnetic fields generated by two electromagnetic solenoids. To illustrate the concept, custom solenoids were fabricated and optimized to generate temporal interfering electric fields for rodent brain stimulation. C-Fos expression was used to track neuronal activation. C-Fos expression was not present in regions impacted by only one high-frequency magnetic field indicating ineffective recruitment of neural activity in non-target regions. In contrast, regions impacted by two fields that interfere to create a low-frequency envelope display a strong increase in c-Fos expression. Therefore, this magnetic temporal interference solenoid-based system provides a framework to perform further stimulation studies that would investigate the advantages it could bring over conventional TMS systems.


title: EagleImp: Fast and Accurate Genome-wide Phasing and Imputation in a Single Tool

abstract:
BackgroundReference-based phasing and genotype imputation algorithms have been developed with sublinear theoretical runtime behaviour, but runtimes are still high in practice when large genome-wide reference datasets are used.

MethodsWe developed EagleImp, a software with algorithmic and technical improvements and new features for accurate and accelerated phasing and imputation in a single tool.

ResultsWe compared accuracy and runtime of EagleImp with Eagle2, PBWT and prominent imputation servers using whole-genome sequencing data from the 1000 Genomes Project, the Haplotype Reference Consortium and simulated data with more than 1 million reference genomes. EagleImp is 2 to 10 times faster (depending on the single or multiprocessor configuration selected) than Eagle2/PBWT, with the same or better phasing and imputation quality in all tested scenarios. For common variants investigated in typical GWAS studies, EagleImp provides same or higher imputation accuracy than the Sanger Imputation Service, Michigan Imputation Server and the newly developed TOPMed Imputation Server, despite larger (not publicly available) reference panels. It has many new features, including automated chromosome splitting and memory management at runtime to avoid job aborts, fast reading and writing of large files, and various user-configurable algorithm and output options.

ConclusionsDue to the technical optimisations, EagleImp can perform fast and accurate reference-based phasing and imputation for future very large reference panels with more than 1 million genomes. EagleImp is freely available for download from https://github.com/ikmb/eagleimp.

category: bioinformatics


title: GoPeaks: Histone Modification Peak Calling for CUT&Tag

abstract: Genome-wide mapping of the histone modification landscape is critical to understanding tran-scriptional regulation. Cleavage Under Targets and Tagmentation (CUT&Tag) is a new method for profiling the localization of covalent histone modifications, offering improved sensitivity and decreased cost compared with Chromatin Immunoprecipitation Sequencing (ChIP-seq). Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. GoPeaks implements a Binomial distribution and stringent read count cut-off to nominate candidate genomic regions. We compared the performance of GoPeaks against commonly used peak calling algorithms to detect H3K4me3, H3K4me1, and H3K27Ac peaks from CUT&Tag data. These histone modifications display a range of peak profiles and are frequently used in epigenetic studies. We found GoPeaks robustly detects genome-wide histone modifications and, notably, identifies H3K27Ac with improved sensitivity compared to other standard peak calling algorithms.


title: Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres

abstract: Nanopore long-read genome sequencing is emerging as a potential approach for the study of genomes including long repetitive elements like telomeres. Here, we report extensive basecalling induced errors at telomere repeats across nanopore datasets, sequencing platforms, basecallers, and basecalling models. We found that telomeres which are represented by (TTAGGG)n and (CCCTAA)n repeats in many organisms were frequently miscalled (~40-50% of reads) as (TTAAAA)n, or as (CTTCTT)n and (CCCTGG)n repeats respectively in a strand-specific manner during nanopore sequencing. We showed that this miscalling is likely caused by the high similarity of current profiles between telomeric repeats and these repeat artefacts, leading to mis-assignment of electrical current profiles during basecalling. We further demonstrated that tuning of nanopore basecalling models, and selective application of the tuned models to telomeric reads led to improved recovery and analysis of telomeric regions, with little detected negative impact on basecalling of other genomic regions. Our study thus highlights the importance of verifying nanopore basecalls in long, repetitive, and poorly defined regions of the genome, and showcases how such artefacts in regions like telomeres can potentially be resolved by improvements in nanopore basecalling models.


