bluuebunny/crossref_metadata_2025 huggingface dataset:
Quality versus quantity: The balance between egg and clutch size among Australian amphibians is related to life history and environmental conditions
Authors: Gould John , Beranek Chad , Valdez Jose , Mahony Michael
Published: March 2020

An inverse relationship between egg and clutch size has been found repeatedly across animal groups, including birds, reptiles and amphibians, and is considered to be a result of resource limitations and physical constraints on the reproducing female. However, few studies have contextualised this relationship with respect to various environmental selecting pressures and life history traits that have also likely influenced the selection of an optimal egg/clutch size combination, while even fewer have tested these interrelationships using robust natural history datasets. In this study, we aimed to test current hypothesises regarding these relationships on both egg and clutch sizes among the Australian Anurans, which to date have not received this kind of investigation. Specifically, we looked at the influence of environmental selecting pressures (egg laying location, environment persistence and bioregion) and life history traits (adult female body size, egg development type, parental care level, breeding period and temporal breeding pattern). As expected, a clear inverse relationship was found between egg and clutch size, while female body size was positively related to both. Generally speaking, smaller clutches of larger eggs tended to be produced by species that i) oviposit terrestrially, ii) showcase direct development and iii) possess high levels of parental care. Temporal breeding pattern was strongly related to clutch size only, with large clutches occurring in explosive breeding species, while breeding habitat was strongly related to egg size only, with large eggs sizes occurring in terrestrial species. Altogether, these findings indicate that numerous factors have likely influenced the evolution of an optimal clutch type in this group, highlighting the importance of incorporating such variables into animal studies on egg and clutch sizes.
An emergent clade of SARS-CoV-2 linked to returned travellers from Iran
Authors: Eden John-Sebastian , Rockett Rebecca , Carter Ian , Rahman Hossinur , de Ligt Joep , Hadfield James , Storey Matthew , Ren Xiaoyun , Tulloch Rachel , Basile Kerri , Wells Jessica , Byun Roy , Gilroy Nicky , O’Sullivan Matthew V , Sintchenko Vitali , Chen Sharon C , Maddocks Susan , Sorrell Tania C , Holmes Edward C , Dwyer Dominic E , Kok Jen ,   for the 2019-nCoV Study Group
Published: March 2020

The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.
A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein
Authors: Joyce M. Gordon , Sankhala Rajeshwer S. , Chen Wei-Hung , Choe Misook , Bai Hongjun , Hajduczki Agnes , Yan Lianying , Sterling Spencer L. , Peterson Caroline E. , Green Ethan C. , Smith Clayton , de Val Natalia , Amare Mihret , Scott Paul , Laing Eric D. , Broder Christopher C. , Rolland Morgane , Michael Nelson L. , Modjarrad Kayvon
Published: March 2020

SARS-CoV-2 is a zoonotic virus that has caused a pandemic of severe respiratory disease—COVID-19— within several months of its initial identification. Comparable to the first SARS-CoV, this novel coronavirus’s surface Spike (S) glycoprotein mediates cell entry via the human ACE-2 receptor, and, thus, is the principal target for the development of vaccines and immunotherapeutics. Molecular information on the SARS-CoV-2 S glycoprotein remains limited. Here we report the crystal structure of the SARS-CoV-2 S receptor-binding-domain (RBD) at a the highest resolution to date, of 1.95 Å. We identified a set of SARS-reactive monoclonal antibodies with cross-reactivity to SARS-CoV-2 RBD and other betacoronavirus S glycoproteins. One of these antibodies, CR3022, was previously shown to synergize with antibodies that target the ACE-2 binding site on the SARS-CoV RBD and reduce viral escape capacity. We determined the structure of CR3022, in complex with the SARS-CoV-2 RBD, and defined a broadly reactive epitope that is highly conserved across betacoronaviruses. This epitope is inaccessible in the “closed” prefusion S structure, but is accessible in “open” conformations. This first-ever resolution of a human antibody in complex with SARS-CoV-2 and the broad reactivity of this set of antibodies to a conserved betacoronavirus epitope will allow antigenic assessment of vaccine candidates, and provide a framework for accelerated vaccine, immunotherapeutic and diagnostic strategies against SARS-CoV-2 and related betacoronaviruses.

HIGHLIGHTS

High resolution structure of the SARS-CoV-2 Receptor-Binding-Domain (RBD).

Recognition of the SARS-CoV-2 RBD by SARS-CoV antibodies.

Structure of the SARS-COV-2 RBD in complex with antibody CR3022.

Identification of a cryptic site of vulnerability on the SARS-CoV-2 Spike.
Accurate Diagnosis of Colorectal Cancer Based on Histopathology Images Using Artificial Intelligence
Authors: Wang Kuan-Song , Yu Gang , Xu Chao , Meng Xiang-He , Zhou Jianhua , Zheng Changli , Deng Zhenghao , Shang Li , Liu Ruijie , Su Shitong , Zhou Xunjian , Li Qingling , Li Juanni , Wang Jing , Ma Kewen , Qi Jialin , Hu Zhenmin , Tang Ping , Deng Jeffrey , Qiu Xiang , Li Bo-Yang , Shen Wen-Di , Quan Ru-Ping , Yang Jun-Ting , Huang Lin-Ying , Xiao Yao , Yang Zhi-Chun , Li Zhongming , Wang Sheng-Chun , Ren Hongzheng , Liang Changjiang , Guo Wei , Li Yanchun , Xiao Heng , Gu Yonghong , Yun Jing-Ping , Huang Dan , Song Zhigang , Fan Xiangshan , Chen Ling , Yan Xiaochu , Li Zhi , Huang Zhong-Chao , Huang Jufang , Luttrell Joseph , Zhang Chao-Yang , Zhou Weihua , Zhang Kun , Yi Chunhui , Shen Hui , Wang Yu-Ping , Xiao Hong-Mei , Deng Hong-Wen
Published: March 2020

Background

Accurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients’ treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on their daily image analyses.

