bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATP2, the essential P4-ATPase of malaria parasites, catalyzes lipid-dependent ATP hydrolysis in complex with a Cdc50 β-subunit
Authors: Lamy Anaïs , Macarini-Bruzaferro Ewerton , Perálvarez-Marín Alex , le Maire Marc , Vázquez-Ibar José Luis 
Published: June 2020

ABSTRACTEfficient mechanisms of lipid transport are indispensable for thePlasmodiummalaria parasite along the different stages of its intracellular life-cycle. Gene targeting approaches have recently revealed the irreplaceable role of thePlasmodium-encodedtype 4 P-type ATPases (P4-ATPases or lipid flippases), ATP2, together with its potential involvement as antimalarial drug target. In eukaryotic membranes, P4-ATPases assure their asymmetric phospholipid distribution by translocating phospholipids from the outer to the inner leaflet. As ATP2 is a yet putative transporter, in this work we have used a recombinantly-producedP. chabaudiATP2, PcATP2, to gain insights into the function and structural organization of this essential transporter. Our work demonstrates that PcATP2 heterodimerizes with two of the threePlasmodium-encodedCdc50 proteins: PcCdc50B and PcCdc50A, indispensable partners for most P4-ATPases. Moreover, the purified PcATP2/PcCdc50B complex catalyses ATP hydrolysis in the presence of phospholipids containing either phosphatidylserine, phosphatidylethanolamine or phosphatidylcholine head groups, and that this activity is upregulated by phosphatidylinositol 4-phosphate. Overall, our work provides the first study of the function and quaternary organization of ATP2, a promising antimalarial drug target candidate.
Mismatch repair deficiency predicts response to HER2 blockade in HER2-negative breast cancer
Authors: Punturi Nindo B , Seker Sinem , Devarakonda Vaishnavi , Kalra Rashi , Chen Ching-Hui , Mazumder Aloran , Li Shunqiang , Primeau Tina , Ellis Matthew J , Kavuri Shyam M , Haricharan Svasti 
Published: June 2020

AbstractEstrogen receptor positive (ER+) breast cancer is a leading cause of cancer-related death globally. Resistance to standard of care endocrine treatment occurs in at least 30% of ER+breast cancer patients resulting in ~40,000 deaths every year in the US alone. Preclinical studies strongly implicate activation of growth factor receptor, HER2 in endocrine treatment resistance of ER+breast cancer that is HER2-at diagnosis1,2. However, clinical trials of pan-HER inhibitors in ER+/HER2-patients have disappointed, likely due to a lack of predictive biomarkers3-6. Here we demonstrate that loss ofMLH1, a principal mismatch repair gene, causally activates HER2 in ER+/HER2-breast cancer upon endocrine treatment. Additionally, we show that HER2 activation is indispensable for endocrine treatment resistant growth of MLH1-cellsin vitroandin vivo.Consequently, inhibiting HER2 restores sensitivity to endocrine treatment in multiple experimental models including patient-derived xenograft tumors. Patient data from multiple clinical datasets (TCGA, METABRIC, Alliance (Z1031) and E-GEOD-28826) supports an association betweenMLH1loss, HER2 upregulation, and sensitivity to trastuzumab in endocrine treatment-resistant ER+/HER2-patients. These results provide strong rationale that MLH1 could serve as a first-in-class predictive marker of sensitivity to combinatorial treatment with endocrine drugs and HER inhibitors in endocrine treatment-resistant ER+/HER2-breast cancer patients. Implications of this study extend beyond breast cancer to Lynch Syndrome cancers.One Sentence SummaryDefective mismatch repair activates HER2 in HER2-negative breast cancer cells and renders them susceptible to HER2 inhibitors.
SF3B1-targeted Splicing Inhibition Triggers Global Alterations in Transcriptional Dynamics and R-Loop Metabolism
Authors: Castillo-Guzman Daisy , Hartono Stella R. , Sanz Lionel A. , Chédin Frédéric 
Published: June 2020

