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https://www.readbyqxmd.com/read/29334255/ngs-based-methylation-profiling-differentiates-tcf3-hlf-and-tcf3-pbx1-positive-b-cell-acute-lymphoblastic-leukemia
#1
Priyadarshini Kachroo, Silke Szymczak, Femke-Anouska Heinsen, Michael Forster, Jörn Bethune, Georg Hemmrich-Stanisak, Lewis Baker, Martin Schrappe, Martin Stanulla, Andre Franke
AIM: To determine whether methylation differences between mostly fatal TCF3-HLF and curable TCF3-PBX1 pediatric acute lymphoblastic leukemia subtypes can be associated with differential gene expression and remission. MATERIALS & METHODS: Five (extremely rare) TCF3-HLF versus five (very similar) TCF3-PBX1 patients were sampled before and after remission and analyzed using reduced representation bisulfite sequencing and RNA-sequencing. RESULTS: We identified 7000 differentially methylated CpG sites between subtypes, of which 78% had lower methylation levels in TCF3-HLF...
January 15, 2018: Epigenomics
https://www.readbyqxmd.com/read/29332189/the-arabidopsis-histone-chaperone-fact-is-required-for-stress-induced-expression-of-anthocyanin-biosynthetic-genes
#2
Alexander Pfab, Matthias Breindl, Klaus D Grasser
The histone chaperone FACT is involved in the expression of genes encoding anthocyanin biosynthetic enzymes also upon induction by moderate high-light and therefore contributes to the stress-induced plant pigmentation. The histone chaperone FACT consists of the SSRP1 and SPT16 proteins and associates with transcribing RNAPII (RNAPII) along the transcribed region of genes. FACT can promote transcriptional elongation by destabilising nucleosomes in the path of RNA polymerase II, thereby facilitating efficient transcription of chromatin templates...
January 13, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29331478/comprehensive-analysis-of-lncrnas-and-mrnas-with-associated-co-expression-and-cerna-networks-in-c2c12-myoblasts-and-myotubes
#3
Rui Chen, Ting Jiang, Yanling She, Sidong Xie, Shanyao Zhou, Cheng Li, Jun Ou, Yulin Liu
Long non-coding RNAs (lncRNAs) are emerging as important regulators in the modulation of muscle development and muscle-related diseases. To explore potential regulators of muscle differentiation, we determined the expression profiles of lncRNAs and mRNAs in C2C12 mouse myoblast cell line using microarray analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to explore their function. We also constructed co-expression, cis/trans-regulation, and competing endogenous RNA (ceRNA) networks with bioinformatics methods...
January 10, 2018: Gene
https://www.readbyqxmd.com/read/29331323/regulation-of-inflammatory-factors-by-double-stranded-rna-receptors-in-breast-cancer-cells
#4
Amritha Venkatesh, Harika Nandigam, Maria Muccioli, Manindra Singh, Tiffany Loftus, Deana Lewis, Michelle Pate, Fabian Benencia
Malignant cells are not the only components of a tumor mass since other cells (e.g., fibroblasts, infiltrating leukocytes and endothelial cells) are also part of it. In combination with the extracellular matrix, all these cells constitute the tumor microenvironment. In the last decade the role of the tumor microenvironment in cancer progression has gained increased attention and prompted efforts directed to abrogate its deleterious effects on anti-cancer therapies. The immune system can detect and attack tumor cells, and tumor-infiltrating lymphocytes (particularly CD8 T cells) have been associated with improved survival or better response to therapies in colorectal, melanoma, breast, prostate and ovarian cancer patients among others...
November 22, 2017: Immunobiology
https://www.readbyqxmd.com/read/29330790/transcriptional-profiling-using-rna-seq-to-study-hypoxia-mediated-gene-regulation
#5
Surendra K Shukla, Ryan J King, Pankaj K Singh
Exposing cells to a hypoxic environment leads to significant physiological and molecular alterations. Most of the hypoxic responses are regulated by the transcription factors known as hypoxia-inducible factors (HIFs). HIF1, a heterodimer of hypoxia-stabilized subunit HIF-1alpha and a constitutively expressed subunit HIF-1beta, serves as a key transcription factor that regulates gene expressions which are involved in cell growth, metabolism, and proliferation. The global expression patterns can be analyzed by utilizing RNA-Seq to understand the cellular alterations in hypoxia...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29330750/immunologic-and-gene-expression-profiles-of-spontaneous-canine-oligodendrogliomas
#6
Anna Filley, Mario Henriquez, Tanmoy Bhowmik, Brij Nath Tewari, Xi Rao, Jun Wan, Margaret A Miller, Yunlong Liu, R Timothy Bentley, Mahua Dey
Malignant glioma (MG), the most common primary brain tumor in adults, is extremely aggressive and uniformly fatal. Several treatment strategies have shown significant preclinical promise in murine models of glioma; however, none have produced meaningful clinical responses in human patients. We hypothesize that introduction of an additional preclinical animal model better approximating the complexity of human MG, particularly in interactions with host immune responses, will bridge the existing gap between these two stages of testing...
