bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic hallmarks of tumor‐stromal interactions in brain metastasis
Authors: Nguyen Don 
Published: June 2021

The central nervous system (CNS) is a major site of relapse for several types of treatment refractory cancers including tumors from the lung, skin, and breast. The incidence of brain metastasis associated deaths is rising, because of the limited delivery of drugs across the blood brain barrier (BBB) and morbidity of metastasis once spread in the CNS. One of the most rate limiting steps of CNS metastasis is the ability of disseminated tumor cells (DTC) to outgrow after extravasating across the BBB. Deciphering the molecular interactions which dictate this step in vivo remains a challenge due to the heterogeneous patterns of tumor outgrowth in the CNS and the unique nature of this tumor microenvironment (TME).To address this challenge, we optimized a novel method for RNA sequencing analysis which leverages xenograft models and overcomes the confounding analytic effects incurred during the isolation of cells ex‐vivo. Using this method, we could decipher molecular alterations that are specific to the tumor cells or the stroma in situ with increased accuracy and sensitivity, revealing striking new insights into brain‐specific transcriptional co‐adaptation of malignant cells and their neuroinflammatory milieu. These gene expression programs are linked to specific patterns of metastatic outgrowth, anatomical location in the brain, and interaction with neuronal cell types. Our study provides a molecular framework to understand the heterogeneous biological manifestation of brain metastasis while revealing novel epigenetic and phenotypic state(s) utilized by metastatic cells to persist and outgrow in the CNS.Support or Funding InformationThis study was funded by grants from the National Cancer Institute (R01CA166376 and R01CA191489).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Leveraging mouse liver co‐expression networks and human lipid GWAS data to identify and validate cholesterol metabolism genes
Authors: Parks Brian Wesley , Li Zhonggang , Nguyen Jenny , Leyva‐Jaimes Fernanda 
Published: June 2021

Genetic factors play an important role in contributing to variation in plasma lipid levels across the human population. Large genome‐wide association studies (GWAS) in humans have identified more than 100 loci significantly associated with plasma levels of low‐density lipoprotein (LDL) cholesterol, high‐density lipoprotein (HDL) cholesterol, triglycerides and total cholesterol (TC). To prioritize genes that are involved in cholesterol metabolism we developed a systematic approach to leverage genome‐wide liver transcriptomic and proteomic data from multiple mouse reference populations along with human lipid GWAS data. We constructed global co‐expression networks from 12 distinct mouse liver datasets and identified a conserved module of genes highly enriched for cholesterol biosynthetic processes. Based on replication across mutiple datasets we prioritized 112 unique genes. Intersection with human GWAS data for LDL, HDL, TC, and triglycerides identified 54 of these genes to be within 100 kilobases of a significant or suggestive significant single nucleotide polymorphism (SNP). 29 of the 54 prioritized genes have well documented biological roles in cholesterol metabolism, such as LDLR, PCSK9, and INSIG1. With the 25 identified genes with no documented role in cholesterol metabolism, we tested for sensitivity to cholesterol modulation and performed a functional screen by siRNA knockdown. From this analysis we identified, Sestrin1, as a candidate gene that is responsive to cholesterol manipulation and capable of modulating cellular cholesterol levels. Using Sestrin1 targeted mice we show that Sestrin1 heterozygous or homozygous knockout mice have elevated levels of plasma cholesterol when fed a diet enriched in cholesterol. Collectively, through a systematic approach we have identified 25 highly prioritized genes that have no documented role in cholesterol metabolism. One of these genes, Sestrin1, we validate in vivo and in vitro as a modulator of cholesterol metabolism.Support or Funding InformationBWP is supported by NIH R00‐HL123021This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Protein kinase R modulates NLRP3 inflammasome in cardiac fibroblasts in sepsis
Authors: Xu Xuemei , Tao Aibin , Kao Raymond , Martin Claudio , Rui Tao 
Published: June 2021