SUMMARYEfficient co-transcriptional splicing is thought to suppress the formation of genome-destabilizing R-loops upon interaction between nascent RNA and the DNA template. Inhibition of the SF3B splicing complex using Pladienolide B (PladB) in human K562 cells caused widespread intron retention and nearly 2,000 instances of R-loops gains. However, only minimal overlap existed between these events, arguing that unspliced introns do not cause excessive R-loops. R-loop gains were instead driven by readthrough transcription resulting from loss of transcription termination over a subset of stress-response genes, defining a new class of aberrant “downstream of genes” (DoG) R-loops. Such DoG R-loops were temporally and spatially uncoupled from loci experiencing DNA damage. Unexpectedly, the predominant response to splicing inhibition was a global R-loop loss resulting from accumulation of promoter-proximal paused RNA polymerases and defective elongation. Thus, SF3B1-targeted splicing inhibition triggered profound alterations in transcriptional dynamics, leading to unexpected disruptions in the global R-loop landscape.HIGHLIGHTSIntron retention caused by SF3B1 inhibition does not lead to excessive R-loopsA subset of genes shows readthrough transcription and accompanying R-loop gainsSF3B1 inhibition causes broad reduction in nascent transcription and R-loop lossR-loop gains and DNA damage are temporally and spatially uncoupled
Dorsal horn CGRP-expressing interneurons contribute to nerve injury-induced mechanical hypersensitivity
Authors: Löken LS , Etlin A , Bernstein M , Steyert M , Kuhn J , Hamel K , Llewellyn-Smith I , Braz JM , Basbaum AI 
Published: June 2020

AbstractPrimary sensory neurons are generally considered the only source of dorsal horn calcitonin gene-related peptide (CGRP), a neuropeptide critical to the transmission of pain messages. Using a tamoxifen-inducible CGRPCreERtransgenic mouse, here we identified a distinct population of CGRP-expressing excitatory interneurons in lamina III of the spinal cord dorsal horn and trigeminal nucleus caudalis. These interneurons have spine-laden, dorsally-directed, dendrites and ventrally-directed axons. Neither innocuous nor noxious stimulation provoked significant Fos expression in these neurons. However, synchronous, electrical non-nociceptive Aβ primary afferent stimulation of dorsal roots depolarized the CGRP interneurons, consistent with their receipt of a VGLUT1 innervation. In contrast, chemogenetic activation produced a significant mechanical hypersensitivity. Importantly, the CGRP interneurons could be activated after peripheral nerve injury, but only with concurrent innocuous, brush stimulation. These findings suggest that hyperexcitability of dorsal horn CGRP interneurons is an important contributor to the circuits that render touch painful after peripheral nerve damage.
DIFFERENTIAL BIOENERGETICS IN ADULT RAT CARDIOMYOCYTES ISOLATED FROM THE RIGHT VERSUS LEFT VENTRICLE
Authors: Nguyen Quyen L. , Rao Krithika , Mullett Steven J. , Wendell Stacy G. , Croix Claudette St. , Goetzman Eric , Shiva Sruti 
Published: June 2020

ABSTRACTThe right and left ventricle of the heart have distinctly different developmental origins and are affected differently by similar pathological stimuli. Though it is well established that the heart relies almost entirely on mitochondrial function to sustain energy production, it remains unclear whether bioenergetics differ in the two ventricles. Herein, we define a novel methodology to optimize the isolation of intact cardiomyocytes from the right versus the left ventricle. We demonstrate that this segmental Langendorff-free methodology yields viable cardiomyocytes with intact mitochondrial function. Further, we compare bioenergetics in right versus left ventricle cardiomyocytes and show that cardiomyocytes from the right ventricle have a greater maximal capacity for respiration and enhanced glycolytic rate. This increase in respiration was concomitant with increased fatty acid oxidation and levels of fatty acid oxidation proteins, but no change in mitochondrial electron transport complex expression. These data validate a potentially powerful tool to evaluate differences in right and left ventricular function and advance the understanding of cardiac bioenergetic differences. These data will be discussed in the context of differential responses by the right versus ventricle in pathology.
Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer
Authors: Hanley CJ , Waise S , Parker R , Lopez MA , Taylor J , Kimbley LM , West J , Ottensmeier CH , Rose-Zerilli MJJ , Thomas GJ 
Published: June 2020

