title: Chromatin accessibility and transcription factors in invasive lobular and ductal breast cancers

abstract: Background: Invasive lobular breast carcinoma (ILC), the second most prevalent histological subtype of breast cancer, exhibits unique molecular features compared with the more common invasive ductal carcinoma (IDC). While genomic and transcriptomic features of ILC and IDC have been characterized, genome-wide chromatin accessibility pattern differences between ILC and IDC remain largely unexplored. Methods: Here, we characterized tumor-intrinsic chromatin accessibility differences between ILC and IDC using primary tumors from The Cancer Genome Atlas (TCGA) breast cancer assay for transposase-accessible chromatin with sequencing (ATAC-seq) dataset. Results: We identified distinct patterns of genome-wide chromatin accessibility in ILC and IDC. Inferred patient-specific transcription factor (TF) motif activities revealed regulatory differences between and within ILC and IDC tumors. EGR1, RUNX3, TP63, STAT6, SOX family, and TEAD family TFs were higher in ILC, while ATF4, PBX3, SPDEF, PITX family, and FOX family TFs were higher in IDC. Conclusions: This study reveals the distinct epigenomic features of ILC and IDC and the active TFs driving cancer progression that may provide valuable information on patient prognosis.


title: Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas

category: cancer biology


title: A novel Pyk2-derived peptide inhibits invadopodia-mediated breast cancer metastasis

abstract: The non-receptor tyrosine kinase Pyk2 is highly expressed in breast cancer, where it mediates invadopodia formation and function via interaction with the actin-nucleation promoting factor cortactin. Here, we designed a cell-permeable peptide inhibitor that contains the second proline-rich region (PRR2) sequence of Pyk2, which binds to the SH3 domain of cortactin and blocks spontaneous lung metastasis in immune-competent mice by inhibiting invadopodia maturation and function. The native structure of the Pyk2-PRR2:cortactin-SH3 complex was determined using nuclear magnetic resonance (NMR), revealing an extended class II interaction surface spanning the canonical binding groove and a second hydrophobic surface which significantly contributes to ligand affinity. Using structure-guided design, we created a mutant peptide lacking critical residues involved in binding that failed to inhibit invadopodia maturation and function and consequent metastatic dissemination in mice. Our findings shed light on the specific molecular interactions between Pyk2 and cortactin and suggest that their inhibition may be used as a novel strategy for blocking breast cancer metastasis.


title: Hypoxia-mediated suppression of pyruvate carboxylase drives tumor microenvironment immunosuppression

abstract: Metabolic reprogramming and immune evasion are established hallmarks of the tumor microenvironment (TME). Growing evidence supports tumor metabolic dysregulation as an important mediator of tumor immune evasion. High TME levels of lactate potently suppress antitumor immunity. Pyruvate carboxylase (PC), the enzyme responsible for the anaplerotic conversion of pyruvate to oxaloacetate, is essential for lung metastasis in breast cancer. Moreover, PC may be dispensable in some cells within the TME, and loss of PC expression is associated with immunosuppression. Here we test whether PC suppression alters tumor metabolism and immunosuppression. Using multiple animal models of breast cancer, we identify a dimorphic role for PC expression in mammary cancer cells. Specifically, PC supports metastatic colonization of the lungs, while suppression of PC promotes primary tumor growth and suppresses histological and transcriptomic markers of antitumor immunity. We demonstrate that PC is potently suppressed by hypoxia, and that PC is frequently suppressed in solid tumors, particularly those with higher levels of hypoxia. Using metabolomics, high-resolution respirometry, and extracellular flux analysis, we show that PC-suppressed cells produce more lactate and undergo less oxidative phosphorylation than controls. Finally, we identify lactate metabolism as a targetable dependency of PC-suppressed cells, which is sufficient to restore T cell populations to the TME of PC-suppressed tumors. Taken together, these data demonstrate that elevated lactate following PC suppression by hypoxia may be a key mechanism through which primary tumors limit antitumor immunity. Thus, these data highlight that PC-directed tumor metabolism is a nexus of tumor progression and antitumor immunity.


title: Identification of plasma proteins associated with oesophageal cancer chemotherapeutic treatment outcomes using SWATH-MS

abstract: Oesophageal adenocarcinoma (OAC) is an aggressive cancer with a five-year survival of <15%. Current chemotherapeutic strategies only benefit a minority (20-30%) of patients and there are no methods available to differentiate between responders and non-responders. We performed quantitative proteomics using Sequential Window Acquisition of all THeoretical fragment-ion spectra-Mass Spectrometry (SWATH-MS) on albumin/IgG-depleted and non-depleted plasma samples from 23 patients with locally advanced OAC prior to treatment. Individuals were grouped based on tumour regression (TRG) score (TRG1/2/3 vs TRG4/5) after chemotherapy, and differentially abundant proteins were compared. Protein depletion of highly abundant proteins led to the identification of around twice as many proteins. SWATH-MS revealed significant quantitative differences in the abundance of several proteins between the two groups. These included complement c1q subunit proteins, C1QA, C1QB and C1QC, which were of higher abundance in the low TRG group. Of those that were found to be of higher abundance in the high TRG group, GSTP1 was found to exhibit the lowest p-value and highest classification accuracy and Cohens kappa value. Concentrations of these proteins were further examined using ELISA-based assays. This study provides quantitative information relating to differences in the plasma proteome that underpin response to chemotherapeutic treatment in oesophageal cancers.


title: Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells

abstract:
Acute myeloid leukemias (AML) are comprised of multiple cell types with distinct capabilities to propagate the disease and resist therapy. Approximately 20% of AML patients carry gain- of-function mutations in IDH1 or IDH2 that result in over-production of the onco-metabolite 2-HG. Although IDH inhibitors can induce complete morphological remission, almost all patients eventually relapse. Analysis of clinical samples suggests that a population of IDH mutant cells is able to persist during treatment eventually acquiring 2-HG independence and drug resistance. Herein we characterized the molecular and cellular responses to the clinical IDH1 inhibitor AG-120 at high resolution using a novel multi-allelic mouse model of IDH1 mutant AML. We demonstrate that AG-120 exerts cell type-dependent effects on leukemic cells promoting delayed disease regression. Although IDH1 inhibition alone was not able to fully eradicate the disease, we uncovered that it increases cycling of rare leukemic stem cells and triggers transcriptional upregulation of the pyrimidine salvage pathway. Accordingly, AG-120 sensitized IDH1 mutant AML to azacitidine with the combination of AG-120 and azacitidine showing vastly improved efficacy in vivo. Our data highlight the impact of non- genetic heterogeneity on treatment response and provide mechanistic rationale for a drug combination that is being tested in clinical trials.

STATEMENT OF SIGNIFICANCEInhibition of mutant IDH1 in AML is insufficient to eliminate the disease but promotes proliferation of quiescent leukemic stem cells. Our data provide a mechanistic explanation for the observed synergy between IDH inhibitors and azacitidine and suggest that IDH inhibitors may also synergize with other drugs that preferentially target actively dividing cells.


title: Discovery of a novel mesothelin specific human antibody VH domain

abstract: Antibody based therapeutics targeting mesothelin (MSLN) have shown limited anti-tumor activities in clinical trials. Novel antibodies with high affinity and better therapeutic developability properties are needed as preclinical candidates. In the present study, we have isolated and characterized a novel VH domain 3C9 from a large size human immunoglobulin heavy chain variable (VH) domain library. 3C9 exhibited high affinity [KD (dissociation constant) < 3nM] and demonstrated good specificity in a membrane proteome array (MPA). Both CAR-T cells and antibody domain drug conjugations (DDCs) generated with 3C9, showed effective killing of MSLN positive cells in vitro without off-target effects. This is also the first report of the crystal structure of MSLN based on the analysis of the MSLN-3C9 complex which was solved at 2.9 [A] resolution. The newly identified antibody domain is a promising candidate therapeutic against cancer.


title: Divergent MEK/ERK and AMPK signaling dictate lipogenic plasticity and dependence on fatty acid synthesis in Glioblastoma

abstract: Deregulated de novo lipid synthesis (DNLS) is a potential druggable vulnerability in Glioblastoma (GBM), a highly lethal and incurable cancer. Yet the molecular mechanisms that determine susceptibility to DNLS-targeted therapies remain unknown, and the lack of brain-penetrant inhibitors of DNLS has prevented their clinical evaluation as GBM therapeutics. Here, we report that YTX-7739, a clinical-stage, brain-penetrant inhibitor of stearoyl CoA desaturase (SCD), triggers lipotoxicity in patient-derived GBM stem-like cells (GSCs) and inhibits fatty acid desaturation in GSCs orthotopically implanted in mice. When administered as a single agent, or particularly in combination with the first line GBM chemotherapy, Temozolomide (TMZ), YTX-7739 showed therapeutic efficacy in orthotopic GSC mouse models owing to its lipotoxicity and its ability to impair DNA damage repair. Leveraging genetic, pharmacological, and physiological manipulation of key signaling nodes in gliomagenesis, we uncover that aberrant MEK/ERK signaling and its repression of the energy sensor AMP-activated protein kinase (AMPK) primarily drives therapeutic vulnerability to SCD and other DNLS inhibitors. Conversely, AMPK activation mitigates lipotoxicity and renders GSCs impervious to the loss of DNLS, both in culture and in vivo, by decreasing the saturation state of phospholipids and diverting toxic lipids into lipid droplets. Altogether, our findings reveal mechanisms of metabolic plasticity in GSCs and provide a framework for rational integration of DNLS-targeted therapies for the treatment of GBM.


title: Modelling the spatial dynamics of oncolytic virotherapy in the presence of virus-resistant tumor cells

abstract: Oncolytic virotherapy is a promising form of cancer treatment that uses native or genetically engineered viruses to target, infect and kill cancer cells. Unfortunately, this form of therapy is not effective in a substantial proportion of cancer patients, partly due to the occurrence of infection-resistant tumor cells. To shed new light on the mechanisms underlying therapeutic failure and to discover strategies that improve therapeutic efficacy we designed a cell-based model of viral infection. The model allows to investigate the dynamics of infection-sensitive and infection-resistant cells in tumor tissue in presence of the virus. To reflect the importance of the spatial configuration of the tumor on the efficacy of virotherapy, we compare three variants of the model: two 2D models of a monolayer of tumor cells and a 3D model. In all model variants, we systematically investigate how the therapeutic outcome is affected by properties of the virus (e.g. the rate of viral spread), the tumor (e.g. production rate of resistant cells, cost of resistance), the healthy stromal cells (e.g. degree of resistance to virus) and the timing of treatment. We find that various therapeutic outcomes are possible when resistant cancer cells arise at low frequency in the tumor. These outcomes depend in an intricate but predictable way on the death rate of infected cells, where faster death leads to rapid virus clearance and cancer persistence. Our simulations reveal three different causes of therapy failure: rapid clearance of the virus, rapid selection of resistant cancer cells, and a low rate of viral spread due to the presence of infection-resistant healthy cells. Our models suggest that improved therapeutic efficacy can be achieved by sensitizing healthy stromal cells to infection, although this remedy has to be weighed against the toxicity induced in the healthy tissue.


