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https://www.readbyqxmd.com/read/29155520/high-expression-level-of-long-non-coding-rna-hotair-is-associated-with-poor-overall-survival-in-gastric-cancer-patients-evidence-from-meta-analysis
#1
Mingxu Da, Jichun Ma, Yongbin Zhang, Jian Yang, Jibin Yao, Boyuan Huang, Hong Ma, Long Ge
PURPOSE: Although several studies have investigated the association between the development of gastric cancer (GC) and the expression level of long non-coding (lnc) RNA HOTAIR, no clear evidence about whether its expression is associated with the overall survival (OS) of GC patients exists. In this study we tried to explore the association between lncRNA HOTAIR expression levels with OS and other clinical features in GC patients. METHODS: Databases including PubMed, EMBASE and the Cochrane Library were used to search eligible studies...
July 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29141248/association-of-functional-genetic-variants-of-hotair-with-hepatocellular-carcinoma-hcc-susceptibility-in-a-chinese-population
#2
Hao Li, Xian-Mei Tang, Yangchen Liu, Weizhen Li, Qiaoyun Chen, Yan Pan
BACKGROUND/AIMS: The HOX transcript antisense intergenic RNA (HOTAIR), a long non-coding RNA (lncRNA), plays an important role in the pathogenesis and progression of multiple tumors. The aim of the present study was to evaluate whether common single nucleotide polymorphisms (SNPs) in HOTAIR are related to hepatocellular carcinoma (HCC) susceptibility in a Chinese population. METHODS: We genotyped three SNPs of HOTAIR in a hepatocellular carcinoma (HCC) case-control study, including 482 cases and 520 control subjects...
November 15, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29138205/long-term-prognosis-of-young-breast-cancer-patients-%C3%A2-40-years-who-did-not-receive-adjuvant-systemic-treatment-protocol-for-the-paradigm-initiative-cohort-study
#3
Gwen Mhe Dackus, Natalie D Ter Hoeve, Mark Opdam, Willem Vreuls, Zsuzsanna Varga, Esther Koop, Stefan M Willems, Carolien Hm Van Deurzen, Emilie J Groen, Alicia Cordoba, Jos Bart, Antien L Mooyaart, Jan G van den Tweel, Vicky Zolota, Jelle Wesseling, Anna Sapino, Ewa Chmielik, Ales Ryska, Frederic Amant, Annegien Broeks, Ron Kerkhoven, Nikolas Stathonikos, Mitko Veta, Adri Voogd, Katarzyna Jozwiak, Michael Hauptmann, Marlous Hoogstraat, Marjanka K Schmidt, Gabe Sonke, Elsken van der Wall, Sabine Siesling, Paul J van Diest, Sabine C Linn
INTRODUCTION: Currently used tools for breast cancer prognostication and prediction may not adequately reflect a young patient's prognosis or likely treatment benefit because they were not adequately validated in young patients. Since breast cancers diagnosed at a young age are considered prognostically unfavourable, many treatment guidelines recommend adjuvant systemic treatment for all young patients. Patients cured by locoregional treatment alone are, therefore, overtreated. Lack of prognosticators for young breast cancer patients represents an unmet medical need and has led to the initiation of the PAtients with bReAst cancer DIaGnosed preMenopausally (PARADIGM) initiative...
November 14, 2017: BMJ Open
https://www.readbyqxmd.com/read/29127278/the-north-american-bullfrog-draft-genome-provides-insight-into-hormonal-regulation-of-long-noncoding-rna
#4
S Austin Hammond, René L Warren, Benjamin P Vandervalk, Erdi Kucuk, Hamza Khan, Ewan A Gibb, Pawan Pandoh, Heather Kirk, Yongjun Zhao, Martin Jones, Andrew J Mungall, Robin Coope, Stephen Pleasance, Richard A Moore, Robert A Holt, Jessica M Round, Sara Ohora, Branden V Walle, Nik Veldhoen, Caren C Helbing, Inanc Birol
Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there are currently no genomic resources for the former, important group of amphibians. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines...
