bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nix induced mitochondrial fission, mitophagy, and myocyte insulin resistance are abrogated by PKA phosphorylation
Authors: da Silva Rosa Simone Cristina , Martens Matthew D. , Field Jared T. , Nguyen Lucas , Kereliuk Stephanie M. , Hai Yan , Chapman Donald , Diehl-Jones William , Aliani Michel , West Adrian R. , Thliveris James , Ghavami Saeid , Rampitsch Christof , Dolinsky Vernon W. , Gordon Joseph W. 
Published: November 2019

AbstractLipotoxicity is a form of cellular stress caused by the accumulation of lipids resulting in mitochondrial dysfunction and insulin resistance in muscle. Previously, we demonstrated that the mitophagy receptor Nix is responsive to lipotoxicity and accumulates in response to diacylglycerols induced by high-fat (HF) feeding. In addition, previous studies have implicated autophagy and mitophagy in muscle insulin sensitivity. To provide a better understanding of these observations, we undertook gene expression array and shot-gun metabolomics studies in soleus muscle from rodents on an HF diet. Interestingly, we observed a modest reduction in several autophagy-related genes including Beclin-1, ATG3, and -5. Moreover, we observed alterations in the fatty acyl composition of cardiolipins and phosphatidic acids. Given the previously reported roles of these phospholipids and Nix in mitochondrial dynamics, we investigated aberrant mitochondrial fission and turn-over as a mechanism of myocyte insulin resistance. In a series of gain-of-function and loss-of-function experiments in rodent and human myotubes, we demonstrate that Nix accumulation triggers mitochondrial depolarization, fragmentation, calcium-dependent activation of DRP1, and mitophagy. In addition, Nix-induced mitochondrial fission leads to myotube insulin resistance through activation of mTOR-p70S6 kinase inhibition of IRS1, which is contingent on phosphatidic acids and Rheb. Finally, we demonstrate that Nix-induced mitophagy and insulin resistance can be reversed by direct phosphorylation of Nix by PKA, leading to the translocation of Nix from the mitochondria and sarcoplasmic reticulum to the cytosol. These findings provide insight into the role of Nix-induced mitophagy and myocyte insulin resistance during an overfed state when overall autophagy-related gene expression is reduced. Furthermore, our data suggests a mechanism by which exercise or pharmacological activation of PKA may overcome myocyte insulin resistance.Graphical Abstract
Candidate methylation sites associated with endocrine therapy resistance in the TCGA ER+/HER2- breast cancer cohort
Authors: Soleimani Maryam , Borgoni Simone , Sofyalı Emre , Verschure Pernette J. , Wiemann Stefan , Moerland Perry D. , van Kampen Antoine H.C. 
Published: November 2019

AbstractBackgroundEstrogen receptor (ER) positive breast cancer is often effectively treated with drugs that inhibit ER signaling, i.e., tamoxifen (TAM) and aromatase inhibitors (AIs). However, about 30% of ER+ breast cancer patients develop resistance to therapy leading to tumour recurrence. Changes in the methylation profile have been implicated as one of the mechanisms through which therapy resistance develops. Therefore, we aimed to identify methylation loci associated with endocrine therapy resistance.MethodsWe used genome-wide DNA methylation profiles of primary ER+ tumors from The Cancer Genome Atlas in combination with curated data on survival and treatment to predict development of endocrine resistance. Association of individual DNA methylation markers with survival was assessed using Cox proportional hazards models in a cohort of ER+/HER2- tumours (N=552) and two sub-cohorts corresponding to the endocrine treatment (AIs or TAM) that patients received (N=210 and N=172, respectively). Models were adjusted for clinical variables tumour stage, age, AI treatment and luminal subtype. We also identified signatures of multiple methylation loci associated with survival using Cox proportional hazards models with elastic net regularization. Individual markers and multivariable signatures were compared with DNA methylation profiles generated in a time course experiment using the T47D ER+ breast cancer cell line treated with tamoxifen or deprived from estrogen.ResultsWe identified 132, 9 and 1 CpGs for which DNA methylation is significantly associated with survival in the ER+/HER2-, TAM and AI cohorts respectively. Corresponding multi-locus signatures consisted of 171, 50 and 160 CpGs and showed a large overlap with the corresponding single-locus signatures. Single-locus signatures for the ER+/HER2- and TAM cohorts were conserved among the loci that were differentially methylated in endocrine-resistant T47D cells. Similarly, multi-locus signatures for the ER+/HER2- and AI cohorts were conserved in endocrine-resistant T47D cells.ConclusionsWe identified individual and multivariable DNA methylation markers associated with therapy resistance independently of luminal status. Our results suggest that these markers identified from primary tumours and prior to any endocrine treatment are associated with development of endocrine resistance.
Enzalutamide-induced PTH1R-mediated TGFBR2 decrease in osteoblasts contributes to resistance in prostate cancer bone metastases
Authors: Su Shang , Cao Jingchen , Meng Xiangqi , Liu Ruihua , Ark Alexandra Vander , Woodford Erica , Zhang Reian , Stiver Isabelle , Zhang Xiaotun , Madaj Zachary B. , Bowman Megan J. , Wu Yingying , Xu H. Eric , Chen Bin , Yu Haiquan , Li Xiaohong 
Published: November 2019