Methods

Based on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC prediction/diagnosis using weakly labeled pathological whole slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, >14,680 WSIs, from >9,631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, U.S., and Germany.

Results

Our innovative AI tool was consistently nearly perfectly agreed with (average Kappa-statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multi-centers. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.981 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells.

Conclusions

This first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. Hence, it will drastically alleviate the heavy clinical burden of daily pathology diagnosis, and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.
Master Regulator Analysis of the SARS-CoV-2/Human interactome
Authors: Guzzi Pietro Hiram , Mercatelli Daniele , Ceraolo Carmine , Giorgi Federico M.
Published: March 2020

the recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In this paper, we set out to shed light on the SARS-CoV-2/host receptor recognition, a crucial factor for successful virus infection. Based on the current knowledge of the interactome between SARS-CoV-2 and host cell proteins, we performed Master Regulator Analysis to detect which parts of the human interactome are most affected by the infection. We detected, amongst others, affected apoptotic and mitochondrial mechanisms, and a downregulation of the ACE2 protein receptor, notions that can be used to develop specific therapies against this new virus.
Cross-reactive antibody response between SARS-CoV-2 and SARS-CoV infections
Authors: Lv Huibin , Wu Nicholas C. , Tsang Owen Tak-Yin , Yuan Meng , Perera Ranawaka A. P. M. , Leung Wai Shing , So Ray T. Y. , Chun Chan Jacky Man , Yip Garrick K. , Hong Chik Thomas Shiu , Wang Yiquan , Chung Choi Chris Yau , Lin Yihan , Ng Wilson W. , Zhao Jincun , Poon Leo L. M. , Malik Peiris J. S. , Wilson Ian A. , Mok Chris K. P.
Published: March 2020

The World Health Organization has recently declared the ongoing outbreak of COVID-19, which is caused by a novel coronavirus SARS-CoV-2, as pandemic. There is currently a lack of knowledge in the antibody response elicited from SARS-CoV-2 infection. One major immunological question is concerning the antigenic differences between SARS-CoV-2 and SARS-CoV. We address this question by using plasma from patients infected by SARS-CoV-2 or SARS-CoV, and plasma obtained from infected or immunized mice. Our results show that while cross-reactivity in antibody binding to the spike protein is common, cross-neutralization of the live viruses is rare, indicating the presence of non-neutralizing antibody response to conserved epitopes in the spike. Whether these non-neutralizing antibody responses will lead to antibody-dependent disease enhancement needs to be addressed in the future. Overall, this study not only addresses a fundamental question regarding the antigenicity differences between SARS-CoV-2 and SARS-CoV, but also has important implications in vaccine development.
GAS6-AXL signaling triggers actin remodeling and macropinocytosis that drive cancer cell invasion
Authors: Zdżalik-Bielecka Daria , Poświata Agata , Kozik Kamila , Jastrzębski Kamil , Schink Kay Oliver , Brewińska-Olchowik Marta , Piwocka Katarzyna , Stenmark Harald , Miączyńska Marta
Published: March 2020

AXL, a member of the TAM (TYRO3, AXL, MER) receptor tyrosine kinase family, and its ligand GAS6 are implicated in oncogenesis and metastasis of many cancer types. However, the exact cellular processes activated by GAS6-AXL remain largely unexplored. Here, we identified an interactome of AXL and revealed its associations with proteins regulating actin dynamics. Consistently, GAS6-mediated AXL activation triggered actin remodeling manifested by peripheral membrane ruffling and circular dorsal ruffles (CDRs). This further promoted macropinocytosis that mediated the internalization of GAS6-AXL complexes and sustained survival of glioblastoma cells grown under glutamine-deprived conditions. GAS6-induced CDRs contributed to focal adhesion (FA) turnover, cell spreading and elongation. Consequently, AXL activation by GAS6 drove invasion of cancer cells in a spheroid model. All these processes required the kinase activity of AXL but not TYRO3, and downstream activation of PI3K. We propose that GAS6-AXL signaling induces multiple actin-driven cytoskeletal rearrangements and macropinocytosis that jointly contribute to cancer cell invasion.
Emergence of evidence during disease outbreaks: lessons learnt from the Zika virus outbreak
Authors: Counotte Michel J , Meili Kaspar W , Low Nicola
Published: March 2020

Introduction

Outbreaks of infectious diseases trigger an increase in scientific research and output. Early in outbreaks, evidence is scarce, but it accumulates rapidly. We are continuously facing new disease outbreaks, including the new coronavirus (SARS-nCoV-2) in December 2019.The objective of this study was to describe the accumulation of evidence during the 2013-2016 Zika virus (ZIKV) outbreak in the Pacific and the Americas related to aetiological causal questions about congenital abnormalities and Guillain-Barré syndrome.

