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https://www.readbyqxmd.com/read/28927099/interleukin-6-identified-as-an-important-factor-in-hypoxia-and-aldehyde-dehydrogenase-based-gefitinib-adaptive-resistance-in-non-small-cell-lung-cancer-cells
#1
Shi-Min An, Hui-Min Lei, Xu-Ping Ding, Fan Sun, Chun Zhang, Ya-Bin Tang, Hong-Zhuan Chen, Ying Shen, Liang Zhu
Gefitinib resistance and relapse of the disease were the greatest challenges facing clinical therapy of non-small-cell lung cancer (NSCLC). Of note, regarding the hypoxia condition in solid tumor tissues in vivo, roles of hypoxia in gefitinib adaptive resistance and its association with lung cancer stem cells (LCSCs) have not been fully elucidated. In the present study, the role of hypoxia in gefitinib adaptive resistance and its association with aldehyde dehydrogenase (ALDH)-based LCSC gefitinib resistance were comparatively studied using RNA-sequencing (RNA-seq) technology...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28925390/alterations-of-micrornas-throughout-the-malignant-evolution-of-cutaneous-squamous-cell-carcinoma-the-role-of-mir-497-in-epithelial-to-mesenchymal-transition-of-keratinocytes
#2
A Mizrahi, A Barzilai, D Gur-Wahnon, I Z Ben-Dov, S Glassberg, T Meningher, E Elharar, M Masalha, J Jacob-Hirsch, H Tabibian-Keissar, I Barshack, J Roszik, R Leibowitz-Amit, Y Sidi, D Avni
Skin carcinogenesis is known to be a multi-step process with several stages along its malignant evolution. We hypothesized that transformation of normal epidermis to cutaneous squamous cell carcinoma (cSCC) is causally linked to alterations in microRNAs (miRNA) expression. For this end we decided to evaluate their alterations in the pathologic states ending in cSCC. Total RNA was extracted from formalin fixed paraffin embedded biopsies of five stages along the malignant evolution of keratinocytes towards cSCC: Normal epidermis, solar elastosis, actinic keratosis KIN1-2, advanced actinic keratosis KIN3 and well-differentiated cSCC...
September 18, 2017: Oncogene
https://www.readbyqxmd.com/read/28924923/plant-insects-and-mites-uptake-double-stranded-rna-upon-its-exogenous-application-on-tomato-leaves
#3
Anupam Gogoi, Nomi Sarmah, Athanasios Kaldis, Dionysios Perdikis, Andreas Voloudakis
Exogenously applied double-stranded RNA (dsRNA) molecules onto tomato leaves, moved rapidly from local to systemic leaves and were uptaken by agricultural pests namely aphids, whiteflies and mites. Four small interfering RNAs, deriving from the applied dsRNA, were molecularly detected in plants, aphids and mites but not in whiteflies. Double-stranded RNA (dsRNA) acts as the elicitor molecule of the RNA silencing (RNA interference, RNAi), the endogenous and evolutionary conserved surveillance system present in all eukaryotes...
September 18, 2017: Planta
https://www.readbyqxmd.com/read/28924511/barcoded-ns31-aml2-primers-for-sequencing-of-arbuscular-mycorrhizal-communities-in-environmental-samples
#4
Benjamin S T Morgan, Louise M Egerton-Warburton
PREMISE OF THE STUDY: Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples...
August 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28923972/small-genome-symbiont-underlies-cuticle-hardness-in-beetles
#5
Hisashi Anbutsu, Minoru Moriyama, Naruo Nikoh, Takahiro Hosokawa, Ryo Futahashi, Masahiko Tanahashi, Xian-Ying Meng, Takashi Kuriwada, Naoki Mori, Kenshiro Oshima, Masahira Hattori, Manabu Fujie, Noriyuki Satoh, Taro Maeda, Shuji Shigenobu, Ryuichi Koga, Takema Fukatsu
Beetles, representing the majority of the insect species diversity, are characterized by thick and hard cuticle, which plays important roles for their environmental adaptation and underpins their inordinate diversity and prosperity. Here, we report a bacterial endosymbiont extremely specialized for sustaining beetle's cuticle formation. Many weevils are associated with a γ-proteobacterial endosymbiont lineage Nardonella, whose evolutionary origin is estimated as older than 100 million years, but its functional aspect has been elusive...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28922562/association-between-polymorphisms-in-microrna-target-sites-and-survival-in-early-stage-non-small-cell-lung-cancer
#6
Seung Soo Yoo, Mi Jeong Hong, Jang Hyuck Lee, Jin Eun Choi, Shin Yup Lee, Jaehee Lee, Seung Ick Cha, Chang Ho Kim, Yangki Seok, Eungbae Lee, Sukki Cho, Sanghoon Jheon, Jae Yong Park
A high-throughput mapping method of RNA-RNA interactions by crosslinking, ligation, and sequencing of hybrids (CLASH) can not only provide information about canonical but also non-canonical interactions. We evaluated the associations between variants in microRNA target sites using CLASH data and survival outcomes of 782 early-stage non-small cell lung cancer (NSCLC) patients who underwent curative surgical resection. Among the 100 variants studied, two variants showed significant association with survival outcomes...
