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apoptosis transcriptome

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https://www.readbyqxmd.com/read/28525372/overexpression-of-a-novel-candidate-oncogene-kif14-correlates-with-tumor-progression-and-poor-prognosis-in-prostate-cancer
#1
Yixiang Zhang, Yeqing Yuan, Pei Liang, Zhaoxia Zhang, Xiaojing Guo, Ligang Xia, Yingying Zhao, Xing-Sheng Shu, Shengkun Sun, Ying Ying, Yingduan Cheng
Prostate cancer (PCa) is the second leading cause of death from cancer in men. The mechanism underlying tumorigenesis and development of PCa is largely unknown. Here, we identified Kinesin family member 14 (KIF14) as a novel candidate oncogene in PCa. We found that KIF14 was overexpressed in multiple PCa cell lines and primary PCa tissues. Knockdown of KIF14 in DU145 and PC3 prostate cancer cells suppressed cell proliferation, induced cell cycle arrest and apoptosis. Transcriptome analysis by RNA-sequencing demonstrated that KIF4 suppression led to transcriptional changes of genes involved in p53 and TGF-beta signaling pathway...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28514740/differential-expression-of-circulating-biomarkers-of-tumor-phenotype-and-outcomes-in-previously-treated-non-small-cell-lung-cancer-patients-receiving-erlotinib-vs-cytotoxic-chemotherapy
#2
Mary Jo Fidler, Casey Frankenberger, Richard Seto, Gabriela C Lobato, Cristina L Fhied, Selina Sayidine, Sanjib Basu, Mark Pool, Reem Karmali, Marta Batus, Wen-Rong Lie, David Hayes, Jehangir Mistry, Philip Bonomi, Jeffrey A Borgia
BACKGROUND: The objective of this study was to identify serum biomarkers capable of predicting clinical outcomes in previously-treated NSCLC patients with wild-type for EGFR activating mutations or insufficient tissue for mutation status determination. METHODS: Sixty-six Luminex immunoassays representative of biological themes that emerged from a re-analysis of transcriptome data from the Cancer Genome Atlas (TCGA) were evaluate against pretreatment serum specimens from previously-treated advanced NSCLC patients received either cytotoxic chemotherapy (n=32) or erlotinib (n=79)...
April 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28504646/the-rna-binding-protein-tristetraprolin-schedules-apoptosis-of-pathogen-engaged-neutrophils-during-bacterial-infection
#3
Florian Ebner, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael Sixt, Pavel Kovarik
Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity...
May 15, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28503089/anticancer-chemodiversity-of-ranunculaceae-medicinal-plants-molecular-mechanisms-and-functions
#4
REVIEW
Da-Cheng Hao, Chun-Nian He, Jie Shen, Pei-Gen Xiao
The buttercup family, Ranunculaceae, comprising more than 2,200 species in at least 62 genera, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine since the beginning of human civilization. Various medicinal phytometabolites have been found in Ranunculaceae plants, many of which, such as alkaloids, terpenoids, saponins, and polysaccharides, have shown anti-cancer activities in vitro and in vivo. Most concerns have been raised for two epiphany molecules, the monoterpene thymoquinone and the isoquinoline alkaloid berberine...
February 2017: Current Genomics
https://www.readbyqxmd.com/read/28500849/transcriptomic-profiles-of-human-foreskin-fibroblast-cells-in-response-to-orf-virus
#5
Daxiang Chen, Mingjian Long, Bin Xiao, Yufeng Xiong, Huiqin Chen, Yu Chen, Zhenzhan Kuang, Ming Li, Yingsong Wu, Daniel L Rock, Daoyuan Gong, Yong Wang, Haijian He Fang Liu, Shuhong Luo, Wenbo Hao
Orf virus has been utilized as a safe and efficient viral vector against not only diverse infectious diseases, but also against tumors. However, the nature of the genes triggered by the vector in human cells is poorly characterized. Using RNA sequencing technology, we compared specific changes in the transcriptomic profiles in human foreskin fibroblast cells following infection by the orf virus. The results indicated that orf virus upregulates or downregulates expression of a variety of genes, including genes involved in antiviral immune response, apoptosis, cell cycle and a series of signaling pathways, such as the IFN and p53-signaling pathways...