January 12, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29330721/transcriptomic-analysis-and-discovery-of-genes-in-the-response-of-arachis-hypogaea-to-drought-stress
#7
Xiaobo Zhao, Chunjuan Li, Shubo Wan, Tingting Zhang, Caixia Yan, Shihua Shan
The peanut (Arachis hypogaea) is an important crop species that is threatened by drought stress. The genome sequences of peanut, which was officially released in 2016, may help explain the molecular mechanisms that underlie drought tolerance in this species. We report here a gene expression profiling of A. hypogaea to gain a global view of its drought resistance. Using whole-transcriptome sequencing, we analysed differential gene expression in response to drought stress in the drought-resistant peanut cultivar J11...
January 12, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29330702/ptac10-an-s1-domain-containing-component-of-the-transcriptionally-active-chromosome-complex-is-essential-for-plastid-gene-expression-in-arabidopsis-thaliana-and-is-phosphorylated-by-chloroplast-targeted-casein-kinase-ii
#8
Qing-Bo Yu, Tuan-Tuan Zhao, Lin-Shan Ye, Ling Cheng, Ying-Qian Wu, Chao Huang, Zhong-Nan Yang
In higher plant chloroplasts, the plastid-encoded RNA polymerase (PEP) consists of four catalytic subunits and numerous nuclear-encoded accessory proteins, including pTAC10, an S1-domain-containing protein. In this study, pTAC10 knockout lines were characterized. Two ptac10 mutants had an albino phenotype and severely impaired chloroplast development. The pTAC10 genomic sequence fused to a four-tandem MYC tag driven by its own promoter functionally complemented the ptac10-1 mutant phenotype. pTAC10 was present in both the chloroplast stroma and thylakoids...
January 12, 2018: Photosynthesis Research
https://www.readbyqxmd.com/read/29330429/tissue-and-serum-microrna-profile-of-oral-squamous-cell-carcinoma-patients
#9
Augusto Schneider, Berta Victoria, Yury Nunez Lopez, Wiktoria Suchorska, Wojciech Barczak, Agnieszka Sobecka, Wojciech Golusinski, Michal M Masternak, Pawel Golusinski
Head and neck cancer is characterized by malignant tumors arising from the epithelium covering the upper aerodigestive tract, and the majority of these epithelial malignancies are squamous cell carcinomas (SCCs) of the oral cavity (OSCCs). The aim of the current work was to identify miRNAs regulated in OSCC cancerous tissue when compared to a healthy adjacent tissue and to verify the presence of the same miRNAs in the circulation of these patients. For that serum samples and biopsies of healthy and tumor tissues were collected from five patients diagnosed with OSCC of the oral cavity, RNA was extracted from these samples and microRNAs libraries were prepared and sequenced...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330365/engineered-nanointerfaces-for-microfluidic-isolation-and-molecular-profiling-of-tumor-specific-extracellular-vesicles
#10
Eduardo Reátegui, Kristan E van der Vos, Charles P Lai, Mahnaz Zeinali, Nadia A Atai, Berent Aldikacti, Frederick P Floyd, Aimal H Khankhel, Vishal Thapar, Fred H Hochberg, Lecia V Sequist, Brian V Nahed, Bob S Carter, Mehmet Toner, Leonora Balaj, David T Ting, Xandra O Breakefield, Shannon L Stott
Extracellular vesicles (EVs) carry RNA, DNA, proteins, and lipids. Specifically, tumor-derived EVs have the potential to be utilized as disease-specific biomarkers. However, a lack of methods to isolate tumor-specific EVs has limited their use in clinical settings. Here we report a sensitive analytical microfluidic platform (EVHB-Chip) that enables tumor-specific EV-RNA isolation within 3 h. Using the EVHB-Chip, we achieve 94% tumor-EV specificity, a limit of detection of 100 EVs per μL, and a 10-fold increase in tumor RNA enrichment in comparison to other methods...