Methods

We hypothesised that the temporal sequence would follow a pre-specified order, according to study design. We assessed 1) how long it takes before findings from a specific study design appear, 2) how publication of preprints could reduce the time to publication and 3) how time to publication evolves over time.

Results

We included 346 publications published between March 6, 2014 and January 1, 2019. In the 2013-–2016 ZIKV outbreak, case reports, case series and basic research studies were published first. Case-control and cohort studies appeared between 400–700 days after ZIKV was first detected in the region of the study origin. Delay due to the publication process were lowest at the beginning of the outbreak. Only 4.6% of the publications was available as preprints.

Discussion

The accumulation of evidence over time in new causal problems generally followed a hierarchy. Preprints reduced the delay to initial publication. Our methods can be applied to new emerging infectious diseases.
Gut microbiota impacts bone via B.vulgatus-valeric acid-related pathways
Authors: Lin Xu , Xiao Hong-Mei , Liu Hui-Min , Lv Wan-Qiang , Greenbaum Jonathan , Yuan Si-Jie , Gong Rui , Zhang Qiang , Chen Yuan-Cheng , Peng Cheng , Xu Xue-Juan , Pan Dao-Yan , Chen Zhi , Li Zhang-Fang , Zhou Rou , Wang Xia-Fang , Lu Jun-Min , Ao Zeng-Xin , Song Yu-Qian , Zhang Yin-Hua , Su Kuan-Jui , Meng Xiang-He , Ge Chang-Li , Lv Feng-Ye , Shi Xing-Ming , Zhao Qi , Guo Bo-Yi , Yi Neng-Jun , Shen Hui , Papasian Christopher J. , Shen Jie , Deng Hong-Wen
Published: March 2020

Although gut microbiota influences osteoporosis risk, the individual species involved, and underlying mechanisms, are unknown. We performed integrative analyses in a Chinese cohort with metagenomics/targeted metabolomics/whole-genome sequencing. Bacteroides vulgatus was found negatively associated with bone mineral density (BMD), this association was validated in US Caucasians. Serum valeric acid was positively associated with BMD, and B.vulgatus causally downregulated it. Ovariectomized mice fed B.vulgatus had decreased bone formation and increased bone resorption, lower BMD and poorer bone micro-structure. Valeric acid suppressed NF-κB p65 protein production (pro-inflammatory), and enhanced IL-10 mRNA expression (anti-inflammatory), leading to suppressed maturation of osteoclast-like cells, and enhanced maturation of osteoblasts in vitro. B.vulgatus and valeric acid represent promising targets for osteoporosis prevention/treatment.
Comparison of Population Characteristics in Real-World Clinical Oncology Databases in the US: Flatiron Health, SEER, and NPCR
Authors: Ma Xinran , Long Lura , Moon Sharon , Adamson Blythe J.S. , Baxi Shrujal S.
Published: March 2020

Background and Objective

The Surveillance, Epidemiology, and End Results Program (SEER) program and the National Program of Cancer Registries (NPCR), are authoritative sources for population cancer surveillance and research in the US. An increasing number of recent oncology studies are based on the electronic health record (EHR)-derived de-identified databases created and maintained by Flatiron Health. This report describes the differences in the originating sources and data development processes, and compares baseline demographic characteristics in the cancer-specific databases from Flatiron Health, SEER, and NPCR, to facilitate interpretation of research findings based on these sources.

Methods

Patients with documented care from January 1, 2011 through May 31, 2019 in a series of EHR-derived Flatiron Health de-identified databases covering multiple tumor types were included. SEER incidence data (obtained from the SEER 18 database) and NPCR incidence data (obtained from the US Cancer Statistics public use database) for malignant cases diagnosed from January 1, 2011 to December 31, 2016 were included. Comparisons of demographic variables were performed across all disease-specific databases, for all patients and for the subset diagnosed with advanced-stage disease.

Results

As of May 2019, a total of 201,570 patients with 19 different cancer types were included in Flatiron Health datasets. In an overall comparison to national cancer registries, patients in the Flatiron Health databases had similar sex, age at initial diagnosis, and geographic distributions but appeared to be diagnosed with later stages of disease compared with patients in other datasets. For variables such as stage and race, Flatiron Health databases had a greater degree of incompleteness. There are variations in these trends by cancer types.

Conclusions

These three databases present general similarities in demographic and geographic distribution, but there are overarching differences across the populations they cover. Differences in data sourcing (medical oncology EHRs vs cancer registries), and disparities in sampling approaches and rules of data acquisition may explain some of these divergences. Furthermore, unlike the steady information flow entered into registries, the availability of medical oncology EHR-derived information reflects the extent of involvement of medical oncology clinics at different points in the specialty management of individual diseases, resulting in inter-disease variability. These differences should be considered when interpreting study results obtained with these databases.
Recapitulation of SARS-CoV-2 Infection and Cholangiocyte Damage with Human Liver Organoids
Authors: Zhao Bing , Ni Chao , Gao Ran , Wang Yuyan , Yang Li , Wei Jinsong , Lv Ting , Liang Jianqing , Zhang Qisheng , Xu Wei , Xie Youhua , Wang Xiaoyue , Yuan Zhenghong , Liang Junbo , Zhang Rong , Lin Xinhua
Published: March 2020