April 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28493484/cytoplasmic-overexpression-of-rna-binding-protein-hur-is-a-marker-of-poor-prognosis-in-meningioma-and-hur-knockdown-decreases-meningioma-cell-growth-and-resistance-to-hypoxia
#6
Guillaume Gauchotte, Sébastien Hergalant, Charlène Vigouroux, Jean-Matthieu Casse, Rémi Houlgatte, Tony Kaoma, Déborah Helle, Lydia Brochin, Fabien Rech, Matthieu Peyre, François Labrousse, Laurent Vallar, Jean-Louis Gueant, Jean-Michel Vignaud, Shyue-Fang Battaglia-Hsu
HuR regulates cytoplasmic mRNA stability and translatability, and the HuR expression level has been shown to correlate with poor disease outcome in several cancer types; however, the prognostic value and potential pro-oncogenic properties of HuR in meningioma remain unclear. Thus, in the present study we analyzed 85 meningioma tissue samples to establish the relationship between HuR expression, tumor-cell proliferation, and/or patient survival. In addition, we examined the anti-proliferative effects of HuR knockdown in two meningioma cell lines (IOMM-Lee and Ben-Men1), and conducted transcriptome-wide analyses (IOMM-Lee cells) to elucidate the molecular consequences of HuR knockdown...
May 11, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28490743/allelic-imbalance-of-somatic-mutations-in-cancer-genomes-and-transcriptomes
#7
Je-Keun Rhee, Sejoon Lee, Woong-Yang Park, Young-Ho Kim, Tae-Min Kim
Somatic mutations in cancer genomes often show allelic imbalance (AI) of mutation abundance between the genome and transcriptome, but there is not yet a systematic understanding of AI. In this study, we performed large-scale DNA and RNA AI analyses of >100,000 somatic mutations in >2,000 cancer specimens across five tumor types using the exome and transcriptome sequencing data of the Cancer Genome Atlas consortium. First, AI analysis of nonsense mutations and frameshift indels revealed that nonsense-mediated decay is typical in cancer genomes, and we identified the relationship between the extent of AI and the location of mutations in addition to the well-recognized 50-nt rules...
May 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28489891/rna-seq-approach-to-analysis-of-gene-expression-profiles-in-dark-green-islands-and-light-green-tissues-of-cucumber-mosaic-virus-infected-nicotiana-tabacum
#8
Lijuan Chen, Chunyan Fei, Lin Zhu, Zhenpeng Xu, Wenshan Zou, Ting Yang, Honghui Lin, Dehui Xi
Dark green islands (DGIs) surrounded by light green tissues (LGTs) are common leaf symptoms of plants that are systemically infected by various viruses that induce leaf mosaic in infected plants. The inoculation of Cucumber mosaic virus (CMV) in Nicotiana tabacum produced a commonly occurring sequence of classic patterns of DGIs and LGTs. Previous studies confirmed that there are significant differences between DGIs and LGTs in terms of physiology, biochemistry and molecular biology, but the mechanisms by which DGIs form remain unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28487480/microbiota-promotes-systemic-t-cell-survival-through-suppression-of-an-apoptotic-factor
#9
Raymond Soto, Charisse Petersen, Camille L Novis, Jason L Kubinak, Rickesha Bell, W Zac Stephens, Thomas E Lane, Robert S Fujinami, Alberto Bosque, Ryan M O'Connell, June L Round
Symbiotic microbes impact the severity of a variety of diseases through regulation of T-cell development. However, little is known regarding the molecular mechanisms by which this is accomplished. Here we report that a secreted factor, Erdr1, is regulated by the microbiota to control T-cell apoptosis. Erdr1 expression was identified by transcriptome analysis to be elevated in splenic T cells from germfree and antibiotic-treated mice. Suppression of Erdr1 depends on detection of circulating microbial products by Toll-like receptors on T cells, and this regulation is conserved in human T cells...
May 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28485999/igf2-mrna-binding-protein-3-imp3-mediated-regulation-of-transcriptome-and-translatome-in-glioma-cells
#10
Shruti Bhargava, Vikas Patil, Riyaz Ahmad Shah, Kumaravel Somasundaram
RNA binding proteins mediate global regulation at the level of transcriptome and translatome of a cell. We studied the global level expression changes regulated by IMP3 in transcriptome and translatome by performing microarray using total cellular RNA and heavy polysome derived RNA of IMP3 silenced glioma cells respectively. Differentially regulated transcripts at the transcriptome level (n = 2388) and at the level of translatome (n = 479) were identified. Further, these transcripts were classified as direct and indirect targets on the basis of presence of IMP3 binding site...
May 9, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28482796/effects-of-cold-acclimation-on-gene-expression-in-fall-field-cricket-gryllus-pennsylvanicus-ionoregulatory-tissues
#11
Lauren E Des Marteaux, Alexander H McKinnon, Hiroko Udaka, Jantina Toxopeus, Brent J Sinclair
BACKGROUND: Cold tolerance is a key determinant of temperate insect distribution and performance. Chill-susceptible insects lose ion and water homeostasis during cold exposure, but prior cold acclimation improves both cold tolerance and defense of homeostasis. The mechanisms underlying these processes are mostly unknown; cold acclimation is thought to enhance ion transport in the cold and/or prevent leak of water and ions. To identify candidate mechanisms of cold tolerance plasticity we generated transcriptomes of ionoregulatory tissues (hindgut and Malpighian tubules) from Gryllus pennsylvanicus crickets and compared gene expression in warm- and cold-acclimated individuals...
