bluuebunny/crossref_metadata_2025_split huggingface dataset:
New insights from The Cancer Genome Atlas: Implications for GPCR expression in cell compartments in solid tumors
Authors: Sriram Krishna , Moyung Kevin , Insel Paul A. 
Published: April 2020

Assessment of the transcriptome of tumors via high‐throughout methods such as RNA‐sequencing (RNA‐seq) has yielded insights that enable understanding of tumor biology and facilitate drug discovery efforts. A challenge with using such “omics” methods is the presence of technical variation between groups of samples (often termed ‘batch effects’) which arise from differences in sample collection, handling and processing, especially with large, multi‐center, consortium‐based efforts such as The Cancer Genome Atlas (TCGA). Approaches to correct for technical artifacts should seek to minimize variance introduced by known technical factors, while preserving the biological variability within the dataset. We present a workflow for assessing the magnitude of identifiable technical artifacts within RNA‐seq data in TCGA and to identify the most relevant sources of variation are most relevant and steps to correct for such artifacts using bioinformatics tools. We show that certain TCGA datasets are highly impacted by technical variation and that correction for these artifacts can alter downstream analyses such as association studies and survival analysis. Correction for these effects using batch correction tools removes the influence of technical artifacts, while preserving biological variation and the overall structure and integrity of the data. We use these corrected data to establish an updated list of significant genes that impact survival in a range of solid tumor types in TCGA . In addition, we use methods to identify networks of co‐expressed and co‐regulated genes and identify genes that are sensitive to molecular features of tumors, such as the presence of specific driver mutations.Using these “tidied‐up” datasets, we analyzed the expression of GPCRs (G protein‐coupled receptors) in tumors to identify the cellular compartments within the tumor microenvironment that express particular GPCRs. Due to their widespread utility as pharmacological targets and numerous recent results re‐emphasizing a role for GPCRs in cancer, such analyses provide a valuable tool for drug discovery. We document a number of GPCRs that are widely expressed in immune cells in a range of solid tumors and that whose functions may impact the phenotype of immune cells, including in cancer. Such widely expressed immune‐associated GPCRs are examples of novel putative targets in the rapidly growing field of immuno‐oncology. These analyses for GPCRs can be expanded to other classes of targets as well, providing a general tool for using large databases of gene expression to identify and evaluate genes that are likely to be expressed in cell types within tumors in vivo, thereby avoiding pitfalls that arise when working with isolated cells or single‐cell based approaches.Support or Funding InformationASPET David Lehr Award
Butyrate Priming Improves Gut Health by Modulating Host Protease Activity in Murine Non‐Alcoholic Fatty Liver Disease
Authors: Mondal Ayan , Seth Ratanesh , Bose Dipro , Nagarkatti Mitzi , Nagarkatti Prakash , Chatterjee Saurabh 
Published: April 2020

Reports from clinical investigations implicate a strong association of non‐alcoholic fatty liver disease (NAFLD) and inflammatory bowel diseases (IBD). Recently we reported a rapid alteration of gut microbiome in murine NAFLD model that resulted in gut leaching, tight junction protein alteration and intestinal inflammation. Advancing our present understanding, we show that altered gut microbiome in murine NAFLD significantly decreased microbial proteases content in the host gut micro‐environment. Dysbiosis significantly increased expression of host proteases derived from gut immune cells which were associated with intestinal inflammation and gut leaching. Results also showed significant upregulated expression of a disintegrin and metalloproteinase 17 (ADAM17) and serine proteases Granzyme M, Cathepsin G and Proteinase 3 in intestines of NAFLD mice. Increased expression of these proteases were associated with activation of protease activated receptor 1 (PAR1), significant over production of pro inflammatory cytokines TNFα and IL‐1β, decreased expression of Occludin, and increased expression of Claudin2. Most interestingly administration of butyrate to NAFLD mouse group significantly increased microbial protease content in gut, decreased expression of ADAM17, Granzyme M and Cathepsin G, and increased expression of protective matrix metalloproteinases 7 and 2 (MMP7 and MMP2). Decreased expression of ADAM17, Granzyme M and Cathepsin G improved gut leaching by upregulation of Occludin and down regulation of Claudin 2 expression, decreased PAR1 expression, and decreased TNFα and IL‐1β secretion. Furthermore, increased expression of MMP 2 and MMP 7 showed elevated expression of anti‐inflammatory cytokines IL‐4 and IL‐10 in small intestine. Thus, in conclusion our present study demonstrates that butyrate plays a crucial role in gut homeostasis by a previously unknown function of modulating host protease activity in NAFLD and can be of significant therapeutic value.Support or Funding InformationThis project has been supported by NIH grants # 2P01AT003961 (Project 4) and #P20GM103641‐07(Project3) to Dr. Saurabh Chatterjee
Protein structure, a new constraint for glycosyltransferase specificity: Template‐like association between the glycoprotein surface on glycan structure
Authors: Kellman Benjamin P. , Lewis Nathan E. 
Published: April 2020

