bluuebunny/crossref_metadata_2025 huggingface dataset:
An expedited approach towards the rationale design of non-covalent SARS-CoV-2 main protease inhibitors with in vitro antiviral activity
Authors: Kitamura Naoya , Sacco Michael Dominic , Ma Chunlong , Hu Yanmei , Townsend Julia Alma , Meng Xiangzhi , Zhang Fushun , Zhang Xiujun , Kukuljac Adis , Marty Michael Thomas , Schultz David , Cherry Sara , Xiang Yan , Chen Yu , Wang Jun
Published: December 2020

The main protease (Mpro) of SARS-CoV-2 is a validated antiviral drug target. Several Mproinhibitors have been reported with potent enzymatic inhibition and cellular antiviral activity, including GC376, boceprevir, calpain inhibitors II and XII, each containing a reactive warhead that covalently modifies the catalytic Cys145. In this study, we report an expedited drug discovery approach by coupling structure-based design and Ugi four-component (Ugi-4CR) reaction methodology to the design of non-covalent Mproinhibitors. The most potent compound23Rhad cellular antiviral activity similar to covalent inhibitors such as GC376. Our designs were guided by overlaying the structure of SARS-CoV Mpro+ ML188 (R), a non-covalent inhibitor derived from Ug-4CR, with the X-ray crystal structures of SARS-CoV-2 Mpro+ calpain inhibitor XII/GC376/UAWJ247. Binding site analysis suggests a strategy of extending the P2 and P3 substitutions in ML188 (R) to achieve optimal shape complementary with SARS-CoV-2 Mpro. Lead optimization led to the discovery of23R, which inhibits SARS-CoV-2 Mproand SARS-CoV-2 viral replication with an IC50of 0.31 μM and EC50of 1.27 μM, respectively. The binding and specificity of23Rto SARS-CoV-2 Mprowere confirmed in a thermal shift assay and native mass spectrometry assay. The co-crystal structure of SARS-CoV-2 Mprowith23Rrevealed the P2 biphenyl fits snuggly into the S2 pocket and the benzyl group in the α-methylbenzyl faces towards the core of the enzyme, occupying a previously unexplored binding site located in between the S2 and S4 pockets. Overall, this study revealed the most potent non-covalent SARS-CoV-2 Mproinhibitors reported to date and a novel binding pocket that can be explored for Mproinhibitor design.
Vertical inheritance governs biosynthetic gene cluster evolution and chemical
diversification
Authors: Chase Alexander B. , Sweeney Douglas , Muskat Mitchell N. , Guillén-Matus Dulce , Jensen Paul R.
Published: December 2020

While specialized metabolites are thought to mediate ecological
interactions, the evolutionary processes driving their diversification,
particularly among closely related lineages, remain poorly understood. Here, we
examine the evolutionary dynamics governing the distribution of natural product
biosynthetic gene clusters (BGCs) using 118 strains within the marine
actinomycete genus Salinispora. While previous
evidence indicated that horizontal gene transfer (HGT) largely contributed to
BGC diversity, we find that a majority of BGCs in
Salinispora genomes are conserved through
processes of vertical descent. In particular, vertical inheritance maintained
BGCs over evolutionary timescales (millions of years) allowing for BGC
diversification among Salinispora species. By
coupling the genomic analyses with high-resolution tandem mass spectrometry
(LC-MS/MS), we identified that BGC evolution in
Salinispora proceeds largely through gene
gain/loss events and constrained recombination that contributes to interspecies
diversity at the gene, pathway, and metabolite levels. Consequently, the
evolutionary processes driving BGC diversification had direct consequences for
compound production and contributed to chemical diversification, as exemplified
in our case study of the medically relevant proteosome inhibitors, the
salinosporamides. Together, our results support the concept that specialized
metabolites, and their cognate BGCs, represent functional traits associated with
niche differentiation among Salinispora
species.

GRAPHICAL ABSTRACT

SIGNIFICANCE

Natural products are traditionally exploited for their
pharmaceutical potential; yet what is often overlooked is that the
evolution of the biosynthetic gene clusters (BGCs) encoding these
small molecules likely affects the diversification of the produced
compounds and implicitly has an impact on the compounds’ activities
and ecological functions. And while the prevailing dogma in natural
product research attributes frequent and widespread horizontal gene
transfer (HGT) as an integral driver of BGC evolution, we find that
the majority of BGC diversity derives from processes of vertical
descent, with HGT events being rare. This understanding can
facilitate informed biosynthetic predictions to identify novel
natural products, in addition to uncovering how these specialized
metabolites contribute to the environmental distribution of
microbes.
Adaptive integration of self-motion and goals in posterior parietal cortex
Authors: Alexander Andrew S. , Tung Janet C. , Chapman G. William , Shelley Laura E. , Hasselmo Michael E. , Nitz Douglas A.
Published: December 2020