BackgroundWe have reported that sepsis leads to an activation of NLRP3 inflammasome in cardiac fibroblasts (CF) resulting in IL‐1β maturation and extracellular release. Increase in IL‐1β by the CF induces myocardial dysfunction. The aim of the present study is to identify a modulation pathway that activates NLRP3 inflammasome in the CF.Materials and MethodsCF were isolated and cultured from adult mouse hearts. The CF were primed with LPS (1 μg/ml) for 6 hrs followed by 30 min of ATP (3 mM) treatment to activate NLRP3 inflammasome. PKR activation was assessed by PKR phosphorylation (Western). NLRP3 inflammasome activation was assessed by detecting CF caspase‐1 p20 (Western) and IL‐1β release (ELISA).ResultsLPS priming of CF resulted in PKR activation as indicated by increase in PKR phosphorylation at Thr451, and increase in NLRP3 and pro‐IL‐1β protein expression. Inhibition of PKR (PKR inhibitor and siRNA) prevented the LPS‐induced NLRP3 and pro‐IL‐1β expression in the CF. Inhibition of PKR in CF primed with LPS before ATP showed no effect on NLRP3 and pro‐IL‐1β expression, but prevented the NLRP3 inflammasome activation as indicated by abolishing the caspase‐1 activation and IL‐1β releasing. In addition, pretreatment of CF with peroxynitrite (ONOO−) decomposition catalyst, FeTPPs, before LPS, prevented the LPS induced PKR phosphorylation, NLRP3 and pro‐IL‐1β expression in CF. Furthermore, pretreatment of CF with FeTPPs before ATP prevented the NLRP3 inflammsome activation in CF.Conclusionour results indicate that ONOO−/PKR pathway modulates priming and activation of NLRP3 inflammasome in CF in sepsis.Support or Funding InformationIRF of Lawson Health Research Institute (IRF 2014–25); The Natural Science Foundation of Jiangsu Province, China (BK2015‐1332).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identification of a Novel Phenotype of Myeloid Cells in Classical Hodgkin Lymphoma
Authors: Post Ginell R. , Yuan Youzhong , Post Steven R. 
Published: June 2021

Classical Hodgkin lymphoma (cHL) characteristically shows few malignant cells in a microenvironment comprised of inflammatory cells. Although cHL is associated with a high cure rate, recent studies have associated poor prognosis with increased macrophages in involved lymph nodes (LN). It was recently reported that in cHL patients with relapsed disease post‐allotransplant, tumor‐infiltrating macrophages are derived from circulating monocytes and not resident macrophages. Thus, the role of monocytic infiltration and differentiation in cHL may be more relevant to defining prognosis in cHL patients and potentially have therapeutic implications. Most studies identify tumor associated macrophages using markers (e.g., CD68) that detect the entire myeloid lineage. In contrast to other myeloid markers, SR‐A is expressed by tissue macrophages but not monocytic precursors. In this study, we examined expression of the Class A Scavenger Receptor (SR‐A/CD204) in cHL LNs. We confirmed a high prevalence of cells that stained with the myeloid markers CD68, CD163, and CD14 in cHL LNs. However, SR‐A protein expression determined by immunohistochemistry was limited to macrophages localized in sclerotic bands characteristic of nodular sclerosing cHL. In contrast, SR‐A protein was readily detectable in solid tumor metastasis to LNs and in resident macrophages in control tissue (spleen, lung, liver). The results of SRA protein expression paralleled the expression of SR‐A message determined by quantitative RT‐PCR indicating transcriptional regulation of SR‐A expression. These data provide evidence for a unique macrophage phenotype, perhaps reflecting altered differentiation of myeloid cells, in LNs of cHL patients.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Patient‐derived and cell line xenograft growth in the B6;129‐Rag2tm1FwaIL2rgtm1Rsky/DwlHsd (R2G2) mouse model
Authors: Naden Jamie 
Published: June 2021