title: Predicting patient treatment response and resistance via single-cell transcriptomics of their tumors

abstract: Tailoring the best treatments to cancer patients is an important open challenge. Here, we build a precision oncology data science and software framework for PERsonalized single-Cell Expression-based Planning for Treatments In Oncology (PERCEPTION). Our approach capitalizes on recently published matched bulk and single-cell transcriptome profiles of large-scale cell-line drug screens to build treatment response models from patients single-cell (SC) tumor transcriptomics. First, we show that PERCEPTION successfully predicts the response to monotherapy and combination treatments in screens performed in cancer and patient-tumor-derived primary cells based on SC-expression profiles. Second, it successfully stratifies responders to combination therapy based on the patients tumors SC-expression in two very recent multiple myeloma and breast cancer clinical trials. Thirdly, it captures the development of clinical resistance to five standard tyrosine kinase inhibitors using tumor SC-expression profiles obtained during treatment in a lung cancer patients cohort. Notably, PERCEPTION outperforms state-of-the-art bulk expression-based predictors in all three clinical cohorts. In sum, this study provides a first-of-its-kind conceptual and computational method that is predictive of response to therapy in patients, based on the clonal SC gene expression of their tumors.


title: Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

abstract:
The development of cancer therapies may be improved by the discovery of tumor-specific molecular dependencies. The requisite tools include genetic and chemical perturbations, each with its strengths and limitations. Drug perturbations can be readily applied to primary cancer samples at a large scale, but mechanistic understanding of hits and further pharmaceutical development is often complicated by the fact that a small compound has a range of affinities to multiple proteins.

To computationally infer the molecular dependencies of individual cancers from their ex-vivo drug sensitivity profiles, we developed a mathematical model that deconvolutes these data using measurements of protein-drug affinity profiles.

Our method, DepInfeR, correctly identified known dependencies, including EGFR dependence in Her2+ breast cancer cell line, FLT3 dependence in AML tumors with FLT3-ITD mutations and the differential dependencies on the B-cell receptor pathway in two major subtypes of chronic lymphocytic leukemia (CLL). Furthermore, our method uncovered new subgroup-specific dependencies, including a previously unreported dependence of high-risk CLL on Checkpoint kinase 1 (CHEK1). The method also produced a more accurate map of the molecular dependencies in a heterogeneous set of 117 CLL samples.

The ability to deconvolute polypharmacological phenotypes into underlying causal molecular dependencies should increase the utility of high-throughput drug response assays for functional precision oncology.


title: ProtFinder: finding subcellular locations of proteins using protein interaction networks

abstract: AO_SCPLOWBSTRACTC_SCPLOWProtein subcellular localization prediction plays a crucial role in improving our understanding of different diseases and consequently assists in building drug targeting and drug development pipelines. Proteins are known to co-exist at multiple subcellular locations which make the task of prediction extremely challenging. A protein interaction network is a graph that captures interactions between different proteins. It is safe to assume that if two proteins are interacting, they must share some subcellular locations. With this regard, we propose ProtFinder - the first deep learning-based model that exclusively relies on protein interaction networks to predict the multiple subcellular locations of proteins. We also integrate biological priors like the cellular component of Gene Ontology to make ProtFinder a more biology-aware intelligent system. ProtFinder is trained and tested using the STRING and BioPlex databases whereas the annotations of proteins are obtained from the Human Protein Atlas. Our model obtained an AUC-ROC score of 90.00% and an MCC score of 83.42% on a held-out set of proteins. We also apply ProtFinder to annotate proteins that currently do not have confident location annotations. We observe that ProtFinder is able to confirm some of these unreliable location annotations, while in some cases complementing the existing databases with novel location annotations. The source code for ProtFinder is available at https://github.com/UCLouvain-CBIO/ProtFinder.


title: PEGPH20, a PEGylated Human Hyaluronidase, Induces Radiosensitization by Reoxygenation In Pancreatic Cancer Xenografts. A Molecular Imaging Study

abstract: PEGylated human hyaluronidase (PEGPH20) enzymatically depletes hyaluronan, an important component of the extracellular matrix, in tumors. The resultant improvement in vascular patency and perfusion has been shown to increase the delivery of therapeutic molecules. We show that PEGPH20 also improves the efficacy of radiation therapy in a human pancreatic adenocarcinoma BxPC3 mouse model overexpressing hyaluronan synthase 3 (BxPC3-HAS3) while exerting little effect on the corresponding wild type tumors. Mice overexpressing HAS3 developed fast growing, radiation resistant tumors that became rapidly more hypoxic as time progressed. Treatment with PEGPH20 increased survival times when used in combination with radiation therapy, significantly more than either radiation therapy or PEGPH20 alone. Radiosensitization in BxPC3-HAS3 tumors was attributed to an increase in local pO2 as studied by by EPR imaging. No effect on survival, radiation treatment, or pO2 was seen in wild type tumors after PEGPH20 treatment. Dynamic contrast enhanced (DCE) MRI and MRI based blood volume imaging showed improved perfusion/permeability and local blood volume, respectively, in BxPC3-HAS3 tumors after PEGPH20 treatment, accounting for the increase in tumor oxygenation. Photoacoustic imaging indicated immediate changes in tumor oxygenation after treatment. Metabolic MRI using hyperpolarized [1-13C] pyruvate suggested a metabolic shift towards decreased glycolytic flux after PEGPH20 treatment. In summary, the results showed that PEGPH20 may be useful for radiosensitization of pancreatic cancer but only in the subset of tumors with substantial hyaluronan accumulation and the response of the treatment may potentially be monitored non-invasive imaging of the hemodynamic and metabolic changes in the tumor microenvironment.