Animals engage in a variety of navigational behaviors that require different regimes of behavioral control. In the wild, rats readily switch between foraging and more complex behaviors such as chase, wherein they pursue other rats or small prey. These tasks require vastly different tracking of multiple behaviorally-significant variables including self-motion state. It is unknown whether changes in navigational context flexibly modulate the encoding of these variables. To explore this possibility, we compared self-motion processing in the multisensory posterior parietal cortex while rats performed alternating blocks of free foraging and visual target pursuit. Animals performed the pursuit task and demonstrated predictive processing by anticipating target trajectories and intercepting them. Relative to free exploration, pursuit sessions yielded greater proportions of parietal cortex neurons with reliable sensitivity to self-motion. Multiplicative gain modulation was observed during pursuit which increased the dynamic range of tuning and led to enhanced decoding accuracy of self-motion state. We found that self-motion sensitivity in parietal cortex was history-dependent regardless of behavioral context but that the temporal window of self-motion tracking was extended during target pursuit. Finally, many self-motion sensitive neurons conjunctively tracked the position of the visual target relative to the animal in egocentric coordinates, thus providing a potential coding mechanism for the observed gain changes to self-motion signals. We conclude that posterior parietal cortex dynamically integrates behaviorally-relevant information in response to ongoing task demands.
Polyamine biosynthesis and eIF5A hypusination are modulated by the DNA tumor virus KSHV and promote KSHV viral infection
Authors: Fiches Guillaume N. , Biswas Ayan , Zhou Dawei , Kong Weili , Jean Maxime , Santoso Netty G. , Zhu Jian
Published: December 2020

Polyamines are critical metabolites involved in various cellular processes and often dysregulated in cancers. Kaposi’s sarcoma associated Herpesvirus (KSHV) is a defined oncogenic virus belonging to the sub-family of human gamma-herpesviruses. KSHV infection leads to the profound alteration of host metabolic landscape to favor the development of KSHV-associated malignancies. In our studies, we identified that polyamine biosynthesis and eIF5A hypusination are dynamically regulated by KSHV infection likely through the modulation of key enzymes of these pathways, such as ODC1, and that in return these metabolic pathways are required for both KSHV lytic switch from latency andde novoinfection. The further analysis unraveled that translation of critical KSHV latent and lytic proteins (LANA, RTA) depends on eIF5A hypusination. We also demonstrated that KSHV infection can be efficiently and specifically suppressed by using inhibitors targeting either polyamine biosynthesis or eIF5A hypusination. Above all, our results illustrated that the dynamic and profound interaction of a DNA tumor virus (KSHV) with host polyamine biosynthesis and eIF5A hypusination metabolic pathways promote viral propagation and oncogenesis, which serve as new therapeutic targets to treat KSHV-associated malignancies.
Genomic analysis provides novel insights into diversification and taxonomy ofAllorhizobium vitis(i.e.Agrobacterium vitis)
Authors: Kuzmanović Nemanja , Biondi Enrico , Overmann Jörg , Puławska Joanna , Verbarg Susanne , Smalla Kornelia , Lassalle Florent
Published: December 2020

Background

Allorhizobium vitis(formerly namedAgrobacterium vitisorAgrobacteriumbiovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. We obtained and analyzed whole-genome sequences of diverseAll. vitisstrains to get insights into their diversification and taxonomy.

Results

Pairwise genome comparisons and phylogenomic analysis of variousAll. vitisstrains clearly indicated thatAll. vitisis not a single species, but represents a species complex composed of several genomic species. Thus, we emended the description ofAll. vitis, which now refers to a restricted group of strains within theAll. vitisspecies complex (i.e.All. vitis sensu stricto) and proposed a description of a novel species,All. ampelinumsp. nov. The type strain ofAll. vitis sensu strictoremains the current type strain ofAll. vitis, K309T. The type strain ofAll. ampelinumsp. nov. is S4T. We also identified sets of gene clusters specific to theAll. vitisspecies complex,All. vitis sensu strictoandAll. ampelinum, respectively, for which we predicted the biological function and infer the role in ecological diversification of these clades, including some we could experimentally validate.All. vitisspecies complex-specific genes confer tolerance to different stresses, including exposure to aromatic compounds. Similarly,All. vitis sensu stricto-specific genes confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid.All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. Congruently with the genome-based classification,All. vitis sensu strictoandAll. ampelinumwere clearly delineated by MALDI-TOF MS analysis. Moreover, our genome-based analysis indicated thatAllorhizobiumis clearly separated from other genera of the familyRhizobiaceae.

Conclusions

Comparative genomics and phylogenomic analysis provided novel insights into the diversification and taxonomy ofAllorhizobium vitisspecies complex, supporting our redefinition ofAll. vitis sensu strictoand description ofAll. ampelinum. Our pan-genome analyses suggest that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche.
Structural insights into glycine reuptake inhibition
Authors: Shahsavar Azadeh , Stohler Peter , Bourenkov Gleb , Zimmermann Iwan , Siegrist Martin , Guba Wolfgang , Pinard Emmanuel , Seeger Markus A. , Schneider Thomas R. , Dawson Roger J.P. , Nissen Poul
Published: December 2020

