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https://www.readbyqxmd.com/read/27746256/proteomic-analysis-of-pancreatic-cancer-stem-cells-functional-role-of-fatty-acid-synthesis-and-mevalonate-pathways
#1
Jessica Brandi, Ilaria Dando, Elisa Dalla Pozza, Giulia Biondani, Rosalind Jenkins, Victoria Elliott, Kevin Park, Giuseppina Fanelli, Lello Zolla, Eithne Costello, Aldo Scarpa, Daniela Cecconi, Marta Palmieri
: Recently, we have shown that the secretome of pancreatic cancer stem cells (CSCs) is characterized by proteins that participate in cancer differentiation, invasion, and metastasis. However, the differentially expressed intracellular proteins that lead to the specific characteristics of pancreatic CSCs have not yet been identified, and as a consequence the deranged metabolic pathways are yet to be elucidated. To identify the modulated proteins of pancreatic CSCs, iTRAQ-based proteomic analysis was performed to compare the proteome of Panc1 CSCs and Panc1 parental cells, identifying 230 modulated proteins...
October 13, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27695474/genome-wide-identification-evolution-and-co-expression-network-analysis-of-mitogen-activated-protein-kinase-kinase-kinases-in-brachypodium-distachyon
#2
Kewei Feng, Fuyan Liu, Jinwei Zou, Guangwei Xing, Pingchuan Deng, Weining Song, Wei Tong, Xiaojun Nie
Mitogen-activated protein kinase (MAPK) cascades are the conserved and universal signal transduction modules in all eukaryotes, which play the vital roles in plant growth, development, and in response to multiple stresses. In this study, we used bioinformatics methods to identify 86 MAPKKK protein encoded by 73 MAPKKK genes in Brachypodium. Phylogenetic analysis of MAPKKK family from Arabidopsis, rice, and Brachypodium has classified them into three subfamilies, of which 28 belonged to MEKK, 52 to Raf, and 6 to ZIK subfamily, respectively...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27602765/genomic-characterization-of-pediatric-t-cell-acute-lymphoblastic-leukemia-reveals-novel-recurrent-driver-mutations
#3
Jean-François Spinella, Pauline Cassart, Chantal Richer, Virginie Saillour, Manon Ouimet, Sylvie Langlois, Pascal St-Onge, Thomas Sontag, Jasmine Healy, Mark D Minden, Daniel Sinnett
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with variable prognosis. It represents 15% of diagnosed pediatric ALL cases and has a threefold higher incidence among males. Many recurrent alterations have been identified and help define molecular subgroups of T-ALL, however the full range of events involved in driving transformation remain to be defined. Using an integrative approach combining genomic and transcriptomic data, we molecularly characterized 30 pediatric T-ALLs and identified common recurrent T-ALL targets such as FBXW7, JAK1, JAK3, PHF6, KDM6A and NOTCH1 as well as novel candidate T-ALL driver mutations including the p...
September 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27313588/comparative-proteomic-analysis-of-the-response-of-maize-zea-mays-l-leaves-to-long-photoperiod-condition
#4
Liuji Wu, Lei Tian, Shunxi Wang, Jun Zhang, Ping Liu, Zhiqiang Tian, Huimin Zhang, Haiping Liu, Yanhui Chen
Maize (Zea mays L.), an important industrial material and food source, shows an astonishing environmental adaptation. A remarkable feature of its post-domestication adaptation from tropical to temperate environments is adaptation to a long photoperiod (LP). Many photoperiod-related genes have been identified in previous transcriptomics analysis, but proteomics shows less evidence for this mechanism of photoperiod response. In this study, we sampled newly expanded leaves of maize at the three- and six-leaf stages from an LP-sensitive introgression line H496, the donor CML288, LP-insensitive inbred line, and recurrent parent Huangzao4 (HZ4) grown under long days (15 h light and 9 h dark)...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/26980266/genome-wide-identification-and-functional-prediction-of-novel-and-fungi-responsive-lincrnas-in-triticum-aestivum
#5
Hong Zhang, Weiguo Hu, Jilei Hao, Shikai Lv, Changyou Wang, Wei Tong, Yajuan Wang, Yanzhen Wang, Xinlun Liu, Wanquan Ji
BACKGROUND: Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Increasingly evidences suggest that long intergenic ncRNAs (lincRNAs) are developmentally regulated and play important roles in development and stress responses of plants. However, identification of lincRNAs in wheat is still limited comparing with functional gene expression. RESULTS: The transcriptome of the hexaploid wheat line N9134 inoculated with the Chinese Pst race CYR31 and Bgt race E09 at 1, 2, and 3 days post-inoculation was recapitulated to detect the lincRNAs...
