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https://www.readbyqxmd.com/read/28535155/elevated-apobec3b-expression-drives-a-kataegic-like-mutation-signature-and-replication-stress-related-therapeutic-vulnerabilities-in-p53-defective-cells
#1
Jenni Nikkilä, Rahul Kumar, James Campbell, Inger Brandsma, Helen N Pemberton, Fredrik Wallberg, Kinga Nagy, Ildikó Scheer, Beata G Vertessy, Artur A Serebrenik, Valentina Monni, Reuben S Harris, Stephen J Pettitt, Alan Ashworth, Christopher J Lord
BACKGROUND: Elevated APOBEC3B expression in tumours correlates with a kataegic pattern of localised hypermutation. We assessed the cellular phenotypes associated with high-level APOBEC3B expression and the influence of p53 status on these phenotypes using an isogenic system. METHODS: We used RNA interference of p53 in cells with inducible APOBEC3B and assessed DNA damage response (DDR) biomarkers. The mutational effects of APOBEC3B were assessed using whole-genome sequencing...
May 23, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28534968/functional-significance-of-the-long-non-coding-rna-rp11-169d4-1-as-a-metastasis-suppressor-in-laryngeal-squamous-cell-carcinoma-by-regulating-cdh1
#2
Jing Zhao, Kexing Lv, Zeng-Hong Li, Jianhui Wu, Wei Gao, Thian-Sze Wong, Jie Luo, Hao Qin, Bin Wang, Qingling Fu, Wen-Bin Lei
The present study investigated the expression profile and the function of RP11-169D4.1 and explored its potential mechanisms in laryngeal squamous cell carcinoma. The biological function of RP11-169D4.1 was examined using the MTT assay, flow cytometric analysis, wound healing and transwell assays. The relationship between RP11-169D4.1 and miR-205-5p was discovered by Argonaute 2 protein immunoprecipitation. The target gene of RP11-169D4.1 was CDH1 which was assessed by Pearson's correlation analysis, RT-PCR and western blot assay...
May 16, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28534714/profiling-and-bioinformatics-analyses-reveal-differential-circular-rna-expression-in-hypertensive-patients
#3
Na Wu, Ling Jin, Jun Cai
OBJECTIVES: CircRNAs, a novel class of noncoding RNAs, have been reported in many diseases. However, their role in hypertension remains unclear. Here, we aimed to determine the circRNA expression profile in hypertension patients and further construct a circRNA-miRNA-mRNA network for mechanism exploration. METHODS: Plasma circRNA expression profiles were screened by circRNA microarrays and verified by qRT-PCR method. CircRNA-miRNA-mRNA network was established to predict the circRNA targets...
May 23, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/28534222/identification-of-innate-lymphoid-cells-in-single-cell-rna-seq-data
#4
Madeleine Suffiotti, Santiago J Carmona, Camilla Jandus, David Gfeller
Innate lymphoid cells (ILCs) consist of natural killer (NK) cells and non-cytotoxic ILCs that are broadly classified into ILC1, ILC2, and ILC3 subtypes. These cells recently emerged as important early effectors of innate immunity for their roles in tissue homeostasis and inflammation. Over the last few years, ILCs have been extensively studied in mouse and human at the functional and molecular level, including gene expression profiling. However, sorting ILCs with flow cytometry for gene expression analysis is a delicate and time-consuming process...
May 22, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28533983/comparative-transcriptome-analyses-of-a-late-maturing-mandarin-mutant-and-its-original-cultivar-reveals-gene-expression-profiling-associated-with-citrus-fruit-maturation
#5
Lu Wang, Qingzhu Hua, Yuewen Ma, Guibing Hu, Yonghua Qin
Characteristics of late maturity in fruit are good agronomic traits for extending the harvest period and marketing time. However, underlying molecular basis of the late-maturing mechanism in fruit is largely unknown. In this study, RNA sequencing (RNA-Seq) technology was used to identify differentially expressed genes (DEGs) related to late-maturing characteristics from a late-maturing mutant 'Huawan Wuzishatangju' (HWWZSTJ) (Citrus reticulata Blanco) and its original line 'Wuzishatangju' (WZSTJ). A total of approximately 17...
