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https://www.readbyqxmd.com/read/28103507/circular-banp-an-upregulated-circular-rna-that-modulates-cell-proliferation-in-colorectal-cancer
#1
Mingchen Zhu, Yijun Xu, Yun Chen, Feng Yan
Circular RNAs (circRNAs) are recently identified as widespread and diverse endogenous noncoding RNAs that may harbor vital functions in human and animals. However, the role of circRNAs in the process of tumorigenesis and development of colorectal cancer (CRC) remains vague. Here we characterized the circRNA expression profile from three paired CRC cancerous and adjacent normal tissues by human circRNA array, and identified 136 significantly overexpressed circRNAs and 243 downregulated circRNAs in CRC cancerous tissues (>2-fold changes)...
January 16, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28103252/comparative-and-evolutionary-analysis-of-grass-pollen-allergens-using-brachypodium-distachyon-as-a-model-system
#2
Akanksha Sharma, Niharika Sharma, Prem Bhalla, Mohan Singh
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses...
2017: PloS One
https://www.readbyqxmd.com/read/28102850/japanese-encephalitis-virus-induces-human-neural-stem-progenitor-cell-death-by-elevating-grp78-phb-and-hnrnpc-through-er-stress
#3
Sriparna Mukherjee, Noopur Singh, Nabonita Sengupta, Mahar Fatima, Pankaj Seth, Anita Mahadevan, Susarla Krishna Shankar, Arindam Bhattacharyya, Anirban Basu
Japanese encephalitis virus (JEV), which is a causative agent of sporadic encephalitis, harbours itself inside the neural stem/progenitor cells. It is a well-known fact that JEV infects neural stem/progenitor cells and decreases their proliferation capacity. With mass spectrometry-based quantitative proteomic study, it is possible to reveal the impact of virus on the stem cells at protein level. Our aim was to perceive the stem cell proteomic response upon viral challenge. We performed a two-dimensional gel electrophoresis-based proteomic study of the human neural stem cells (hNS1 cell line) post JEV infection and found that 13 proteins were differentially expressed...
January 19, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28102444/patients-with-bicuspid-and-tricuspid-aortic-valve-exhibit-distinct-regional-microrna-signatures-in-mildly-dilated-ascending-aorta
#4
Sebastian Albinsson, Alessandro Della Corte, Azra Alajbegovic, Katarzyna K Krawczyk, Ciro Bancone, Umberto Galderisi, Marilena Cipollaro, Marisa De Feo, Amalia Forte
MicroRNAs are able to modulate gene expression in a range of diseases. We focused on microRNAs as potential contributors to the pathogenesis of ascending aorta (AA) dilatation in patients with stenotic tricuspid (TAV) or bicuspid aortic valve (BAV). Aortic specimens were collected from the 'concavity' and the 'convexity' of mildly dilated AAs and of normal AAs from heart transplant donors. Aortic RNA was analyzed through PCR arrays, profiling the expression of 84 microRNAs involved in cardiovascular disease...
January 19, 2017: Heart and Vessels
https://www.readbyqxmd.com/read/28102366/aurora-kinase-a-is-a-biomarker-for-bladder-cancer-detection-and-contributes-to-its-aggressive-behavior
#5
Aaron Mobley, Shizhen Zhang, Jolanta Bondaruk, Yan Wang, Tadeusz Majewski, Nancy P Caraway, Li Huang, Einav Shoshan, Guermarie Velazquez-Torres, Giovanni Nitti, Sangkyou Lee, June Goo Lee, Enrique Fuentes-Mattei, Daniel Willis, Li Zhang, Charles C Guo, Hui Yao, Keith Baggerly, Yair Lotan, Seth P Lerner, Colin Dinney, David McConkey, Menashe Bar-Eli, Bogdan Czerniak
The effects of AURKA overexpression associated with poor clinical outcomes have been attributed to increased cell cycle progression and the development of genomic instability with aneuploidy. We used RNA interference to examine the effects of AURKA overexpression in human bladder cancer cells. Knockdown had minimal effects on cell proliferation but blocked tumor cell invasion. Whole genome mRNA expression profiling identified nicotinamide N-methyltransferase (NNMT) as a downstream target that was repressed by AURKA...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101198/elevated-expression-of-nrf2-mediates-multidrug-resistance-in-cd133-head-and-neck-squamous-cell-carcinoma-stem-cells
#6
Bao-Cai Lu, Jing Li, Wen-Fa Yu, Guo-Zheng Zhang, Hui-Min Wang, Hui-Min Ma