The multitude of glycans on any cell surface can appear homogeneous overall, but a more site‐specific perspective suggests some deliberate diversity. Many have argued that site‐specific microheterogeneity arises from the influence of protein structure on glycan synthesis, yet, the prevailing consensus is that glycan synthesis is non‐template driven. We examine the possibility that the diversity of site‐specific glycoprofiles is a result of the affinity for glycosyltransferases to various regions of that protein. In this study, we examine an empirical glycoprotein database containing evidence of site‐specific glycosylation events. Each glycan substructures was correlated to site‐specific protein structure features (e.g. secondary structure, proximal amino acids). By characterizing correlations between glycan substructures and local protein chemistry, we have produced a draft template which we have applied to further our understanding of the HIV envelope mannosylation, predict temporospatial changes in flu glycosylation, explain discrepancies in amino acid substitutions matrices, predict TAPBP dependence in HLA, and predict secretion rates. In an attempt to share our advance, we are currently predicting glycosylation throughout PDB and SWISSMOD and identifying mutations in ClinVar most likely to be glycan‐modulated. By determining occlusion of GTs on structurally annotated sites, we can learn about the structural specificities of these impactful proteins thereby increasing our capacity to understand and predict their behavior.Support or Funding InformationNIH 1 R21 HD088953, NNF10CC1016517
Proteolytic activation of the epithelial sodium channel: role of pro‐protein convertases and prostasin
Authors: Svenningsen Per , Granhoj Jeff , Dimke Henrik 
Published: April 2020

The epithelial sodium channel (ENaC) is essential for regulating renal sodium excretion. Cleavage of the γENaC subunit increases ENaC activity both in vitro and in vivo; however, the involved endogenous proteases remain ambiguous. This study investigates the mechanistic roles of the pro‐protein convertase (PCSK) family and the serine protease prostasin in proteolytic activation of ENaC.We used the M‐1 mouse collecting duct cell line that natively expresses functional ENaC channels for pharmacological inhibition studies with pro‐protein convertase inhibitor decanoyl‐RVKR‐chloromethyl ketone (dec‐RVKR‐cmk) and serine protease inhibitor camostat mesilate (CM). Knockout cell lines of prostasin and three PCSKs were generated with the CRISPR/Cas9 system in M‐1 cells. As an index of ENaC activity, amiloride‐sensitive short‐circuit current (ISC) and transepithelial voltage (VTE) was measured on polarized cells on transwell filter supports in Ussing chambers. γENaC membrane levels and cleavage were tested by western blotting of surface biotinylated M‐1 cells with an antibody against the C‐terminal of γENaC. All values are means SE, compared with students t‐test or ANOVA as appropriate.Pro‐protein convertase inhibition decreased the amiloride‐sensitive ISC in M‐1 cells compared with controls (25.9 1.9 μA, n=5, vs. 45.7 7.0 μA, n=6, p<0.05). Similarly, serine protease inhibition decreased VTE (−34.5 7.8 mV, n=3, vs. −74.2 0.9 mV, n=3, p<0.05) but ISC was not significantly lower (68.0 8.5, n=3, vs. 74.0 2.3, n=3, n.s.). Preliminary evidence suggests that although both inhibitors decreased membrane expression of γENaC, only serine protease inhibitor treatment reduced γENaC cleavage (n=1). Knockout of the Psck3 (furin) gene by CRISPR completely abolished ENaC activity, while knockout of Pcsk4, Pcsk7, and prostasin all showed decreased ENaC activity compared to wild‐type M‐1 cells. Knockout of PCSKs reduced γENaC surface expression, but only knockout of prostasin reduced γENaC cleavage.We propose that PCSKs are not directly involved in proteolytic ENaC activation. Both pharmacological inhibition and knockout of prostasin decreased ENaC activity and γENaC cleavage, thus suggesting a potential role in proteolytic ENaC activation.Support or Funding Information The Danish Medical Research Council
Insulin Similar to Activator of KCNQ1 Channel Recovers the Prolonged Repolarization of Ventricular Cardiomyocytes from Insulin Resistant Aged Rats
Authors: Turan Belma , Olgar Yusuf , Durak Aysegul , Tuncay Erkan 
Published: April 2020