The newly emerged pandemic coronavirus, SARS-CoV-2, has posed a significant public health threat worldwide. However, the mode of virus transmission and tissue tropism is not well established yet. Recent findings of substantial liver damage in patients and ACE2+ cholangiocytes in healthy liver tissues prompted us to hypothesize that human liver ductal organoids could serve as a model to determine the susceptibility and mechanisms underlining the liver damage upon SARS-CoV-2 infection. By single-cell RNA sequencing, we found that long-term liver ductal organoid culture preserved the human specific ACE2+ population of cholangiocytes. Moreover, human liver ductal organoids were permissive to SARS-CoV-2 infection and support robust replication. Notably, virus infection impaired the barrier and bile acid transporting functions of cholangiocytes through dysregulation of genes involved in tight junction formation and bile acid transportation, which could explain the bile acid accumulation and consequent liver damage in patients. These results indicate that control of liver damage caused directly by viral infection should be valued in treating COVID-19 patients. Our findings also provide an application of human organoids in investigating the tropism and pathogenesis of SARS-CoV-2, which would facilitate novel drug discovery.
Single-cell transcriptomic analysis of the adult mouse spinal cord
Authors: Blum Jacob A. , Klemm Sandy , Nakayama Lisa , Kathiria Arwa , Guttenplan Kevin A. , Hoang Phuong T. , Shadrach Jennifer L. , Kaltschmidt Julia A. , Greenleaf William J. , Gitler Aaron D.
Published: March 2020

The spinal cord is a fascinating structure responsible for coordinating all movement in vertebrates. Spinal motor neurons control the activity of virtually every organ and muscle throughout the body by transmitting signals that originate in the spinal cord. These neurons are remarkably heterogeneous in their activity and innervation targets. However, because motor neurons represent only a small fraction of cells within the spinal cord and are difficult to isolate, the full complement of motor neuron subtypes remains unknown. Here we comprehensively describe the molecular heterogeneity of motor neurons within the adult spinal cord. We profiled 43,890 single-nucleus transcriptomes using fluorescence-activated nuclei sorting to enrich for spinal motor neuron nuclei. These data reveal a transcriptional map of the adult mammalian spinal cord and the first unbiased characterization of all transcriptionally distinct autonomic and somatic spinal motor neuron subpopulations. We identify 16 sympathetic motor neuron subtypes that segregate spatially along the spinal cord. Many of these subtypes selectively express specific hormones and receptors, suggesting neuromodulatory signaling within the autonomic nervous system. We describe skeletal motor neuron heterogeneity in the adult spinal cord, revealing numerous novel markers that distinguish alpha and gamma motor neurons—cell populations that are specifically affected in neurodegenerative disease. We also provide evidence for a novel transcriptional subpopulation of skeletal motor neurons. Collectively, these data provide a single-cell transcriptional atlas for investigating motor neuron diversity as well as the cellular and molecular basis of motor neuron function in health and disease.
HARMONIES: A Hybrid Approach for Microbiome Networks Inference via Exploiting Sparsity
Authors: Jiang Shuang , Xiao Guanghua , Koh Andrew Young , Yao Bo , Li Qiwei , Zhan Xiaowei
Published: March 2020

The human microbiome is a collection of microorganisms. They form complex communities and collectively affect host health. Recently, the advances in next-generation sequencing technology enable the high-throughput profiling of the human microbiome. This calls for a statistical model to construct microbial networks from the microbiome sequencing count data. As microbiome count data are high-dimensional and suffer from uneven sampling depth, over-dispersion, and zero-inflation, these characteristics can bias the network estimation and require specialized analytical tools. Here we propose a general framework, HARMONIES, a Hybrid Approach foR MicrobiOme Network Inferences via Exploiting Sparsity, to infer a sparse microbiome network. HARMONIES first utilizes a zero-inflated negative binomial (ZINB) distribution to model the skewness and excess zeros in the microbiome data, as well as incorporates a stochastic process prior for sample-wise normalization. This approach infers a sparse and stable network by imposing non-trivial regularizations based on the Gaussian graphical model. In comprehensive simulation studies, HARMONIES outperformed four other commonly used methods. When using published microbiome data from a colorectal cancer study, it discovered a novel community with disease-enriched bacteria. In summary, HARMONIES is a novel and useful statistical framework for microbiome network inference, and it is available athttps://github.com/shuangj00/HARMONIES.
The vesicular trafficking system component MIN7 is required for minimizingFusarium graminearuminfection
Authors: Machado Wood Ana K. , Panwar Vinay , Grimwade-Mann Mike , Ashfield Tom , Hammond-Kosack Kim E. , Kanyuka Kostya
Published: March 2020

Plants have developed intricate defense mechanisms, referred to as innate immunity, to defend themselves against a wide range of pathogens. Plants often respond rapidly to pathogen attack by the synthesis and delivery of various antimicrobial compounds, proteins and small RNA in membrane vesicles to the primary infection sites. Much of the evidence regarding the importance of vesicular trafficking in plant-pathogen interactions comes from the studies involving model plants whereas this process is relatively understudied in crop plants. Here we assessed whether the vesicular trafficking system components previously implicated in immunity inArabidopsis thalianaplay a role in the interaction withFusarium graminearum, a fungal pathogen notoriously famous for its ability to cause Fusarium head blight (FHB) disease in wheat. Among the analyzed vesicular trafficking mutants, two independent T-DNA insertion mutants in theAtMin7gene displayed a markedly enhanced susceptibility toF. graminearum. Earlier studies identified this gene, encoding an ARF-GEF protein, as a target for the HopM1 effector of the bacterial pathogenPseudomonas syringaepv.tomato, which destabilizes AtMIN7 leading to its degradation and weakening host defenses. To test whether this key vesicular trafficking component may also contribute to defense in crop plants, we identified the candidateTaMin7genes in wheat and knocked-down their expression through Virus induced gene silencing. Wheat plants in whichTaMIN7were silenced displayed significantly more FHB disease. This suggests that disruption of MIN7 function in both model and crop plants compromises the trafficking of innate immunity signals or products resulting in hyper-susceptibility to various pathogens.