2016: BMC Genomics
https://www.readbyqxmd.com/read/26828373/u6-snrna-intron-insertion-occurred-multiple-times-during-fungi-evolution
#6
Sebastian Canzler, Peter F Stadler, Jana Hertel
U6 small nuclear RNAs are part of the splicing machinery. They exhibit several unique features setting them appart from other snRNAs. Reports of introns in structured non-coding RNAs have been very rare. U6 genes, however, were found to be interrupted by an intron in several Schizosaccharomyces species and in 2 Basidiomycota. We conducted a homology search across 147 currently available fungal genome and identified the U6 genes in all but 2 of them. A detailed comparison of their sequences and predicted secondary structures showed that intron insertion events in the U6 snRNA were much more common in the fungal lineage than previously thought...
2016: RNA Biology
https://www.readbyqxmd.com/read/26819475/jumonji-domain-containing-protein-6-is-decreased-in-human-preeclamptic-placentas-and-regulates-sflt-1-splice-variant-production
#7
Kirsten R Palmer, Stephen Tong, Laura Tuohey, Ping Cannon, Louie Ye, Natalie J Hannan, Fiona C Brownfoot, Sebastián E Illanes, Tu'uhevaha J Kaitu'u-Lino
The anti-angiogenic protein, soluble fms-like tyrosine kinase-1 (sFLT-1), plays a central role in preeclamptic pathophysiology. A splice variant of FLT-1 (VEGF receptor 1), sFLT-1 is released in excessive amounts from the preeclamptic placenta into the maternal circulation, where it causes endothelial dysfunction manifesting as end-organ disease. However, the mechanisms regulating its production within the placenta remain poorly understood. Recently it was shown in endothelial cells that Jumonji domain containing protein 6 (JMJD6) hydroxylates U2 small nuclear ribonucleoprotein auxiliary factor 65-kDa subunit (U2AF65, a component of the splicesome)...
March 2016: Biology of Reproduction
https://www.readbyqxmd.com/read/26508027/genetic-landscape-of-recurrent-asxl1-u2af1-sf3b1-srsf2-and-ezh2-mutations-in-304-chinese-patients-with-myelodysplastic-syndromes
#8
Lingyun Wu, Luxi Song, Lan Xu, Chunkang Chang, Feng Xu, Dong Wu, Qi He, Jiying Su, Liyu Zhou, Chao Xiao, Zheng Zhang, Youshan Zhao, Saijuan Chen, Xiao Li
We determined the biological and prognostic significance of five recurrent genetic aberrations in Chinese patients with myelodysplastic syndromes (MDS). A total of 304 Chinese MDS patients were screened for known mutations in five genes (ASXL1, U2AF1, SF3B1, SRSF2, and EZH2) using next-generation sequencing. Of these, 97 patients (31.9 %) harbored at least one mutation in the five genes, and patients harboring these mutations had distinct clinical features. Incidence ratios for mutations in ASXL1, U2AF1, SF3B1, SRSF2, and EZH2 were 11...
April 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/25993305/maldi-mass-spectrometric-imaging-revealing-hypoxia-driven-lipids-and-proteins-in-a-breast-tumor-model
#9
Lu Jiang, Kamila Chughtai, Samuel O Purvine, Zaver M Bhujwalla, Venu Raman, Ljiljana Paša-Tolić, Ron M A Heeren, Kristine Glunde
Hypoxic areas are a common feature of rapidly growing malignant tumors and their metastases and are typically spatially heterogeneous. Hypoxia has a strong impact on tumor cell biology and contributes to tumor progression in multiple ways. To date, only a few molecular key players in tumor hypoxia, such as hypoxia-inducible factor-1 (HIF-1), have been discovered. The distribution of biomolecules is frequently heterogeneous in the tumor volume and may be driven by hypoxia and HIF-1α. Understanding the spatially heterogeneous hypoxic response of tumors is critical...
June 16, 2015: Analytical Chemistry
https://www.readbyqxmd.com/read/25888565/nuclear-import-of-the-u1a-splicesome-protein-is-mediated-by-importin-%C3%AE-%C3%AE-and-ran-in-living-mammalian-cells
#10
Miki Hieda, Taro Tachibana, Masahiro Fukumoto, Yoshihiro Yoneda
No abstract text is available yet for this article.