title: RNA decay defines the therapeutic response to transcriptional perturbation in cancer

abstract:
Transcriptionally dysregulated cancers are sensitive to the inhibition of RNA Polymerase II (RNAPII) - driven gene expression. The therapeutic effect is attributed to selective inhibition of discrete oncogenes regulated at the chromatin level, however the role of RNA stability remains largely unexplored. Using integrated transcriptomic technologies, we discovered that RNA decay is a key determinant in defining gene expression responses to transcriptional perturbation, where total RNA signatures are dominated with genes that have short transcript half-lives, including oncogenic drivers such as c-MYC. Experimentally increasing c-MYC RNA stability maintained total c-MYC RNA levels following RNAPII perturbation, despite a concordant decrease in nascent RNA. Taken together, these data demonstrate that RNA decay shapes the molecular and therapeutic response to transcriptional perturbation in cancer.

HIGHLIGHTSO_LISelective inhibition of oncogenic transcription in response to epigenetic and transcriptional inhibitors in cancer under-estimates the role of RNA decay
C_LIO_LIGene intrinsic RNA decay rates are a key determinant in shaping the total mRNA response to transcriptional perturbation in cancer
C_LIO_LISelective disruption of core-transcription factor networks is a result of short transcript half-lives
C_LIO_LIModulation of c-MYC decay rates can render it insensitive to transcriptional targeting
C_LI


title: Mapping phenotypic heterogeneity in melanoma onto the epithelial-hybrid-mesenchymal axis

abstract: Epithelial to mesenchymal transition (EMT) is a well-studied hallmark of epithelial-like cancers that is characterized by loss of epithelial markers and gain of mesenchymal markers. Interestingly, melanoma, which is derived from melanocytes of the skin, also undergo phenotypic plasticity toward mesenchymal-like phenotypes under the influence of various micro-environmental cues. Our study connects EMT to the phenomenon of de-differentiation (i.e., transition from proliferative to more invasive phenotypes) observed in melanoma cells during drug treatment. By analyzing 78 publicly available transcriptomic melanoma datasets, we found that de-differentiation in melanoma is accompanied by upregulation of mesenchymal genes, but not necessarily a concomitant loss of an epithelial program, suggesting a more "one-dimensional" EMT that leads to a hybrid epithelial/ mesenchymal phenotype. Samples lying in the hybrid epithelial/mesenchymal phenotype also correspond to the intermediate phenotypes in melanoma along the proliferative-invasive axis - neural crest and transitory ones. Interestingly, as melanoma cells progress along the invasive axis, the mesenchymal signature does not increase monotonically. Instead, we observe a peak in mesenchymal scores followed by a decline, as cells further de-differentiate. This biphasic response recapitulates the dynamics of melanocyte development, suggesting close interactions among genes controlling differentiation and mesenchymal programs in melanocytes. Similar trends were noted for metabolic changes often associated with EMT in carcinomas in which progression along mesenchymal axis correlates with the downregulation of oxidative phosphorylation, while largely maintaining glycolytic capacity. Overall, these results provide an explanation for how EMT and dedifferentiation axes overlap with respect to their transcriptional and metabolic programs in melanoma.


title: Propofol disrupts alpha dynamics in distinct thalamocortical networks underlying sensory and cognitive function during loss of consciousness

abstract: During propofol-induced general anesthesia, alpha rhythms undergo a striking shift from posterior to anterior, termed anteriorization. We combined human intracranial recordings with diffusion imaging to show that anteriorization occurs with opposing dynamics in two distinct thalamocortical subnetworks. The cortical and thalamic anatomy involved, as well as their known functional roles, suggest multiple means by which propofol dismantles sensory and cognitive processes to achieve loss of consciousness.

category: neuroscience


title: Unaltered T cell responses to common antigens in individuals with Parkinson's disease

abstract:
Background and ObjectivesParkinsons disease (PD) is associated with a heightened inflammatory state, including activated T cells. However, it is unclear whether these PD T cell responses are antigen specific or more indicative of generalized hyperresponsiveness. Our objective was to measure and compare antigen-specific T cell responses directed towards antigens derived from commonly encountered human pathogens/vaccines in patients with PD and age-matched healthy controls (HC).

MethodsPeripheral blood mononuclear cells (PBMCs) from 20 PD patients and 19 age-matched HCs were screened. Antigen specific T cell responses were measured by flow cytometry using a combination of the activation induced marker (AIM) assay and intracellular cytokine staining.

ResultsHere we show that both PD patients and HCs show similar T cell activation levels to several antigens derived from commonly encountered human pathogens/vaccines in the general population. Similarly, we also observed no difference between HC and PD in the levels of CD4 and CD8 T cell derived cytokines produced in response to any of the common antigens tested. These antigens encompassed both viral (coronavirus, rhinovirus, respiratory syncytial virus, influenza, cytomegalovirus) and bacterial (pertussis, tetanus) targets.

ConclusionsThese results suggest the T cell dysfunction observed in PD may not extend itself to abnormal responses to commonly encountered or vaccine-target antigens. Our study supports the notion that the targets of inflammatory T cell responses in PD may be more directed towards autoantigens like -synuclein (-syn) rather than common foreign antigens.

category: immunology


title: Reactive Oxygen Species Signaling Differentially Controls Wound Healing and Regeneration

abstract: Reactive oxygen species (ROS), such as hydrogen peroxide, are conserved and critical components of both wound healing and regeneration. Even though millions are affected each year by poor wound healing and an inability to restore functional tissue, how the same ROS-mediated signaling regulates these two different processes is not fully understood. Here, we investigate the role(s) of ROS during planarian wound healing and regeneration. We show ROS accumulate after injury and are required for wound closure (by promoting cytoskeletal movements) and regrowth (by promoting blastema formation). We found that different threshold levels of ROS regulate separate downstream targets to control wound healing (jun-1) versus regeneration (hsp70). By only manipulating ROS levels, we were able to control which injury-induced program was initiated: failure to close (chronic wound), healing only (no blastema), or full regeneration. Our results demonstrate that healing versus regenerative outcomes are based on differential ROS-mediated gene expression soon after injury. This study highlights ROS signaling as a potential therapeutic means to control wound repair mechanisms in multiple contexts. Therefore, investigating the mechanisms by which ROS control different tissue repair processes will be necessary not only for regenerative medicine but to improve clinical outcomes for chronic wounds and fibrosis.

category: developmental biology


title: Epistasis between synonymous and nonsynonymous mutations in Dictyostelium discoideum ammonium transporter amtA drives functional complementation in Saccharomyces cerevisiae.

abstract:
Role of Horizontal Gene Transfer (HGT) in evolution transcends across the three domains of life. Ammonium transporters are present in all species and therefore offer an excellent paradigm to study protein evolution following HGT. While investigating HGT through complementation assay, we observed that synonymous and nonsynonymous mutations follow an epistastic relationship. As a proxy for HGT, we attempted to complement a mep1mep2mep3{Delta} strain of S. cerevisiae (triple deletion strain) which cannot grow on ammonium as a sole nitrogen source below a concentration of 3 mM, with amtA of D. discoideum. As the wild type amtA did not complement, we isolated two mutant derivatives of amtA that complemented the triple deletion strain of S. cerevisiae. amtA M1 bears three nonsynonymous and two synonymous substitutions and these substitutions are necessary for its functionality. amtA M2 bears two nonsynonymous and one synonymous substitution, all of which are necessary for functionality. These mutants were then studied at phenotypic, cell biological, and biochemical level. Interestingly, AmtA M1 transports ammonium but does not confer toxicity to methylamine while AmtA M2 transports ammonium as well as confers methylamine toxicity, demonstrating functional diversification. Based on the results presented, we suggest that protein evolution cannot be fathomed by studying nonsynonymous and synonymous substitutions separately. This is because, protein evolution entails an interaction between synonymous and nonsynonymous substitution, which seems to have gone unnoticed thus far. Above observations have significant implications in various facets of biological processes and are discussed in detail.

HighlightsO_LIAmmonium transporters (Amts) from bacteria to humans complement in yeast
C_LIO_LIAmtA of D. discoideum does not complement yeast defective for ammonium uptake
C_LIO_LISynonymous & nonsynonymous mutations are essential for AmtA functionality in yeast
C_LIO_LIConformational differences underlie functionality & functional diversification
C_LIO_LIProtein evolution entails interaction of synonymous & nonsynonymous mutations
C_LI

category: genetics


title: Deploying genomics workflows on high performance computing (HPC) platforms: storage, memory, and compute considerations

abstract: Next Generation Sequencing (NGS) workloads largely consist of pipelines of tasks with heterogeneous compute, memory, and storage requirements. Identifying the optimal system configuration has historically required expertise in both system architecture and bioinformatics. This paper outlines infrastructure recommendations for one commonly used genomics workload based on extensive benchmarking and profiling, along with recommendations on how to tune genomics workflows for high performance computing (HPC) infrastructure. The demonstrated methodology and learnings can be extended for other genomics workloads and for other infrastructures such as the cloud.

category: bioinformatics


title: SOX9 binds TCFs to mediate Wnt/β catenin target gene activation

abstract: Activation of the Wnt/{beta}-catenin pathway regulates gene expression by promoting the formation of a {beta}-catenin-TCF complex on target gene chromatin. The transcription factor SOX9 antagonises Wnt signalling in many contexts through its ability to down-regulate {beta}-catenin protein levels. Here, we find that SOX9 promotes the proliferation of Wnt-driven colorectal cancer (CRC) cells. We identify multiple enhancers activated by SOX9 working in concert with the Wnt pathway. These enhancers are co-occupied by TCFs and SOX9 and contain TCF and SOX9 binding sites that are necessary for transcriptional activation. In addition, we identify a physical interaction between the DNA-binding domains of TCFs and SOX9 and show that TCF-SOX9 interactions are important for target gene regulation and CRC cell growth. Our work demonstrates a highly context-dependent effect of SOX9 on Wnt targets, with activation or repression being dependent on the presence or absence of SOX9 binding sites on Wnt-regulated enhancers respectively.