Enhanced expression of the ATP-binding cassette (ABC) transporter protein ABC sub-family G member 2 (ABCG2) in cancer stem cells (CSCs) plays a major role in chemotherapeutic drug efflux, which results in therapy failure and tumor relapse. In addition to downregulating apoptosis in CSCs, it has been reported that the transcriptional upregulation of the redox sensing factor Nrf2 is involved in the upregulation of ABCG2 expression and consequent chemoresistance. The current study investigated the presence of cancer stem-like side population (SP) cells from head and neck squamous cell carcinoma (HNSCC) samples, and evaluated the Nrf2 expression profile and multidrug resistance properties of HNSCC stem cells...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28101126/characterisation-of-microbial-communities-within-aggressive-prostate-cancer-tissues
#7
Melissa A Yow, Sepehr N Tabrizi, Gianluca Severi, Damien M Bolton, John Pedersen, Graham G Giles, Melissa C Southey
BACKGROUND: An infectious aetiology for prostate cancer has been conjectured for decades but the evidence gained from questionnaire-based and sero-epidemiological studies is weak and inconsistent, and a causal association with any infectious agent is not established. We describe and evaluate the application of new technology to detect bacterial and viral agents in high-grade prostate cancer tissues. The potential of targeted 16S rRNA gene sequencing and total RNA sequencing was evaluated in terms of its utility to characterise microbial communities within high-grade prostate tumours...
2017: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/28100188/high-expression-of-micro-rna-135a-in-hepatocellular-carcinoma-is-associated-with-recurrence-within-12%C3%A2-months-after-resection
#8
Johann von Felden, Denise Heim, Kornelius Schulze, Till Krech, Florian Ewald, Björn Nashan, Ansgar W Lohse, Henning Wege
BACKGROUND: Hepatocellular carcinoma has a dismal prognosis due to recurrence rates of up to 70% after curative resection. Early recurrence is driven by synchronous microscopic intrahepatic metastases. The predictive value of histological parameters is discussed controversially and adjuvant therapy is not established. The aim of this study was to identify patients at high risk for early intrahepatic recurrence by expression profiling of selected micro RNAs. METHODS: In 52 patients undergoing HCC resection between 2011 and 2014, liver and tumor tissue was collected during surgery...
January 18, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28100173/whole-genome-wide-transcript-profiling-to-identify-differentially-expressed-genes-associated-with-seed-field-emergence-in-two-soybean-low-phytate-mutants
#9
Fengjie Yuan, Xiaomin Yu, Dekun Dong, Qinghua Yang, Xujun Fu, Shenlong Zhu, Danhua Zhu
BACKGROUND: Seed germination is important to soybean (Glycine max) growth and development, ultimately affecting soybean yield. A lower seed field emergence has been the main hindrance for breeding soybeans low in phytate. Although this reduction could be overcome by additional breeding and selection, the mechanisms of seed germination in different low phytate mutants remain unknown. In this study, we performed a comparative transcript analysis of two low phytate soybean mutants (TW-1 and TW-1-M), which have the same mutation, a 2 bp deletion in GmMIPS1, but show a significant difference in seed field emergence, TW-1-M was higher than that of TW-1 ...
January 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28099854/single-cell-transcriptomic-analysis-defines-heterogeneity-and-transcriptional-dynamics-in-the-adult-neural-stem-cell-lineage
#10
Ben W Dulken, Dena S Leeman, Stéphane C Boutet, Katja Hebestreit, Anne Brunet
Neural stem cells (NSCs) in the adult mammalian brain serve as a reservoir for the generation of new neurons, oligodendrocytes, and astrocytes. Here, we use single-cell RNA sequencing to characterize adult NSC populations and examine the molecular identities and heterogeneity of in vivo NSC populations. We find that cells in the NSC lineage exist on a continuum through the processes of activation and differentiation. Interestingly, rare intermediate states with distinct molecular profiles can be identified and experimentally validated, and our analysis identifies putative surface markers and key intracellular regulators for these subpopulations of NSCs...