May 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28481732/human-cap10-like-protein-46%C3%A2-kda-gene-promotes-malignancy-in-colorectal-cancer
#12
Honghong Fang, Qiaoyun Chu, Jie Zhang, Hao Wang, Xinwei Yu, Siqi Ge, Manshu Song, Lijuan Wu, Minglin Lang, Naibai Chang, Youxin Wang, Wei Wang
Colon cancer patients have major unmet needs in terms of robust diagnostics and molecular biomarkers for personalized therapeutics. We have previously reported that human CAP10-like protein 46 kDa (hCLP46) is overexpressed in human acute myelogenous leukemia, T acute lymphoblastic leukemia, and leukemia cell lines. We extend this line of biomarker and diagnostic discovery research by investigating hCLP46 expression in colorectal cancer (CRC) tissues and examine the possibility of hCLP46 as a candidate biomarker for diagnosis and prognosis of CRC...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481231/zeolite-containing-mixture-supplementation-ameliorated-dextran-sodium-sulfate-induced-colitis-in-mice-by-suppressing-the-inflammatory-bowel-disease-pathway-and-improving-apoptosis-in-colon-mucosa
#13
Weida Lyu, Huijuan Jia, Chuanzong Deng, Kenji Saito, Seigo Yamada, Hisanori Kato
Inflammatory bowel disease (IBD) is induced by multiple environmental factors, and there is still no known treatment capable of curing the disease completely. We propose a zeolite-containing mixture (Hydryeast(®), HY)-a multi-component nutraceutical of which the main ingredients are Azumaceramics (mixture of zeolite and oyster shell burned under high temperature), citric acid, red rice yeast (monascus) and calcium stearate-as a nutraceutical intervention in IBD to ameliorate dextran sodium sulfate (DSS)-induced colitis...
May 6, 2017: Nutrients
https://www.readbyqxmd.com/read/28473620/prognostic-and-biologic-significance-of-long-non-coding-rna-profiling-in-younger-adults-with-cytogenetically-normal-acute-myeloid-leukemia
#14
Dimitrios Papaioannou, Deedra Nicolet, Stefano Volinia, Krzysztof Mrózek, Pearlly Yan, Ralf Bundschuh, Andrew J Carroll, Jessica Kohlschmidt, William Blum, Bayard L Powell, Geoffrey L Uy, Jonathan E Kolitz, Eunice S Wang, Ann-Kathrin Eisfeld, Shelley J Orwick, David M Lucas, Michael A Caligiuri, Richard M Stone, John C Byrd, Ramiro Garzon, Clara D Bloomfield
Long non-coding RNAs are a novel class of RNA molecules, which are increasingly recognized as important molecular players in solid and hematologic malignancies. Herein we investigated whether long non-coding RNA expression is associated with clinical and molecular features, as well as outcome of younger adults (aged <60 years) with de novo cytogenetically normal acute myeloid leukemia. Whole transcriptome profiling (RNA-seq) was performed in a training (n=263) and a validation set (n=114). Using the training set, we identified 24 long non-coding RNAs associated with event-free survival...
May 4, 2017: Haematologica
https://www.readbyqxmd.com/read/28472080/transcriptome-analysis-of-muskrat-scented-glands-degeneration-mechanism
#15
Yimeng Li, Tianxiang Zhang, Juntong Zhou, Shuang Yang, Mengyuan Fan, Xiaoning Sun, Meishan Zhang, Shanghua Xu, Muha Cha, Xiaolong Hu, Lei Qi, Shaobi Lin, Shuqiang Liu, Defu Hu
The scented gland, a musk-secreting organ of male muskrats, shows clear seasonal changes. When entering the secreting season in March, scented glands gradually increase in size and active secretion starts. In September, scented glands become gradually smaller and secretion decreases. By November, scented glands are gradually replaced by adipose tissue. In this study, six healthy adult male muskrats were analysed: three from the secreting season (March) and three from the non-secreting season (November). Using RNA-Seq analysis, gene expression profiles of scented glands from both seasons were determined...