title: Mathematical models of tumor volume dynamics in response to radiotherapy

abstract: From the beginning of the usage of radiotherapy (RT) for cancer treatment, mathematical modeling has been integral to understanding radiobiology and for designing treatment approaches and schedules. There has been extensive modeling of response to RT with the inclusion of various degrees of biological complexity. Here we focus on models of tumor volume dynamics. There has been much discussion on the implications of different models of tumor growth, and it is just important to consider the implications of selecting different models for response to RT. In this study, we compare three models of tumor volume dynamics: (1) exponential growth with RT directly reducing tumor volume, (2) logistic growth with direct tumor volume reduction, and (3) logistic growth with RT reducing the tumor carrying capacity. For all three models, we: performed parameter sensitivity and identifiability analyses; investigated the impact of the parameter sensitivity on the tumor volume trajectories; and examined the rates of change in tumor volume ({Delta}V/{Delta}t) during and RT treatment course. The parameter identifiability and sensitivity analyses revealed the interdependence of the different model parameters and may inform parameter calibration in any further usage of these models. In examining the {Delta}V/{Delta}t trends, we coined a new metric - the point of maximum reduction of tumor volume (MRV) - to quantify the magnitude and timing of the expected largest impact of RT during a treatment course. Ultimately, the results of these analyses help us to better understand the implications of model selection while simultaneously generating many hypotheses about the underlying radiobiology that need to be tested on time-resolved measurements of tumor volume from appropriate pre-clinical or clinical data. The answers to these questions and more detailed study of these and similar models of tumor volume dynamics may enable more appropriate model selection on a disease-site or patient-by-patient basis.


title: Functional plasticity and recurrent cell states of malignant B cells in follicular lymphoma

abstract: Follicular lymphoma (FL) derives from malignant transformation of germinal center (GC) B cells. FL malignant B cells are heterogeneous and diverge from their GC B cell-of-origin, but the diversity, function, and location of malignant B cell states remain to be addressed. Based on integrative single-cell RNA-seq, we identified and studied recurrent FL malignant B cell states and dynamics. Most FL B cells spanned a continuum of states from proliferating GC-like to quiescent memory (Mem)-like cell states. That GC-to-Mem axis was the main source of intra-tumor transcriptional heterogeneity. While FL B cell states were independent from subclonal B cell receptor genetics divergence, T follicular helper (TFH) cell-derived signals controlled the transition from Mem-like to GC-like states. GC-like, TFH-activated and Mem-like FL B cells tended to occupy distinct niches within and around tumor follicles. Our study characterizes novel malignant cell states recurrent in B cell lymphomas, and highlights the functional plasticity of malignant B cells.


title: Sexual dimorphism versus biomechanical loading in occipital bone morphological variation

abstract:
This research explores the contribution of biomechanical activity to several metric and non- metric aspects of occipital bone variation. Previous studies note that occipital traits including robusticity and size can often be used to illicit estimates of ancestry and sex. The utility of occipital traits in fragmentary human remains for population affinity or sex however may be compromised by a previously unexplored contribution from biomechanical stress. Through the examination of traits highly associated with biological sex (foramen magnum area, external occipital protuberance depth, lambda-inion length, bicondylar breadth, occipital form, and nuchal line rugosity) this study examined the potential sex estimation against a reflection of gender specific lifestyle differences or changes in activity patterns over time in occipital dimensions. Directly collected data and previously published data were analyzed from several sites, including Archaic hunter-gatherers from Florida, Agricultural groups from South Dakota, and modern populations from FSU teaching collection and the Terry and Hamann-Todd collections. Findings suggest that the foramen magnum area is not sufficiently dimorphic amongst our samples to accurately estimate biological sex and significant inter-group variation in bicondylar breadth and lambda-inion may indicate activity related differences.

HighlightsO_LIThis study examines biological sex estimation reliability from fragmentary occipital material.
C_LIO_LIThis study compares prehistoric, historic, and modern population occipital bone variation.
C_LIO_LIThis study analyzes potential effects of activity on traditionally dimorphic occipital traits.
C_LI

category: physiology


title: Excess ribosomal protein production unbalances translation in Fragile X Syndrome

abstract: Dysregulated protein synthesis is a core pathogenic mechanism in Fragile X Syndrome (FX). The mGluR Theory of FX predicts that pathological synaptic changes arise from the excessive translation of mRNAs downstream of mGlu1/5 activation. Here, we use a combination of CA1 pyramidal neuron-specific TRAP-seq and proteomics to identify the overtranslating mRNAs supporting exaggerated mGlu1/5-induced long-term synaptic depression (mGluR-LTD) in the FX mouse model (Fmr1-/y). Surprisingly, our results identify a robust translation of ribosomal proteins (RPs) upon mGlu1/5 stimulation that coincides with a reduced translation of long mRNAs encoding synaptic proteins. These changes are mimicked and occluded in Fmr1-/y neurons. Inhibiting RP translation significantly impairs mGluR-LTD and prevents the length-dependent shift in the translating population. Together, these results suggest that pathological changes in FX result from a length-dependent alteration in the translating population that is supported by excessive RP translation.


title: A genetic variant of the Wnt receptor LRP6 accelerates synapse degeneration during ageing and in Alzheimer's disease

abstract: Synapse loss strongly correlates with cognitive decline in Alzheimers Disease (AD), but the underlying mechanisms are poorly understood. Studies suggest that deficient Wnt signalling, a pathway required for neuronal connectivity, contributes to synapse dysfunction and loss in AD. Consistent with this idea, a variant of Lrp6, (Lrp6-val), which confers reduced Wnt signalling, has been linked to late onset AD. However, the impact of Lrp6-val on synapses in the healthy and AD brain has not been examined. Using CRISPR/Cas9 genome editing, we generated a novel knock-in mouse model carrying this Lrp6 variant to study its role in synaptic integrity. Lrp6-val mice develop normally and do not exhibit morphological brain abnormalities. Hippocampal neurons from Lrp6-val mice do not respond to Wnt7a, a Wnt ligand that promotes synaptic assembly through the Frizzled-5 (Fz5) receptor. Activation of the Wnt pathway by Wnt ligands leads to the formation of a complex between LRP6 and Fz5. In contrast, LRP6-Val impairs the formation of the LRP6-Fz5 complex elicited by Wnt7a, as detected by proximity ligation assay (PLA). We demonstrate that Lrp6-val mice exhibit structural and functional synaptic defects that become more pronounced with age, consistent with decreased canonical Wnt signalling during ageing. To investigate the contribution of this variant to AD, Lrp6-val mice were crossed to hAPPNL-G-F/NL-G-F (NL-G-F), a knock-in AD mouse model. The presence of the Lrp6-val variant significantly exacerbates synapse loss around amyloid-{beta} plaques in NL-G-F mice. Our findings uncover a novel role for the Lrp6-val variant in synapse vulnerability during ageing and its contribution to synapse degeneration in AD.


title: An EcR probe reveals mechanisms of the ecdysone-mediated switch from repression-to-activation on target genes in the larval wing disc

abstract: Fluctuating levels of steroid hormones provide both systemic and local cues to synchronize metazoan development and control germline and homeostatic processes. The main steroid hormone in Drosophila is ecdysone (Ec), which upon binding of its active form (20E) converts its receptor, EcR, from a transcriptional repressor to activator. Multiple co-repressors and co-activators are proposed to act with EcR in different tissues to control diverse targets and processes, including apoptosis, cell migration, and proliferation. Despite these diverse roles, relatively little is known regarding how EcR translates Ec temporal gradients into modulation of individual target genes. Here we use an Ec-binding fragment of EcR (EcRLBD) as a  sponge to sequester coregulators and probe the state of EcR activity as larval wing cells traverse the 3rd instar Ec gradient. This approach reveals a dramatic and rapid shift from EcR mediated repression-to-activation in late L3 cells, and that the extent of repression varies between targets. An Ala483Thr mutation that disrupts binding of the co-repressor Smr compromises the ability of EcRLBD to derepress reporters, but also limits its ability to block activation, suggesting either that a coactivator shares an EcR-interaction interface with Smr or that Smr-repression primes targets for 20E activation. Molecular and genetic data reveal that EcRLBD sequesters 20E, and that EcRLBD phenotypes can be modulated by manipulating intracellular 20E levels with Ec importer (EcI) and Cyp18a1, which inactivates 20E. Finally, we provide evidence that Smr repression of EcR activity varies spatially and by target in the wing disc. In sum these data reveal that relief of EcR-Smr repression is a major contributor to 20E induction of EcR targets in larval wing discs and highlight EcRLBD as an effective probe to define EcR-20E gene regulatory mechanisms in vivo.


title: Heat and humidity sensors that alert mosquitoes to nearby human hosts

abstract: Mosquito-borne diseases sicken >500,000,000 people annually, killing >500,0001. Mosquito host-seeking is guided by multiple host-associated cues, which combine to drive blood feeding in a manner that remains poorly understood2,3. While heat is a powerful mosquito attractant, recent studies indicate that disruption of heat seeking has little impact on host detection by the malaria vector Anopheles gambiae4, suggesting other cues act alongside heat in the complex sensory environment of a human host. Here we show mosquitoes require Ir93a (an Ionotropic Receptor5) to maintain attraction to a human host and feed on warmed blood. Using Ir93a, we uncover the previously uncharacterized mosquito hygrosensory system, and show Ir93a is required for humidity detection by humidity sensors (hygrosensors) as well as temperature detection by thermosensors, and for attraction to each stimulus. These findings indicate that hygrosensation and thermosensation function in parallel, driving host proximity detection in response to the overlapping heat and humidity gradients humans produce6,7. These host cue sensors appear to have arisen by co-opting existing sensors of physical cues rather than de novo, as Ir93a-dependent thermo- and hygro-sensors support physiological homeostasis in non-blood-feeding insects8-11. While Ir93a is conserved among arthropods, reliance on heat and humidity evolved independently in multiple blood-feeding lineages, suggesting multiple, vector-specific implementations of this common host-seeking strategy.