April 17, 2015: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/25803894/-sequence-characterization-and-differential-expression-of-a-glutathione-s-transferase-gene-vv-gto1-from-volvariella-volvacea
#11
Junjie Yan, Lixian Guo, Jingjing Zhao, Baogui Xie
OBJECTIVE: Based on the analysis of omics data of Volvariella volvacea, a gene encoding glutathione S- transferase (GSTs) named vv-gtol was obtained. To reveal the role of GSTs in the growth and development in edible fungi, the structure, the sequence characters and the expression profile of a GST gene vv-gto1 of Volvariella volvacea were analyzed. METHODS: ZOOM software was used to map sequencing read (reads) from genome and transcriptome against the splicing sequence of genome, to confirm the complete length and the accuracy of the gene sequence, and to visualize gene structure...
October 4, 2014: Wei Sheng Wu Xue Bao, Acta Microbiologica Sinica
https://www.readbyqxmd.com/read/25345011/-differential-proteome-analysis-of-carbon-tetrachloride-induced-mouse-liver-fibrosis
#12
Gaigai Guo, Hongxing Wu, Mingwei Liu, Chen Ding, Jun Qin, Xiaoming Yang
To explore the differential proteome pattern in mouse fibrosis liver in comparison to wild type. Mice were fed with carbon tetrachloride or olive oil vehicle for 15 weeks. Mouse livers from both groups were collected and submitted to MS platform for proteome screening. GO (Gene Ontology) biological process and KEGG (Kyoto Enyoolpedia of Genes and Genomes) pathway enrichment analysis were used to analyze differentially expressed proteins. As the results, we identified 17 382 and 20 486 unique peptides in control and carbon tetrachloride-induced groups, respectively...
July 2014: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/25335912/vitamin-d-receptor-and-rxr-in-the-post-genomic-era
#13
REVIEW
Mark D Long, Lara E Sucheston-Campbell, Moray J Campbell
Following the elucidation of the human genome and components of the epigenome, it is timely to revisit what is known of vitamin D receptor (VDR) function. Early transcriptomic studies using microarray approaches focused on the protein coding mRNA that were regulated by the VDR, usually following treatment with ligand. These studies quickly established the approximate size and surprising diversity of the VDR transcriptome, revealing it to be highly heterogenous and cell type and time dependent. Investigators also considered VDR regulation of non-protein coding RNA and again, cell and time dependency was observed...
April 2015: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/25078136/activators-of-pkm2-in-cancer-metabolism
#14
REVIEW
Steven L Warner, Kent J Carpenter, David J Bearss
Pyruvate kinase converts phosphoenolpyruvate to pyruvate, catalyzing the rate-limiting step of glycolysis. The M1 isoenzyme of pyruvate kinase (PKM1) is found in adult tissues; whereas, PKM2 is a splicesome variant found in embryonic and cancer cells. PKM2 expression in malignant cells is a result of the tumor microenvironment and is responsible for maintaining a glycolytic phenotype. PKM2 has other nonmetabolic functions in malignant cells, including transcriptional coactivation and protein kinase activity...
June 2014: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/24753405/targeting-vertebrate-intron-encoded-box-c-d-2-o-methylation-guide-rnas-into-the-cajal-body
#15
Aline Marnef, Patrica Richard, Natalia Pinzón, Tamás Kiss
Post-transcriptional pseudouridylation and 2'-O-methylation of splicesomal small nuclear ribonucleic acids (snRNAs) is mediated by box H/ACA and box C/D small Cajal body (CB)-specific ribonucleoproteins (scaRNPs), respectively. The WD-repeat protein 79 (WDR79) has been proposed to interact with both classes of modification scaRNPs and target them into the CB. The box H/ACA scaRNAs carry the common CAB box motif (consensus, ugAG) that is required for both WDR79 binding and CB-specific accumulation. Thus far, no cis-acting CB-localization element has been reported for vertebrate box C/D scaRNAs...
June 2014: Nucleic Acids Research
https://www.readbyqxmd.com/read/24608750/deep-rna-sequencing-reveals-hidden-features-and-dynamics-of-early-gene-transcription-in-paramecium-bursaria-chlorella-virus-1
#16
Guillaume Blanc, Michael Mozar, Irina V Agarkova, James R Gurnon, Giane Yanai-Balser, Janet M Rowe, Yuannan Xia, Jean-Jack Riethoven, David D Dunigan, James L Van Etten
Paramecium bursaria chlorella virus 1 (PBCV-1) is the prototype of the genus Chlorovirus (family Phycodnaviridae) that infects the unicellular, eukaryotic green alga Chlorella variabilis NC64A. The 331-kb PBCV-1 genome contains 416 major open reading frames. A mRNA-seq approach was used to analyze PBCV-1 transcriptomes at 6 progressive times during the first hour of infection. The alignment of 17 million reads to the PBCV-1 genome allowed the construction of single-base transcriptome maps. Significant transcription was detected for a subset of 50 viral genes as soon as 7 min after infection...