title: Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks

abstract:
Muscle-invasive bladder cancer (BLCA) is an aggressive disease. Consensus BLCA transcriptomic subtypes have been proposed, with two major Luminal and Basal subgroups, presenting distinct molecular and clinical characteristics. However, how these distinct subtypes are regulated remains unclear. We hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of BLCA subtypes.

Through integrated RNA-sequencing and epigenomic profiling of histone marks in primary tumours, cancer cell lines, and normal human urothelia, we established the first integrated epigenetic map of BLCA and demonstrated the link between subtype and epigenetic control. We identified the repertoire of activated super-enhancers and highlighted Basal, Luminal and Normal-associated SEs. We revealed the super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal subgroups including FOXA1 and ZBED2 respectively. FOXA1 CRISPR-Cas9 mutation triggered a shift from Luminal to Basal phenotype, confirming its role in Luminal identity regulation and induced ZBED2 overexpression. In parallel, we showed that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in cancer cells through STAT2 inhibition.

Our study furthers the understanding of epigenetic regulation of muscle-invasive BLCA and identifies a co-regulated network of super-enhancers and associated transcription factors providing potential targets for the treatment of this aggressive disease.


title: mTORC2 Drives ZFX-mediated Ganglioside Biosynthesis to Promote Breast Cancer Progression.

abstract: Sphingolipid and ganglioside metabolic pathways are crucial components of cell signalling, having established roles in tumor cell proliferation, invasion, and migration. However, regulatory mechanisms controlling sphingolipid and ganglioside synthesis in mammalian cells is less known. Here, we show that RICTOR, the regulatory subunit of mTORC2, regulates the synthesis of sphingolipids and gangliosides in Luminal breast cancer-specific MCF-7 cells through transcriptional and epigenetic mechanisms. RICTOR regulates glucosylceramide levels by modulating the expression of UDP-Glucose Ceramide Glucosyl transferase (UGCG). We identify Zinc Finger protein X-linked (ZFX) as a RICTOR-responsive transcription factor whose recruitment to the UGCG promoter is regulated by DNA methyltransferases and histone demethylase (KDM5A) that are known AKT substrates. We further demonstrate that RICTOR regulates the synthesis of GD3 gangliosides through ZFX and UGCG, and triggers the activation of the EGFR signalling pathway, thereby promoting tumor growth. In line with our findings in cell culture and mice models, we observe an elevated expression of RICTOR, ZFX, and UGCG in Indian Luminal breast cancer patient samples, and in TCGA and METABRIC datasets. Together, we establish a key regulatory circuit, RICTOR-AKT-ZFX-UGCG-Ganglioside-EGFR-AKT, and elucidate its contribution to breast cancer progression.


title: Uncovering potential interventions for pancreatic cancer patients via mathematical modeling

abstract: Pancreatic Ductal Adenocarcinoma (PDAC) is widely known for its poor prognosis because it is often diagnosed when the cancer is in a later stage. We built a model to analyze the microenvironment of pancreatic cancer in order to better understand the interplay between pancreatic cancer, stellate cells, and their signaling cytokines. Specifically, we have used our model to study the impact of inducing four common mutations: KRAS, TP53, SMAD4, and CDKN2A. After implementing the various mutation combinations, we used our stochastic simulator to derive aggressiveness scores based on simulated attractor probabilities and long-term trajectory approximations. These aggression scores were then corroborated with clinical data. Moreover, we found sets of control targets that are effective among common mutations. These control sets contain nodes within both the pancreatic cancer cell and the pancreatic stellate cell, including PIP3, RAF, PIK3 and BAX in pancreatic cancer cell as well as ERK and PIK3 pancreatic stellate cell. Many of these nodes were found to be differentially expressed among pancreatic cancer patients in the TCGA database. Furthermore, literature suggests that many of these nodes can be targeted by drugs currently in circulation. The results herein help provide a proof of concept in the path towards personalized medicine through a means of mathematical systems biology. All data and code used for running simulations, statistical analysis, and plotting is available on a GitHub repository at https://github.com/drplaugher/PCC_Mutations.

category: systems biology