AbstractFibroblasts are functionally heterogeneous cells, capable of promoting and suppressing tumour progression. Across cancer types, the extent and cause of this phenotypic diversity remains unknown. We used single-cell RNA sequencing and multiplexed immunohistochemistry to examine fibroblast heterogeneity in human lung and non-small cell lung cancer (NSCLC) samples. This identified seven fibroblast subpopulations: including inflammatory fibroblasts and myofibroblasts (representing terminal differentiation states), quiescent fibroblasts, proto-myofibroblasts (x2) and proto-inflammatory fibroblasts (x2). Fibroblast subpopulations were variably distributed throughout tissues but accumulated at discrete niches associated with differentiation status. Bioinformatics analyses suggested TGF-β1 and IL-1 as key regulators of myofibroblastic and inflammatory differentiation respectively. However,in vitroanalyses showed that whilst TGF-β1 stimulation in combination with increased tissue tension could induce myofibroblast marker expression, it failed to fully re-capitulateex-vivophenotypes. Similarly, IL-1β treatment only induced upregulation of a subset of inflammatory fibroblast marker genes.In silicomodelling of ligand-receptor signalling identified additional pathways and cell interactions likely to be involved in fibroblast activation, which can be examined using publicly available R shiny applications (at the following links:myofibroblast activationandinflammatory fibroblast activation). This highlighted a potential role for IL-11 and IL-6 (among other ligands) in myofibroblast and inflammatory fibroblast activation respectively. This analysis provides valuable insight into fibroblast subtypes and differentiation mechanisms in NSCLC.
Activation-induced re-organization of chromatin in human T cells
Authors: Bediaga Naiara G. , Coughlan Hannah D. , Johanson Timothy M. , Garnham Alexandra L. , Naselli Gaetano , Schröder Jan , Fearnley Liam G. , Bandala-Sanchez Esther , Allan Rhys S. , Smyth Gordon K. , Harrison. Leonard C. 
Published: June 2020

ABSTRACTRemodelling of chromatin architecture is known to regulate gene expression and has been well characterized in cell lineage development but less so in response to cell perturbation. Activation of T cells, which triggers extensive changes in transcriptional programs, serves as an instructive model to elucidate how changes in genome organization orchestrate gene expression in response to cell perturbation. To characterize coordinate changes at different levels of chromatin architecture, we analysed chromatin accessibility, chromosome conformation and gene expression after activation of human T cells. T cell activation led to widespread changes in chromatin interactions and accessibility that were mostly shared between CD4+and CD8+T cells. Differential chromatin interactions were associated with upregulation or downregulation of linked target genes. Moreover, activation was associated with the formation of shorter chromatin interactions, partitioning of topologically associating domains (TADs) and acquisition of new TAD boundaries characterized by higher nucleosome occupancy, and lower chromatin accessibility and gene expression. These findings render an integrated and multiscale characterization of activation-induced re-organization of chromatin architecture underlying gene transcription in human T cells.
Single-cell RNA transcriptomics identifies Hivep3 as essential in regulating the development of innate-like T lymphocytes
Authors: Krovi Sai Harsha , Zhang Jingjing , Michaels-Foster Mary Jessamine , Brunetti Tonya , Loh Liyen , Scott-Browne James , Gapin Laurent 
Published: June 2020

SummaryMost T lymphocytes leave the thymus as naïve cells with limited functionality. However, unique populations of T cells, commonly known as innate-like T cells, differentiate into functionally distinct effector subsets during thymic development under the influence of the transcription factor PLZF. Here, we profiled >10,000 differentiating thymic iNKT cells using single-cell RNA sequencing to provide a comprehensive transcriptional landscape of their maturation, function, and fate decision in steady state. We identifiedHivep3, a zinc finger transcription factor and adaptor protein, as a key factor that is expressed in early precursors and regulates the post-selection proliferative burst, differentiation and functions of iNKT cells. Importantly, we extended these results to other PLZF+innate-like T cell populations, highlighting the unique and common requirement ofHivep3to the development of all innate-like T cells.
Enrichment and physiological characterization of a novel comammoxNitrospiraindicates ammonium inhibition of complete nitrification
Authors: Sakoula Dimitra , Koch Hanna , Frank Jeroen , Jetten Mike SM , van Kessel Maartje AHJ , Lücker Sebastian 
Published: June 2020