2014: PloS One
https://www.readbyqxmd.com/read/24258465/a-phase-i-open-label-single-arm-dose-escalation-study-of-e7107-a-precursor-messenger-ribonucleic-acid-pre-mrna-splicesome-inhibitor-administered-intravenously-on-days-1-and-8-every-21-days-to-patients-with-solid-tumors
#17
D S Hong, R Kurzrock, A Naing, J J Wheler, G S Falchook, J S Schiffman, N Faulkner, M J Pilat, J O'Brien, P LoRusso
The aim of this study was to determine the maximum tolerated dose, dose-limiting toxicities, and pharmacokinetic profile of E7107 in patients with advanced solid tumors. Patients in this phase I, open-label, single-arm, dose-escalation study had metastatic or locally advanced solid tumors and received E7107 as a 30-minute intravenous infusion at doses of 0.6, 1.2, 1.8, 2.4, 3.2, 4.3, and 5.7 mg/m(2). Twenty-six patients were enrolled in the study. At 5.7 mg/m(2), two patients experienced dose-limiting toxicities including diarrhea, vomiting, dehydration, and myocardial infarction on Days 1-3 following E7107 administration...
June 2014: Investigational New Drugs
https://www.readbyqxmd.com/read/23736079/inhibition-of-glutathione-biosynthesis-alters-compartmental-redox-status-and-the-thiol-proteome-in-organogenesis-stage-rat-conceptuses
#18
Craig Harris, Daniel Z Shuster, Rosaicela Roman Gomez, Karilyn E Sant, Matthew S Reed, Jan Pohl, Jason M Hansen
Developmental signals that control growth and differentiation are regulated by environmental factors that generate reactive oxygen species (ROS) and alter steady-state redox environments in tissues and fluids. Protein thiols are selectively oxidized and reduced in distinct spatial and temporal patterns in conjunction with changes in glutathione/glutathione disulfide (GSH/GSSG) and cysteine/cystine (Cys/CySS) redox potentials (E(h)) to regulate developmental signaling. The purpose of this study was to measure compartment-specific thiol redox status in cultured organogenesis-stage rat conceptuses and to evaluate the impact of thiol oxidation on the redox proteome...
October 2013: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/23686287/a-conformational-switch-in-prp8-mediates-metal-ion-coordination-that-promotes-pre-mrna-exon-ligation
#19
Matthew J Schellenberg, Tao Wu, Dustin B Ritchie, Sebastian Fica, Jonathan P Staley, Karim A Atta, Paul LaPointe, Andrew M MacMillan
Splicing of pre-mRNAs in eukaryotes is catalyzed by the spliceosome, a large RNA-protein metalloenzyme. The catalytic center of the spliceosome involves a structure comprising the U2 and U6 snRNAs and includes a metal bound by U6 snRNA. The precise architecture of the splicesome active site, however, and the question of whether it includes protein components, remains unresolved. A wealth of evidence places the protein PRP8 at the heart of the spliceosome through assembly and catalysis. Here we provide evidence that the RNase H domain of PRP8 undergoes a conformational switch between the two steps of splicing, rationalizing yeast prp8 alleles that promote either the first or second step...
June 2013: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/23269276/autoantibody-signatures-involving-glycolysis-and-splicesome-proteins-precede-a-diagnosis-of-breast-cancer-among-postmenopausal-women
#20
Jon J Ladd, Timothy Chao, Melissa M Johnson, Ji Qiu, Alice Chin, Rebecca Israel, Sharon J Pitteri, Jianning Mao, Mei Wu, Lynn M Amon, Martin McIntosh, Christopher Li, Ross Prentice, Nora Disis, Samir Hanash
We assessed the autoantibody repertoire of a mouse model engineered to develop breast cancer and the repertoire of autoantibodies in human plasmas collected at a preclinical time point and at the time of clinical diagnosis of breast cancer. In seeking to identify common pathways, networks, and protein families associated with the humoral response, we elucidated the dynamic nature of tumor antigens and autoantibody interactions. Lysate proteins from an immortalized cell line from a MMTV-neu mouse model and from MCF7 human breast cancers were spotted onto nitrocellulose microarrays and hybridized with mouse and human plasma samples, respectively...
March 1, 2013: Cancer Research
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