The human glycine transporter 1 (GlyT1) regulates glycine mediated neuronal excitation and inhibition through sodium- and chloride-dependent reuptake of the neurotransmitter1-3. Inhibition of glycine reuptake via GlyT1 prolongs neurotransmitter signaling and has long served as a key therapeutic development strategy for treatment of a broad range of central nervous system disorders including schizophrenia and cognitive impairments4. Using an inhibition state-selective sybody and serial synchrotron crystallography, we determined the structure of GlyT1 in complex with a benzoylpiperazine chemotype inhibitor at 3.4 Å resolution. The inhibitor locks GlyT1 in an inward-open conformation and binds at the intracellular gate of the release pathway, overlapping with the glycine release site. The inhibitor likely reaches GlyT1 from the cytoplasmic leaflet of the plasma membrane. The study defines the mechanism of non-competitive inhibition and enables the rational design of new, clinically efficacious GlyT1 inhibitors.
Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020
Authors: Leung Kathy , Shum Marcus HH , Leung Gabriel M , Lam Tommy TY , Wu Joseph T
Published: December 2020

Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor binding domain of the spike protein have rapidly become prevalent in the UK. We estimated that the earlier 501Y lineage without amino acid deletion Δ69/Δ70 circulating mainly between early September to mid-November was 10% (6-13%) more transmissible than the 501N lineage, and the currently dominant 501Y lineage with amino acid deletion Δ69/Δ70 circulating since late September was 75% (70-80%) more transmissible than the 501N lineage.
Effect of Complete Respiratory Muscle Training (cRMT) on Dysphonia following Single CVA: A retrospective pilot study
Authors: Arnold Robert J. , Gaskill Christopher S , Bausek Nina
Published: December 2020

Background

Although dysphonia is less prevalent than dysphagia following cerebrovascular accidents, dysphonia does contribute to the burden of disease resulting from stroke. Strengthening muscles of the larynx and respiratory tract through respiratory muscle training (RMT) has proven effective in improving voice after neurological insult. However, approaches to strengthen only the expiratory muscle groups (EMST) dominate the clinical study literature, with variable outcomes. By focusing on exhalation, the contribution of inspiratory muscles to phonation may have been overlooked. This study investigated the effect of combined respiratory muscle training (cRMT) to improve voice function in stroke patients.

Methods

Recorded data of twenty patients with dysphonia following stroke were allocated to an intervention (IG) or a control group (CG) based upon whether they chose cRMT or not while awaiting pro bono voice therapy services. The intervention group (N=10) was treated daily with three 5-minute sessions of complete resistive respiratory muscle training for 28 days, while the control group (N=10) received no cRMT or other exercise intervention. Perceptual and acoustic measurements as well as a pulmonary function test were assessed pre-and post-intervention.

Results

The intervention group demonstrated significant improvements after 28 days of combined respiratory muscle training (cRMT) in peak flow (127%), patient self-perception of voice improvement (84.41%), as well as in five of the six categories of the Consensus Auditory-Perceptual Evaluation of Voice (CAPE-V) overall severity (63.22%), breathiness (61.06%), strain (63.43%), pitch range (48.11%) and loudness (57.51%), compared to the control group who did not receive treatment. Furthermore, cRMT also led to significant improvements in maximum phonation time (212.5%) and acoustic parameters of vocal intensity and semitone range.

Conclusion

This pilot study shows promise of the feasibility and effectiveness of cRMT to lessen the signs and symptoms of dysphonia while simultaneously improving breath support.
Stepwise transmigration cascade of T and B cells through the perivascular channel in lymph node high endothelial venules
Authors: Choe Kibaek , Moon Jieun , Lee Soo Yun , Song Eunjoo , Back Ju Hee , Song Joo-Hye , Hyun Young-Min , Uchimura Kenji , Kim Pilhan
Published: December 2020

High endothelial venules (HEVs) effectively recruit circulating lymphocytes from the blood to lymph nodes. HEVs have endothelial cells (ECs) and perivascular sheaths consisting of fibroblastic reticular cells (FRCs). Many studies have characterized the multiple steps of lymphocyte migration interacting with ECs at the luminal side of HEVs. However, post-luminal migration steps are not well elucidated. Herein, we performed intravital imaging to investigate post-luminal T and B cell migration, consisting of trans-EC migration, crawling in the perivascular channel (a narrow space between ECs and FRCs) and trans-FRC migration. The post-luminal migration of T cells occurred in a PNAd-dependent manner. Remarkably, we found hot spots for the trans-EC and trans-FRC migration of T and B cells. Interestingly, T and B cells preferentially shared trans-FRC migration hot spots but not trans-EC migration hot spots. Furthermore, the trans-FRC T cell migration was confined to fewer sites than trans-EC T cell migration, and trans-FRC migration of T and B cells preferentially occurred at FRCs covered by CD11c+ dendritic cells in HEVs. These results suggest that HEV ECs and FRCs with perivascular DCs delicately regulate T and B cell entry into lymph nodes.
In vitro characterization of engineered red blood cells as potent viral traps against HIV-1 and SARS-CoV-2
Authors: Hoffmann Magnus A. G. , Kieffer Collin , Bjorkman Pamela J.
Published: December 2020