Immunodeficient mouse models are helping to advance the field of oncology. A new model on the market, the B6;129‐Rag2tm1FwaIL2rgtm1Rsky/DwlHsd (R2G2) knockout mouse, lacks responsiveness to common gamma chain cytokines, including IL‐2, IL‐4, IL‐7, IL‐9 and IL‐15. In addition, this model exhibits defects in lymphoid development and so lacks mature lymphocytes of the B, T, and natural killer (NK) cell lineages. Herein we describe growth of multiple patient‐derived (PDX) and tumor cell line xeno‐ (CDX) and allo‐grafts in the R2G2 immunodeficient mouse model. The PDXs examined include colorectal and head and neck cancers. The CDXs studied include esophageal (OE33 and FLO1) and stomach cancer (AGS). Tumor growth data was also collected from two allografts of murine colorectal cancer (CT26) and B‐cell lymphoma (A20) cells. Colorectal PDX tissue was subcutaneously implanted bilaterally into five male R2G2 and five male NSG mice. Growth was comparable between the R2G2 and the NSG mouse models, however the standard error was much lower in the R2G2 strain. Head and neck PDX 626 and 635 was transplanted in 2.2 mm2 tissues into 4 sections of each of 2 R2G2 mice each (n=2/PDX), and 100% of mice developed either one or two tumors. The human esophageal adenocarcinoma OE33 cells were implanted into the left and right flanks of three each of R2G2, Athymic Nude and SCID mice. There was a 100% take rate in R2G2 mice, 0% in SCID mice and 17% in Athymic Nude mice. The human esophageal adenocarcinoma FLO1 cells were examined in two studies. In both studies, cells were injected into both flanks of R2G2 and SCID mice. Study A also examined growth in Athymic Nude mice. In study A, no tumor growth was seen in Athymic Nude or SCID mice, whereas the take rate was 100% in R2G2 mice. In study B, the take rate was 100% in both the R2G2 and the SCID mice, although differences were seen in growth rate. Human gastric adenocarcinoma AGS cells were implanted in both flanks of four each of R2G2 and SCID mice. The take rate was 75% in R2G2 mice and 0% in SCID mice. Head and neck squamous cell carcinoma SQ20b cells were implanted in twenty R2G2 mice and take rate was 90%. Growth of two allogeneic tumor lines was also examined. The mouse colon carcinoma CT26 cells were implanted in ten R2G2 mice and took in 100% of the mice. Mouse B‐cell lymphoma A20 cells were implanted in ten R2G2 mice and take rate was 100%. Both allografts grew to 1000mm3 by 13 days post implantation. These data provide evidence that the R2G2 mouse model is a valuable tool for oncology programs including cell line tumor models research, with high take rates and quick growth of allogeneic models.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Significant Reduction in Full Metabolic Syndrome in Saudi Subjects with Elevated Fasting Glucose through an Intensive Lifestyle Monitoring Programme of 12 months
Authors: Alfawaz Hanan A. , AL‐Daghri Nasser M. 
Published: June 2021

BackgroundThe present interventional study in adult Saudi subjects with elevated fasting glucose was aimed to determine the health benefits, in terms of reduction in full metabolic syndrome, of a 12‐month intensive lifestyle monitoring programme with emphasis on lowering dietary fat intake; exercise and increasing sunlight exposure.MethodsBetween April‐2012 and March‐2017, 300 Saudi subjects with baseline fasting glucose at 5.6 to 6.9mmol/l were screened and randomly divided into 3 groups: 1) General advice (GA) group who received a standard lifestyle change advice at recruitment and at 6‐months, 2) Intensive lifestyle monitoring programme (ILMP) group who was followed with a rigorous lifestyle modification support and 3) Metformin (GA+Met) group who was advised to take 3 tablets/day of 500 mg metformin hydrochloride. Basic anthropometric, glycemic, and lipid estimations were obtained at baseline and after 6‐months and 12‐months. The data for 85(GA), 73(ILMP) and 59(GA+Met) subjects was analyzed after removing those lost in follow‐up etc. The percentages of full metabolic syndrome and its five components were calculated for all three groups at different time points.ResultsThe mean fasting glucose at baseline, 6‐months and 12‐months respectively was 5.97±0.4, 6.07±0.7 and 5.92±0.9 (p=0.49) for GA group; 6.06±0.4, 5.66±0.8 and 5.67±0.8 (p<0.01) for ILMP group; and 6.57±0.5, 6.01±1.3 and 5.76±1.7 (p<0.01) for GA+Met group. 37.3 %( N=22) in GA+Met group were able to reduce their weight by atleast 5% from baseline while this number was 11 %( N=8) and 10.6 %( N=9) in ILMP and GA respectively. Full Metabolic syndrome at end of study compared to the baseline was 64.7%(N=55) vs 72.9%(62) (% change: Δ= −8.2%, p=not significant) for GA group; 35.6%(26) vs 61.6%(45) (Δ= −26%, p<0.01) for ILMP group and 64.4%(38) vs 83.1%(49) (Δ= −18.7%, p<0.01) for GA+Met group.ConclusionsThis study highlights the clinical potency of intensive lifestyle modification programme versus other anti‐diabetic management options in reducing full metabolic syndrome in Saudi adults with elevated fasting glucose.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Type‐I interferon‐mediated Akt/mTORC2 signaling regulates autophagy and inflammasome activation in mouse liver injury/sepsis model
Authors: Wells Jakob , Kader Muhamuda , Tamama Kenichi , Yates Cecelia , Scott Melanie , Ismail Nahed 
Published: June 2021