title: Primary cilia loss promotes reactivation of morphogenesis and cyst-fission through a deregulated TGFβ-ECM-Integrin axis in polycystic liver disease.

abstract: Pathological liver cysts are an important comorbidity in multiple diseases and syndromes(1, 2) driven by dysfunction of the primary cilium (PC), a complex sensory organelle that protrudes from the apical surface of biliary epithelial cells (BECs)(3, 4). The essential nature of PC in liver development(5, 6) makes understanding the molecular role of this organelle in the structural maintenance of the adult bile duct challenging. Here, we show that PC loss deletion of Wdr35 in adult mouse BECs is sufficient to cause bile duct expansion, driving cyst formation through the de novo production of a fibronectin-rich pro-cystic microenvironment. This newly formed niche promotes both cell-autonomous changes in cell shape and duct-level mechanical rearrangements that converge to drive cyst-fission, a novel process whereby single, large cysts undergo morphological splitting. This process gives rise to many, smaller polycystic progeny and can be halted by pharmacological inhibition of a specific pro-cystic integrin receptor.

category: cell biology


title: Interoperability of RTN1A in dendrite dynamics and immune functions in human Langerhans cells

abstract:
Skin is an active immune organ where professional antigen-presenting cells such as epidermal Langerhans cells (LCs) link innate and adaptive immune responses. While Reticulon 1A (RTN1A) was recently identified in LCs and dendritic cells in cutaneous and lymphoid tissues of humans and mice, its function is still unclear. Here, we studied the involvement of this protein in cytoskeletal remodeling and immune responses towards pathogens by stimulation of Toll-like receptors (TLRs) in resident LCs (rLCs) and emigrated LCs (eLCs) in human epidermis ex vivo and in a transgenic THP-1 RTN1A+ cell line. Hampering RTN1A functionality through an inhibitory antibody induced significant dendrite retraction of rLCs and inhibited their emigration. Similarly, expression of RTN1A in THP-1 cells significantly altered their morphology, enhanced aggregation potential and inhibited the Ca2+ flux. Differentiated THP-1 RTN1A+ macrophages exhibited long cell protrusions and a larger cell body size in comparison to wild type cells. Further, stimulation of epidermal sheets with bacterial lipoproteins (TLR1/2 and TLR2) and single-stranded RNA (TLR7) resulted in the formation of substantial clusters of rLCs and a significant decrease of RTN1A expression in eLCs. Together, our data indicate involvement of RTN1A in dendrite dynamics and structural plasticity of primary LCs. Moreover, we discovered a relation between activation of TLRs, clustering of LCs and downregulation of RTN1A within the epidermis, thus indicating an important role of RTN1A in LC residency and maintaining tissue homeostasis.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/487626v1_ufig1.gif" ALT="Figure 1">
View larger version (42K):
org.highwire.dtl.DTLVardef@8011c8org.highwire.dtl.DTLVardef@f784borg.highwire.dtl.DTLVardef@1a28a1corg.highwire.dtl.DTLVardef@195b0f_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIBlocking of RTN1A induces dendrite retraction of resident LCs (rLCs) in epidermal explants.
C_LIO_LIDespite a roundish morphology rLCs exhibit reduced migration capacity.
C_LIO_LIRTN1A has an inhibitory effect on the calcium flux.
C_LIO_LIToll-like receptor-activated rLCs form vast clusters and significantly diminish RTN1A expression after emigration.
C_LIO_LIRTN1A plays a central role in LC residency and maintaining tissue homeostasis.
C_LI


title: A dominant negative mutation uncovers cooperative control of caudal Wolffian Duct development by Sprouty genes

abstract: The Wolffian Ducts (WD) are paired epithelial tubules central to the development of the mammalian genitourinary tract. Outgrowths from the WD known as the ureteric buds (UB) generate the collecting ducts of the kidney. Later during development, the caudal portion of the WD will form the vas deferens, epididymis and seminal vesicle in males, and will degenerate in females. While the genetic pathways controlling the development of the UB are firmly established, less is known about those governing development of WD portions caudal to the UB. Sprouty proteins are inhibitors of receptor tyrosine kinase (RTK) signaling in vivo. We have recently shown that homozygous mutation of a conserved tyrosine (Tyr53) of Spry1 results in UB defects indistinguishable from that of Spry1 null mice. Here we show that heterozygosity for the Spry1 Y53A allele causes caudal WD developmental defects consisting on ectopically branched seminal vesicles in males and persistent WD in females, without affecting kidney development. Detailed analysis reveals that this phenotype also occurs in Spry1+/- mice but with a much lower penetrance, indicating that removal of tyrosine 53 generates a dominant negative mutation in vivo. Supporting this notion, concomitant deletion of one allele of Spry1 and Spry2 also recapitulates the genital phenotype of Spry1Y53A/+ mice with high penetrance. Mechanistically, we show that unlike the effects of Spry1 in kidney development, these caudal WD defects are independent of Ret signaling, but can be completely rescued by lowering the genetic dosage of Fgf10. In conclusion, mutation of tyrosine 53 of Spry1 generates a dominant-negative allele that uncovers fine-tuning of caudal WD development by Sprouty genes.


title: Hydrogens and hydrogen-bond networks in macromolecular MicroED data

abstract: Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that scattered electrons carry informing about the charged state of atoms and can provide strong contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for drug discovery and electron microscopy can enable such visualization. Using subatomic resolution MicroED data obtained from triclinic hen egg-white lysozyme, we identified hundreds of individual hydrogen atom positions and directly visualize hydrogen bonding interactions and the charged states of residues. Over a third of all hydrogen atoms are identified from strong difference peaks, the most complete view of a macromolecular hydrogen network visualized by electron diffraction to date. These results show that MicroED can provide accurate structural information on hydrogen atoms and non-covalent hydrogen bonding interactions in macromolecules. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering and understanding the hydrogen bonding interactions underlying protein structure and function.

category: biochemistry


title: Myosin Heavy Chain Converter Domain Mutations Drive Early-Stage Changes in Extracellular Matrix Dynamics in Hypertrophic Cardiomyopathy

abstract: More than 60% of hypertrophic cardiomyopathy (HCM)-causing mutations are found in the gene loci encoding cardiac myosin-associated proteins including myosin heavy chain (MHC) and myosin binding protein C (MyBP-C). Moreover, patients with more than one independent HCM mutation may be at increased risk for more severe disease expression and adverse outcomes. However detailed mechanistic understanding, especially at early stages of disease progression, is limited. To identify early-stage HCM triggers, we generated single (MYH7 c.2167C>T [R723C] with a known pathogenic significance in the MHC converter domain) and double (MYH7 c.2167C>T [R723C]; MYH6 c.2173C>T [R725C] with unknown significance) myosin gene mutations in human induced pluripotent stem cells (hiPSCs) using a base-editing strategy. Cardiomyocytes (CMs) derived from hiPSCs with either single or double mutation exhibited phenotypic characteristics consistent with later-stage HCM including hypertrophy, multinucleation, altered calcium handling, metabolism and arrhythmia. We then probed mutant CMs at time points prior to the detection of known HCM characteristics. We found MYH7/MYH6 dual mutation dysregulated extracellular matrix (ECM) remodeling, altered integrin expression, and interrupted cell-ECM adhesion by limiting the formation of focal adhesions. These results point to a new phenotypic feature of early-stage HCM and reveal novel therapeutic avenues aimed to delay or prohibit disease onset.

category: bioengineering


title: Parallel cryo electron tomography on in situ lamellae

abstract: In situ cryo electron tomography of cryo focused ion beam milled samples emerged in recent years as a powerful technique for structural studies of macromolecular complexes in their native cellular environment. The lamella-shaped samples, however, have a limited area and are created with a necessary pretilt. This severely limits the possibilities for recording tomographic tilt series in a high-throughput manner. Here, we utilise a geometrical sample model and optical image shift to record tens of tilt series in parallel, thereby saving time and gaining sample areas conventionally used for tracking of specimen movement. The parallel cryo electron tomography (PACE-tomo) method achieves a throughput faster than 5 min per tilt series and allows the collection of sample areas that were previously unreachable, thus maximising the amount of data from each lamella. Performance testing with ribosomes in vitro and in situ on state-of-the-art and general-purpose microscopes demonstrated the high-throughput and high-quality of PACE-tomo.

category: biophysics


title: Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle

abstract: During cell division, the spindle generates force to move chromosomes. In mammals, microtubule bundles called kinetochore-fibers (k-fibers) attach to and segregate chromosomes. To do so, k-fibers must be robustly anchored to the dynamic spindle. We previously developed microneedle manipulation to mechanically challenge k-fiber anchorage, and observed spatially distinct response features revealing the presence of heterogeneous anchorage (Suresh et al. 2020). How anchorage is precisely spatially regulated, and what forces are necessary and sufficient to recapitulate the k-fibers response to force remain unclear. Here, we develop a coarse-grained k-fiber model and combine with manipulation experiments to infer underlying anchorage using shape analysis. By systematically testing different anchorage schemes, we find that forces solely at k-fiber ends are sufficient to recapitulate unmanipulated k-fiber shapes, but not manipulated ones for which lateral anchorage over a 3 m length scale near chromosomes is also essential. Such anchorage robustly preserves k-fiber orientation near chromosomes while allowing pivoting around poles. Anchorage over a shorter length scale cannot robustly restrict pivoting near chromosomes, while anchorage throughout the spindle obstructs pivoting at poles. Together, this work reveals how spatially regulated anchorage gives rise to spatially distinct mechanics in the mammalian spindle, which we propose are key for function.