Engineered red blood cells (RBCs) expressing viral receptors could be used therapeutically as viral traps as RBCs lack nuclei and other organelles required for viral replication. Here we show that the combination of a powerful erythroid-specific expression system and transgene codon optimization yields high expression levels of the HIV-1 receptors CD4 and CCR5, as well as a CD4-glycophorin A (CD4-GpA) fusion protein on enucleated RBCs. Engineered RBCs expressing CD4 and CCR5 were efficiently infected by HIV-1, but CD4 or CD4-GpA expression in the absence of CCR5 was sufficient to potently neutralize HIV-1 in vitro. To facilitate continuous large-scale production of engineered RBCs, we generated erythroblast cell lines stably expressing CD4-GpA or ACE2-GpA fusion proteins, which produced potent RBC viral traps against HIV-1 and SARS-CoV-2. Our results suggest that this approach warrants further investigation as a potential treatment against viral infections.
Modelling the contribution of iodised salt in industrially processed foods to iodine intake in Macedonia
Authors: Milevska-Kostova Neda , Karanfilski Borislav , Knowles Jacky , Codling Karen , Lazarus John H
Published: December 2020

Evidence from the 1950s showed that Macedonia was iodine deficient. After the introduction of mandatory universal salt iodisation, the country saw a steady increase in iodine intake and decline in goitre prevalence, earning iodine-deficiency free status in 2003. Iodine status assessments in 2007 and 2016 showed adequate iodine intake among school age children (median urinary iodine concentration of 241 µg/L and 236 µg/L respectively). Macedonia participated in the 2019 piloting of the Iodine Global Network Programme Guidance on the use of iodised salt in industrially processed foods to better understand salt and iodised salt intake from food sources other than household salt.

Aggregated data from the 2017 Household Consumption and Expenditure Survey (HCES) was used to determine household salt consumption, to identify widely-consumed, salt-containing industrially processed foods and estimate typical daily intake of these foods. The salt content of these foods was estimated using national standards and the Danish food composition database. The percentage of this salt that was iodised was assessed using customs data for salt imports.

Although the study has its limitations, including a relatively small selection of foods, the results indicate potential iodine intake from iodised household salt and iodised salt in the selected foods of above 300% of the Estimated Average Requirement and over 220% of the Recommended Nutrient Intake for adults. This was approximately 50% of the tolerable safe Upper Level for iodine intake. The study confirmed high daily salt intake (11.2 grams from household salt only). Successful salt reduction would be expected to reduce iodine intake, however, modelling with 10% and 30% reduction implied this is unlikely to put any population group at risk of deficiency. It is recommended that design and implementation of salt iodisation and salt reduction policies are harmonized, alongside continued regular iodine status monitoring for different population groups.
CellVGAE: An unsupervised scRNA-seq analysis workflow with graph attention networks
Authors: Buterez David , Bica Ioana , Tariq Ifrah , Andrés-Terré Helena , Liò Pietro
Published: December 2020

Abstract

Currently, single-cell RNA sequencing (scRNA-seq) allows high-resolution views of individual cells, for libraries of up to (tens of) thousands of samples. In this study, we introduce the use of graph neural networks (GNN) in the unsupervised study of scRNA-seq data, namely for dimensionality reduction and clustering. Motivated by the success of non-neural graph-based techniques in bioinformatics, as well as the now common feedforward neural networks being applied to scRNA-seq measurements, we develop an architecture based on a variational graph autoencoder with graph attention layers that works directly on the connectivity of cells. With the help of three case studies, we show that our model, named CellVGAE, can be effectively used for exploratory analysis, even on challenging datasets, by extracting meaningful features from the data and providing the means to visualise and interpret different aspects of the model. Furthermore, we evaluate the dimensionality reduction and clustering performance on 9 well-annotated datasets, where we compare with leading neural and non-neural techniques. CellVGAE outperforms competing methods in all 9 scenarios. Finally, we show that CellVGAE is more interpretable than existing architectures by analysing the graph attention coefficients. The software and code to generate all the figures are available at https://github.com/davidbuterez/CellVGAE.
DNA sequence-dependent formation of heterochromatin nanodomains
Authors: Thorn Graeme J. , Clarkson Christopher T. , Rademacher Anne , Mamayusupova Hulkar , Schotta Gunnar , Rippe Karsten , Teif Vladimir B.
Published: December 2020

The mammalian epigenome contains thousands of heterochromatin nanodomains (HNDs) marked by di- and trimethylation of histone H3 at lysine 9, which have a typical size of 3-10 nucleosomes. However, the (epi)genetic determinants of their location and boundaries are only partly understood. Here, we compare four HND types in mouse embryonic stem cells, that are defined by histone methylases SUV39H1/2 or GLP, transcription factor ADNP or chromatin remodeller ATRX. Based on a novel chromatin hierarchical lattice framework termed ChromHL, we are able to predict HND maps with singe-nucleotide resolution. We find that HND nucleation can be rationalized by DNA sequence specific protein binding to PAX3/9, ADNP and LINE1 repeats. Depending on type of microdomains, boundaries are determined either by CTCF binding sites or by nucleosome-nucleosome and nucleosome-HP1 interactions. Our new framework allows predicting how patterns of H3K9me2/3 and other chromatin nanodomains are established and changed in processes such as cell differentiation.
Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning
Authors: Körtel Nadine , Rücklé Cornelia , Zhou You , Busch Anke , Hoch-Kraft Peter , Sutandy FX Reymond , Haase Jacob , Pradhan Mihika , Musheev Michael , Ostareck Dirk , Ostareck-Lederer Antje , Dieterich Christoph , Hüttelmaier Stefan , Niehrs Christof , Rausch Oliver , Dominissini Dan , König Julian , Zarnack Kathi
Published: December 2020