November 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/29121981/intrinsic-dna-curvature-in-trypanosomes
#5
Pablo Smircich, Najib M El-Sayed, Beatriz Garat
BACKGROUND: Trypanosoma cruzi and Trypanosoma brucei are protozoan parasites causing Chagas disease and African sleeping sickness, displaying unique features of cellular and molecular biology. Remarkably, no canonical signals for RNA polymerase II promoters, which drive protein coding genes transcription, have been identified so far. The secondary structure of DNA has long been recognized as a signal in biological processes and more recently, its involvement in transcription initiation in Leishmania was proposed...
November 9, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29119346/structure-target-specificity-and-expression-of-pn_lnc_n13-a-long-non-coding-rna-differentially-expressed-in-apomictic-and-sexual-paspalum-notatum
#6
Ana Ochogavía, Giulio Galla, José Guillermo Seijo, Ana María González, Michele Bellucci, Fulvio Pupilli, Gianni Barcaccia, Emidio Albertini, Silvina Pessino
KEY MESSAGE: ncRNA PN_LNC_N13 shows contrasting expression in reproductive organs of sexual and apomictic Paspalum notatum genotypes. Apomictic plants set genetically maternal seeds whose embryos derive by parthenogenesis from unreduced egg cells, giving rise to clonal offspring. Several Paspalum notatum apomixis related genes were identified in prior work by comparative transcriptome analyses. Here, one of these candidates (namely N13) was characterized. N13 belongs to a Paspalum gene family including 30-60 members, of which at least eight are expressed at moderate levels in florets...
November 8, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29108274/chromosome-preference-of-disease-genes-and-vectorization-for-the-prediction-of-non-coding-disease-genes
#7
Hui Peng, Chaowang Lan, Yuansheng Liu, Tao Liu, Michael Blumenstein, Jinyan Li
Disease-related protein-coding genes have been widely studied, but disease-related non-coding genes remain largely unknown. This work introduces a new vector to represent diseases, and applies the newly vectorized data for a positive-unlabeled learning algorithm to predict and rank disease-related long non-coding RNA (lncRNA) genes. This novel vector representation for diseases consists of two sub-vectors, one is composed of 45 elements, characterizing the information entropies of the disease genes distribution over 45 chromosome substructures...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29106417/high-throughput-annotation-of-full-length-long-noncoding-rnas-with-capture-long-read-sequencing
#8
Julien Lagarde, Barbara Uszczynska-Ratajczak, Silvia Carbonell, Sílvia Pérez-Lluch, Amaya Abad, Carrie Davis, Thomas R Gingeras, Adam Frankish, Jennifer Harrow, Roderic Guigo, Rory Johnson
Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines targeted RNA capture with third-generation long-read sequencing. Here we present an experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues that resulted in novel transcript models for 3,574 and 561 gene loci, respectively...
November 6, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29099871/the-role-of-h19-a-long-non-coding-rna-in-mouse-liver-postnatal-maturation
#9
Chad Pope, Stephanie C Piekos, Liming Chen, Shashank Mishra, Xiao-Bo Zhong
H19 RNA is highly expressed at early postnatal ages and precipitously decreases at a specific time corresponding with increases in expression of genes important for mature liver function, such as drug metabolizing enzymes. H19's role in the regulation of liver maturation is currently unknown. Using an H19 knockout mouse model to determine the role of H19 in liver development, we quantified gene expression for insulin growth factor signaling, Wnt signaling, key cytochrome P450 (P450) enzymes known to change as the liver develops, and fetal and adult plasma protein produced in liver...
2017: PloS One
https://www.readbyqxmd.com/read/29091957/hepatitis-e-virus-hev-egress-role-of-bst2-tetherin-and-interferon-induced-long-non-coding-rna-lncrna-bispr
#10
Daizy Paliwal, Prashant Joshi, Subrat Kumar Panda
BACKGROUND: The biology of Hepatitis E Virus (HEV), a common cause of epidemic and sporadic hepatitis, is still being explored. HEV exits liver through bile, a process which is essential for its natural transmission by feco-oral route. Though the process of this polarised HEV egress is not known in detail, HEV pORF3 and hepatocyte actin cytoskeleton have been shown to play a role. METHODS: Our transcriptome analysis in Hepatitis E virus (HEV) replicon transfected Huh7 cells at 24 and 72 hrs indicated that at 24hrs, both LncBISPR and BST2, expressed by a bidirectional promoter were highly upregulated whereas at 72 hrs, BST2 expression was comparatively reduced accompanied by normal levels of BISPR...