January 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29330289/brca1-through-its-e3-ligase-activity-regulates-the-transcription-factor-oct1-and-carbohydrate-metabolism
#11
Karina Vázquez-Arreguín, Jessica Maddox, Jinsuk Kang, Dongju Park, Reuben R Cano, Rachel E Factor, Thomas Ludwig, Dean Tantin
The tumor suppressor BRCA1 regulates the DNA damage response (DDR) and other processes that remain incompletely defined. Among these, BRCA1 heterodimerizes with BARD1 to ubiquitylate targets via its N-terminal E3 ligase activity. Here it is demonstrated that BRCA1 promotes oxidative metabolism by degrading Oct1 (POU2F1), a transcription factor with pro-glycolytic and tumorigenic effects. BRCA1 E3 ubiquitin ligase mutation skews cells towards a glycolytic metabolic profile while elevating Oct1 protein. CRISPR-mediated Oct1 deletion reverts the glycolytic phenotype...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330203/personalized-rna-medicine-for-pancreatic-cancer
#12
Maud-Emmanuelle Gilles, Liangliang Hao, Ling Huang, Rajesha Rupaimoole, Pedro P Lopez-Casas, Emilia Pulver, Jong Cheol Jeong, Senthil K Muthuswamy, Manuel Hidalgo, Sangeeta N Bhatia, Frank J Slack
PURPOSE: Since drug responses vary between patients, it is crucial to develop pre-clinical or co-clinical strategies that forecast patient response. In this study, we tested whether RNA-based therapeutics were suitable for personalized medicine by using patient-derived-organoid (PDO) and patient-derived-xenograft (PDX) models.  Experimental Design: We performed microRNA (miRNA) profiling of PDX samples to determine the status of miRNA deregulation in individual pancreatic ductal adenocarcinoma (PDAC) patients...
January 12, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29330162/transcriptome-analyses-of-mosaic-msc-mitochondrial-mutants-of-cucumber-in-a-highly-inbred-nuclear-background
#13
Tomasz L Mróz, Sebastian Eves-van den Akker, Agata Bernat, Agnieszka Skarzyńska, Leszek Pryszcz, Madeline Olberg, Michael J Havey, Grzegorz Bartoszewski
Cucumber (Cucumis sativus L.) has a large, paternally transmitted mitochondrial genome. Cucumber plants regenerated from cell cultures occasionally show paternally transmitted mosaic (MSC) phenotypes, characterized by slower growth, chlorotic patterns on the leaves and fruit, lower fertility, and rearrangements in their mitochondrial DNAs (mtDNAs). MSC lines 3, 12, and 16 originated from different cell cultures all established using the highly-inbred, wild-type line B. These MSC lines possess different rearrangements and under-represented regions in their mtDNAs...
January 12, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29329543/stat3-induced-lncrna-haglros-overexpression-contributes-to-the-malignant-progression-of-gastric-cancer-cells-via-mtor-signal-mediated-inhibition-of-autophagy
#14
Jin-Fei Chen, Peng Wu, Rui Xia, Jian Yang, Xin-Ying Huo, Dong-Ying Gu, Cui-Ju Tang, Wei De, Fen Yang
BACKGROUND: Long noncoding RNAs (lncRNAs) are an important class of functional regulators involved in human cancers development, including gastric cancer (GC). Studying aberrantly expressed lncRNAs may provide us with new insights into the occurrence and development of gastric cancer by acting as oncogenes or tumor suppressors. In this study, we aim to examine the expression pattern of lncRNA HAGLROS in GC and its clinical significance as well as its biological role in tumor progression...
January 12, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29329292/transcriptome-profiling-with-focus-on-potential-key-genes-for-wing-development-and-evolution-in-megaloprepus-caerulatus-the-damselfly-species-with-the-world-s-largest-wings
#15
Wiebke Feindt, Sara J Oppenheim, Robert DeSalle, Paul Z Goldstein, Heike Hadrys
The evolution, development and coloration of insect wings remains a puzzling subject in evolutionary research. In basal flying insects such as Odonata, genomic research regarding bauplan evolution is still rare. Here we focus on the world's largest odonate species-the "forest giant" Megaloprepus caerulatus, to explore its potential for looking deeper into the development and evolution of wings. A recently discovered cryptic species complex in this genus previously considered monotypic is characterized by morphological differences in wing shape and color patterns...