N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based approach to map m6A sites with single-nucleotide resolution. However, due to broad antibody reactivity, reliable identification of m6A sites from miCLIP data remains challenging. Here, we present miCLIP2 in combination with machine learning to significantly improve m6A detection. The optimised miCLIP2 results in high-complexity libraries from less input material. Importantly, we established a robust computational pipeline to tackle the inherent issue of false positives in antibody-based m6A detection. The analyses are calibrated withMettl3knockout cells to learn the characteristics of m6A deposition, including m6A sites outside of DRACH motifs. To make our results universally applicable, we trained a machine learning model, m6Aboost, based on the experimental and RNA sequence features. Importantly, m6Aboost allows prediction of genuine m6A sites in miCLIP2 data without filtering for DRACH motifs or the need for Mettl3 depletion. Using m6Aboost, we identify thousands of high-confidence m6A sites in different murine and human cell lines, which provide a rich resource for future analysis. Collectively, our combined experimental and computational methodology greatly improves m6A identification.

Highlights

miCLIP2 produces complex libraries to map m6A RNA modifications

Mettl3KO miCLIP2 allows to identify Mettl3-dependent RNA modification sites

Machine learning predicts genuine m6A sites from human and mouse miCLIP2 data withoutMettl3KO

m6A modifications occur outside of DRACH motifs and associate with alternative splicing
A Systematic Review and Network Meta-Analysis for COVID-19 Treatments
Authors: Zhang Chenyang , Jin Huaqing , Wen Yifeng , Yin Guosheng
Published: December 2020

Background

Numerous interventions for coronavirus disease 2019 (COVID-19) have been investigated by randomized controlled trials (RCTs). This systematic review and Bayesian network meta-analysis (NMA) aim to provide a comprehensive evaluation of efficacy of available treatments for COVID-19.

Methods

We searched for candidate COVID-19 studies in WHO COVID-19 Global Research Database, PubMed, PubMed Central, LitCovid, Proquest Central and Ovid up to December 19, 2020. RCTs for suspected or confirmed COVID-19 patients were included, regardless of publication status or demographic characteristics. Bayesian NMA with fixed effects was conducted to estimate the effect sizes using posterior means and 95% equal-tailed credible intervals (CrIs), while that with random effects was carried out as well for sensitivity analysis. Bayesian hierarchical models were used to estimate effect sizes of treatments grouped by their drug classifications.

Results

We identified 96 eligible RCTs with a total of 51187 patients. Compared with the standard of care (SOC), this NMA showed that dexamethasone led to lower risk of mortality with an odds ratio (OR) of 0.85 (95% CrI [0.76, 0.95]; moderate certainty) and lower risk of mechanical ventilation (MV) with an OR of 0.68 (95% CrI [0.56, 0.83]; low certainty). For hospital discharge, remdesivir (OR 1.37, 95% CrI [1.15, 1.64]; moderate certainty), dexamethasone (OR 1.20, 95% CrI [1.08, 1.34]; low certainty), interferon beta (OR 2.15, 95% CrI [1.26, 3.74]; moderate certainty), tocilizumab (OR 1.40, 95% CrI [1.05, 1.89]; moderate certainty) and baricitinib plus remdesivir (OR 1.75, 95% CrI [1.28, 2.39]; moderate certainty) could all increase the discharge rate respectively. Recombinant human granulocyte colony-stimulating factor indicated lower risk of MV (OR 0.20, 95% CrI [0.10, 0.40]; moderate certainty); and patients receiving convalescent plasma resulted in better viral clearance (OR 2.28, 95% CrI [1.57, 3.34]; low certainty). About two-thirds of the studies included in this NMA were rated as high risk of bias, and the certainty of evidence was either low or very low for most of the comparisons.

Conclusion

The Bayesian NMA identified superiority of several COVID-19 treatments over SOC in terms of mortality, requirement of MV, hospital discharge and viral clearance. These results provide a comprehensive comparison of current COVID-19 treatments and shed new light on further research and discovery of potential COVID-19 treatments.
Iliski, a software for robust calculation of transfer functions
Authors: Aydin Ali-Kemal , Haselden William D. , Dang Julie , Drew Patrick J. , Charpak Serge , Boido Davide
Published: December 2020

1.

Understanding the relationships between biological events is paramount to unravel pathophysiological mechanisms. These relationships can be modeled with Transfer Functions (TFs), with no need of a priori hypotheses as to the shape of the transfer function. Here we present Iliski, a software dedicated to TFs computation between two signals. It includes different pre-treatment routines and TF computation processes: deconvolution, deterministic and non-deterministic optimization algorithms that are adapted to disparate datasets. We apply Iliski to data on neurovascular coupling, an ensemble of biological events that link neuronal activity to local changes of blood flow, highlighting the software benefits and caveats in the computation and evaluation of TFs. We also propose a workflow that will help users to choose the best computation according to the dataset. Iliski is available under the open-source license CC BY 4.0 on GitLab (https://gitlab.com/AliK_A/iliski) and can be used on the most common operating systems, either within the MATLAB environment, or as a standalone application.
EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape
Authors: Ungerleider Nathan , Bullard Whitney , Kara Mehmet , Wang Xia , Roberts Claire , Renne Rolf , Tibbetts Scott , Flemington Erik
Published: December 2020

Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt’s Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and a BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validatedin vivothrough the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in TCGA GC dataset. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing the host immune response.