January 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/28099853/a-tissue-mapped-axolotl-de-novo-transcriptome-enables-identification-of-limb-regeneration-factors
#11
Donald M Bryant, Kimberly Johnson, Tia DiTommaso, Timothy Tickle, Matthew Brian Couger, Duygu Payzin-Dogru, Tae J Lee, Nicholas D Leigh, Tzu-Hsing Kuo, Francis G Davis, Joel Bateman, Sevara Bryant, Anna R Guzikowski, Stephanie L Tsai, Steven Coyne, William W Ye, Robert M Freeman, Leonid Peshkin, Clifford J Tabin, Aviv Regev, Brian J Haas, Jessica L Whited
Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorly understood, partly because the enormous and incompletely sequenced genomes of axolotls have hindered the study of genes facilitating regeneration. We assembled and annotated a de novo transcriptome using RNA-sequencing profiles for a broad spectrum of tissues that is estimated to have near-complete sequence information for 88% of axolotl genes...
January 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/28099441/puma-and-nf-kb-are-cell-signaling-predictors-of-reovirus-oncolysis-of-breast-cancer
#12
Chandini Thirukkumaran, Zhong-Qiao Shi, Ponnampalam Thirukkumaran, Joanne Luider, Karen Kopciuk, Jason Spurrell, Kate Elzinga, Don Morris
BACKGROUND AND PURPOSE: Reovirus is a ubiquitous RNA virus that exploits aberrant signaling pathways for its replication. The oncolytic potential of reovirus against numerous cancers under pre-clinical/clinical conditions has been documented by us and others. Despite its proven clinical activity, the underlying mechanisms of reovirus oncolysis is still not well elucidated. If reovirus therapy is to be optimized for cancer, including breast cancer patients, it is imperative to understand the mechanisms of reovirus oncolysis, especially in treatment of resistant tumour...
2017: PloS One
https://www.readbyqxmd.com/read/28099430/pooled-crispr-screening-with-single-cell-transcriptome-readout
#13
Paul Datlinger, André F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler, Johanna Klughammer, Linda C Schuster, Amelie Kuchler, Donat Alpar, Christoph Bock
CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome profiling, but at much lower throughput. Here we combine pooled CRISPR screening with single-cell RNA sequencing into a broadly applicable workflow, directly linking guide RNA expression to transcriptome responses in thousands of individual cells...
January 18, 2017: Nature Methods
https://www.readbyqxmd.com/read/28099146/long-non-coding-rna-growth-arrest-specific-transcript-5-acts-as-a-tumour-suppressor-in-colorectal-cancer-by-inhibiting-interleukin-10-and-vascular-endothelial-growth-factor-expression
#14
Yuan Li, Yan Li, Shengkai Huang, Kun He, Mei Zhao, Hong Lin, Dongdong Li, Jiaming Qian, Caihong Zhou, Yuhua Chen, Changzhi Huang
Long non-coding RNAs (lncRNAs) are highly involved in diverse biological processes of human malignancies. The expression profile and underlying mechanism of lncRNA growth arrest specific transcript 5 (GAS5) in colorectal cancer (CRC) is poorly understood. In this study, we found that GAS5 was commonly downregulated in CRC tissues, serum of CRC patients and CRC cell lines. Knockdown of GAS5 promoted CRC cell proliferation and colony formation, whereas overexpression of GAS5 produced the opposite result. We further demonstrated that knockdown of GAS5 increased the expression and secretion of interleukin-10 (IL-10) and vascular endothelial growth factor (VEGF-A) via NF-κB and Erk1/2 pathways...
January 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28098833/role-of-electron-driven-proton-transfer-processes-in-the-ultrafast-deactivation-of-photoexcited-anionic-8-oxoguanine-adenine-and-8-oxoguanine-cytosine-base-pairs
#15
Xiuxiu Wu, Tolga N V Karsili, Wolfgang Domcke
It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required...