One sentence summary

Disruption of an ARF-GEF protein encoding geneAtMin7inArabidopsis thalianaand silencing of the orthologous gene in wheat result in hyper susceptibility to the fungal pathogenFusarium graminearum.
Rational design and implementation of a chemically inducible hetero-trimerization system
Authors: Wu Helen D. , Kikuchi Masaki , Dagliyan Onur , Aragaki Adam K. , Nakamura Hideki , Dokholyan Nikolay V. , Umehara Takashi , Inoue Takanari
Published: March 2020

Chemically inducible dimerization (CID) uses a small molecule to induce binding of two different proteins. CID tools exemplified by the FKBP/FRB/rapamycin system have been widely employed to probe molecular events inside and outside cells. While various CID tools are available, chemically inducible trimerization (CIT) has not been developed, due to inherent challenges in designing or identifying a chemical that simultaneously binds three proteins with high affinity and target specificity. Nevertheless, by introducing a third recruitable component, CIT could enable versatile applications. Here, we devised the CIT by rationally splitting FRB and FKBP. Based on cellular and structural datasets, select split pairs of FRB or FKBP underwent efficient trimerization with full length FKBP or FRB, respectively, upon addition of rapamycin. We also demonstrated its potential for cellular applications by rapidly inducing tri-organellar plasma membrane-ER-mitochondria junctions, and by perturbing intended membrane lipids exclusively at the plasma membrane-ER membrane contact sites. By conferring one additional condition to what is achievable with CID, CIT expands the types of manipulation in single live cells, to address cell biology questions otherwise intractable, and engineer cell functions for future synthetic biology applications.
A CTGF-YAP regulatory pathway is essential for angiogenesis and barriergenesis in the retina
Authors: Moon Sohyun , Lee Sangmi , Caesar JoyAnn , Pruchenko Sarah , Leask Andew , Knowles James A. , Sinon Jose , Chaqour Brahim
Published: March 2020

Connective tissue growth factor (CTGF) or CCN2 is a matricellular protein essential for normal embryonic development and tissue repair. CTGF exhibits cell- and context-dependent activities, but the CTGF function in vascular development and permeability barrier is not known. Here we show that endothelial cells (ECs) are one of the major cellular sources of CTGF in the developing and adult retinal vasculature. Mice lacking CTGF expression either globally or specifically in ECs exhibit impaired vascular cell growth and morphogenesis, and blood barrier breakdown. The global molecular signature of CTGF includes cytoskeletal and extracellular matrix protein, growth factor, and transcriptional co-regulator genes such as yes-associated protein (YAP). YAP, itself a transcriptional activator of the CTGF gene, mediates several CTGF-controlled angiogenic and barriergenic transcriptional programs. Re-expression of YAP rescues, at least partially, angiogenesis and barriergenesis in CTGF mutant mouse retinas. Thus, the CTGF-YAP angiomodulatory pathway is critical for vascular development and barrier function.
In vitroevolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells
Authors: Jado Juan Carlos , Dow Michelle , Carolino Krypton , Klie Adam , Fonseca Gregory J. , Ideker Trey , Carter Hannah , Winzeler Elizabeth A.
Published: March 2020

Background

In vitroevolution and whole genome analysis has proven to be a powerful method for studying the mechanism of action of small molecules in many haploid microbes but has generally not been applied to human cell lines in part because their diploid state complicates the identification of variants that confer drug resistance. To determine if haploid human cell could be used in MOA studies, we evolved resistance to five different anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel) using a near-haploid cell line (HAP1) and then analyzed the genomes of the drug resistant clones, developing a bioinformatic pipeline that involved filtering for high frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound. Applying the filter to sequences from 28 drug resistant clones identified a set of 21 genes which was strongly enriched for known resistance genes or known drug targets (TOP1, TOP2A, DCK, WDR33, SLCO3A1). In addition, some lines carried structural variants that encompassed additional known resistance genes (ABCB1, WWOX and RRM1). Gene expression knockdown and knockout experiments of 10 validation targets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, discovered and studied in an isogenic background.
Patient-derived xenografts and organoids model therapy response in prostate cancer
Authors: Karkampouna Sofia , La Manna Federico , De Filippo Maria R. , Kiener Mirjam , De Menna Marta , Zoni Eugenio , Grosjean Joël , Klima Irena , Garofoli Andrea , Bolis Marco , Theurillat Jean-Philippe , Genitsch Vera , Keller David , Booij Tijmen H. , Stirnimann Christian U. , Eng Kenneth , Sboner Andrea , Ng Charlotte K. Y. , Piscuoglio Salvatore , PC Gray , Spahn Martin , Rubin Mark A. , Thalmann George N. , Julio Marianna Kruithof-de
Published: March 2020