title: Redox regulation of yeast Hsp70 modulates protein quality control while directly triggering an Hsf1-dependent cytoprotective response

abstract: Neurodegenerative disease affects millions of Americans every year, through diagnoses such as Alzheimers, Parkinsons, and Huntingtons diseases. One factor linked to formation of these aggregates is damage sustained to proteins by oxidative stress. Cellular protein homeostasis (proteostasis) relies on the ubiquitous Hsp70 chaperone family. Hsp70 activity has been previously shown to be modulated by modification of two key cysteines in the ATPase domain by oxidizing or thiol-modifying compounds. To investigate the biological consequences of cysteine modification on the Hsp70 Ssa1 in budding yeast, we generated cysteine null (cysteine to serine) and oxidomimetic (cysteine to aspartic acid) mutant variants of both C264 and C303 and demonstrate reduced ATP binding, hydrolysis and protein folding properties in both the oxidomimetic as well as hydrogen peroxide-treated Ssa1. In contrast, cysteine nullification rendered Ssa1 insensitive to oxidative inhibition. The oxidomimetic ssa1-2CD (C264D, C303D) allele was unable to function as the sole Ssa1 isoform in yeast cells and also exhibited dominant negative effects on cell growth and viability. Ssa1 binds to and represses Hsf1, the major transcription factor controlling the heat shock response, and the oxidomimetic Ssa1 failed to stably interact with Hsf1, resulting in constitutive activation of the heat shock response. Consistent with the in vitro findings, ssa1-2CD cells were compromised for de novo folding, post-stress protein refolding and in regulated degradation of a model terminally misfolded protein. Together these findings pinpoint Hsp70 as a key link between oxidative stress and proteostasis, information critical to understanding cytoprotective systems that prevent and manage cellular insults underlying complex disease states.


title: Dictyostelium discoideum cells sense their local density and retain nutrients when the cells are about to overgrow their food source

abstract: Dictyostelium discoideum is a unicellular eukaryote that eats bacteria, and eventually overgrows the bacteria. D. discoideum cells accumulate extracellular polyphosphate (polyP), and the polyP concentration increases as the local cell density increases. At high cell densities, the correspondingly high extracellular polyP concentrations allow cells to sense that they are about to overgrow their food supply and starve, causing the D. discoideum cells to inhibt their proliferation. In this report, we show that high extracellular polyP inhibits exocytosis of undigested or partially digested nutrients. PolyP decreases cell membrane fluidity and plasma membrane recycling, and this requires the G protein-coupled polyP receptor GrlD, the polyphosphate kinase Ppk1, and the inositol hexakisphosphate kinase I6kA. PolyP did not affect random cell motility, cell speed, or F-actin levels. PolyP decreased membrane saturated fatty acids and altered lipid and protein contents in detergent-insoluble lipid microdomains. Together, these data suggest that D. discoideum cells use polyP as a signal to sense their local cell density and reduce cell membrane fluidity and membrane recycling, perhaps as a mechanism to retain ingested food when the cells are about to starve.


title: The HH-GLI2-CKS1B network regulates the proliferation-to-maturation transition of human cardiomyocytes

abstract: Cardiomyocyte (CM) proliferation and maturation are highly linked processes, however, the extent to which these processes are controlled by a single signaling axis is unclear. Here, we find the Hedgehog (HH)-GLI2-CKS1B cascade regulates the transition between proliferation and maturation in hiPSC-CMs. Initially, we found a significant enrichment of GLI2-signaling in CMs from patients with ischemic heart failure (HF) or dilated-cardiomyopathy (DCM), indicating initiation of fetal programs in the stressed heart. Developmentally, we showed downregulation of GLI-signaling in adult human CM, adult murine CM, and in late-stage hiPSC-CM. In early-stage, proliferative hiPSC-CM, inhibition of Hh- or GLI-proteins enhanced CM maturation. Mechanistically, we identified CKS1B, a new effector of GLI2 and showed that GLI2 binds the CKS1B promoter to regulate its expression. CKS1B overexpression in late-stage hiPSC-CMs led to increased proliferation with loss of maturation. Thus, the Hh-GLI2-CKS1B axis regulates the proliferation-maturation transition and provides targets to enhance cardiac tissue engineering and regenerative therapies.


title: Trim33 conditions the lifespan of primitive macrophages and onset of definitive macrophage production

abstract: TRIM33 (Tif1-{gamma}) is a transcriptional regulator notably involved in several aspects of hematopoiesis. It is essential for the production of erythrocytes in zebrafish, and for the proper functionning and aging of hematopoietic stem and progenitor cells (HSPCs) in mice. Here we have found that in zebrafish development, Trim33 is essential cell-autonomously for the lifespan of the yolk sac derived primitive macrophages, as well as for the initial production of definitive (HSPC-derived) macrophages in the first niche of definitive hematopoiesis, the caudal hematopoietic tissue. Moreover, Trim33 deficiency leads to an excess production of definitive neutrophils and thrombocytes. Our data indicate that Trim33 radically conditions the differentiation ouput of aorta-derived HSPCs in all four erythro-myeloid cell types, in a niche-specific manner.


title: A Comprehensive Roadmap of Human Placental Development in vitro

abstract: Human pluripotent stem cells (hPSCs) represent a powerful model system to study early developmental processes. However, lineage specification into trophectoderm (TE) remains poorly understood and access to well-characterized placental cells for biomedical research is limited, largely depending on fetal tissues or cancer cell lines. Here, we developed novel strategies enabling highly efficient TE specification that generates cytotrophoblast (CTB) and multinucleated primary syncytiotrophoblast (STB) followed by establishment of trophoblast stem cells (TSCs) capable of differentiating into extravillous trophoblast (EVT) and STB after long-term expansion. We confirmed stepwise induction of lineage- and cell-type-specific genes and substantiated typical features of placental cells using morphological, biochemical, integrated multi-omics, and single-cell analyses. Our data provide conclusive evidence that conventional hPSCs can be directly and exclusively converted into TE, thereby providing an unlimited source of diverse placental cell types suitable for a broad range of biomedical applications.


title: Intraspecific diversity based on low temperature induced arrhythmia in embryonic heart of medaka (Oryzias latipes)

abstract:
BackgroundCold tolerance during embryonic development, especially blood circulation is important for growth in poikilothermic animals. Medaka (Oryzias latipes), has cold tolerance and is distributed in the highest latitudes occupied by the genus Oryzias. Regarding cold tolerance in embryogenesis, Hd-rR strain belonging to the southern Japanese (S.JPN) group showed arrhythmia when the embryo was exposed to 15 {degrees}C in the heartbeat initiation period (st. 24), whereas the embryo of Odate medaka, which belongs to the northern Japanese (N.JPN) group, showed stable heartbeats.

ResultsIn this study, to verify the sensitivity to low temperature in the medaka wild populations, heartbeat intervals of st. 24 embryos derived from three N.JPN, eight S.JPN, and two western Korean/Chinese (W.KOR) populations were investigated at an arbitrary temperature range of 12-15 {degrees}C. There was no significant difference in the mean values of the heart rates and the coefficient of variation (CV) of interbeat intervals in the N.JPN, S.JPN, and W.KOR groups. A temperature dependency of the CV within 12-15 {degrees}C was observed only in five S.JPN specimens, whereas three S.JPN, the N.JPN and the W.KOR specimens showed no alteration in CV with temperature. Temperature dependency of the heart rate was also varied in the S.JPN specimens.

ConclusionsThese results suggest that the temperature dependency of the CV under 12-15 {degrees}C during the heartbeat initiation period is a variation within the S.JPN after the divergence from the N.JPN.


title: DOT1L activity affects cell lineage progression in the developing brain by controlling metabolic programs

abstract: Cortical neurogenesis depends on the tight balance between self-renewal and differentiation of apical progenitors (APs), the key progenitor type generating all other neural cells including neocortical neurons. We here report the activity of the histone methyltransferase DOT1L as a gatekeeper for AP cell identity. Combining lineage tracing with single-cell RNA sequencing of clonally related cells, we explore consequences of DOT1L inhibition on AP lineage progression during neurogenesis in the embryonic mouse neocortex. At the cellular level, DOT1L inhibition led to increased neurogenesis driven by a shift from asymmetric self-renewing to symmetric neurogenic divisions of APs. At the molecular level, we show that DOT1L activity preserved AP identity by promoting transcription of a gene set involved in AP metabolism. On a mechanistic level, DOT1L inhibition increased expression of metabolic genes, including microcephaly-associated Asparagine synthetase (Asns) and overexpression of ASNS in APs resulted in increased neuronal differentiation. Asns expression was predicted to be controlled through EZH2 and we show that DOT1L activity allows PRC2-mediated repression of Asns expression. Importantly, inhibition of ASNS activity rescued increased AP differentiation upon DOT1L inhibition. Our data show that DOT1L activity/PRC2 crosstalk controls AP lineage progression by regulating AP metabolism, and they provide a mechanistic view on how DOT1L activity might affect neocortical neurogenesis.


title: Cytoneme-mediated transport of active Wnt5b/Ror2 complexes in zebrafish gastrulation

abstract: Chemical signaling is the primary means by which cells communicate in the embryo. The underlying principle refers to a group of ligand-producing cells and a group of cells that respond to this signal because they express the appropriate receptors. In the zebrafish embryo, Wnt5b binds to the receptor Ror2 to trigger the Wnt/Planar Cell Polarity (Wnt/PCP) signaling pathway to regulate tissue polarity and cell migration. However, it is still unclear how this lipophilic ligand is transported from the source cells through the aqueous extracellular space to the target tissue. Here we show that Wnt5b, together with Ror2, is loaded on long protrusions. The active Wnt5b/Ror2 complexes are handed over from these cytonemes to the receiving cell to trigger Wnt/PCP signaling, regardless of whether the cell expresses functional receptors. On the tissue level, we show that cytoneme-dependent spreading of active Wnt5b/Ror2 affects convergence and extension in the zebrafish gastrula.


title: Cochlear Neurotrophin-3 overexpression at mid-life prevents age-related cochlear synaptopathy and slows age-related hearing loss

abstract: Age-related hearing loss (ARHL) is the most prevalent sensory deficit in the elderly. This progressive pathology often has psychological and medical comorbidities, including social isolation, depression, and cognitive decline. Despite ARHLs enormous impact, no therapies to prevent or slow its progression exist. Loss of synapses between inner hair cells (IHCs) and spiral ganglion neurons (SGNs), a.k.a. cochlear synaptopathy, is an early event in ARHL, preceding neuronal and hair cell loss. To determine if age-related cochlear synaptopathy can be prevented, and if this impacts the time-course of ARHL, we tested the effects of cochlear overexpression of neurotrophin-3 (Ntf3) starting at middle-age. We chose Ntf3 because this neurotrophin regulates the formation of IHC-SGN synapses in the neonatal period. We now show that triggering Ntf3 overexpression by cochlear supporting cells starting in middle age rapidly increases the amplitude of sound-evoked neural potentials, indicating that Ntf3 improves cochlear function when pathology is minimal. Furthermore, near the end of their lifespan, Ntf3-overexpressing mice have milder ARHL, with enhanced cochlear neural function and reduced cochlear synaptopathy. Our results provide evidence that age-related decrease in cochlear Ntf3 expression contributes to ARHL. and Ntf3 supplementation could serve as a therapeutic for this prevalent disorder. Furthermore, these findings suggest that increased expression of factors that regulate synaptogenesis during development might prevent age-related synaptopathy, a process involved in several central nervous system degenerative disorders.