January 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28098181/profiling-single-guide-rna-specificity-reveals-a-mismatch-sensitive-core-sequence
#16
Ting Zheng, Yingzi Hou, Pingjing Zhang, Zhenxi Zhang, Ying Xu, Letian Zhang, Leilei Niu, Yi Yang, Da Liang, Fan Yi, Wei Peng, Wenjian Feng, Ying Yang, Jianxin Chen, York Yuanyuan Zhu, Li-He Zhang, Quan Du
Targeting specificity is an essential issue in the development of CRISPR-Cas technology. Using a luciferase activation assay, off-target cleavage activity of sgRNA was systematically investigated on single nucleotide-mismatched targets. In addition to confirming that PAM-proximal mismatches are less tolerated than PAM-distal mismatches, our study further identified a "core" sequence that is highly sensitive to target-mismatch. This sequence is of 4-nucleotide long, located at +4 to +7 position upstream of PAM, and positioned in a steric restriction region when assembled into Cas9 endonuclease...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28098170/targeting-the-pi3k-akt-pathway-via-gli1-inhibition-enhanced-the-drug-sensitivity-of-acute-myeloid-leukemia-cells
#17
Hui Liang, Qi-Li Zheng, Peng Fang, Jian Zhang, Tuo Zhang, Wei Liu, Min Guo, Christopher L Robinson, Shui-Bing Chen, Xiao-Ping Chen, Fang-Ping Chen, Hui Zeng
Combination targeted therapy is commonly used to treat acute myeloid leukemia (AML) patients, particularly in refractory/relapse (RR) population. However, concerns have been raised regarding the safety and patient tolerance of combination chemotherapy. It is critical to choose the appropriate treatment for precision therapy. We performed genome-wide RNA profiling using RNA-Seq to compare the RR group and the complete remission (CR) group (a total of 42 adult AML patients). The Hedgehog (Hh) and PI3K/AKT pathways were upregulated in the RR population, which was further confirmed by western blot and/or qPCR...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096363/an-rna-based-signature-enables-high-specificity-detection-of-circulating-tumor-cells-in-hepatocellular-carcinoma
#18
Mark Kalinich, Irun Bhan, Tanya T Kwan, David T Miyamoto, Sarah Javaid, Joseph A LiCausi, John D Milner, Xin Hong, Lipika Goyal, Srinjoy Sil, Melissa Choz, Uyen Ho, Ravi Kapur, Alona Muzikansky, Huidan Zhang, David A Weitz, Lecia V Sequist, David P Ryan, Raymond T Chung, Andrew X Zhu, Kurt J Isselbacher, David T Ting, Mehmet Toner, Shyamala Maheswaran, Daniel A Haber
Circulating tumor cells (CTCs) are shed into the bloodstream by invasive cancers, but the difficulty inherent in identifying these rare cells by microscopy has precluded their routine use in monitoring or screening for cancer. We recently described a high-throughput microfluidic CTC-iChip, which efficiently depletes hematopoietic cells from blood specimens and enriches for CTCs with well-preserved RNA. Application of RNA-based digital PCR to detect CTC-derived signatures may thus enable highly accurate tissue lineage-based cancer detection in blood specimens...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096131/nutrition-micrornas-and-human-health
#19
REVIEW
Juan Cui, Beiyan Zhou, Sharon A Ross, Janos Zempleni
MicroRNAs (miRs) hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA. Over 60% of human protein-coding genes are regulated by miRs, and 1881 high-confidence miRs are encoded in the human genome. Evidence suggests that miRs not only are synthesized endogenously, but also might be obtained from dietary sources, and that food compounds alter the expression of endogenous miR genes. The main food matrices for studies of biological activity of dietary miRs include plant foods and cow milk...
January 2017: Advances in Nutrition
https://www.readbyqxmd.com/read/28096076/a-landscape-of-synthetic-viable-interactions-in-cancer
#20
Yunyan Gu, Ruiping Wang, Yue Han, Wenbin Zhou, Zhangxiang Zhao, Tingting Chen, Yuanyuan Zhang, Fuduan Peng, Haihai Liang, Lishuang Qi, Wenyuan Zhao, Da Yang, Zheng Guo
Synthetic viability, which is defined as the combination of gene alterations that can rescue the lethal effects of a single gene alteration, may represent a mechanism by which cancer cells resist targeted drugs. Approaches to detect synthetic viable (SV) interactions in cancer genome to investigate drug resistance are still scarce. Here, we present a computational method to detect synthetic viability-induced drug resistance (SVDR) by integrating the multidimensional data sets, including copy number alteration, whole-exome mutation, expression profile and clinical data...
January 17, 2017: Briefings in Bioinformatics
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