September 18, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/28922552/an-individualized-gene-expression-signature-for-prediction-of-lung-adenocarcinoma-metastases
#7
Lishuang Qi, Tianhao Li, Gengen Shi, Jiasheng Wang, Xin Li, Sainan Zhang, Libin Chen, Yuan Qin, Yunyan Gu, Wenyuan Zhao, Zheng Guo
Our laboratory previously reported an individual-level signature consisting of nine gene pairs, named 9-GPS. This signature was developed by training on microarray expression data and validated using three independent integrated microarray data sets, with samples of stage I non-small cell lung cancer after complete surgical resection. In this study, we first validated the cross-platform robustness of 9-GPS by demonstrating that 9-GPS could significantly stratify the overall survival of 213 stage I lung adenocarcinoma (LUAD) patients detected with RNA-sequencing platform in The Cancer Genome Atlas (log-rank p = 0...
September 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28922394/sequence-features-of-viral-and-human-internal-ribosome-entry-sites-predictive-of-their-activity
#8
Alexey A Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal
Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be involved in this process. However due to the small number of IRESs known, there have been no systematic investigations of the determinants of IRES activity. With the recent discovery of thousands of novel IRESs in human and viruses, the next challenge is to decipher the sequence determinants of IRES activity...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28921648/rna-therapeutics-in-oncology-advances-challenges-and-future-directions
#9
A Robert MacLeod, Stanley T Crooke
RNA-based therapeutic technologies represent a rapidly expanding class of therapeutic opportunities with the power to modulate cellular biology in ways never before possible. With RNA-targeted therapeutics, inhibitors of previously undruggable proteins, gene expression modulators, and even therapeutic proteins can be rationally designed based on sequence information alone, something that is not possible with other therapeutic modalities. The most advanced RNA therapeutic modalities are antisense oligonucleotides (ASOs) and small interfering RNAs...
October 2017: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28919018/de-novo-transcriptome-assembly-of-the-calanoid-copepod-neocalanus-flemingeri-a-new-resource-for-emergence-from-diapause
#10
Vittoria Roncalli, Matthew C Cieslak, Stephanie A Sommer, Russell R Hopcroft, Petra H Lenz
Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N...
September 14, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28918562/crispr-cas9-genome-editing-in-wheat
#11
Dongjin Kim, Burcu Alptekin, Hikmet Budak
Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile tool for genome editing which enables editing of multiple genes based on the guidance of small RNAs. Even though the efficiency of CRISPR/Cas9 system has been shown with several studies from diploid plants, its application remains a challenge for plants with polyploid and complex genome...
September 16, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28918093/topological-structure-determination-of-rna-using-small-angle-x-ray-scattering
#12
Yuba R Bhandari, Linxin Fan, Xianyang Fang, George Zaki, Eric A Stahlberg, Wei Jiang, Charles D Schwieters, Jason R Stagno, Yun-Xing Wang
Knowledge of RNA three-dimensional topological structures provides important insight into the relationship between RNA structural components and function. It is often likely that near complete sets of biochemical and biophysical data containing structural restraints are not available but one still wants to obtain knowledge about approximate topological folding of RNA. In this regard, general methods for determining such topological structures with minimum readily available restraints are lacking. Naked RNAs are difficult to crystallize and NMR spectroscopy is generally limited to small RNA fragments...