title: Speech Production in Intracranial Electroencephalography: iBIDS Dataset

abstract: Speech production is an intricate process involving a large number of muscles and cognitive processes. The neural processes underlying speech production are not completely understood. As speech is a uniquely human ability, it can not be investigated in animal models. High-fidelity human data can only be obtained in clinical settings and is therefore not easily available to all researchers. Here, we provide a dataset of 10 participants reading out individual words while we measured intracranial EEG from a total of 1103 electrodes. The data, with its high temporal resolution and coverage of a large variety of cortical and sub-cortical brain regions, can help in understanding the speech production process better. Simultaneously, the data can be used to test speech decoding and synthesis approaches from neural data to develop speech Brain-Computer Interfaces and speech neuroprostheses.


title: Plant-produced RBD and cocktail-based vaccine candidates are highly effective against SARS-CoV-2, independently of its emerging variants

abstract: SARS-CoV-2 is a novel and highly pathogenic coronavirus, which has caused an outbreak in Wuhan City, China, in 2019 and then spread rapidly throughout the world. Although several COVID-19 vaccines are currently available for mass immunization, they are less effective against emerging SARS-CoV-2 variants, especially the Omicron (B.1.1.529). Recently, we successfully produced receptor-binding domain (RBD) variants of spike (S) protein of SARC-CoV-2 and an antigen cocktail in Nicotiana benthamiana, which are highly produced in plants and elicited high-titer antibodies with potent neutralizing activity against SARS-CoV-2. In this study, we demonstrate that these protein-based vaccine candidates are highly effective against Delta and Omicron variants. These data support that plant produced RBD and cocktail-based antigens are most promising vaccine candidates and may protect against Delta and Omicron-mediated COVID-19. Based on the neutralization ability, plant produced RBD and cocktail-based vaccine candidates are highly effective against SARS-CoV-2, independently of its emerging variants.


title: Chemical conversion of human conventional Pluripotent Stem Cells to Trophoblast Stem Cells

abstract: In human embryos, naive pluripotent cells of the inner cell mass generate epiblast, primitive endoderm and Trophectoderm (TE) lineage, whence trophoblast cells derive. In vitro, naive pluripotent stem cells (PSCs) retain this potential and can generate trophoblast stem cells (TSCs), while conventional PSCs form amnion-like cells and lack the competence to generate TSCs. Transient histone deacetylase and MEK inhibitions with LIF stimulation can be used to chemically reset conventional to naive PSCs. Here we report that chemical resetting induced expression of both naive and TSC markers and of placental imprinted genes. A modified chemical resetting protocol allowed for the fast and efficient conversion of conventional PSCs into TSCs, entailing shutdown of pluripotency genes and full activation of the trophoblast master regulators, without induction of amnion markers. Chemical resetting generates a responsive intermediate state, in which conventional PSCs rapidly acquire competence to form TSCs without the need of stabilisation and expansion in a naive state. The efficiency and rapidity of our system will be useful for the study of cell fate transitions, and to generate models of placental disorders.


title: Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons.

abstract: Neuron-specific morphology and function are fundamentally tied to differences in gene expression across the nervous system. We previously generated a single cell RNA-seq dataset for every anatomical neuron class in the C. elegans hermaphrodite. Here we present a complementary set of bulk RNA-seq samples for 41 of the 118 neuron classes in C. elegans. We show that the bulk dataset captures both lowly expressed and noncoding RNAs that are missed in the single cell dataset, but also includes false positives due to contamination by other cell types. We present an integrated analytical strategy that effectively resolves both the low sensitivity of single cell RNA-seq data and the reduced specificity of bulk RNA-Seq. We show that this integrated dataset enhances the sensitivity and accuracy of transcript detection and quantification of differentially expressed genes. We propose that our approach provides a new tool for interrogating gene expression, by bridging the gap between old (bulk) and new (single cell) methodologies for transcriptomic studies. We suggest that these datasets will advance the goal of delineating the mechanisms that define neuronal morphology and connectivity in C. elegans.


title: Paired Associates Learning is Disrupted After Unilateral Parietal Lobe Controlled Cortical Impact in Rats: A Trial-by-Trial Behavioral Analysis

abstract:
Approximately 60-70 million people suffer from a traumatic brain injury (TBI) each year. As animal models continue to be paramount in understanding and treating cognitive impairment following TBI, the necessity of testing intervention strategies in clinically relevant settings cannot be ignored. This study used a unilateral parietal lobe controlled cortical impact (CCI) model of TBI and tested rats on a touchscreen-based associative learning task, Paired Associates Learning (PAL). In humans, PAL has been used to assess cognitive deficits in stimulus-location association in a multitude of disease states, including TBI. To date, the extent to which a rat model of TBI produces deficits in PAL has not yet been reported, although the usage of PAL will be important for understanding the clinical consequences of cognitive impairment post-injury and throughout intervention treatment. This study details the behavioral and histological consequences of the CCI injury model and closes a translational research gap between basic and clinical TBI research.

HIGHLIGHTSO_LIPAL performance declines in a rat model of TBI.
C_LIO_LIResponse-driven bias in PAL becomes elevated after TBI.
C_LIO_LIInflammatory microglial response in the thalamus correlates with PAL deficit.
C_LI

category: animal behavior and cognition


title: Microphysiological Drug-Testing Platform For Identifying Responses To Prodrug Treatment In Primary Leukemia

abstract: Despite increasing survival rates of pediatric leukemia patients over the past decades, the outcome of some leukemia subtypes has remained dismal. Drug sensitivity and resistance testing on patient-derived leukemia samples provides important information to tailor treatments for high-risk patients. However, currently used well-based drug screening platforms are severely limited in predicting the effects of prodrugs, a class of therapeutics that require metabolic activation to become effective. To address this limitation, we developed a microphysiological drug-testing platform that enables co-culturing of patient-derived leukemia cells, human bone marrow mesenchymal stromal cells, and human liver microtissues within the same microfluidic platform that, at the same time, regulates the physical interaction between the diverse cell types. Our model recapitulates hepatic prodrug activation of ifosfamide, which cannot be assessed in traditional well-based assays. By testing the susceptibility of primary patient-derived leukemia samples to the prodrug ifosfamide, we identified sample-specific sensitivities to ifosfamide in primary leukemia samples. Our microfluidic platform enables the recapitulation of physiologically relevant conditions and the testing of prodrugs, particularly with short-lived and unstable metabolites, which provides a basis for clinical translation and precision chemotherapy selection.


title: EcoFun-MAP: An Ecological Function Oriented Metagenomic Analysis Pipeline

abstract: Annotating ecological functions of environmental metagenomes is challenging due to a lack of specialized reference databases and computational barriers. Here we present the Ecological Function oriented Metagenomic Analysis Pipeline (EcoFun-MAP) for efficient analysis of shotgun metagenomes in the context of ecological functions. We manually curated a reference database of EcoFun-MAP which is used for GeoChip design. This database included [~]1,500 functional gene families that were catalogued by important ecological functions, such as carbon, nitrogen, phosphorus, and sulfur cycling, metal homeostasis, stress responses, organic contaminant degradation, antibiotic resistance, microbial defense, electron transfer, virulence and plant growth promotion. EcoFun-MAP has five optional workflows from ultra-fast to ultra-conservative, fitting different research needs from functional gene exploration to stringent comparison. The pipeline is deployed on High Performance Computing (HPC) infrastructure with a highly accessible web-based interface. We showed that EcoFun-MAP is accurate and can process multi-million short reads in a minute. We applied EcoFun-MAP to analyze metagenomes from groundwater samples and revealed interesting insights of microbial functional traits in response to contaminations. EcoFun-MAP is available as a public web server at http://iegst1.rccc.ou.edu:8080/ecofunmap/.


title: scROSHI - robust supervised hierarchical identification of single cells

abstract: Identifying cell types based on expression profiles is a pillar of single cell analysis. Existing machine-learning methods identify predictive features from annotated training data, which are often not available in early-stage studies. This can lead to overfitting and inferior performance when applied to new data. To address these challenges we present scROSHI, which utilizes previously obtained cell type-specific gene sets and does not require training or the existence of annotated data. By respecting the hierarchical nature of cell type relationships and assigning cells consecutively to more specialized identities, excellent prediction performance is achieved. In a benchmark based on publicly available PBMC data sets, scROSHI outperforms competing methods when training data are limited or the diversity between experiments is large.


title: Identification and comparison of somatic antigen composition for bacteria from Providencia genus

abstract:
Providencia is a genus of Gram-negative bacteria belonging to the Morganellaceae family. This genus includes nine species (P. stuartii, P. sneebia, P. rettgeri, P. rustigianii, P. heimbachae, P. burhodogranariea, P. alcalifaciens, P. huaxiensis, and P. vermicola) with varying degrees of virulence, capable of infecting humans and insects [1, 2].

For Gram-negative bacteria, the somatic antigen (O-antigen) has become one of the key virulence factors. It is the highly immunogenic part of lipopolysaccharides due to the distal location. O-antigens are characterized by structural heterogeneity, providing varying degrees of inter- and intraspecific virulence. At the genetic level, somatic antigens have an operon structure. Operon genes responsible for the synthesis and transformation of O-polysaccharide are transcribed together. Analysis of O-antigen operon organization determines genes specific for each O-serogroup. It is beneficial for molecular typing of strains and for studies of bacterial evolution.