2017: PloS One
https://www.readbyqxmd.com/read/29079634/small-rna-mediated-regulation-of-dna-dosage-in-the-ciliate-oxytricha
#11
Jaspreet S Khurana, Derek Clay, Sandrine Moreira, Xing Wang, Laura F Landweber
Dicer-dependent small non-coding RNAs play important roles in gene regulation in a wide variety of organisms. Endogenous small interfering RNAs (siRNAs) are part of an ancient pathway of transposon control in plants and animals. The ciliate, Oxytricha trifallax, has approximately 16,000 gene-sized chromosomes in its somatic nucleus. Long non-coding RNAs establish high ploidy levels at the onset of sexual development, but the factors that regulate chromosome copy numbers during cell division and growth have been a mystery...
October 27, 2017: RNA
https://www.readbyqxmd.com/read/29056500/emerging-role-of-non-coding-rna-in-oral-cancer
#12
REVIEW
Fatemeh Momen-Heravi, Shashi Bala
Oral squamous cell carcinoma (OSCC) is characterized by genomic and epigenomic alterations. However, the mechanisms underlying oral squamous cell carcinoma tumorigenesis and progression remain to be elucidated. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and extracellular RNAs (exRNAs) are emerging groups of regulatory RNAs, which possess low or no protein-coding potential. Emerging lines of evidence indicates that deregulated expression of lncRNAs and circular RNAs are associated with the induction and progression of various cancers, including oral cancer, through epigenetic, transcriptional, and post-transcriptional alterations...
October 19, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/29053596/elucidating-the-role-of-host-long-non-coding-rna-during-viral-infection-challenges-and-paths-forward
#13
REVIEW
David J Lemler, Hayden N Brochu, Fang Yang, Erin A Harrell, Xinxia Peng
Research over the past decade has clearly shown that long non-coding RNAs (lncRNAs) are functional. Many lncRNAs can be related to immunity and the host response to viral infection, but their specific functions remain largely elusive. The vast majority of lncRNAs are annotated with extremely limited knowledge and tend to be expressed at low levels, making ad hoc experimentation difficult. Changes to lncRNA expression during infection can be systematically profiled using deep sequencing; however, this often produces an intractable number of candidate lncRNAs, leaving no clear path forward...
October 20, 2017: Vaccines
https://www.readbyqxmd.com/read/29039502/long-non%C3%A2-coding-rna-hottip-promotes-hepatocellular-carcinoma-tumorigenesis-and-development-a-comprehensive-investigation-based-on-bioinformatics-qrt%C3%A2-pcr-and-meta%C3%A2-analysis-of-393-cases
#14
Yu Zhang, Jia-Cheng Huang, Kai-Teng Cai, Xi-Bing Yu, You-Rong Chen, Wen-Ya Pan, Ze-Liang He, Jun Lv, Zhen-Bo Feng, Gang Chen
HOTTIP functions as an independent biomarker in multiple cancers. However, the role of HOTTIP in hepatocellular carcinoma (HCC) remains unclear. In this study, we sought to investigate the HOTTIP expression in HCC and normal liver. We combined quantitative reverse transcription-polymerase chain reactions (qRT‑PCR), Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), Multi Experiment Matrix (MEM) and Oncomine database to assess the clinical role and the potential molecular mechanism of HOTTIP in HCC...