Background: Sepsis is a clinical syndrome due to dysregulated systemic immune response to infection and tissue injury that causes life‐threatening multiple organ failure. In murine model of sepsis and hepatic inflammatory injury induced by infection with Ehrlichia, an obligate intracellular bacteria targeting liver that compromises the immune system, we have shown that type I interferon (IFN‐I) signaling triggered liver injury, excessive inflammation, and impaired bacterial clearance. We and others have also showed that Ehrlichia exploits autophagy proteins for their own survival and replication. This study was designed to investigate the role of IFN‐I signaling in the regulation of autophagy and inflammatory responses in immune and non‐immune cells such as macrophages and hepatocytes, respectively, during sepsis.Results: In this study, we found that IFN‐I signaling promotes autophagy and activates non‐canonical inflammasome pathway mediated by caspase 11 in primary murine macrophages and hepatocytes. Enhancement of autophagy in hepatocytes and macrophages via IFN‐I stimulation or rapamycin treatment increased bacterial replication. Conversely, inhibition of autophagy in macrophages using type III Phosphatidylinositol 3‐kinases (PI‐3K) inhibitor (3‐MA) or blocking IFN‐I receptor (IFNAR) signaling attenuated autophagy, abrogated caspase 11 activation, and decreased intracellular bacteria. These data suggest that IFN‐I signaling impair anti‐bacterial immunity via induction of autophagy. Further, IFN‐I signaling also induced secretion of several chemokines and growth factors (e.g. MIP1alpha, MCP‐1, RANTES, KC, GM‐CSF and VEGF) by hepatocytes that are known to promote excessive infiltration of immune and inflammatory cells into the liver. Finally, microarray analysis identified mTORC2, rapamycin‐insensitive companion of mTOR, and WNT, elevated in sepsis, signaling components to be enhanced in IFN‐I stimulated and infected hepatocytes, which may play a role in IFN‐mediated enhancement of autophagy and inflammation.Conclusions: Together, our novel findings identify the IFN‐1‐mediated Akt/autophagy axis as a key regulator of innate inflammatory response in the mouse liver cells. By identifying molecular mechanisms of IFN‐1‐mediated Akt/autophagy/mTORC2 signaling during sepsis, our study provides a rationale for therapeutic approaches to manage inflammation and liver injury during sepsis.Support or Funding InformationThis work was supported by grants from NIAMS, NIGMD, and NIAID (AR68317 CCY, GM102146 MS, and R56A1097679 NI)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Critical Role of Plasmin in Macrophage Activation During Liver Injury
Authors: Roth Katherine , Joshi Nikita , Albee Ryan , Luyendyk James P. , Copple Bryan 
Published: June 2021

Activation of hepatic macrophages is critical for liver repair after injury. The mechanism by which liver injury stimulates macrophage activation is not fully understood. We tested the hypothesis that the fibrinolytic enzyme, plasmin, is critical for macrophage activation after liver injury. To test this hypothesis, mice were exposed to a hepatotoxic dose of acetaminophen followed by treatment with tranexamic acid (1200 mg/kg i.p., administered twice daily), a drug that inhibits the conversion of plasminogen to plasmin. Exposure of mice to acetaminophen stimulated rapid macrophage activation, increasing cytokine production and macrophage‐mediated phagocytosis of necrotic cells. This activation was reduced by plasmin inhibition, leading to impaired liver repair. Next, we determined whether plasmin directly activates macrophages. Treatment of either bone marrow‐derived macrophages or Kupffer cells with plasmin increased expression of the proinflammatory cytokines Cxcl1, Cxcl2, and tumor necrosis factor‐α in an Erk1/2 and p38‐dependent manner. Studies have indicated a role for high‐mobility group B1 protein (HMGB1), a damage‐associated molecular pattern molecule, in the activation of macrophages. Therefore, we determined whether HMGB1 affects plasmin‐mediated activation of macrophages. While HMGB1 alone at concentrations that are detected in the serum of acetaminophen‐treated mice did not increase expression of proinflammatory cytokines in macrophages, it synergistically enhanced plasmin‐mediated upregulation of cytokines. Furthermore, necrotic hepatocytes from wild‐type mice enhanced plasmin‐mediated activation of macrophages, whereas necrotic hepatocytes from hepatocyte‐specific HMGB1 knockout mice did not. Collectively, these studies demonstrate that plasmin is an important activator of macrophages after liver injury. Further characterization of this pathway could lead to the development of novel therapies aimed at enhancing macrophage‐mediated liver repair in patients suffering from acute liver injury.Support or Funding InformationNIH grant 2 R01 DK073566NIH Training Grant T32 ES007255This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Hepatocyte specific ablation of β and γ‐catenin leads to altered hepatocyte polarity and microvillae association
Authors: Pradhan Tirthadipa , Adebayo Adeola , Molina Laura , Monga Satdarshan Pal 
Published: June 2021