Both cardiac dysfunction and systemic insulin resistance mostly observed together with advancing aging or metabolic syndrome (MetS), while the exact underlying mechanisms of heart‐specific insulin resistance and cardiac dysfunction still remain unclear. There also are relations between delayed ventricular repolarization, increased risk in arrhythmia and QT‐prolongation in ECG with diabetes, aging and MetS. They also showed that the mutations/functional alterations in QT‐prolongation related K+‐channels such as KCNQ1‐channels might be responsible for these changes. In addition, most of recent observations that insulin sensitivity of glucose metabolism are affected by a new molecule KCNQ1, which brings up a thought on possible relation of development of insulin resistance, changes in this channel and QT‐prolongations in senescent mammalian cardiomyocytes. Therefore, we aimed to clarify a possible association between prolonged action potential duration and alterations in KCNQ1‐channel function as well as insulin application in ventricular cardiomyocytes from either insulin resistant aged or MetS rats. Our data showed that there is a significant prolongation in action potential repolarization phase in isolated cardiomyocytes from insulin‐resistant aged or MetS rats, while those animals have a significant prolonged‐QT in ECG and can respond to insulin application. Besides, application of KCNQ1‐channel activator reduced the prolonged action potential repolarizations and this indicates the contribution of KCNQ1‐currents and possible benefits of insulin on action potential prolongation of both aged and MetS cardiomyocytes. Our present study also showed that the protein expression level of KCNQ1 and KCNE1 remained unchanged. Overall, our present results can reveal important information on the contributions of these parameters on the aging‐related or metabolic syndrome‐related cardiac dysfunction and the effect of insulin on these alterations. Therefore, our findings will contribute to the literature and the clinical applications with a new therapeutic approach by revealing the molecular mechanisms of insulin treatment on insulin resistant aged or MetS mammalian cardiac dysfunction.Support or Funding InformationSupported through TUBITAK SBAG‐119S661
Identification of Critical MCUR1 Domains in the Mitochondrial Calcium Uniporter Complex that Regulates Cellular Metabolism
Authors: Enslow Benjamin Troy , Madaris Travis , Ravichandran Joel , Jacob Reggie , Srikantan Subramanya , Stathopulos Peter , Muniswamy Madesh 
Published: April 2020

