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https://www.readbyqxmd.com/read/29343745/malaria-infected-red-blood-cells-release-small-regulatory-rnas-through-extracellular-vesicles
#1
Kehinde Adebayo Babatunde, Smart Mbagwu, María Andrea Hernández-Castañeda, Swamy R Adapa, Michael Walch, Luis Filgueira, Laurent Falquet, Rays H Y Jiang, Ionita Ghiran, Pierre-Yves Mantel
The parasite Plasmodium falciparum causes the most severe form of malaria. Cell communication between parasites is an important mechanism to control population density and differentiation. The infected red blood cells (iRBCs) release small extracellular vesicles (EVs) that transfer cargoes between cells. The EVs synchronize the differentiation of the asexual parasites into gametocytes to initiate the transmission to the mosquito. Beside their role in parasite communication, EVs regulate vascular function. So far, the exact cargoes responsible for cellular communication remain unknown...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320459/the-landscape-of-small-non-coding-rnas-in-triple-negative-breast-cancer
#2
Yan Guo, Hui Yu, Jing Wang, Quanhu Sheng, Shilin Zhao, Ying-Yong Zhao, Brian D Lehmann
Triple-negative breast cancer (TNBC) is an operational term for breast cancers lacking targetable estrogen receptor expression and HER2 amplifications. TNBC is, therefore, inherently heterogeneous, and is associated with worse prognosis, greater rates of metastasis, and earlier onset. TNBC displays mutational and transcriptional diversity, and distinct mRNA transcriptional subtypes exhibiting unique biology. High-throughput sequencing has extended cancer research far beyond protein coding regions that include non-coding small RNAs, such as miRNA, isomiR, tRNA, snoRNAs, snRNA, yRNA, 7SL, and 7SK...
January 10, 2018: Genes
https://www.readbyqxmd.com/read/29287594/comprehensive-molecular-biomarker-identification-in-breast-cancer-brain-metastases
#3
Hans-Juergen Schulten, Mohammed Bangash, Sajjad Karim, Ashraf Dallol, Deema Hussein, Adnan Merdad, Fatma K Al-Thoubaity, Jaudah Al-Maghrabi, Awatif Jamal, Fahad Al-Ghamdi, Hani Choudhry, Saleh S Baeesa, Adeel G Chaudhary, Mohammed H Al-Qahtani
BACKGROUND: Breast cancer brain metastases (BCBM) develop in about 20-30% of breast cancer (BC) patients. BCBM are associated with dismal prognosis not at least due to lack of valuable molecular therapeutic targets. The aim of the study was to identify new molecular biomarkers and targets in BCBM by using complementary state-of-the-art techniques. METHODS: We compared array expression profiles of three BCBM with 16 non-brain metastatic BC and 16 primary brain tumors (prBT) using a false discovery rate (FDR) p < 0...
December 29, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29283311/snornas-associate-with-mrna-3-processing-complex-new-wine-in-old-bottles
#4
Junjie Shi, Chunliu Huang, Shanshan Huang, Chengguo Yao
3' end processing is required for the maturation of all eukaryotic RNAs. Current model suggests that canonical mRNA 3' processing is carried out exclusively within a protein complex termed mRNA 3' processing complex. In a recent study, by using RNA-biotin based pull-down assay and high-throughput sequencing, we reported that a subset of small nucleolar RNAs (snoRNAs) were physically associated with this macromolecular machinery. Through detailed characterization of one of these snoRNAs, SNORD50A, we revealed that non-coding RNA, such as snoRNA, may play a regulatory role in mRNA 3' processing...
December 28, 2017: RNA Biology
https://www.readbyqxmd.com/read/29235389/extracellular-genomic-biomarkers-of-osteoarthritis
#5
Emma Budd, Giovanna Nalesso, Ali Mobasheri
Introduction Osteoarthritis (OA), a chronic, debilitating and degenerative disease of the joints, is the most common form of arthritis. The seriousness of this prevalent and chronic disease is often overlooked. Disease modifying OA drug development is hindered by the lack of soluble biomarkers to detect OA early. The objective of OA biomarker research is to identify early OA prior to the appearance of radiographic signs and the development of pain. Areas covered This review has focused on extracellular genomic material that could serve as biomarkers of OA...
December 13, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/29219730/a-comprehensive-profile-of-circulating-rnas-in-human-serum
#6
Sinan Uğur Umu, Hilde Langseth, Cecilie Bucher-Johannessen, Bastian Fromm, Andreas Keller, Eckart Meese, Marianne Lauritzen, Magnus Leithaug, Robert Lyle, Trine B Rounge
Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA)...