This study focuses on identifying and comparing candidates for O-antigen operons in Providencia species with different levels of virulence. The hypothesis is the presence of an association between the O-antigen operon composition and the bacteria lifestyle. Data processing and analysis are carried out by a pipeline developed by the authors. Pipeline combines five steps of the genome analysis: genome quality evaluation, assembly annotation, operon identification with verification of operon boundaries, and visualization of O-antigen operons. The results reveal previously undescribed O-antigen genes and the changes in the O-antigen operons structure. Among the changes are a transposon insertion leading to tetracycline resistance and the presence of IS elements.


title: Chromenone derivatives as novel pharmacological chaperones for retinitis pigmentosa-linked rod opsin mutants

abstract: The correct expression of folded, functional rhodopsin (Rho) is critical for visual perception. However, this seven-transmembrane helical G protein-coupled receptor (GPCR) is prone to mutations with pathological consequences of retinal degeneration in retinitis pigmentosa (RP) due to Rho misfolding. Pharmacological chaperones that stabilize the inherited Rho variants by assisting their folding and membrane targeting could slow the progression of RP. In this study, we employed virtual screening of synthetic compounds with natural product scaffold in conjunction with in vitro and in vivo evaluations to discover a novel chromenone-containing small molecule with favorable pharmacological properties that stabilizes rod opsin. This compound reversibly binds to unliganded bovine rod opsin with an EC50 value comparable to the 9-cis-retinal chromophore analog and partially rescued membrane trafficking of multiple RP-related rod opsin variants in vitro. Importantly, this novel ligand of rod opsin was effective in vivo in murine models, protecting photoreceptors from deterioration caused either by bright light or genetic insult. Together, our current study suggests potential broad therapeutic implications of the new chromenone-containing non-retinoid small molecule against retinal diseases associated with photoreceptor degeneration.

category: pharmacology and toxicology


title: Metformin disrupts Danio rerio metabolism at environmentally relevant concentrations: A generational study

abstract:
Metformin (MET) is an anti-diabetic pharmaceutical with a large-scale consumption, which is increasingly detected in surface waters. However, current knowledge on the generational effects of MET exposure in the metabolism of non-target organisms is limited. The present study aimed at investigating the effects of MET in the model freshwater teleost Danio rerio, following a generational exposure (from egg up to 9 months exposure) to environmentally relevant concentrations ranging from 361 ng/L to 13 000 ng/L. Biochemical markers were used to determine cholesterol and triglycerides levels, as well as mitochondrial complex I activity in males and females zebrafish liver. mRNA transcript changes were also assessed in the liver of both sexes by means of an exploratory RNA-seq analysis and expression levels of key genes involved in the energy metabolism and lipid homeostasis, i.e. acaca, acadm, cox5aa, idh3a, hmgcra, prkaa1, were determined using qRT-PCR analysis. The findings here reported revealed that MET was able to significantly disrupt critical biochemical and molecular processes involved in zebrafish metabolism, such as cholesterol and fatty acid biosynthesis, the mitochondrial electron transport chain and the tricarboxylic acid cycle, concomitantly to changes on the hepatosomatic index. Non-monotonic dose response curves were frequently detected in the gene expression profile, with higher effects observed for 361 ng/L and 2 166 ng/L concentrations. Collectively, the obtained results suggest that environmentally relevant concentrations of MET are able to severely disrupt D. rerio metabolism, with potential impacts at the ecological level, supporting the need to update the environmental quality standard (EQS) and predicted no-effect concentration (PNEC) for MET.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/487223v1_ufig1.gif" ALT="Figure 1">
View larger version (31K):
org.highwire.dtl.DTLVardef@e9baecorg.highwire.dtl.DTLVardef@eedd72org.highwire.dtl.DTLVardef@c87a5org.highwire.dtl.DTLVardef@9d7c55_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIDanio rerio was exposed to metformin for a full generation;
C_LIO_LIMET affected COX I activity, as well as Chol and TGL content in zebrafish liver;
C_LIO_LIMET altered mRNA levels of genes involved in energy metabolism and lipid content;
C_LIO_LINon-monotonic dose-response curves were frequently detected;
C_LIO_LIDue to the results obtained, MET PNEC should be reviewed.
C_LI


title: Isometric Spiracular Scaling in Scarab Beetles: Implications for Diffusive and Advective Oxygen Transport

abstract: The scaling of respiratory structures has been hypothesized to be a major driving factor in the evolution of many aspects of animal physiology. Here we provide the first assessment of the scaling of the spiracles in insects using ten scarab beetle species differing 180x in mass, including some of the most massive extant insect species. Using X-ray microtomography, we measured the cross-sectional area and depth of all eight spiracles, enabling the calculation of their diffusive and advective capacities. Each of these metrics scaled with geometric isometry. Because diffusive capacities scale with lower slopes than metabolic rates, the largest beetles measured require 10-fold higher PO2 gradients across the spiracles to sustain metabolism by diffusion compared to the smallest species. Large beetles can exchange sufficient oxygen for resting metabolism by diffusion across the spiracles, but likely no scarab beetle can do so during flight. In contrast, spiracular advective capacities scale more steeply than metabolic rates, so larger beetles should require less pressure to drive sufficient ventilation to meet oxygen demands, assuming similar extraction efficiencies. These data illustrate a general principle of gas exchange: scaling of respiratory transport structures with geometric isometry diminishes the potential for diffusive gas exchange but enhances advective capacities; combining such structural scaling with muscle-driven ventilation allows larger animals to achieve high metabolic rates when active.


title: A snapshot of statistical methods used in experimental immunoblotting: A scoping review

abstract: Among the many avenues considered to make life science more reproducible, the improvement of the quality and openness of statistical methods has taken centre stage. However, although disparities across research fields and techniques are not unknown, they remain largely unexplored. The present scoping review aims to provide a first overview of statistical methods used in biochemical research involving immunoblotting (also referred to as western blotting), a technique frequently used to quantify proteins of interest. A reverse chronological systematic sampling was implemented to explore the PubMed online browser and analyse 2932 experimental conditions (i.e., experimental groups) in quantitative immunoblots from 64 articles published at the end of 2021. The statistical test (actual study size n = 67) and software (actual study size n = 61) used for each article and the sample size for each experimental condition were documented. The results indicate an omnipresence of parametric tests, mostly one-way analysis of variance (ANOVA, 15/67) and Students t-test (13/67), but for many articles the statistical procedure was not clearly divulged (23/67). GraphPad Prism was the most commonly used statistical package (36/61), but many (14/61) articles did not reveal the package used. Finally, the sample size was clearly disclosed in only 1054/2932 conditions in which its median value was 3 (IQR = [3 - 6]). This study suggests that the transparency of reporting might be suboptimal in immunoblotting research and prompts more comprehensive systematic reviews in future.

category: scientific communication and education


title: Topological Data Analysis of Human Brain Networks Through Order Statistics

abstract:
Understanding the topological characteristics of the brain network across a population is central to understanding brain functions. The abstraction of human connectome as a graph has been pivotal in gaining insights on the topological features of the brain network. The development of group-level statistical inference procedures in brain graphs while accounting for the heterogeneity and randomness still remains a difficult task. In this study, we develop a robust statistical framework based on persistent homology using the order statistics for analyzing brain networks. The use of order statistics greatly simplifies the computation of the persistent barcodes. We validate the proposed methods using comprehensive simulation studies and subsequently apply to the resting-state functional magnetic resonance images. We conclude a statistically significant topological difference between the male and female brain networks.

Author summaryWe fit a random graph model to the brain network and compute the expected persistent barcodes using order statistics. This novel approach significantly simplifies the computation of expected persistent barcodes, which otherwise requires complex theoretical constructs. Subsequently, the proposed statistical framework is used to discriminate if two groups of brain networks are topologically different. The method is applied in determining the sexual dimorphism in the shape of resting-state functional magnetic resonance images.


title: Formalism for the sequential estimation of neural membrane time constant and input-output curve towards selective and closed-loop transcranial magnetic stimulation

abstract: This paper describes a novel tool for closed-loop system identification of the activation dynamics of the neural target of transcranial magnetic stimulation (TMS). The method operates in real time, selects ideal stimulus parameters, detects and processes the response, and estimates the input-output (IO) curve and the neural membrane time constant representing a first-order approximation of the activated neural target. First, the neural membrane response and depolarization factor, which leads to motor evoked potentials (MEPs) are analytically computed and discussed. Then, an integrated model is developed which combines the neural membrane time constant and the input-output curve in TMS. Identifiability of the proposed integrated model is discussed. A condition is derived, which assures SPE of the proposed integrated model. Finally, a real-time and sequential parameter estimation (SPE) formalism is described to identify the neural membrane time constant and IO curve parameters in closed-loop TMS, where TMS pulses are administered sequentially based on the automatic analysis of the electromyography (EMG) data in real time. Optimal sampling based on maximization of the Fisher information matrix (FIM) and more conventional and intuitive uniform sampling methods both are addressed in this paper. The effectiveness of the proposed parameter tuning method is evaluated via simulations. Without loss of generality, this paper focuses on a specific case of cTMS pulses. The method is directly applicable to other cTMS pulse shapes with no new point of principals. The Matlab code is available online on Github.


title: Neuroscout, a unified platform for generalizable and reproducible fMRI research

abstract: Functional magnetic resonance imaging (fMRI) has revolutionized cognitive neuroscience, but methodological barriers limit the generalizability of findings from the lab to the real world. Here, we present Neuroscout, an end-to-end platform for analysis of naturalistic fMRI data designed to facilitate the adoption of robust and generalizable research practices. Neuroscout leverages state-of-the-art machine learning models to automatically annotate stimuli from dozens of naturalistic fMRI studies, allowing researchers to easily test neuroscientific hypotheses across multiple ecologically-valid datasets. In addition, Neuroscout builds on a robust ecosystem of open tools and standards to provide an easy-to-use analysis builder and a fully automated execution engine that reduce the burden of reproducible research. Through a series of meta-analytic case studies, we validate the automatic feature extraction approach and demonstrate its potential to support more robust fMRI research. Owing to its ease of use and a high degree of automation, Neuroscout makes it possible to overcome modeling challenges commonly arising in naturalistic analysis and to easily scale analyses within and across datasets, democratizing generalizable fMRI research.


title: High frequency spike inference with particle Gibbs sampling

abstract: Fluorescent calcium indicators are an indispensable tools for monitoring the spiking activity of large neuronal populations in animal models. However, despite the plethora of algorithms developed over the last decades, accurate spike time inference methods for rates greater than 20 Hz are lacking. More importantly, little attention has been devoted to the quantification the statistical uncertainties in spike time estimation, which is essential for assigning a confidence in the inference for a particular recording. To address these challenges, we introduce an auto-regressive generative model that accounts for bursting neuronal activity and baseline fluorescence modulation, and it also applies recent sequential Monte Carlo approaches to obtain joint posterior distributions of static and dynamic model parameters. We show that our inference method is competitive with state-of-the-art algorithms by analysing the CASCADE benchmark datasets. We also show that spike time intervals as short as five milliseconds can be inferred from fluorescence transients recorded using a state-of-the-art genetically encoded indicator. Overall, our study describes a Bayesian inference method to detect neuronal spiking patterns and their uncertainty. The use of particle Gibbs samplers allows for unbiased estimates of all model parameters and it provides a statistical framework to test more specific models of calcium indicators.


title: ROStrace detects oxidative stress in vivo and predicts progression of Alzheimer's disease pathology in APP/PS1 mice.

abstract:
PurposeOxidative stress is implicated in the pathogenesis of the most common neurodegenerative diseases, such as Alzheimers disease (AD). However, tracking oxidative stress in the brain has proven difficult and impeded its use as a biomarker. Herein, we investigate the utility of a novel positron emission tomography (PET) tracer, [18F]ROStrace, as a biomarker of oxidative stress throughout the course of AD in the well-established APP/PS1 double mutant mouse model.