September 13, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28918033/six-highly-conserved-targets-of-rnai-revealed-in-hiv-1-infected-patients-from-russia-are-also-present-in-many-hiv-1-strains-worldwide
#13
Olga V Kretova, Daria M Fedoseeva, Maria A Gorbacheva, Natalya M Gashnikova, Maria P Gashnikova, Nataliya V Melnikova, Vladimir R Chechetkin, Yuri V Kravatsky, Nickolai A Tchurikov
RNAi has been suggested for use in gene therapy of HIV/AIDS, but the main problem is that HIV-1 is highly variable and could escape attack from the small interfering RNAs (siRNAs) due to even single nucleotide substitutions in the potential targets. To exhaustively check the variability in selected RNA targets of HIV-1, we used ultra-deep sequencing of six regions of HIV-1 from the plasma of two independent cohorts of patients from Russia. Six RNAi targets were found that are invariable in 82%-97% of viruses in both cohorts and are located inside the domains specifying reverse transcriptase (RT), integrase, vpu, gp120, and p17...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28916650/differential-expression-of-mirnas-in-the-respiratory-tree-of-the-sea-cucumber-apostichopus-japonicus-under-hypoxia-stress
#14
Da Huo, Lina Sun, Xiaoni Li, Xiaoshang Ru, Shilin Liu, Libin Zhang, Lili Xing, Hongsheng Yang
Sea cucumber, an important economic species, has encountered high mortality since 2013 in northern China because of seasonal environmental stress such as hypoxia, high temperature, and low salinity. MicroRNAs (miRNAs) are important in regulating gene expression in marine organisms in response to environmental change. In the present study, high-throughput sequencing was used to investigate alterations in miRNA expression in the sea cucumber under different levels of dissolved oxygen (DO). Nine small RNA libraries were constructed from the sea cucumber respiratory trees...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28916639/small-rna-seq-during-acute-maximal-exercise-reveal-rnas-involved-in-vascular-inflammation-and-cardiometabolic-health
#15
Ravi Shah, Ashish S Yeri, Avash Das, Amanda Courtright-Lim, Olivia Ziegler, Ernest Gervino, Jeffrey Ocel, Pablo Quintero Pinzon, Luke Wooster, Cole Shields Bailey, Kahraman Tanriverdi, Lea Beaulieu, Jane E Freedman, Ionita Ghiran, Gregory D Lewis, Kendall Van Keuren-Jensen, Saumya Das
OBJECTIVE: Exercise improves cardiometabolic and vascular function, though mechanisms remain unclear. Our objective was to demonstrate the diversity of circulating extracellular RNA (ex-RNA) release during acute exercise in humans and its relevance to exercise-mediated benefits on vascular inflammation. Approach and Results: We performed plasma small RNA sequencing (RNA-seq) in 26 individuals undergoing symptom-limited maximal treadmill exercise, with replication of our top candidate miRNA in a separate cohort of 59 individuals undergoing bicycle ergometry...
September 15, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28912272/the-transcription-factor-hoxb7-regulates-erk-kinase-activity-and-thereby-stimulates-the-motility-and-invasiveness-of-pancreatic-cancer-cells
#16
Makiko Tsuboi, Keisuke Taniuchi, Takahiro Shimizu, Motoaki Saito, Toshiji Saibara
HOX genes encode transcription factors that function as sequence-specific transcription factors that are involved in cellular proliferation, differentiation, and death. The aim of this study was to investigate the role of a HOX family protein, HOXB7, in the motility and invasiveness of pancreatic cancer cells. We previously identified a HOXB7 transcript that is one of a number of transcripts that are preferentially translated in membrane protrusions in pancreatic cancer cells. Immunocytochemistry showed that HOXB7 was localized to the cell protrusions of migrating pancreatic cancer cells...
September 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28911330/extensive-transcriptomic-and-epigenomic-remodelling-occurs-during-arabidopsis-thaliana-germination
#17
Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G Lewsey, James Whelan
BACKGROUND: Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination...
September 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28911107/web-based-ngs-data-analysis-using-mirmaster-a-large-scale-meta-analysis-of-human-mirnas
#18
Tobias Fehlmann, Christina Backes, Mustafa Kahraman, Jan Haas, Nicole Ludwig, Andreas E Posch, Maximilian L Würstle, Matthias Hübenthal, Andre Franke, Benjamin Meder, Eckart Meese, Andreas Keller
The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28905886/time-series-oligonucleotide-count-to-assign-antiviral-sirnas-with-long-utility-fit-in-the-big-data-era
#19
K Wada, Y Wada, Y Iwasaki, T Ikemura
Oligonucleotides are key elements of nucleic acid therapeutics such as small interfering RNAs (siRNAs). Influenza and Ebolaviruses are zoonotic RNA viruses mutating very rapidly, and their sequence changes must be characterized intensively to design therapeutic oligonucleotides with long utility. Focusing on a total of 182 experimentally validated siRNAs for influenza A, B and Ebolaviruses compiled by the siRNA database, we conducted time-series analyses of occurrences of siRNA targets in these viral genomes...
September 14, 2017: Gene Therapy
https://www.readbyqxmd.com/read/28905147/evaluation-and-control-of-mirna-like-off-target-repression-for-rna-interference
#20
REVIEW
Heeyoung Seok, Haejeong Lee, Eun-Sook Jang, Sung Wook Chi
RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes...
September 13, 2017: Cellular and Molecular Life Sciences: CMLS
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