AbstractOver 80% of prostate cancer (PCa) patients in the United States die with bone metastases. Second-line hormonal therapies, such as enzalutamide, improve overall survival in about 50% of patients with bone metastases, but almost all responsive patients eventually develop enzalutamide resistance. Our study showed that although enzalutamide significantly inhibited the tumor growth of subcutaneously or orthotopically grafted PCa C4-2B cells, it had no effect on the bone lesion development when C4-2B tumors were grafted in the bone, suggesting a crucial role of the microenvironment in enzalutamide resistance in PCa bone metastasis. We found that enzalutamide significantly decreased the amount of the TGFBR2 (TGF-β type II receptor) in osteoblasts, both in vitro and in patient samples. The osteoblast-specific knockout of Tgfbr2 significantly induced bone metastasis. We showed that the enzalutamide-induced TGFBR2 decrease in osteoblasts was mediated by increased PTH1R (parathyroid hormone/parathyroid hormone-related peptide receptor), which resulted in TGFBR2 degradation, and that blocking PTH1R rescued the TGFBR2 decrease. Furthermore, we found that PTH1R up-regulation by enzalutamide was correlated with increased Pth1r promoter occupancy by transcription factor NR2F1. Our findings highlight a potential enzalutamide-resistance mechanism through TGFBR2 decrease in osteoblasts, thus suggesting future PTH1R-blocking approaches to overcome enzalutamide resistance in PCa bone metastasis.
Ancient balancing selection maintains incompatible versions of a conserved metabolic pathway in yeast
Authors: Boocock James , Sadhu Meru J , Bloom Joshua S , Kruglyak Leonid 
Published: November 2019

AbstractDifferences in nutrient availability have led to the evolution of diverse metabolic strategies across species, but within species these strategies are expected to be similar. Here, we discovered that the galactose metabolic pathway in the yeastSaccharomyces cerevisiaeexists in two functionally distinct, incompatible states maintained by ancient balancing selection. We identified a genetic interaction for growth in galactose among the metabolic genesGAL2, GAL1/10/7, andPGM1. We engineered strains with all allelic combinations at these loci and showed that the reference allele ofPGM1is incompatible with the alternative alleles of the other genes. We observed a strong signature of ancient balancing selection at all three loci and found that the alternative alleles diverged from the reference alleles before the birth of theSaccharomyces sensu strictospecies cluster 10-20 million years ago. Strains with the alternative alleles are found primarily in galactose-rich dairy environments, and they grow faster in galactose, but slower in glucose, revealing a tradeoff on which balancing selection may have acted.
Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading into euchromatic islands
Authors: Méteignier Louis-Valentin , Lecampion Cécile , Velay Florent , Vriet Cécile , Dimnet Laura , Térèse Michel , Rougée Martin , Breuer Christian , Soubigou-Taconnat Ludivine , Sugimoto Keiko , Barneche Fredy , Laloi Christophe 
Published: November 2019

AbstractThe organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of theArabidopsis thalianagenome are specifically downregulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some TE loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine (SAM) synthase MAT3, which is required for H3K9me2 deposition. Topoisomerase VI promotes MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a mechanistic insight into the essential role of Topoisomerase VI in the delimitation of chromatin domains.
Epigenomic profiling of neuroblastoma cell lines
Authors: Upton Kristen , Modi Apexa , Patel Khushbu , Conkrite Karina L. , Sussman Robyn T. , Way Gregory P. , Adams Rebecca N. , Sacks Gregory I. , Fortina Paolo , Diskin Sharon J. , Maris John M. , Rokita Jo Lynne 
Published: November 2019

AbstractUnderstanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.
Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population
Authors: Tsuji Satsuki , Maruyama Atsushi , Miya Masaki , Ushio Masayuki , Sato Hirotoshi , Minamoto Toshifumi , Yamanaka Hiroki 
Published: November 2019

AbstractEnvironmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high-throughput sequencing, denoising was performed using two of the most widely used denoising packages, UNOISE3 and DADA2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (UNOISE3) and 41 (DADA2) haplotypes were detected by eDNA analysis. When DADA2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. This study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large-scale capture-based conventional methods, suggesting that it could become a more efficient survey method for investigating intraspecific genetic diversity in the field.
Automaticity in the reading circuitry
Authors: Joo Sung Jun , Tavabi Kambiz , Caffarra Sendy , Yeatman Jason D. 
Published: November 2019

AbstractSkilled reading requires years of practice associating visual symbols with speech sounds. Over the course of the learning process, this association becomes effortless and automatic. Here we test whether automatic activation of spoken-language circuits in response to visual words is a hallmark of skilled reading. Magnetoencephalography was used to measure word-selective responses under multiple cognitive tasks (N = 42, 7-12 years of age). Even when attention was drawn away from the words by performing an attention-demanding fixation task, strong word-selective responses were found in a language region (i.e., superior temporal gyrus) starting at ~300 ms after stimulus onset. Critically, this automatic word-selective response was indicative of reading skill: the magnitude of word-selective responses correlated with individual reading skill. Our results suggest that automatic recruitment of spoken-language circuits is a hallmark of skilled reading; with practice, reading becomes effortless as the brain learns to automatically translate letters into sounds and meaning.
Fibrin fragment E potentiates TGF-β-induced myofibroblast activation and recruitment
Authors: Fuchs Peder Fredlund , Heindryckx Femke , Calitz Carlemi , Binet François , Øie Solbak Sara Marie , Danielson Helena U. , Kreuger Johan , Gerwins Pär 
Published: November 2019

SummaryBackgroundFibrin is an essential constituent of the coagulation cascade, and the formation of hemostatic fibrin clots is central to wound healing. Fibrin clots are over time degraded into fibrin degradation products as the injured tissue is replaced by granulation tissue.Objectivesstudy the role of the fibrin degradation product fragment E (FnE) in fibroblast activation and migration.MethodsRat kidney fibroblasts (NRK-49F), human fetal lung fibroblasts (HFL1) and immortalized human foreskin fibroblasts (BJ) were exposed to FnE and TGF-β. Fibroblast activation was measured via quantitative RT-PCR and western blot for α-SMA and Collagen Iα1. A microfluidic chemotaxis assay was used to study directional migration. To investigate if FnE interacts with integrins, direct binding experiments were performed using surface plasmon resonance biosensor technology. Infusion pumps releasing FnE were implanted subcutaneously in mice and profibrotic effects of FnE were analyzed using immunohistochemical staining of the wound area.ResultsWe present evidence that FnE is a chemoattractant for fibroblasts and that FnE can potentiate TGF-β-induced myofibroblast formation. FnE forms a stable complex with αVβ3integrin, and the integrin β3subunit is required both for FnE-induced fibroblast migration and for potentiation of TGF-β-induced myofibroblast formation. Finally, subcutaneous infusion of FnE in mice results in a fibrotic response in the hypodermis. These results support a model where FnE released from clots in wounded tissue promote wound healing and fibrosis by both recruitment and activation of fibroblasts. Fibrin fragment E could thus represent a therapeutic target for treatment of pathological fibrosis.Essentials–Fibrin is an essential constituent of the coagulation cascade, and fibrin clotting is central to wound healing.–Fibrin clots are over time degraded into fibrin degradation products, including fibrin fragment E (FnE).–FnE is a chemoattractant for fibroblasts and can potentiate TGF-β-induced myofibroblast formation.–FnE released from clots in wounded tissue could promote wound healing and fibrosis.
Human T cells employ conserved AU-rich elements to fine-tune IFN-γ production
Authors: Freen-van Heeren Julian J. , Popović Branka , Guislain Aurélie , Wolkers Monika C. 
Published: November 2019