MethodsPET imaging studies were conducted in wild-type (WT) and APP/PS1 mice at 3 different time points, representing early (5 mo.), middle (10 mo.), and advanced (16 mo.) life (n = 6-12, per sex). Semi-quantitation SUVRs of the plateau phase (40-60min post-injection; SUVR40-60) of ten brain subregions were designated by the Mirrione atlas and analyzed by Pmod. Statistical parametric mapping (SPM) was used to distinguish brain regions with elevated ROS in APP/PS1 relative to WT in both sexes. The PET studies were validated by ex vivo autoradiography and immunofluorescence with the parent compound, dihydroethidium.

Results[18F]ROStrace retention was increased in the APP/PS1 brain compared to age-matched controls by 10 mo. of age (p < 0.0001), and preceded the accumulation of oxidative damage in APP/PS1 neurons at 16mo. (p < 0.005). [18F]ROStrace retention and oxidative damages were higher and occurred earlier in female APP/PS1 mice as measured by PET (p < 0.001), autoradiography and immunohistochemistry (p < 0.05). [18F]ROStrace differences emerged mid-life, temporally and spatially correlating with increased A{beta} burden (r2 = 0.36; p = 0.0003), which was also greatest in the female brain (p < 0.001).

Conclusions[18F]ROStrace identifies increased oxidative stress and neuroinflammation in APP/PS1 female mice, concurrent with increased amyloid burden mid-life. Differences in oxidative stress during this crucial time may partially explain the sexual dimorphism in AD. [18F]ROStrace may provide a long-awaited tool to stratify at-risk patients who may benefit from antioxidant therapy prior to irreparable neurodegeneration.


title: The Delta variant SARS-CoV-2 spike protein uniquely promotes aggregation of pseudotyped viral particles

abstract: Individuals infected with the SARS-CoV-2 Delta variant, lineage B.1.617.2, exhibit faster initial infection with a higher viral load than prior variants, and pseudotyped particles bearing the SARS-CoV-2 Delta variant spike protein induce a faster initial infection rate of target cells compared to those bearing other SARS-CoV-2 variant spikes. Here, we show that pseudotyped particles bearing the Delta variant spike form unique aggregates, as evidenced by negative stain and cryogenic electron microscopy (EM), flow cytometry, and nanoparticle tracking analysis. Viral particles pseudotyped with other SARS-CoV-2 spike variants do not show aggregation by any of these criteria. The contribution to infection kinetics of the Delta spikes unique property to aggregate is discussed with respect to recent evidence for collective infection by other viruses. Irrespective of this intriguing possibility, spike-dependent aggregation is a new functional parameter of spike-expressing viral particles to evaluate in future spike protein variants.

category: microbiology


title: Hippo Signaling Pathway Activation during SARS-CoV-2 Infection Contributes to Host Antiviral Response

abstract: SARS-CoV-2, responsible for the COVID-19 pandemic, causes respiratory failure and damage to multiple organ systems. The emergence of viral variants poses a risk of vaccine failures and prolongation of the pandemic. However, our understanding of the molecular basis of SARS-CoV-2 infection and subsequent COVID-19 pathophysiology is limited. In this study, we have uncovered a critical role for the evolutionarily conserved Hippo signaling pathway in COVID-19 pathogenesis. Given the complexity of COVID-19 associated cell injury and immunopathogenesis processes, we investigated Hippo pathway dynamics in SARS-CoV-2 infection by utilizing COVID-19 lung samples, and human cell models based on pluripotent stem cell-derived cardiomyocytes (PSC-CMs) and human primary lung air-liquid interface (ALI) cultures. SARS-CoV-2 infection caused activation of the Hippo signaling pathway in COVID-19 lung and in vitro cultures. Both parental and Delta variant of concern (VOC) strains induced Hippo pathway. The chemical inhibition and gene knockdown of upstream kinases MST1/2 and LATS1 resulted in significantly enhanced SARS-CoV-2 replication, indicating antiviral roles. Verteporfin a pharmacological inhibitor of the Hippo pathway downstream transactivator, YAP, significantly reduced virus replication. These results delineate a direct antiviral role for Hippo signaling in SARS-CoV-2 infection and the potential for this pathway to be pharmacologically targeted to treat COVID-19.


title: The non-random assembly of functional motifs in plant-pollinator networks

abstract: Ecological processes leave distinct structural imprints on the species interactions that shape the topology of mutualistic networks. Detecting those relationships is not trivial since they go beyond pairwise interactions, but may get blurred when considering full network descriptors. Recent work has shown that the network meso-scale can capture this important information. The meso-scale describes network subgraphs representing patterns of interactions between a small number of species (i.e., motifs) that constitute the building blocks of the whole network. Despite the possible implications of network motifs to better capture species interactions, they remain overlooked in natural plant-pollinator networks. By exploring 60 empirical plant-pollinator networks from 18 different studies with wide geographical coverage we show that some motifs are consistently under- or over-represented worldwide, suggesting that the building blocks of plant-pollinator networks are not random. Furthermore, we find that distinct motif positions describing species ecological roles (e.g., generalisation and number of indirect interactions) are occupied by different plant and floral visitor groups on both trophic levels. Bees appear less frequently in specialised motif positions with high number of indirect interactions, while the rest of floral visitor groups are infrequent in generalised motif positions with low number of indirect interactions. All plant groups tend to be over-represented on specialised motif positions, except tall plant species with separated sexes (e.g., woody dioecious or monoecious species), which are more frequent on motif positions with low number of indirect interactions. Interestingly, the realized combinations of different species groups within a motif can not be retrieved from their joint probability distributions, indicating that group combinations are not random either. Our result highlights the non-random structure of the meso-scale on plant-pollinators networks and the association of different plant and floral visitor groups with certain motifs that involve different ecological roles at a macro-ecological scale.

category: ecology


title: Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike

abstract: The BA.2 sub-lineage of the SARS-CoV-2 Omicron variant has gained in proportion relative to BA.1. As differences in spike (S) proteins may underlie differences in their pathobiology, here we determine cryo-EM structures of a BA.2 S ectodomain and compare these to previously determined BA.1 S structures. BA.2 Receptor Binding Domain (RBD) mutations induced remodeling of the internal RBD structure resulting in its improved thermostability and tighter packing within the 3-RBD-down spike. In the S2 subunit, the fusion peptide in BA.2 was less accessible to antibodies than in BA.1. Pseudovirus neutralization and spike binding assays revealed extensive immune evasion while defining epitopes of two RBD-directed antibodies, DH1044 and DH1193, that bound the outer RBD face to neutralize both BA.1 and BA.2. Taken together, our results indicate that stabilization of the 3-RBD-down state through interprotomer RBD-RBD packing is a hallmark of the Omicron variant, and reveal differences in key functional regions in the BA.1 and BA.2 S proteins.


title: Design of an Integrated Microvascularised Human Skin-on-a-Chip Tissue Equivalent Model

abstract: Tissue engineered skin constructs have been under development since the 1980s as a replacement for human skin tissues and animal models for therapeutics and cosmetic testing. These have evolved from simple single cell-assays to increasingly complex models with integrated dermal equivalents and multiple cell types including a dermis, epidermis and vasculature. The development of micro-engineered platforms and biomaterials has enabled scientists to better recreate and capture the tissue microenvironment in vitro, including the vascularization of tissue models and their integration into microfluidic chips. However, to date, microvascularised human skin equivalents in a microfluidic context have not been reported. Here we present the design of a novel skin-on-a-chip model integrating human derived primary and immortalized cells in a full thickness skin equivalent. The model is housed in a microfluidic device, in which a microvasculature was previously established. We characterize the impact of our chip design on the quality of the microvascular networks formed and evidence that this enables the formation of more homogenous networks. We developed a methodology to harvest tissues from embedded chips, after 14 days of culture, and characterize the impact of culture conditions and vascularization (including with pericyte co-cultures) on the stratification of the epidermis in the resulting skin equivalents. Our results indicate that vascularization enhances stratification and differentiation (thickness, architecture and expression of terminal differentiation markers such as involucrin and transglutaminase 1), allowing formation of more mature skin equivalents in microfluidic chips. The skin-on-a-chip tissue equivalents developed, thanks to their realistic microvasculature, may find application for the testing efficacy and safety of therapeutics delivered systemically, in a human context.


title: Protein 3D structure-based neural networks highly improve the accuracy in compound-protein binding affinity prediction

abstract: Theoretically, the accuracy of computational models in predicting compound-protein binding affinities (CPAs) could be improved by the introduction of protein 3D structure information. However, most of these models still suffer from a low accuracy due to the lack of an efficient approach to encode informative protein features. The major challenge is how to combine the multi-modal information such as the residue sequence of the protein, residue atom coordinates and the torsion angles. To tackle this problem, we develop Fast Evolutional Attention and Thoroughgoing-graph Neural Networks (FeatNN) to facilitate the application of protein 3D structure information for predicting CPAs. Specifically, we established a novel end-to-end architecture to jointly embed torsion matrix, discrete distance matrix, and sequence information of protein and extract compound features with deep graph convolution layers. In addition, a new pairwise mapping attention mechanism is introduced to comprehensively learn potential interaction information between proteins and compounds. FeatNN considerably outperforms various state-of-the-art baselines in CPA prediction with the Pearson value elevated by about 35.7%. Thus, FeatNN provides an outstanding method for highly accurate CPA prediction and facilitates high-throughput virtual screening of drug candidates.