Mitochondria are multivariate signal processors that decode diverse cellular inputs into various bioenergetic outputs. One such signal is the calcium (Ca2+) flux between the cytosol and mitochondria which modulates the organelle’s function. Under physiologic cytosolic [Ca2+], energy output (ATP) can be adjusted to meet cellular demands. To maintain the Ca2+ homeostatic circuit, a selective mitochondrial Ca2+ Uniporter (MCU) complex promotes Ca2+ uptake. MCUR1 is an integral mitochondrial inner membrane protein which serves as a scaffold factor for the MCU complex and regulates its functional activity. The resolved NMR structure of the human MCUR1 protein revealed a high degree of conservation for 3 residues within the “head domain” of the protein, A170, L174, V203, and Y204.ObjectiveWe hypothesized that alterations of these critical residues would affect MCUR1 function, and thereby, MCU complex activity.MethodsTo test this hypothesis, MCU‐mediated mitochondrial calcium (mCa2+) uptake, resting matrix mCa2+ levels, and mitochondrial bioenergetics such as NAD(P)H production and oxygen consumption rate (OCR) were evaluated.ResultsRemarkably, cells expressing the MCUR1A170R/L174R mutant demonstrated near complete ablation of MCU‐mediated mCa2+ uptake, NAD(P)H production and OCR. Conversely, cells expressing MCURWT, or the MCURV203R/Y204R mutant demonstrated similar effects on MCU activity and mitochondrial bioenergetics suggesting a nominal change at the structural level.ConclusionCollectively, our results indicate that the MCUR1 head domain is necessary for proper MCU complex activity, and that MCU‐mediated mCa2+ uptake modulates mitochondrial bioenergetics and cell function.Support or Funding InformationThis research was funded by the National Institutes of Health R25R25DK078381 program. (NIHR01GM109882, R01HL086699, R01HL142673, DOD/CDMRP PR181598P and NIH1S10RR027327 to M. Madesh and R25DK078381 to W.B.R. B.T.E. is supported by the National Center For Advancing Translational Sciences of the National Institutes of Health under Award Number TL1TR002647. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
CAROGENIC MICROORGANISMS IN CHILDREN WITH PRIMARY AND MIXED DENTITION
Authors: Rodriguez Patricia Noemi , Mateo Maria Teresa , Iglesias Maria Veronica , Alonso Maria Gabriela , Lifshitz Fima , Molgatini Susana , Friedman Silvia Maria , Canga Liliana 
Published: April 2020

The oral cavity is one of the most important and complex habitats of microorganisms, housing a great diversity of communities, which colonize the mucous membranes and form the dental biofilm. The acidification of biofilm by carbohydrate intake is an important factor for the onset and progression of carious lesions, where the microorganisms involved produce acids and tolerate a low pH medium.ObjectiveDetermine in children with and without carious lesions the composition of the supragingival biofilm according to the type of dentition.Materials and methodsThe study population included 49 children (24 with primary dentition PD, 36–72 months of age and 25 with mixed dentition MD, 74 to 110 months of age), with and without carious lesions. Presence of caries was determined by the visual method ICDAS and dietary history was recorded. To perform microbiological study of acidogenic microorganisms (SM: Streptococcus spp, L: Lactobacillus spp, C: Candida spp. and V: Veillonella spp), a sample of supragingival biofilm plaque was collected from molar.Agar mitis salivarius with bacitracin, MRS agar (Britany®Argentina), selective and differential medium CHROMagar Candida and selective medium for Veillonella with the addition of vancomycin and lacquered blood were inoculated. All were incubated under atmospheric conditions according to the requirements of each of the studied microorganisms. Results were statistically analyzed using ANOVA or Fisher, when appropriate. The study was approved by the Ethics Committee of the School of Dentistry‐UBA.ResultsSM and L counts was higher in PD, regardless of the presence of caries, p< 0.0001. In PD the percentage of positive C cultures was higher in children with caries, differences that were not observed in MD (p=0.0478). With respect to V, only a higher percentage of positive crops were observed in children with caries in MD (p=0.0119).Conclusionthe count of SM and L and the presence of C and V vary with the type of dentition, suggesting a change in the composition of the microbiota, even in teeth without caries.Support or Funding InformationGranted by UBACYT 20720170100005BA.
Subcutaneous grafting of ovaries from newborn rabbits into adult ovariectomized mice does not result in normal folliculogenesis
Authors: Valdez Dominik , Ruiz Saul , Foster Robert , Rodriguez-Sosa Jose Rafael 
Published: April 2020