December 8, 2017: RNA Biology
https://www.readbyqxmd.com/read/29196413/the-fungal-snornaome
#7
Sebastian Canzler, Peter F Stadler, Jana Schoor
Small nucleolar RNAs (snoRNAs) are essential players in the rRNA biogenesis due to their involvement in the nucleolytic processing of the precursor and the subsequent guidance of nucleoside modifications. Within the kingdom Fungi, merely a few species-specific surveys have explored their snoRNA repertoire. However, the wide range of the snoRNA landscape spanning all major fungal lineages has not been mapped so far, mainly because of missing tools for automatized snoRNA detection and functional analysis. For the first time, we report here a comprehensive inventory of fungal snoRNAs together with a functional analysis and an in-depth investigation of their evolutionary history including innovations, deletions, and target switches...
December 1, 2017: RNA
https://www.readbyqxmd.com/read/29189765/phylogenetic-analysis-of-the-snord116-locus
#8
Deborah J Good, Matthew A Kocher
The SNORD116 small nucleolar RNA locus (SNORD116@) is contained within the long noncoding RNA host gene SNHG14 on human chromosome 15q11-q13. The SNORD116 locus is a cluster of 28 or more small nucleolar (sno) RNAs; C/D box (SNORDs). Individual RNAs within the cluster are tandem, highly similar sequences, referred to as SNORD116-1, SNORD116-2, etc., with the entire set referred to as SNORD116@. There are also related SNORD116 loci on other chromosomes, and these additional loci are conserved among primates...
November 30, 2017: Genes
https://www.readbyqxmd.com/read/29175581/application-of-shape-reveals-in-vivo-rna-folding-under-normal-and-growth-stressed-conditions-in-the-human-parasite-entamoeba-histolytica
#9
Ashwini Kumar Ray, Sarah Naiyer, Shashi Shekhar Singh, Alok Bhattacharya, Sudha Bhattacharya
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a versatile sequence independent method to probe RNA structure in vivo and in vitro. It has so far been tried mainly with model organisms. We show that cells of Entamoeba histolytica, a protozoan parasite of humans are hyper-sensitive to the in vivo SHAPE reagent, NAI, and show rapid loss of viability and RNA integrity. We optimized treatment conditions with 5.8S rRNA and Eh_U3 snoRNA to obtain NAI-modification while retaining RNA integrity...
November 22, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29163812/identification-of-metastasis-associated-micrornas-in-serum-from-rectal-cancer-patients
#10
Robin Mjelle, Kjersti Sellæg, Pål Sætrom, Liv Thommesen, Wenche Sjursen, Eva Hofsli
MicroRNAs (miRNAs) are promising prognostic and diagnostic biomarkers due to their high stability in blood. Here we investigate the expression of miRNAs and other noncoding (nc) RNAs in serum of rectal cancer patients. Serum from 96 rectal cancer patients was profiled using small RNA sequencing and expression of small RNAs was correlated with the clinicopathological characteristics of the patients. Multiple classes of RNAs were detected, including miRNAs and fragments of tRNAs, snoRNAs, long ncRNAs, and other classes of RNAs...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155959/the-discovery-potential-of-rna-processing-profiles
#11
Amadís Pagès, Ivan Dotu, Joan Pallarès-Albanell, Eulàlia Martí, Roderic Guigó, Eduardo Eyras
Small non-coding RNAs (sncRNAs) are highly abundant molecules that regulate essential cellular processes and are classified according to sequence and structure. Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence and structure. We developed SeRPeNT, a new computational method that exploits reproducibility across replicates and uses dynamic time-warping and density-based clustering algorithms to identify, characterize and compare sncRNAs by harnessing the power of read profiles...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29141226/a-pan-cancer-analysis-of-the-expression-and-clinical-relevance-of-small-nucleolar-rnas-in-human-cancer
#12
Jing Gong, Yajuan Li, Chun-Jie Liu, Yu Xiang, Chunlai Li, Youqiong Ye, Zhao Zhang, David H Hawke, Peter K Park, Lixia Diao, John A Putkey, Liuqing Yang, An-Yuan Guo, Chunru Lin, Leng Han
Increasing evidence has demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types from The Cancer Genome Atlas. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29137313/rna-seq-reveals-distinctive-rna-profiles-of-small-extracellular-vesicles-from-different-human-liver-cancer-cell-lines
#13
Martina Berardocco, Annalisa Radeghieri, Sara Busatto, Marialucia Gallorini, Chiara Raggi, Clarissa Gissi, Igea D'Agnano, Paolo Bergese, Armando Felsani, Anna C Berardi
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29132127/a-functional-connection-between-dyskerin-and-energy-metabolism
#14
Alberto Angrisani, Nunzia Matrone, Valentina Belli, Rosario Vicidomini, Nunzia Di Maio, Mimmo Turano, Filippo Scialò, Paolo Antonio Netti, Antonio Porcellini, Maria Furia
The human DKC1 gene encodes dyskerin, an evolutionarily conserved nuclear protein whose overexpression represents a common trait of many types of aggressive sporadic cancers. As a crucial component of the nuclear H/ACA snoRNP complexes, dyskerin is involved in a variety of essential processes, including telomere maintenance, splicing efficiency, ribosome biogenesis, snoRNAs stabilization and stress response. Although multiple minor dyskerin splicing isoforms have been identified, their functions remain to be defined...