Therapy resistance and metastatic processes in prostate cancer (PCa) remain undefined, due to lack of experimental models that mimic different disease stages. We describe a novel androgen-dependent PCa patient-derived xenograft (PDX) model from treatment-naïve, soft tissue metastasis (PNPCa). RNA and whole-exome sequencing of the PDX tissue and organoids confirmed transcriptomic and genomic similarity to primary tumor. PNPCa harboursBRCA2 and CHD1somatic mutations, shows anSPOP/FOXA1-like transcriptomic signature and microsatellite instability, which occurs in 3% of advanced PCa and has never been modelledin vivo. Comparison of the treatment-naïve PNPCa with additional metastatic PDXs (BM18, LAPC9), in a medium-throughput organoid screen of FDA-approved compounds, revealed differential drug sensitivities. Multikinase inhibitors (ponatinib, sunitinib, sorafenib) were broadly effective on all PDX- and patient-derived organoids from advanced cases with acquired resistance to standard-of-care compounds. This proof-of-principle study may provide a preclinical tool to screen drug responses to standard-of-care and newly identified, repurposed compounds.
Robustness of epithelial sealing is an emerging property of local ERK feedbacks driven by cell elimination
Authors: Valon Léo , Davidović Anđela , Levillayer Florence , Chouly Mathilde , Cerqueira-Campos Fabiana , Levayer Romain
Published: March 2020

While the pathways regulating apoptosis and cell extrusion are rather well described1,2, what regulates the precise spatio-temporal distribution of cell elimination in tissues remains largely unknown. This is particularly relevant for epithelia with high rates of cell elimination, a widespread situation during embryogenesis3–6and epithelial homeostasis7, where concomitant death of neighbours could impair the maintenance of epithelial sealing. However, the extent to which epithelial tissues can cope with concomitant cell death, and whether any mechanism regulates such occurrence have never been explored so far. Here, using theDrosophilapupal notum (a single layer epithelium) and a new optogenetic tool to trigger caspase activation and cell extrusion, we first show that concomitant death of clusters of at least three cells is sufficient to transiently impair epithelial sealing. Such clustered extrusion was almost never observedin vivo, suggesting the existence of a mechanism preventing concomitant elimination of neighbours. Statistical analysis and simulations of cell death distribution in the notum highlighted a transient and local protective phase occurring near every dying cell. This protection is driven by a transient activation of ERK in the direct neighbours of extruding cells which reverts caspase activation and prevents elimination of cells in clusters. Altogether, this study demonstrates that the distribution of cell elimination in epithelia is an emerging property of transient and local feedbacks through ERK activation which is required to maintain epithelial sealing in conditions of high rate of cell elimination.
DNA methylation is indispensable for leukemia inhibitory factor dependent embryonic stem cells reprogramming
Authors: Wu Baojiang , Li Yunxia , Li Bojiang , Zhang Baojing , Wang Yanqiu , Li Lin , Gao Junpeng , Fu Yuting , Li Shudong , Chen Chen , Surani M. Azim , Tang Fuchou , Li Xihe , Bao Siqin
Published: March 2020

Naïve pluripotency can be maintained by the 2i/LIF supplements (CHIR99021, PD0325901 and LIF), which primarily affect canonical WNT, FGF/ERK, and JAK/STAT3 signaling. However, whether one of these tripartite supplements alone is sufficient to maintain naïve self-renewal remain unclear. Here we show that LIF alone is sufficient to induce reprogramming of 2i/LIF cultured ESCs (2i/L-ESCs) to ESCs with hypermethylated state (L-ESCs).In vitro, upon withdrawal of 2i, 2i/L-ESCs overcome the epigenetic barrier and DNA hypermethylated, which accompanies transcriptional changes and subsequent establishment of epigenetic memory. Global transcriptome features also show that L-ESCs are close to 2i/L-ESCs and in a stable state between naïve and primed pluripotency. Notably, our results demonstrate that DNA methylation was indispensable for LIF-dependent mouse ESCs reprogramming and self-renew. LIF-dependent ESCs reprogramming efficiency is significantly increased in serum treatment and reduced inDnmt3aorDnmt3lknockout ESCs. Importantly, unlike epiblast and EpiSCs, L-ESCs contribute to somatic tissues and germ cells in chimaeras. Such simple culture system of ESCs is more conducive to clarify the molecular mechanism of ESCsin vitroculture.

Significance

Embryonic stem cell (ESCs) exhibit naïve pluripotency which reflects their ability to contribute to all embryonic lineages upon injection into blastocyst. ESCs were originally derived by co-culture with feeder cells and fetal calf serum. In this manuscript, we took a detailed approach to dissect the roles of LIF alone in ESC reprogramming of 2i/LIF cultured ESCs (2i/L-ESCs). Here, for the first time, we derived stable hypermethylated pluripotent ESCs under culture of LIF alone (L-ESCs). We further assessed L-ESCs properties both in vitro and in vivo, and provide molecular insights to the mechanism which allows LIF alone to maintain pluripotency and a hypermethylated state. We believe these findings are novel and valuable for future ESCs study.
Boron induces osteogenesis by stimulating NaBC1 in cooperation with BMPR1A
Authors: Rico Patricia , Rodrigo-Navarro Aleixandre , Sánchez Pérez Laura , Salmeron-Sanchez Manuel
Published: March 2020