2017: PeerJ
https://www.readbyqxmd.com/read/28532450/lps-induced-systemic-inflammation-reveals-an-immunomodulatory-role-for-the-prion-protein-at-the-blood-brain-interface
#6
Ø Salvesen, M R Reiten, A Espenes, M K Bakkebø, M A Tranulis, C Ersdal
BACKGROUND: The cellular prion protein (PrP(C)) is an evolutionary conserved protein abundantly expressed not only in the central nervous system but also peripherally including the immune system. A line of Norwegian dairy goats naturally devoid of PrP(C) (PRNP (Ter/Ter)) provides a novel model for studying PrP(C) physiology. METHODS: In order to explore putative roles for PrP(C) in acute inflammatory responses, we performed a lipopolysaccharide (LPS, Escherichia coli O26:B6) challenge of 16 goats (8 PRNP (+/+) and 8 PRNP (Ter/Ter)) and included 10 saline-treated controls (5 of each PRNP genotype)...
May 22, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28531310/nascent-rna-sequencing-reveals-mechanisms-of-gene-regulation-in-the-human-malaria-parasite-plasmodium-falciparum
#7
Xueqing Maggie Lu, Gayani Batugedara, Michael Lee, Jacques Prudhomme, Evelien M Bunnik, Karine G Le Roch
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28530607/metabolic-and-rna-profiling-elucidates-proanthocyanidins-accumulation-in-aglianico-grape
#8
Alessandra Rinaldi, Clizia Villano, Carmine Lanzillo, Angelo Tamburrino, Michael Jourdes, Pierre-Louis Teissedre, Luigi Moio, Luigi Frusciante, Domenico Carputo, Riccardo Aversano
Aglianico grapes are known for their high content of proanthocyanidins (PAs), which are responsible for the astringency of wines derived from this cultivar. However, the accumulation of PAs and their genetic control during berry development remain largely unexplored. This work aimed to monitor astringency-causing PAs in Aglianico berries and correlate them with the expression of 14 key genes. Berries were collected during ripening and dissected in skins and seeds. PAs were fractionated and the content of total phenolics, flavans, anthocyanins, tannins reactive towards salivary proteins and tannin structural composition were evaluated...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28529717/gene-length-and-detection-bias-in-single-cell-rna-sequencing-protocols
#9
Belinda Phipson, Luke Zappia, Alicia Oshlack
Background: Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thousands of single cells. This technology has led to the discovery of novel cell types and revealed insights into the development of complex tissues. However, many technical challenges need to be overcome during data generation. Due to minute amounts of starting material, samples undergo extensive amplification, increasing technical variability. A solution for mitigating amplification biases is to include unique molecular identifiers (UMIs), which tag individual molecules...
2017: F1000Research
https://www.readbyqxmd.com/read/28529578/long-non-coding-rna-expression-profiles-in-gallbladder-carcinoma-identified-using-microarray-analysis
#10
Jiwen Wang, Han Liu, Xiaokun Shen, Yueqi Wang, Dexiang Zhang, Sheng Shen, Tao Suo, Hongtao Pan, Yue Ming, Kan Ding, Houbao Liu
Gallbladder carcinoma (GBC) is the most common biliary tract cancer and exhibits poor patient prognosis. Previous studies have identified that long non-coding RNAs (lncRNAs) serve important regulatory roles in cancer biology. Alterations in lncRNAs are associated with several types of cancer. However, the contribution of lncRNAs to GBC remains unclear. To investigate the lncRNAs that are potentially involved in GBC, lncRNA profiles were identified in three pairs of human GBC and corresponding peri-carcinomatous tissue samples using microarray analysis...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28529576/increased-mir31hg-lncrna-expression-increases-gefitinib-resistance-in-non-small-cell-lung-cancer-cell-lines-through-the-egfr-pi3k-akt-signaling-pathway
#11
Bing Wang, Hong Jiang, Limin Wang, Xueqin Chen, Kan Wu, Shirong Zhang, Shenglin Ma, Bing Xia