AUTHOR SUMMARY

Burkitt’s Lymphoma and gastric cancer are both associated with EBV, a prolific DNA tumor virus that latently resides in nearly all human beings. Despite mostly restricting viral gene expression to noncoding RNAs, EBV has important influences on the fitness of infected tumor cells. Here, we show that the miRNA class of viral noncoding RNAs are a major viral contributor to remodeling the tumor cell regulatory machinery in patient tumor samples. First, an assessment of miRNA expression in clinical tumor samples showed that EBV miRNAs are expressed at unexpectedly high levels relative to cell miRNAs. Using a highly specific miRNA target identification approach, CLASH, we comprehensively identified both viral and cellular microRNA targets and the relative abundance of each microRNA-mRNA interaction. We also show that viral microRNAs bind to and alter the expression of their mRNA targets more effectively than their cellular microRNA counterparts. Pathway analysis of the most effectively targeted mRNAs revealed enrichment of immune signaling pathways and we show a corresponding inverse correlation between EBV miRNA expression and infiltrating immune cells in EBV positive primary tumors. Altogether, this study shows that EBV miRNAs are key regulators of the tumor cell phenotype and the immune cell microenvironment.
Cetylpyridinium chloride-containing mouthwashes reduce the infectivity of SARS-CoV-2 variantsin vitro
Authors: Muñoz-Basagoiti Jordana , Perez-Zsolt Daniel , León Rubén , Blanc Vanessa , Raïch-Regué Dàlia , Cano-Sarabia Mary , Trinité Benjamin , Pradenas Edwards , Blanco Julià , Gispert Joan , Clotet Bonaventura , Izquierdo-Useros Nuria
Published: December 2020

Oral mouthwashes decrease the infectivity of several respiratory viruses including SARS-CoV-2. However, the precise agents with antiviral activity present in these oral rinses and their exact mechanism of action remain unknown. Here we show that Cetylpyridinium chloride (CPC), a quaternary ammonium compound present in many oral mouthwashes, reduces SARS-CoV-2 infectivity by inhibiting the viral fusion step with target cells after disrupting the integrity of the viral envelope. We also found that CPC-containing mouth rinses decreased more than a thousand times the infectivity of SARS-CoV-2in vitro, while the corresponding vehicles had no effect. This activity was effective for different SARS-CoV-2 variants, including the B.1.1.7 variant, predominant in UK, also in the presence of sterilized saliva. CPC-containing mouth rinses could therefore represent a cost-effective measure to reduce SARS-CoV-2 infectivity in saliva, aiding to reduce viral transmission from infected individuals regardless of the variants they are infected with.
Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning
Authors: Frazer Jonathan , Notin Pascal , Dias Mafalda , Gomez Aidan , Brock Kelly , Gal Yarin , Marks Debora S.
Published: December 2020

Quantifying the pathogenicity of protein variants in human disease-related genes would have a profound impact on clinical decisions, yet the overwhelming majority (over 98%) of these variants still have unknown consequences1–3. In principle, computational methods could support the large-scale interpretation of genetic variants. However, prior methods4–7have relied on training machine learning models on available clinical labels. Since these labels are sparse, biased, and of variable quality, the resulting models have been considered insufficiently reliable8. By contrast, our approach leverages deep generative models to predict the clinical significance of protein variants without relying on labels. The natural distribution of protein sequences we observe across organisms is the result of billions of evolutionary experiments9,10. By modeling that distribution, we implicitly capture constraints on the protein sequences that maintain fitness. Our model EVE (Evolutionary model of Variant Effect) not only outperforms computational approaches that rely on labelled data, but also performs on par, if not better than, high-throughput assays which are increasingly used as strong evidence for variant classification11–23. After thorough validation on clinical labels, we predict the pathogenicity of 11 million variants across 1,081 disease genes, and assign high-confidence reclassification for 72k Variants of Unknown Significance8. Our work suggests that models of evolutionary information can provide a strong source of independent evidence for variant interpretation and that the approach will be widely useful in research and clinical settings.
Identification of Key Genes Potentially Related to Triple Receptor Negative Breast Cancer by Microarray Analysis
Authors: Vastrad Basavaraj , Vastrad Chanabasayya , Kotturshetti Iranna
Published: December 2020