The intrinsic properties of Mesenchymal Stem Cells (MSCs) make them ideal candidates for tissue engineering applications as they are regulated by the different signals present in the stem cell niche. Considerable efforts have been made to control stem cell behavior by designing material system approaches to engineer synthetic extracellular matrices and/or include soluble factors in the media. This work proposes a novel and simple approach based on ion-channel stimulation to determine stem cell fate that avoids the use of growth factors (GFs). We used boron ion - essential item in cell metabolism - transported inside cells by the NaBC1-channel. Addition of boron alone enhanced MSC adhesion and contractility, promoted osteogenesis and inhibited adipogenesis. The stimulated NaBC1 promoted osteogenesis via activation of the BMP canonical pathway (comprising Smad1 and YAP nucleus translocation and osteopontin expression) through a mechanism that involves simultaneous NaBC1/BMPR1A and NaBC1/α5β1/αvβ3co-localization,. We describe a novel function for NaBC1 as a mechanosensitive ion-channel capable of interacting and stimulating GF receptors and fibronectin-binding integrins. Our results open up new biomaterial engineering approaches for biomedical applications by a cost-effective strategy that avoids the use of soluble GFs.
Identification of key candidate genes and pathways in axial Spondyloarthritis through integrated bioinformatics analysis
Authors: Zhang Zhen-zhen , Zeng Jing , Li Hai-hong , Zou Yu-cong , Liang Shuang , Liu Gang
Published: March 2020

Background

Radiographic axial Spondyloarthritis (r-axSpA) is the prototypic form of seronegative spondyloarthritis (SpA). In the present study, we evaluated the key genes related with r-axSpA, and then elucidated the possible molecular mechanisms of r-axSpA.

Material/Methods

The gene expression GSE13782 was downloaded from the GEO database contained five proteoglycan-induced spondylitis mice and three naïve controls. The differentially expressed genes (DEGs) were identified with the Bioconductor affy package in R. Gene Ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were built with the DAVID program followed by construction of a protein-protein interaction (PPI) network performed with Cytoscape. WebGestalt was performed to construct transcriptional regulatory network and microRNAs-target regulatory networks. RT-PCR and immunohistochemical staining were performed to testify the expression of hub genes, transcription factors (TFs) and microRNAs.

Results

A total of 230 DEGs were identified. PPI networks were constructed by mapping DEGs into STRING, in which 20 hub proteins were identified. KEGG pathway analyses revealed that the chemokine, NOD-like receptor, IL-17, and TNF signalling pathways were altered. GO analyses revealed that DEGs were extensively involved in the regulation of cytokine production, the immune response, the external side of the plasma membrane, and G-protein coupled chemoattractant receptor activity. The results of RT-PCR and immunohistochemical staining demonstrated that the expression of DEGs, TFs and microRNAs in our experiment were basically consistent with the predictions.

Conclusions

The results of this study offer insight into the pathomechanisms of r-axSpA and provide potential research directions.
Derivation of macaque trophoblast stem cells
Authors: Schmidt Jenna Kropp , Meyer Michael G. , Wiepz Gregory J. , Block Lindsey N. , Dusek Brittany M. , Kroner Kamryn M. , Bertogliat Mario J. , Keding Logan T. , Koenig Michelle R. , Mean Katherine D. , Golos Thaddeus G.
Published: March 2020

Abstract

Nonhuman primates are excellent models for studying human placentation as experimental manipulationsin vitrocan be translated toin vivopregnancy. Our objective was to develop macaque trophoblast stem cells (TSC) as anin vitroplatform for future assessment of primate trophoblast development and function. Macaque TSC lines were generated by isolating first trimester placental villous cytotrophoblasts followed by culture in TSC medium to “reprogram” the cells to a proliferative state. TSCs grew as mononuclear colonies, whereas upon induction of syncytiotrophoblast (ST) differentiation multinuclear structures appeared, indicative of syncytium formation. Chorionic gonadotropin secretion was >4,000-fold higher in ST culture media compared to TSC media. Characteristic trophoblast hallmarks were defined in TSCs and ST including expression of C19MC miRNAs and macaque placental nonclassical MHC class I molecule, Mamu-AG. TSC differentiation to extravillous trophoblasts (EVTs) with or without the ALK-5 inhibitor A83-01 resulted in differing morphologies but similar expression of Mamu-AG and CD56 as assessed by flow cytometry, hence further refinement of relevant EVT markers is needed. Our preliminary characterization of macaque TSCs suggests that these cells represent a proliferative, self-renewing TSC population capable of differentiating to STsin vitrothereby establishing an experimental model of primate placentation.
dom2vec: Unsupervised protein domain embeddings capture domains structure and function providing data-driven insights into collocations in domain architectures
Authors: Melidis Damianos P. , Malone Brandon , Nejdl Wolfgang
Published: March 2020

Motivation

Word embedding approaches have revolutionized Natural Language Processing NLP research. These approaches aim to map words to a low-dimensional vector space in which words with similar linguistic features are close in the vector space. These NLP approaches also preserve local linguistic features, such as analogy. Embedding-based approaches have also been developed for proteins. To date, such approaches treat amino acids as words, and proteins are treated as sentences of amino acids. These approaches have been evaluated either qualitatively, via visual inspection of the embedding space, or extrinsically, via performance on a downstream task. However, it is difficult to directly assess the intrinsic quality of the learned embeddings.