The aim of the present study was to gain insight into the molecular mechanism of gefitinib resistance in non-small cell lung cancer (NSCLC), and demonstrate whether long noncoding RNA (lncRNA) expression signatures differ between gefitinib-sensitive PC9 and gefitinib-resistant PC9 (PC9-R) cell lines. PC9 and PC9-R cells were treated with gefitinib and, after 48 h, proliferation and apoptosis were analyzed using a Cell Counting Kit-8 (CCK-8) assay and flow cytometry. Microarray expression profiling of lncRNAs was undertaken in both PC9 and PC9-R cells, and the expression profiles were verified by reverse transcription quantitative-polymerase chain reaction...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28529570/the-meaning-of-piwi-proteins-in-cancer-development
#12
Monika Litwin, Anna Szczepańska-Buda, Aleksandra Piotrowska, Piotr Dzięgiel, Wojciech Witkiewicz
Cancer is a histologically and genetically heterogeneous population of tumor cells that exhibits distinct molecular profiles determined by epigenetic alterations. P-element-induced wimpy testis (PIWI) proteins in complex with PIWI-interacting RNA (piRNA) have been previously demonstrated to be involved in epigenetic regulation in germline cells. Recently, reactivation of PIWI expression, primarily PIWI-like protein 1 and 2, through aberrant DNA methylation resulting in genomic silencing has been identified in various types of tumors...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28529506/roles-of-regulatory-rnas-for-antibiotic-resistance-in-bacteria-and-their-potential-value-as-novel-drug-targets
#13
REVIEW
Petra Dersch, Muna A Khan, Sabrina Mühlen, Boris Görke
The emergence of antibiotic resistance mechanisms among bacterial pathogens increases the demand for novel treatment strategies. Lately, the contribution of non-coding RNAs to antibiotic resistance and their potential value as drug targets became evident. RNA attenuator elements in mRNA leader regions couple expression of resistance genes to the presence of the cognate antibiotic. Trans-encoded small RNAs (sRNAs) modulate antibiotic tolerance by base-pairing with mRNAs encoding functions important for resistance such as metabolic enzymes, drug efflux pumps, or transport proteins...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28529452/estradiol-suppresses-tlr4-triggered-apoptosis-of-decidual-stromal-cells-and-drives-an-anti-inflammatory-th2-shift-by-activating-sgk1
#14
Yiyun Lou, Minhao Hu, Qijing Wang, Mu Yuan, Ning Wang, Fang Le, Lejun Li, Shisi Huang, Liya Wang, Xiangrong Xu, Fan Jin
A pro-inflammatory cytokine profile at the feto-maternal interface may predispose immune maladaptation notably in early miscarriages. We investigated the involvement of estradiol (E2)-activated serum-glucocorticoid regulated kinase 1 (SGK1) in preserving the tolerogenic and pro-survival intrauterine microenvironment beneficial to gestation maintenance. Decidual SGK1 was down-regulated in early miscarriage, consistent with the lower serum E2 concentration seen in pregnancy loss. Lipopolysaccharide (LPS)/Toll-like receptors 4 (TLR4) signaling induced apoptosis and the pro-inflammatory T helper type (TH) 1 response of decidual stromal cells (DSCs) were associated with miscarriage...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28529365/long-noncoding-rnas-new-evidence-for-overlapped-pathogenesis-between-major-depressive-disorder-and-generalized-anxiety-disorder
#15
Xuelian Cui, Wei Niu, Lingming Kong, Mingjun He, Kunhong Jiang, Shengdong Chen, Aifang Zhong, Wanshuai Li, Jim Lu, Liyi Zhang
BACKGROUND: About half of patients with major depressive disorder (MDD) have clinically meaningful levels of anxiety. Greater severity of depressive illness and functional impairment has been reported in patients with high levels of anxiety accompanying depression. The pathogenesis for the comorbidity was still unsure. AIM: This study aimed to determine whether there would be molecular link for overlapped pathogenesis between MDD and anxiety disorder. MATERIALS AND METHODS: Using long noncoding RNA (lncRNA) microarray profiling and reverse transcription polymerase chain reaction, six downregulated lncRNAs and three upregulated lncRNAs had been identified to be the potential biomarkers for MDD and generalized anxiety disorder (GAD), respectively...