ABSTRACTLong-lasting CD8+T cell responses are critical in combatting infections and tumors. The pro-inflammatory cytokine IFN-γ is a key effector molecule herein. We recently showed that in murine T cells, the production of IFN-γ is tightly regulated through AU-rich elements (AREs) that are located in the 3’ Untranslated Region (UTR). Loss of AREs resulted in prolonged cytokine production in activated T cells and boosted anti-tumoral T cell responses. Here, we investigated whether these findings can be translated to primary human T cells. Utilizing CRISPR-Cas9 technology, we deleted the ARE region from theIFNG3’UTR in peripheral blood-derived human T cells. Loss of AREs stabilized theIFNGmRNA in T cells and supported a higher proportion of sustained IFN-γ protein-producing T cells. Importantly, this was also true for tumor antigen-specific T cells. MART-1 TCR engineered T cells that were gene-edited for ARE-deletion showed increased percentages of IFN-γ producing MART-1-specific ARE-Del T cells in response to MART-1 expressing tumor cells. Combined, our study reveals that ARE-mediated post-transcriptional regulation is highly conserved between murine and human T cells. Furthermore, generating antigen-specific ARE-Del T cells is feasible, a feature that could potentially be exploited for therapeutical purposes.
Recapitulating idiopathic pulmonary fibrosis related alveolar epithelial dysfunction in an iPSC-derived air-liquid interface model
Authors: Schruf Eva , Schroeder Victoria , Le Huy Q. , Schönberger Tanja , Raedel Dagmar , Stewart Emily L. , Fundel-Clemens Katrin , Bluhmki Teresa , Weigle Sabine , Schuler Michael , Thomas Matthew J. , Heilker Ralf , Webster Megan J. , Dass Martin , Frick Manfred , Stierstorfer Birgit , Quast Karsten , Garnett James P. 
Published: November 2019

ABSTRACTAn abnormal emergence of airway epithelial-like cells within the alveolar compartments of the lung, herein termed bronchiolization, is a process often observed in patients suffering from idiopathic pulmonary fibrosis (IPF), a fatal disease characterized by progressive fibrotic lung remodeling. However, the origin of this dysfunctional epithelium remains unknown.In this study, we aimed to investigate the effects of a pro-fibrotic milieu, similar to that found in an IPF lung, on human alveolar epithelial progenitor cell differentiation. We developed an induced pluripotent stem cell (iPSC)-derived air-liquid interface (ALI) model of alveolar type II (ATII)-like cell differentiation and stimulated it with an IPF-relevant cocktail (IPF-RC), composed of cytokines previously reported to be elevated in IPF lungs. iPSC-derived cultures express ATII markers and contain lamellar body-like structures. Stimulation with IPF-RC during the last two weeks of differentiation increases secretion of IPF biomarkers. Transcriptome analysis of IPF-RC treated cultures reveals significant overlap with human IPF data and enrichment of transcripts associated with extracellular matrix organization. IPF-RC stimulation further impairs ATII differentiation by driving a shift towards an airway epithelial-like expression signature.In conclusion, we show for the first time, the establishment of a human model system that recapitulates aspects of IPF-associated bronchiolizationin vitro. Our findings reveal how aberrant alveolar epithelial progenitor cell differentiation in a pro-fibrotic environment could contribute to alveolar bronchiolization in the distal IPF lung.SOURCE OF SUPPORTThe research was funded by Boehringer Ingelheim Pharma GmbH & Co. KG.
Palmitate-induced toxicity is associated with impaired mitochondrial respiration and accelerated oxidative stress in cultured cardiomyocytes: the critical role of Coenzyme Q9/10
Authors: Dludla Phiwayinkosi V. , Silvestri Sonia , Orlando Patrick , Mazibuko-Mbeje Sithandiwe E. , Johnson Rabia , Marcheggiani Fabio , Cirilli Ilenia , Muller Christo J.F. , Louw Johan , Chellan Nireshni , Obonye Nnini , Nkambule Bongani B. , Tiano Luca 
Published: November 2019

AbstractImpaired mitochondrial function concomitant to enhanced oxidative stress-induced damage are well established mechanisms involved in hyperlipidemia-induced cardiotoxicity. Coenzyme Q9/10 (CoQ) is known to be a critical component of the mitochondrial electron transport chain that efficiently supports the process of bioenergetics in addition to its antioxidant activities. However, there is very limited information on the direct effect of myocardial lipid overload on endogenous CoQ levels in association with mitochondrial respiration and oxidative stress status. Here, such effects were explored by exposing H9c2 cardiomyocytes to various doses (0.15 to 1 mM) of palmitate for 24 hours. The results demonstrated that palmitate doses ≥ 0.25 mM are enough to impair mitochondrial respiration and cause oxidative stress. Although endogenous CoQ levels are enhanced by palmitate doses ≤ 5 mM, this is not enough to counteract oxidative stress, but is sufficient to maintain cell viability of cardiomyocytes, suggesting a compensation mechanism. Palmitate doses > 5 mM caused severe mitochondrial toxicity, including reduction of cell viability. Interestingly, enhancement of CoQ levels with the lowest dose of palmitate (0.15 mM) was accompanied by a significantly reduction of CoQ oxidation status, as well as low cytosolic production of reactive oxygen species. From the overall findings, it appears that CoQ response may be crucial to improve mitochondrial function and thus protect against hyperlipidemia-induced insult. These results further suggest that therapeutic agents that can stimulate endogenous levels of CoQ may be beneficial in protecting the myocardium against diabetes associated complications.