Triple receptor negative breast cancer (TNBC) is the type of gynecological cancer in the elderly women. This study is aimed to explore molecular mechanism of TNBC via bioinformatics analysis. The gene expression profiles of GSE88715 (including 38 TNBC and 38 normal control) was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened using the limma package in R software. Pathway and gene ontology (GO) enrichment analysis were performed based on various pathway dabases and GO database. Then, InnateDb interactome database, Cytoscape and PEWCC1 were applied to construct the protein-protein interaction (PPI) network and screen hub genes. Similarly, miRNet database, NetworkAnalyst database and Cytoscape were applied to construct the target gene - miRNA network and target gene - TF network, and screen targate genes. Pathway and GO enrichment analysis was further performed for hub genes, gene clusters identified via module analysis and targate genes. The expression of hub genes with prognostic values was validated on the UALCAN, cBio Portal, The Human Protein Atlas, receiver operator characteristic (ROC) curve analysis, RT-PCR analysis and immune infiltration analysis. A total of 949 DEGs were identified in TNBC (469 up regulated genes, and 480 down regulated genes), and they were mainly enriched in the terms of phospholipases, toxoplasmosis, immune response, cell surface, glycolysis, biosynthesis of amino acids, carboxylic acid metabolic process and organic substance catabolic process extracellular space. Hub genes including UBD, HLA-B, MYC and HSP90AB1 were identified via PPI network and modules, which were mainly enriched in immune response, antigen processing and presentation, cell cycle and pathways in cancer. Targate genes including CCDC80, PEG10, HOPX and CCNA2 were identified via target gene - miRNA network and target gene - TF network, which were mainly enriched in extracellular structure organization, validated targets of C-MYC transcriptional activation, ensemble of genes encoding core extracellular matrix including ECM glycoproteins and cell cycle. The top five significantly overexpressed mRNA (ADAM15, BATF, NOTCH3, ITGAX and SDC1) and the top five significantly underexpressed mRNA (RPL4, EEF1G, RPL3, RBMX and ABCC2) were selected for further validation in TNBCpatients and healthy controls. Analysis of the expression of genes in the various databases showed that ADAM15, BATF, NOTCH3, ITGAX, SDC1, RPL4, EEF1G, RPL3, RBMX and ABCC2 expressions have a cancer specific pattern in TNBC. Collectively, ADAM15, BATF, NOTCH3, ITGAX, SDC1, RPL4, EEF1G, RPL3, RBMX and ABCC2 may be useful candidate biomarkers for TNBC diagnosis, prognosis and theraputic targates.
Cytopath: Simulation-based inference of differentiation trajectories from RNA velocity fields
Authors: Gupta R. , Cerletti D. , Gut G. , Oxenius A. , Claassen M.
Published: December 2020

Abstract

Trajectory inference from single-cell RNA sequencing data bears the potential to systematically reconstruct complex differentiation processes, however inferring trajectories that accurately model the biological characteristics of varied processes continues to be a challenge, notwithstanding the many available solutions. In general, trajectory and pseudotime inference methods have so far suffered from the ambiguity of static single-cell transcriptome snapshots lacking a concept of directionality and rate of transcriptional activity.

We report Cytopath, a method for trajectory inference that takes advantage of transcriptional activity information from RNA velocity of single-cells to perform trajectory inference. Cytopath performs this task by defining a Markov chain model, simulating an ensemble of possible differentiation trajectories and constructs a consensus trajectory. We show that Cytopath can recapitulate the topological and molecular characteristics of the differentiation process under study. In our analysis we include differentiation trajectories with varying bifurcated, circular, convergent and mixed topology studied in single-snapshot as well as time-series single-cell RNA sequencing experiments. We demonstrate superior and enabling capability to reconstruct differentiation trajectories in comparison to state-of-the art trajectory inference approaches.
Hepatitis B virus envelope proteins can serve as therapeutic targets embedded in the host cell plasma membrane
Authors: Zhao Lili , Chen Fuwang , Quitt Oliver , Festag Marvin , Ringelhan Marc , Wisskirchen Karin , Hasreiter Julia , Yakovleva Luidmila , Sureau Camille , Bohne Felix , Aichler Michaela , Bruss Volker , Shevtsov Maxim , van de Klundert Maarten , Momburg Frank , Möhl Britta S. , Protzer Ulrike
Published: December 2020

Hepatitis B virus (HBV) infection is a major health threat causing 880,000 deaths each year. Available therapies control viral replication, but do not cure HBV leaving patients at risk to develop hepatocellular carcinoma. Here we show that HBV envelope proteins (HBs) - besides their integration into endosomal membranes - become embedded in the plasma membrane where they can be targeted by redirected T-cells. HBs was detected on the surface of HBV-infected cells, in livers of mice replicating HBV and in HBV-induced hepatocellular carcinoma. Staining with HBs-specific recombinant antibody MoMab recognizing a confirmational epitope indicated that membrane-associated HBs remains correctly folded in HBV-replicating cells in cell culture and in livers of HBV-transgenic micein vivo. MoMab coated onto superparamagnetic iron oxide nanoparticles allowed to detect membrane-associated HBs after HBV infection by electron microscopy in distinct stretched of the hepatocyte plasma membrane. Last not least we demonstrate that HBs located to the cell surface allows therapeutic targeting of HBV-positive cells by T-cells either engrafted with a chimeric antigen receptor or redirected by bispecific, T-cell engager antibodies.
Distinct molecular pathways govern presynaptic homeostatic plasticity
Authors: Nair Anu G. , Muttathukunnel Paola , Müller Martin
Published: December 2020