January 2017: Indian Journal of Psychiatry
https://www.readbyqxmd.com/read/28529265/comparative-transcriptomic-analysis-identifies-reprogramming-and-differentiation-genes-differentially-expressed-in-uipscs-and-escs
#16
Liang Shi, Yazhou Cui, Xiaoyan Zhou, Jing Luan, Linli Wang, Jinxiang Han
Embryonic stem cells (ESCs) technology has garnered worldwide attention for its therapeutic applications in vivo. Researchers have previously shown that non-viral induced pluripotent stem cells (iPSCs) can be generated from urine. As a potential alternative, Urinary iPSCs (UiPSCs) are highly similar to embryonic stem cells (ESCs) in many aspects such as morphology, expression of pluripotency markers and the capacity to develop into three germ layers in vitro and in vivo. However, the degree of gene expression similarity between iPSCs and ESCs has not been completely elucidated...
May 20, 2017: Bioscience Trends
https://www.readbyqxmd.com/read/28529082/rice-expression-database-red-an-integrated-rna-seq-derived-gene-expression-database-for-rice
#17
Lin Xia, Dong Zou, Jian Sang, Xingjian Xu, Hongyan Yin, Mengwei Li, Shuangyang Wu, Songnian Hu, Lili Hao, Zhang Zhang
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. Here, we present RED (Rice Expression Database; http://expression.ic4r.org), an integrated database of rice gene expression profiles derived entirely from RNA-Seq data. RED features a comprehensive collection of 284 high-quality RNA-Seq experiments, integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments. Based on massive expression profiles, RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest...
May 4, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28529066/reconstructing-context-specific-gene-regulatory-network-and-identifying-modules-and-network-rewiring-through-data-integration
#18
Tianle Ma, Aidong Zhang
Reconstructing context-specific transcriptional regulatory network is crucial for deciphering principles of regulatory mechanisms underlying various conditions. Recently studies that reconstructed transcriptional networks have focused on individual organisms or cell types and relied on data repositories of context-free regulatory relationships. Here we present a comprehensive framework to systematically derive putative regulator-target pairs in any given context by integrating context-specific transcriptional profiling and public data repositories of gene regulatory networks...
May 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28528185/simvastatin-ameliorate-memory-deficits-and-inflammation-in-clinical-and-mouse-model-of-alzheimer-s-disease-via-modulating-the-expression-of-mir-106b
#19
Wenzhong Huang, Zhenyu Li, Liandong Zhao, Wei Zhao
BACKGROUND: Alzheimer's disease (AD) as a neurodegenerative brain disorder is a devastating pathology leading to disastrous cognitive impairments and dementia, and several studies have shown that AD is closely related to the inflammation, so anti-inflammatory treatment may provide therapeutic benefits. In this study, the effect of simvastatin on inflammation was investigated and the underlying mechanisms were explored. METHODS: First, we tested the effect of simvastatin on AD in clinical research...
May 18, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28527333/transcriptome-wide-analysis-of-jasmonate-treated-by-2-cells-reveals-new-transcriptional-regulators-associated-with-alkaloid-formation-in-tobacco
#20
Yuping Yang, Pengcheng Yan, Che Yi, Wenzheng Li, Yuhui Chai, Lingling Fei, Ping Gao, Heping Zhao, Yingdian Wang, Michael P Timko, Bingwu Wang, Shengcheng Han
Jasmonates (JAs) are well-known regulators of stress, defence, and secondary metabolism in plants, with JA perception triggering extensive transcriptional reprogramming, including both activation and/or repression of entire metabolic pathways. We performed RNA sequencing based transcriptomic profiling of tobacco BY-2 cells before and after treatment with methyl jasmonate (MeJA) to identify novel transcriptional regulators associated with alkaloid formation. A total of 107,140 unigenes were obtained through de novo assembly, and at least 33,213 transcripts (31%) encode proteins, in which 3419 transcription factors (TFs) were identified, representing 72 gene families, as well as 840 transcriptional regulators (TRs) distributed among 19 gene families...
May 4, 2017: Journal of Plant Physiology
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