About 10% (6.1 million) of women in the United States ages 15–44 have difficulty becoming pregnant or staying pregnant. About 1/3 are fertility problems in women. Abnormal ovarian function is a major contributor. A greater understanding of ovarian function and especially follicular development would improve treatment. Follicles form when germ cells arrive in the primitive sex cords, which are derived from the coelomic epithelium. In most species, these cords fragment and the germ cells become covered by precursors of the granulosa cells. Thus primordial follicles form. Pools of these follicles are eventually recruited and undergo maturation; a series of functional and morphological transformations that lead to ovulatory follicles. In species like humans, cattle and pigs, follicles form during the embryonic phase of gestation, while maturation takes place after birth. In contrast, both phases occur postnatally in rabbits and makes them an excellent model to study folliculogenesis. Laboratory studies using non‐rodent species are logistically more difficult and even prohibitive. One alternative is ovarian grafting into immunocompromised mice. When adult ovarian tissue is transplanted from large animals into mice, some primordial follicles survive and undergo maturation. We investigated the rabbit model by transplantation of immature rabbit ovaries under the dorsal skin of adult ovariectomized NCr N
ude mice (1 ovary / mouse). At 4 – 5 weeks, growth of the grafted ovaries was evident. Macroscopically, 50% of the grafts (5/10) had one or two follicle‐like structures on their surface. Histologically the structures were cysts lined by cuboidal cells and contained cells with the germ cell phenotype. In conclusion, ovaries grafted subcutaneously from newborn rabbits into ovariectomized adult mice developed cystic primordial follicles. Normal follicle formation and maturation did not occur.Support or Funding InformationMidwestern University intramural funds
A study on Morphometric Features of Esophagus
Authors: Alimohammadi Majid , Doroudi Majid , Zilabi Golsan , Ebrahimi Azarnoush 
Published: April 2020

Certain data such as weight and dimensions of anatomical structures are important in dosimetry for treating cancer patients using radiotherapy.The objective of this study is to determine the morphometric features of esophagus and discuss the possible correlation between the height and weight of esophagus with other parameters such as height, weight and age of patients. 23 samples were measured using measuring tape and digital scale. The results of measurements showed significant correlation between the age of individuals and the weight and length of esophagus. However, no significant correlation was found between the length and weight of esophagus with either gender, height or weight of individuals.
SPERMIDINE DOES NOT INFLUENCE LIMB MUSCLE MASS FOLLOWING ANDROGEN DEPLETION
Authors: Rossetti Michael L. , Casero Robert A. , Gordon Bradley 
Published: April 2020

Skeletal muscle atrophy increases the risk of morbidity and mortality during various pathological conditions. In males, a decrease in the production and/or bioavailability of androgens (termed hypogonadism) directly contributes to muscle atrophy during such conditions. While it is known that androgens prevent muscle atrophy, the mechanism(s) by which androgens mediate this effect are largely undefined. To identify potential androgen sensitive pathways regulating limb muscle mass, we subjected total RNA from the tibialis anterior (TA) from castrated mice and total RNA from the TA of sham mice to microarray analysis. This approach showed that androgen depletion significant altered the expression of genes involved in the polyamine metabolic pathway. The polyamines, spermidine (Spd), spermine (Spm) and their diamine precursor putrescine, are naturally occurring, polycationic alkylamines that are absolutely required for mammalian cell growth, differentiation, and survival. Accordingly, we confirmed that androgen depletion reduced muscle expression of ornithine decarboxylase (ODC1), S‐adenosylmethionine decarboxylase (AMD1), spermine oxidase (SMOX), and spermidine/spermine N‐1acetyltrasferase (SAT1), which are genes involved with polyamine biosynthesis (ODC1, AMD1) and catabolism (SMOX, SAT1). Changes in the expression of these polyamine metabolic genes following androgen depletion coincided with a preferential decrease in Spd concentration in the TA, and this reduction was strongly related to the degree of muscle atrophy induced by the androgen depletion. To assess the role of Spd in the regulation of limb muscle mass, we treated previously castrated mice with Spd in the drinking water for 8 weeks. Even though Spd treatment completely prevented the decrease in muscle Spd concentrations following androgen depletion, mass of the TA or other limb skeletal muscles was not affected. Moreover, treating previously castrated mice with nandrolone decanoate increased muscle mass and restored expression of the polyamine metabolic genes without restoring Spd values. Thus, the decrease in Spd concentration in the limb muscle following androgen depletion likely mediates processes that are independent of muscle mass regulation.Support or Funding InformationNIH Grant CA204345 to (RAC) Institute for Successful Longevity to (BSG)