Liver is the largest organ in a vertebrate body which is structurally and functionally complex and is considered second to the brain in its complexity. It is highly heterogeneous in nature and consists of various cell types. Hepatocytes are the predominant type of cells present in liver which is responsible for its many important functions including bile production, detoxification, cholesterol synthesis etc. Like any other epithelial cell, hepatocytes are polarized towards the apico‐basal axes. Polarization of hepatocytes is necessary for many functions and requires carefully orchestrated cooperation between cell adhesion molecules, extracellular matrix, cell junctions, cytoskeleton, and intracellular trafficking machinery. Loss of hepatocyte polarity is associated with various liver diseases including cholestasis.Recently, we have shown that absence of adherent junctional protein β and γ catenin in the liver leads to cholestatic liver disease. However, the molecular mechanism that leads to cholestasis in the absence of β‐ γ‐catenin is not known. Therefore, we developed a hepatocyte specific conditional knockout of β and γ catenin to further characterize their role in this disease. TEM and SEM analysis of β‐ γ‐catenin knockout liver showed aberrant tight junctional and adherent junctional structurers. Permeability assay confirmed that barrier function of tight junctions is completely lost in these mice resulting in mixing of the bile with the blood. We also found that bile canaliculi, which is apically located in hepatocytes designated for bile storage is strongly dilated with significant reduction in microvilli inside them. Further analysis revealed that loss of β‐ γ‐catenin leads to reduced expression of HNF4α target genes. Remarkably, we found that loss of HNF4α phenocopies β‐ γ‐catenin knockout liver causing aberrant tight and adherent junctional structure. Studies designed to address the molecular mechanism behind the regulation of β; γ‐catenin in maintaining hepatocyte polarity and association of β; γ‐catenin and HNF4α in promoting hepatocyte polarity are currently underway. Profound understanding of the regulation of hepatocyte polarity by both β ‐and γ‐catenin will be useful in the context of liver development and pathophysiology.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Proton‐Coupled Electron Transfer in Soybean Lipoxygenase: Hydrogen Tunneling, Electrostatics, and Conformational Motions
Authors: Hammes‐Schiffer Sharon 
Published: June 2021

The enzyme soybean lipoxygenase (SLO) serves as a prototype for hydrogen tunneling reactions because of its unusually large deuterium kinetic isotope effect (KIE) of 80 for the wild‐type enzyme and over 500 for a double mutant. The proton‐coupled electron transfer (PCET) reaction catalyzed by SLO has been studied with a vibronically nonadiabatic PCET theory that includes the quantum mechanical effects of the electrons and the transferring proton, as well as the proton donor‐acceptor and solvent motions. The calculations reproduced the experimentally observed magnitude and temperature dependence of the KIE for wild‐type SLO and a series of single mutants. The large KIE was found to arise from the small overlap between the reactant and product proton vibrational wave functions. Theoretical modeling of the double mutant illustrated that the colossal KIE of over 500 arises from a combination of a non‐optimal active site conformation corresponding to longer equilibrium donor‐acceptor distances and reduced sampling of shorter donor‐acceptor distances. Recent quantum mechanical/molecular mechanical (QM/MM) free energy simulations using a finite temperature string method combined with umbrella sampling have provided additional insights about the conformational motions, as well as the significance of electrostatics in this enzymatic reaction. These calculations highlight the critical roles of hydrogen tunneling, electrostatics, and protein conformational motions in enzyme catalysis.Support or Funding InformationNational Institutes of Health Grant GM056207This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.