Presynaptic homeostatic plasticity (PHP) stabilizes synaptic transmission by counteracting impaired neurotransmitter receptor function through increased presynaptic release. PHP is thought to be triggered by impaired receptor function, and to involve a stereotypic signaling pathway. However, here we demonstrate that different receptor perturbations that similarly reduce synaptic activity result in vastly different responses at theDrosophilaneuromuscular junction. While receptor inhibition by the glutamate receptor (GluR) antagonist γ-DGG is not compensated by PHP, the GluR inhibitors PhTx-433 and Gyki induce compensatory PHP. Intriguingly, PHP triggered by PhTx and Gyki involve separable signaling pathways, including inhibition of distinct GluR subtypes, differential modulation of the active-zone scaffold Bruchpilot, and short-term plasticity. Moreover, while PHP upon Gyki treatment does not require genes promoting PhTx-induced PHP, it involves presynaptic Protein Kinase D. Thus, synapses not only respond differentially to similar activity impairments, but achieve homeostatic compensation via distinct mechanisms, highlighting the diversity of homeostatic signaling.
Assessment and comparison of two different methods to extract nucleic acids from individual honey bees
Authors: Swami Rohan , Ganser Brooke , Tarpy David R. , Strand Micheline K. , Li-Byarlay Hongmei
Published: December 2020

The honey bee is an excellent model system to study behavior ecology, behavioral genetics, and sociogenomics. Nucleic acid based analyses enable a broad scope of research in functional genomics, disease diagnostics, mutant screening, and genetic breeding. Multiple levels of analysis lead to a more comprehensive understanding of the causes of phenotypic variation by integrating genomic variation, transcriptomic profiles, and epigenomic information. One limitation, however, is the sample preparation procedures to obtain high quality DNA and RNA simultaneously, particularly from small amounts of material, such as tissues of individual bees. We demonstrate that it is feasible to perform dual extractions of DNA and RNA from a single individual bee and compare the quality and quantity of the extracted nucleic acids using two different types of methods (column based versus ethanol precipitation). We obtained a higher yield of both DNA and RNA with one of the extraction methods over the other, although the quality of the DNA and RNA was not significantly different between methods. We describe here the first validated method for dual extraction of DNA and RNA specifically from individual honey bees.
How to coordinate vaccination and social distancing to mitigate SARS-CoV-2 outbreaks
Authors: Grundel Sara , Heyder Stefan , Hotz Thomas , Ritschel Tobias K. S. , Sauerteig Philipp , Worthmann Karl
Published: December 2020

Most countries have started vaccinating people against COVID-19. However, due to limited production capacities and logistical challenges it will take months/years until herd immunity is achieved. Therefore, vaccination and social distancing have to be coordinated. In this paper, we provide some insight on this topic using optimization-based control on an age-differentiated compartmental model. For real-life decision making, we investigate the impact of the planning horizon on the optimal vaccination/social distancing strategy. We find that in order to reduce social distancing in the long run, without overburdening the healthcare system, it is essential to vaccinate the people with the highest contact rates first. That is also the case if the objective is to minimize fatalities provided that the social distancing measures are sufficiently strict. However, for short-term planning it is optimal to focus on the high-risk group.
An immunogenic model of KRAS-mutant lung cancer for study of targeted therapy and immunotherapy combinations
Authors: Boumelha Jesse , de Carné Trécesson Sophie , Law Emily K. , Romero-Clavijo Pablo , Coelho Matthew A. , Ng Kevin , Mugarza Edurne , Moore Christopher , Rana Sareena , Caswell Deborah R. , Murillo Miguel , Hancock David C. , Argyris Prokopios P. , Brown William L. , Durfee Cameron , Larson Lindsay K. , Vogel Rachel I. , Suárez-Bonnet Alejandro , Priestnall Simon L. , East Philip , Ross Sarah J. , Kassiotis George , Molina-Arcas Miriam , Swanton Charles , Harris Reuben , Downward Julian
Published: December 2020

Mutations in oncogenes such as KRAS and EGFR cause a high proportion of lung cancers. Drugs targeting these proteins cause tumour regression but ultimately fail to cure these cancers, leading to intense interest in how best to combine them with other treatments, such as immunotherapies. However, preclinical systems for studying the interaction of lung tumours with the host immune system are inadequate, in part due to the low tumour mutational burden in genetically engineered mouse models. Here we set out to develop mouse models of mutant KRAS-driven lung cancer with an elevated tumour mutational burden by expressing the human DNA cytosine deaminase, APOBEC3B, to mimic the mutational signature seen in human lung cancer. This failed to substantially increase clonal tumour mutational burden and autochthonous tumours remained refractory to immunotherapy. However, by establishing clonal cell lines from these tumours we generated an immunogenic syngeneic transplantation model of KRAS mutant lung adenocarcinoma that was sensitive to immunotherapy. Unexpectedly, we found that anti-tumour immune responses were not directed against neoantigens but instead targeted derepressed endogenous retroviral antigens. The ability of KRASG12Cinhibitors to cause regression of KRASG12C-expressing versions of these tumours was markedly potentiated by the adaptive immune system, providing a unique opportunity for the study of combinations of targeted and immunotherapies in immune-hot lung cancer.