AbstractThe recent discovery of bacteria within the genusNitrospiracapable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammoxNitrospiraexhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Furthermore, most available genomic information is derived from metagenomic sequencing and high-quality genomes ofNitrospirain general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named “CandidatusNitrospira kreftii”, and performed a detailed genomic and physiological characterization. The complete genome of “Ca.N. kreftii” allowed reconstruction of its basic metabolic traits. Similar toNitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3≈ 0.036 µM), but a higher nitrite affinity (Km(app)_NO2- ≈ 13.8 µM), indicating an adaptation to highly oligotrophic environments. Counterintuitively for a nitrifying microorganism, we also observed an inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This substrate inhibition of “Ca.N. kreftii” indicate that differences in ammonium tolerance rather than affinity can be a niche determining factor for different comammoxNitrospira.
Effects of Renin-Angiotensin Inhibition on ACE2 and TMPRSS2 Expression: Insights into COVID-19
Authors: Wu Congqing , Ye Dien , Mullick Adam E. , Li Zhenyu , Danser A.H. Jan , Daugherty Alan , Lu Hong S. 
Published: June 2020

AbstractAngiotensin-converting enzyme 2 (ACE2), a component of the renin-angiotensin system, is a receptor for SARS-CoV-2, the virus that causes COVID-19. To determine whether the renin-angiotensin inhibition regulates ACE2 expression, either enalapril (an angiotensin-converting enzyme inhibitor) or losartan (an AT1 receptor blocker) was infused subcutaneously to male C57BL/6J mice for two weeks. Neither enalapril nor losartan changed abundance of ACE2 mRNA in lung, ileum, kidney, and heart. Viral entry also depends on transmembrane protease serine 2 (TMPRSS2) to prime the S protein. TMPRSS2 mRNA was abundant in lungs and ileum, modest in kidney, but barely detectable in heart. TMPRSS2 mRNA abundance was not altered by either enalapril or losartan in any of the 4 tissues. Next, we determined whether depletion of angiotensinogen (AGT), the unique substrate of the renin-angiotensin system, changes ACE2 and TMPRSS2 mRNA abundance. AGT antisense oligonucleotides (ASO) were injected subcutaneously to male C57BL/6J mice for 3 weeks. Abundance of ACE2 mRNA was unchanged in any of the 4 tissues, but TMPRSS2 mRNA was significantly decreased in lungs. Our data support that the renin-angiotensin inhibition does not regulate ACE2 and hence are not likely to increase risk for COVID-19.
Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships
Authors: Kirubakaran Palani , Morton George , Zhang Pingfeng , Zhang Hanghang , Gordon John , Abou-Gharbia Magid , Issa Jean-Pierre J. , Wu Jinhua , Childers Wayne , Karanicolas John 
Published: June 2020

AbstractCyclin-dependent kinase 9 (CDK9) plays a key role in transcription elongation, and more recently it was also identified as the molecular target of a series of diaminothiazole compounds that reverse epigenetic silencing in a phenotypic assay. To better understand the structural basis underlying these compounds’ activity and selectivity, we developed a comparative modeling approach that we describe herein. Briefly, this approach draws upon the strong structural conservation across the active conformation of all protein kinases, and their shared pattern of interactions with Type I inhibitors. Because of this, we hypothesized that the large collection of inhibitor/kinase structures available in the Protein Data Bank (PDB) would enable accurate modeling of this diaminothiazole series in complex with each CDK family member. We apply this new comparative modeling pipeline to build each of these structural models, and then demonstrate that these models provide retrospective rationale for the structure-activity relationships that ultimately guided optimization to the lead diaminothiazole compound MC180295 (14e). We then solved the crystal structure of the14e/CDK9 complex, and found the resulting structure to be in excellent agreement with our corresponding comparative model. Finally, inspired by these models, we demonstrate how structural changes to14ecan be used to rationally tune this compound’s selectivity profile. With the emergence of CDK9 as a promising target for therapeutic intervention in cancer, we anticipate that comparative modeling can provide a valuable tool to guide optimization of potency and selectivity of new inhibitors targeting this kinase.
Multi-ancestry Genome- and Phenome-wide Association Studies of Diverticular Disease in Electronic Health Records with Natural Language Processing enriched phenotype algorithm
Authors: Joo Yoonjung Yoonie , Pacheco Jennifer A , Thompson William K , Rasmussen-Torvik Laura J , Rasmussen Luke V , Lin Frederick TJ , de Andrade Mariza , Borthwick Kenneth M , Bottinger Erwin , Cagan Andrew , Carrell David S , Denny Joshua C , Ellis Stephen B , Gottesman Omri , Linneman James G , Pathak Jyotishman , Peissig Peggy L , Shang Ning , Tromp Gerard , Veerappan Annapoorani , Smith Maureen E , Chisholm Rex L , Gawron Andrew , Kho Abel N , Hayes M Geoffrey 
Published: June 2020