2018: PloS One
https://www.readbyqxmd.com/read/29329291/ovule-identity-mediated-by-pre-mrna-processing-in-arabidopsis
#16
Encarnación Rodríguez-Cazorla, Samanta Ortuño-Miquel, Héctor Candela, Lindsay J Bailey-Steinitz, Martin F Yanofsky, Antonio Martínez-Laborda, Juan-José Ripoll, Antonio Vera
Ovules are fundamental for plant reproduction and crop yield as they are the precursors of seeds. Therefore, ovule specification is a critical developmental program. In Arabidopsis thaliana, ovule identity is redundantly conferred by the homeotic D-class genes SHATTERPROOF1 (SHP1), SHP2 and SEEDSTICK (STK), phylogenetically related to the MADS-domain regulatory gene AGAMOUS (AG), essential in floral organ specification. Previous studies have shown that the HUA-PEP activity, comprised of a suite of RNA-binding protein (RBP) encoding genes, regulates AG pre-mRNA processing and thus flower patterning and organ identity...
January 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29328431/bioinformatic-analysis-of-gene-expression-profiling-of-intracranial-aneurysm
#17
Lijuan Bo, Bo Wei, Zhanfeng Wang, Chaohui Li, Zheng Gao, Zhuang Miao
Intracranial aneurysm (IA) is a severe clinical condition of primary concern and currently, there is no effective therapeutic reagent. The present study aimed to investigate the molecular mechanism of IA via bioinformatic analysis. Various gene expression profiles (GSE26969) were downloaded from the Gene Expression Omnibus database, including 3 IA and 3 normal superficial temporal artery samples. Firstly, the limma package in R language was used to identify differentially expressed genes (DEGs; P‑value <0...
December 29, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328377/feature-genes-in-metastatic-breast-cancer-identified-by-metade-and-svm-classifier-methods
#18
Youlin Tuo, Ning An, Ming Zhang
The aim of the present study was to investigate the feature genes in metastatic breast cancer samples. A total of 5 expression profiles of metastatic breast cancer samples were downloaded from the Gene Expression Omnibus database, which were then analyzed using the MetaQC and MetaDE packages in R language. The feature genes between metastasis and non‑metastasis samples were screened under the threshold of P<0.05. Based on the protein‑protein interactions (PPIs) in the Biological General Repository for Interaction Datasets, Human Protein Reference Database and Biomolecular Interaction Network Database, the PPI network of the feature genes was constructed...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328372/differential-microrna-expression-profiles-and-bioinformatics-analysis-between-young-and-aging-spontaneously-hypertensive-rats
#19
Jingfeng Wang, Jingjing Zhang, Xuefeng Ding, Yanyan Wang, Zhiming Li, Weipeng Zhao, Jianguo Jia, Jingmin Zhou, Junbo Ge
MicroRNAs (miRNAs/miRs) serve a role as important regulators in cardiac hypertrophy. The present study aimed to reveal the differential expression profile of miRNAs between young and aging spontaneously hypertensive rats (SHRs) and studied the functional annotation of predicted targets. Briefly, 3‑month‑old and 12‑month‑old SHRs (n=3/group) were subjected to echocardiography, histopathological analysis and dihydroethidium staining. Subsequently, small RNA sequencing and data processing was conducted to identify the differentially expressed miRNAs between these two groups...
January 9, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29325795/insertional-mutagenesis-confounds-the-mechanism-of-the-morbid-phenotype-of-a-plnr9c-transgenic-mouse-line
#20
Alexander Kraev
BACKGROUND: A mouse line with heterozygous transgenic expression of phospholamban carrying a substitution of cysteine for arginine 9 (TgPLNR9C) under the control of α-myosin heavy chain (αMHC) promoter features dilated cardiomyopathy, heart failure and premature death. METHODS AND RESULTS: Determination of transgene chromosomal localization by conventional methods shows that in this line the transgenic array of 13 PLNR9C expression cassettes, arranged in a head-to-tail tandem orientation, has integrated into the bi-directional promoter of the αMHC (Myh6) gene and the gene for the regulatory non-coding RNA Myheart (Mhrt), both of which are known to be involved in cardiac development and pathology...
January 8, 2018: Journal of Cardiac Failure
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