2017: PloS One
https://www.readbyqxmd.com/read/28468592/whole-transcriptome-analysis-reveals-dysregulated-oncogenic-lncrnas-in-natural-killer-t-cell-lymphoma-and-establishes-mir155hg-as-a-target-of-prdm1
#16
Esra Baytak, Qiang Gong, Burcu Akman, Hongling Yuan, Wing C Chan, Can Küçük
Natural killer/T-cell lymphoma is a rare but aggressive neoplasm with poor prognosis. Despite previous reports that showed potential tumor suppressors, such as PRDM1 or oncogenes associated with the etiology of this malignancy, the role of long non-coding RNAs in natural killer/T-cell lymphoma pathobiology has not been addressed to date. Here, we aim to identify cancer-associated dysregulated long non-coding RNAs and signaling pathways or biological processes associated with these long non-coding RNAs in natural killer/T-cell lymphoma cases and to identify the long non-coding RNAs transcriptionally regulated by PRDM1...
May 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28466200/myc-and-raf-key-effectors-in-cellular-signaling-and-major-drivers-in-human-cancer
#17
Eduard Stefan, Klaus Bister
The prototypes of the human MYC and RAF gene families are orthologs of animal proto-oncogenes that were originally identified as transduced alleles in the genomes of highly oncogenic retroviruses. MYC and RAF genes are now established as key regulatory elements in normal cellular physiology, but also as major cancer driver genes. Although the predominantly nuclear MYC proteins and the cytoplasmic RAF proteins have different biochemical functions, they are functionally linked in pivotal signaling cascades and circuits...
May 3, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28465658/impact-of-obesity-with-impaired-glucose-tolerance-on-retinal-degeneration-in-a-rat-model-of-metabolic-syndrome
#18
Kishore Kumar Godisela, Singareddy Sreenivasa Reddy, Chekkilla Uday Kumar, Natarajan Saravanan, Paduru Yadagiri Reddy, Monica M Jablonski, Radha Ayyagari, Geereddy Bhanuprakash Reddy
PURPOSE: Metabolic syndrome (MetS) is associated with several degenerative diseases, including retinal degeneration. Previously, we reported on progressive retinal degeneration in a spontaneous obese rat (WNIN/Ob) model. In this study, we investigated the additional effect of impaired glucose tolerance (IGT), an essential component of MetS, on retinal degeneration using the WNIN/GR-Ob rat model. METHODS: The retinal morphology and ultrastructure of WNIN/GR-Ob and age-matched littermate lean rats were studied by microscopy and immunohistochemistry...
2017: Molecular Vision
https://www.readbyqxmd.com/read/28460635/transcriptomic-profiling-and-quantitative-high-throughput-qhts-drug-screening-of-cdh1-deficient-hereditary-diffuse-gastric-cancer-hdgc-cells-identify-treatment-leads-for-familial-gastric-cancer
#19
Ina Chen, Lesley Mathews-Greiner, Dandan Li, Abisola Abisoye-Ogunniyan, Satyajit Ray, Yansong Bian, Vivek Shukla, Xiaohu Zhang, Raj Guha, Craig Thomas, Berkley Gryder, Athina Zacharia, Joal D Beane, Sarangan Ravichandran, Marc Ferrer, Udo Rudloff
BACKGROUND: Patients with hereditary diffuse gastric cancer (HDGC), a cancer predisposition syndrome associated with germline mutations of the CDH1 (E-cadherin) gene, have few effective treatment options. Despite marked differences in natural history, histopathology, and genetic profile to patients afflicted by sporadic gastric cancer, patients with HDGC receive, in large, identical systemic regimens. The lack of a robust preclinical in vitro system suitable for effective drug screening has been one of the obstacles to date which has hampered therapeutic advances in this rare disease...
May 1, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28455421/therapeutic-rationale-to-target-highly-expressed-cdk7-conferring-poor-outcomes-in-triple-negative-breast-cancer
#20
Bo Li, Triona Ní Chonghaile, Yue Fan, Stephen Madden, Rut Klinger, Aisling E O'Connor, Louise Walsh, Gillian O'Hurley, Girish Mallya Udupi, Jesuchristopher Joseph, Finbarr Tarrant, Emer Conroy, Alexander Gaber, Suet-Feung Chin, Helen A Bardwell, Elena Provenzano, John Crown, Thierry Dubois, Sabine C Linn, Karin Jirstrom, Carlos Caldas, Darran O'Connor, William M Gallagher
Triple-negative breast cancer (TNBC) patients commonly exhibit poor prognosis and high relapse after treatment, but there remains a lack of biomarkers and effective targeted therapies for this disease. Here, we report evidence highlighting the cell cycle-related kinase CDK7 as a driver and candidate therapeutic target in TNBC. Using publicly available transcriptomic data from a collated set of TNBC patients (n = 383) and the METABRIC TNBC dataset (n = 217), we found CDK7 mRNA levels to be correlated with patient prognosis...
April 28, 2017: Cancer Research
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