AbstractBackground and aimsDiverticular disease is among the most prevalent conditions encountered by gastroenterologists, affecting ∼50% of Americans before the age of 60. Our aim was to identify genetic risk variants and clinical phenotypes associated with diverticular disease, utilizing the electronic health record (EHR) with Natural Language Processing (NLP).MethodsWe developed a NLP-enriched phenotype algorithm that incorporated colonoscopy or abdominal imaging reports to accurately identify patients with diverticulosis and diverticulitis from multicenter EHRs. We performed genome-wide association studies (GWAS) of diverticular disease in European, African and multi-ancestry participants, followed by phenome-wide association studies (PheWAS) of the risk variants to identify their potential comorbid/pleiotropic effects in the clinical phenome. For more in-depth investigation of associated clinical phenotypes, we also performed PheWAS with the previously reported 52 GWAS susceptibility variants for diverticular disease.ResultsAncestry-stratified GWAS analyses confirmed the well-established associations betweenARHGAP15loci with diverticular disease in European cohorts, and found similar positive effect sizes in African cohorts but with non-significant p-values. With overall intensified GWAS signals in diverticulitis patients compared to diverticulosis patients, we found substantial genetic correlations between diverticulosis and diverticulitis, up to 0.997 in European ancestry. PheWAS analyses identified associations between the diverticular disease GWAS variants and circulatory system, genitourinary, and neoplastic EHR phenotypes.ConclusionOur multiancestry GWAS-PheWAS study demonstrated an effective use of multidimensional EHR information in disease case/control classification with NLP for more comprehensive and scalable phenotyping, and implementation of an integrative analytical pipeline to facilitate etiological investigation of a disease from a clinical perspective.
Rab5 regulates macropinosome closure through recruitment of the inositol 5-phosphatases OCRL/Inpp5b and the hydrolysis of PtdIns(4,5)P2
Authors: Maxson Michelle E. , Sarantis Helen , Volchuk Allen , Brumell John H. , Grinstein Sergio 
Published: June 2020

AbstractRab5 is required for macropinosome formation, but its site and mode of action remain unknown. We report that Rab5 acts at the plasma membrane, downstream of ruffling, to promote macropinosome sealing and scission. Dominant-negative Rab5, which obliterates macropinocytosis, had no effect on the development of membrane ruffles. However, Rab5-containing vesicles were recruited to circular membrane ruffles, and SNARE-dependent endomembrane fusion was necessary for completion of macropinocytosis. This fusion event coincided with the disappearance of PtdIns(4,5)P2that accompanies macropinosome closure. Counteracting the depletion of PtdIns(4,5)P2by expression of phosphatidylinositol-4-phosphate 5-kinase impaired macropinosome formation. Importantly, we found that removal of PtdIns(4,5)P2is dependent on Rab5, through the Rab5-mediated recruitment of the inositol 5-phosphatases OCRL and Inpp5b, via APPL1. Knockdown of OCRL and Inpp5b, or APPL1 prevented macropinosome closure, without affecting ruffling. We therefore propose that Rab5 is essential for the clearance of PtdIns(4,5)P2needed to complete macropinosome scission from the plasmalemma.
VirusDIP: Virus Data Integration Platform
Authors: Wang Lina , Chen Fengzhen , Guo Xueqin , You Lijin , Yang Xiaoxia , Yang Fan , Yang Tao , Gao Fei , Hua Cong , Ding Yuantong , Cai Jia , Yang Linlin , Huang Wei , Xu Zhicheng , Wan Bo , Tong Jiawei , Peng Chunhua , Yang Yawen , Zhang Lei , Liu Ke , Zhou Feiyu , Zhang Minwen , Tan Cong , Zeng Wenjun , Wang Bo , Wei Xiaofeng 
Published: June 2020

AbstractMotivationThe Coronavirus Disease 2019 (COVID-19) pandemic poses a huge threat to human public health. Viral sequence data plays an important role in the scientific prevention and control of epidemics. A comprehensive virus database will be vital useful for virus data retrieval and deep analysis. To promote sharing of virus data, several virus databases and related analyzing tools have been created.ResultsTo facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. VirusDIP is gradually establishing cooperation with more databases, and paving the way for the analysis of virus origin and evolution. All public data in VirusDIP are freely available for all researchers worldwide.Availabilityhttps://db.cngb.org/virus/Contactweixiaofeng@cngb.org