December 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29036592/gain-and-loss-of-small-rna-classes-characterization-of-small-rnas-in-the-parasitic-nematode-family-strongyloididae
#15
Anja Holz, Adrian Streit
The nematode family Strongyloididae is of particular interest because it contains important parasites of medical and veterinary relevance. In addition, species of this family can form parasitic and free-living generations and it also occupies an interesting phylogenetic position within the nematodes. Nematodes differ in several ways from other taxa with respect to their small non-coding RNAs. Recent comparative studies revealed that there is also considerable variability within the nematodes. However, no Strongyloididae species or close relative was included in these studies...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29032575/decreased-expression-of-ifng-as1-ifng-and-il-1b-inflammatory-genes-in-medicated-schizophrenia-and-bipolar-patients
#16
Hannaneh Ghafelehbashi, Majid Pahlevan Kakhki, Lara Kular, Sahar Moghbelinejad, Seyyed Hossein Ghafelehbashi
Although aberrant expression of cytokines such as IL-1B and IFNG in blood from psychiatric patients supports a role of inflammation in the pathogenesis of disease, little is known about mechanisms underlying their regulation. We aimed to evaluate the putative role of IFNG-AS1 long non-coding RNA (lncRNA) in controlling of IFNG locus in schizophrenia (SZ) and Bipolar (BP) patients. We analyzed the expression levels of IFNG-AS1 long non-coding RNA, and IFNG and IL-1B mRNAs in blood cells from 27 SZ and 30 BP medicated patients and in 32 healthy controls...
October 15, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/29029461/prognostic-value-of-long-non-coding-rna-tug1-in-various-tumors
#17
Na Li, Ke Shi, Xinmei Kang, Wei Li
Taurine up-regulated gene 1 (TUG1) is a long non-coding RNA (lncRNA), has been reported that be dysregulated in various tumors, involved in proliferation and apoptosis in a variety of tumor cells. To detect the clinical significance of TUG1 expression in tumor patients, we carried out current systematic review and meta-analysis investigating its relation with the prognosis and clinicopathological features of cancers. A total of 15 studies comprise 1560 patients were analyzed. The pooled results showed that no significant relationship between high TUG1 expression and overall survival (OS) (HR = 1...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29022495/genetic-polymorphisms-of-hotair-gene-are-associated-with-the-risk-of-breast-cancer-in-a-sample-of-southeast-iranian-population
#18
Shekoufeh Hassanzarei, Mohammad Hashemi, Hedieh Sattarifard, Seyed Mehdi Hashemi, Gholamreza Bahari, Saeid Ghavami
There is an increasing body of evidence which highlights the critical functions of long non-coding RNAs in the carcinogenicity mechanism of a variety of cancers. It has been reported that HOX transcript antisense intergenic RNA, a member of long non-coding RNA family, increases breast cancer risk. To date, no data regarding the association between HOX transcript antisense intergenic RNA polymorphisms and the risk of breast cancer development has been reported in Iran. Here, we examine the possible association between HOX transcript antisense intergenic RNA gene polymorphisms and breast cancer in a sample of southeast Iranian female population...
October 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28989584/expression-analysis-of-long-non-coding-pcat-1in-breast-cancer
#19
Shaghayegh Sarrafzadeh, Lobat Geranpayeh, Soudeh Ghafouri-Fard
Background: The prostate cancer-associated non-coding RNA transcript 1 (PCAT-1) is a newly identified long non- coding RNA whose participation in tumorigenesis of a variety of cancers has been observed. In the present study, we aimed at analysis of its expression in breast cancer patients. Materials and Methods: The expression of PCAT-1 was assessed using real-time reverse transcription polymerase chain reaction in tumor samples obtained from 47newly diagnosed breast cancer patients as well as their corresponding adjacent non-cancerous tissues (ANCTs)...
July 1, 2017: International Journal of Hematology-oncology and Stem Cell Research
https://www.readbyqxmd.com/read/28979716/epigenetics-of-gastroenteropancreatic-neuroendocrine-tumors-a-clinicopathologic-perspective
#20
REVIEW
Brendan M Finnerty, Katherine D Gray, Maureen D Moore, Rasa Zarnegar, Thomas J Fahey Iii
Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are a heterogeneous group of rare tumors whose site-specific tumor incidence and clinical behavior vary widely. Genetic alterations associated with familial inherited syndromes have been well defined; however, the genetic profile of sporadic tumors is less clear as their tumorigenesis does not appear to be controlled by classic oncogenes such as P53, RB, or KRAS. Even within GEP-NETs, there are no common oncogenic drivers; for example, DAXX/ATRX mutations are strongly implicated in the tumorigenesis of pancreatic but not small bowel NETs...
September 15, 2017: World Journal of Gastrointestinal Oncology
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