November 6, 2017: Redox Biology
https://www.readbyqxmd.com/read/29127445/negative-epistasis-in-experimental-rna-fitness-landscapes
#15
REVIEW
Devin P Bendixsen, Bjørn Østman, Eric J Hayden
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast...
November 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29106639/mndr-v2-0-an-updated-resource-of-ncrna-disease-associations-in-mammals
#16
Tianyu Cui, Lin Zhang, Yan Huang, Ying Yi, Puwen Tan, Yue Zhao, Yongfei Hu, Liyan Xu, Enmin Li, Dong Wang
Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA-disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA-disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA-disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29089527/cross-platform-analysis-of-transcriptomic-data-identifies-ageing-has-distinct-and-opposite-effects-on-tendon-in-males-and-females
#17
Louise I Pease, Peter D Clegg, Carole J Proctor, Daryl J Shanley, Simon J Cockell, Mandy J Peffers
The development of tendinopathy is influenced by a variety of factors including age, gender, sex hormones and diabetes status. Cross platform comparative analysis of transcriptomic data elucidated the connections between these entities in the context of ageing. Tissue-engineered tendons differentiated from bone marrow derived mesenchymal stem cells from young (20-24 years) and old (54-70 years) donors were assayed using ribonucleic acid sequencing (RNA-seq). Extension of the experiment to microarray and RNA-seq data from tendon identified gender specific gene expression changes highlighting disparity with existing literature and published pathways...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29064465/small-non-coding-rna-transcriptome-of-the-nci-60-cell-line-panel
#18
Erin A Marshall, Adam P Sage, Kevin W Ng, Victor D Martinez, Natalie S Firmino, Kevin L Bennewith, Wan L Lam
Only 3% of the transcribed human genome is translated into protein, and small non-coding RNAs from these untranslated regions have demonstrated critical roles in transcriptional and translational regulation of proteins. Here, we provide a resource that will facilitate cell line selection for gene expression studies involving sncRNAs in cancer research. As the most accessible and tractable models of tumours, cancer cell lines are widely used to study cancer development and progression. The NCI-60 panel of 59 cancer cell lines was curated to provide common models for drug screening in 9 tissue types; however, its prominence has extended to use in gene regulation, xenograft models, and beyond...
October 24, 2017: Scientific Data
https://www.readbyqxmd.com/read/29062204/repertoire-of-noncoding-rnas-in-corpus-luteum-of-early-pregnancy-in-buffalo-bubalus-bubalis
#19
A Jerome, S M K Thirumaran, S N Kala
AIM: The present study was designed to identify other noncoding RNAs (ncRNAs) in the corpus luteum (CL) during early pregnancy in buffalo. MATERIALS AND METHODS: For this study, CL (n=2) from two buffalo gravid uteri, obtained from the slaughter house, was transported to laboratory after snap freezing in liquid nitrogen (-196°C). The stage of pregnancy was determined by measuring the crown-rump region of the fetus. This was followed by isolation of RNA and deep sequencing...
September 2017: Veterinary World
https://www.readbyqxmd.com/read/29051386/ets2-anchors-the-prometastatic-function-of-mutant-p53-in-osteosarcoma
#20
REVIEW
Daniel D Liu, Yibin Kang
Mutations in the tumor suppressor p53 occur in a majority of human cancers. Some gain-of-function (GOF) p53 mutations endow tumor cells with increased metastatic ability, although our understanding of the underlying mechanism remains incomplete. In this issue of Genes & Development, Pourebrahim and colleagues (pp. 1847-1857) develop a new mouse model of osteosarcoma in which a GOF mutant p53 allele is expressed specifically in osteoblasts, while the tumor microenvironment remains wild type for p53, allowing for the study of cell-autonomous functions...
September 15, 2017: Genes & Development
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