Results

In this paper, we introduce dom2vec, an approach for learning protein domain embeddings. We also present fourintrinsicevaluation strategies which directly assess the quality of protein domain embeddings. We leverage the hierarchy relationship of InterPro domains, known secondary structure classes, Enzyme Commission class information, and Gene Ontology annotations in these assessments. These evaluations allow us to assess the quality of learned embeddings independently of a particular downstream task. Importantly, allow us to draw an analog between the local linguistic features in nature languages and the domain structure and function information in domain architectures, thus providing data-driven insights into the context found in thelanguageof domain architectures. We also show that dom2vec embeddings outperform, or are comparable with, state-of-the-art approaches on downstream tasks.

Availability

The protein domain embeddings vectors and the entire code to reproduce the results are available athttps://github.com/damianosmel/dom2vec.

Contact

melidis@l3s.uni-hannover.de
Repurposing Old Antibodies for New Diseases by Exploiting Cross Reactivity and Multicolored Nanoparticles
Authors: Rodriguez-Quijada Cristina , Gomez-Marquez Jose , Hamad-Schifferli Kimberly
Published: March 2020

We exploit the cross-reactivity of dengue (DENV) and zika (ZIKV) virus polyclonal antibodies for nonstructural protein 1 (NS1) to construct a selective sensor that can detect yellow fever virus (YFV) NS1 in a manner similar to chemical olfaction. DENV and ZIKV antibodies were screened for their ability to bind to DENV, ZIKV, and YFV NS1 by ELISA and in pairs in paper immunoassays. A strategic arrangement of antibodies immobilized on paper and conjugated to different colored gold NPs was used to distinguish the three biomarkers. Machine learning of test area RGB values showed that with two spots, readout accuracies of 100% and 87% were obtained for both pure NS1 and DENV/YFV mixtures, respectively. Additional image pre-processing allowed differentiation between all 4 DENV serotypes with 92% accuracy. The technique was extended to hack a commercial DENV test to detect YFV and ZIKV by augmentation with DENV and ZIKV polyclonal antibodies.

TOC GRAPHIC
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network
Authors: Wu Tianqi , Guo Zhiye , Hou Jie , Cheng Jianlin
Published: March 2020

Motivation

Driven by deep learning techniques, inter-residue contact/distance prediction has been significantly improved and substantially enhancedab initioprotein structure prediction. Currently all the distance prediction methods classify inter-residue distances into multiple distance intervals (i.e. a multi-classification problem) instead of directly predicting real-value distances (i.e. a regression problem). The output of the former has to be converted into real-value distances in order to be used in tertiary structure prediction.

Results

To explore the potentials of predicting real-value inter-residue distances, we develop a multi-task deep learning distance predictor (DeepDist) based on new residual convolutional network architectures to simultaneously predict real-value inter-residue distances and classify them into multiple distance intervals. We demonstrate that predicting the real-value distance map and multi-class distance map at the same time performs better than predicting real-value distances alone, indicating their complementarity. On 43 CASP13 hard domains, the average mean square error (MSE) of DeepDist’s real-value distance predictions is 0.896 Å when filtering out the predicted distance >=16 Å, which is lower than 1.003 Å of DeepDist’s multi-class distance predictions. When the predicted real-value distances are converted to binary contact predictions at 8Å threshold, the precisions of top L/5 and L/2 contact predictions are 78.6% and 64.5%, respectively, higher than the best results reported in the CASP13 experiment. These results demonstrate that the real-value distance prediction can predict inter-residue distances well and improve binary contact prediction over the existing state-of-the-art methods. Moreover, the predicted real-value distances can be directly used to reconstruct protein tertiary structures better than multi-class distance predictions due to the lower MSE.
Loss of SUV420H2 promotes EGFR inhibitor resistance in NSCLC through upregulation of MET via LINC01510
Authors: Pal A.S. , Agredo A.M. , Lanman N.A. , Clingerman J. , Gates K , Kasinski A.L.
Published: March 2020

Epidermal growth factor receptor inhibitors (EGFRi) are standard-of-care treatments administered to patients with non-small cell lung cancer (NSCLC) that harbor EGFR alterations. However, development of resistance within a year post-treatment remains a major challenge. Multiple mechanisms can promote survival of EGFRi treated NSCLC cells, including secondary mutations in EGFR and activation of bypass tracks that circumvent the requirement for EGFR signaling. Nevertheless, mechanisms involved in bypass track activation are understudied, and in a subset of cases the mechanisms are unknown. The findings from this study identified an epigenetic factor, SUV420H2 that when lost drives resistance of NSCLC to multiple EGFRi, including erlotinib, gefitinib, afatinib, and osimertinib. SUV420H2 catalyzes trimethylation of histone H4 lysine-20, a modification required for gene repression and maintenance of heterochromatin. Here we show that loss of SUV420H2 leads to upregulation of an oncogenic long non-coding RNA,LINC01510that promotes transcription of the oncogene MET, a component of a major bypass track involved in EGFRi resistance.

Significance

Due to an incomplete understanding of the mechanisms involved in promoting resistance to EGFRi, patients often succumb to their disease. Here we identified a global mediator of EGFRi resistance, SUV420H2 that helps to uncover an additional mechanism involved in resistance driven via a major bypass track involving the protooncogene MET.