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https://www.readbyqxmd.com/read/28199989/presence-of-cancer-associated-mutations-in-exhaled-breath-condensates-of-healthy-individuals-by-next-generation-sequencing
#1
Omar Youssef, Aija Knuuttila, Päivi Piirilä, Tom Böhling, Virinder Sarhadi, Sakari Knuutila
Exhaled breath condensate (EBC) is a non-invasive source that can be used for studying different genetic alterations occurring in lung tissue. However, the low yield of DNA available from EBC has hampered the more detailed mutation analysis by conventional methods. We applied the more sensitive amplicon-based next generation sequencing (NGS) to identify cancer related mutations in DNA isolated from EBC. In order to apply any method for the purpose of mutation screening in cancer patients, it is important to clarify the incidence of these mutations in healthy individuals...
February 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28183795/med12-is-recurrently-mutated-in-middle-eastern-colorectal-cancer
#2
Abdul K Siraj, Tariq Masoodi, Rong Bu, Poyil Pratheeshkumar, Nasser Al-Sanea, Luai H Ashari, Alaa Abduljabbar, Samar Alhomoud, Fouad Al-Dayel, Fowzan S Alkuraya, Khawla S Al-Kuraya
OBJECTIVE: Colorectal cancer (CRC) is a common cancer and a leading cause of cancer deaths. Previous studies have identified a number of key steps in the evolution of CRC but our knowledge of driver mutations in CRC remains incomplete. Recognising the potential of studying different human populations to reveal novel insights in disease pathogenesis, we conducted genomic analysis of CRC in Saudi patients. DESIGN: In the discovery phase of the study, we conducted whole genome sequencing of tumour and corresponding germline DNA in 27 patients with CRC...
February 9, 2017: Gut
https://www.readbyqxmd.com/read/28171795/multifunctional-silver-nanocluster-hybrid-oligonucleotide-vehicle-for-cell-imaging-and-microrna-targeted-gene-silencing
#3
Hau-Yun Chen, Karunya Albert, Cheng-Che Wen, Pei-Ying Hsieh, Sih-Yu Chen, Nei-Chung Huang, Shen-Chuan Lo, Jen-Kun Chen, Hsin-Yun Hsu
Novel therapeutics is urgently needed to prevent cancer-related deaths. MicroRNAs that act as tumor suppressors have been recognized as a next-generation tumor therapy, and the restoration of tumor-suppressive microRNAs using microRNA replacements or mimics may be a less toxic, more effective strategy due to fewer off-target effects. Here, we designed the novel multifunctional oligonucleotide nanocarrier complex composed of a tumor-targeting aptamer sequence specific to mucin 1 (MUC1), poly-cytosine region for fluorescent silver nanocluster (AgNC) synthesis, and complimentary sequence for microRNA miR-34a loading...
January 30, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28143578/circular-rnas-in-human-cancer
#4
REVIEW
Yumin Wang, Yongzhen Mo, Zhaojian Gong, Xiang Yang, Mo Yang, Shanshan Zhang, Fang Xiong, Bo Xiang, Ming Zhou, Qianjin Liao, Wenling Zhang, Xiayu Li, Xiaoling Li, Yong Li, Guiyuan Li, Zhaoyang Zeng, Wei Xiong
CircRNAs are a novel type of RNAs. With the newly developed technology of next-generation sequencing (NGS), especially RNA-seq technology, over 30,000 circRNAs have already been found. Owing to their unique structure, they are more stable than linear RNAs. CircRNAs play important roles in the carcinogenesis of cancer. The expression of circRNAs is correlated with patients' clinical characteristics, and circRNAs play a vital role in many aspects of malignant phenotypes, including cell cycle, apoptosis, vascularization, and invasion; metastasis as a RNA sponge, binding to RBP; or translation...
January 31, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28096087/diffuse-large-b-cell-lymphoma-genotyping-on-the-liquid-biopsy
#5
Davide Rossi, Fary Diop, Elisa Spaccarotella, Sara Monti, Manuela Zanni, Silvia Rasi, Clara Deambrogi, Valeria Spina, Alessio Bruscaggin, Chiara Favini, Roberto Serra, Antonio Ramponi, Renzo Boldorini, Robin Foa', Gianluca Gaidano
Accessible and real-time genotyping for diagnostic, prognostic or treatment purposes is increasingly impelling in diffuse large B-cell lymphoma (DLBCL). Cell-free DNA (cfDNA) is shed into the blood by tumor cells undergoing apoptosis and can be used as source of tumor DNA for the identification of DLBCL mutations, clonal evolution, and genetic mechanisms of resistance. Here we aimed at tracking the basal DLBCL genetic profile and its modification upon treatment using plasma cfDNA. Ultra-deep targeted next generation sequencing of pre-treatment plasma cfDNA from DLBCL patients correctly discovered DLBCL-associated mutations that were represented in >20% of the alleles of the tumor biopsy with a >90% sensitivity and a ~100% specificity...
January 17, 2017: Blood
https://www.readbyqxmd.com/read/28008282/expression-and-functionality-of-trpv1-in-breast-cancer-cells
#6
Lea V Weber, Klaudia Al-Refae, Gerhard Wölk, Gabriele Bonatz, Janine Altmüller, Christian Becker, Günter Gisselmann, Hanns Hatt
Transient receptor potential (TRP) channels contribute to the regulation of intracellular calcium, which can promote cancer hallmarks in cases of dysregulation of gene transcription and calcium-dependent pro-proliferative or anti-apoptotic mechanisms. Several studies have begun to elucidate the roles of TRPV1, TRPV6, TRPM8, and TRPC1 in cancer progression; however, no study has examined the expression profiles of human TRP channels in breast cancer on a large scale. This study focused on the expression and functionality of TRPV1, a nonselective cation channel that was found to be expressed in different carcinoma tissues...
2016: Breast Cancer: Targets and Therapy
https://www.readbyqxmd.com/read/28007883/evidence-for-amino-acid-snorkeling-from-a-high-resolution-in-vivo-analysis-of-fis1-tail-anchor-insertion-at-the-mitochondrial-outer-membrane
#7
Abdurrahman Keskin, Emel Akdoğan, Cory D Dunn
Proteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of the Saccharomyces cerevisiae Fis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus...
February 2017: Genetics
https://www.readbyqxmd.com/read/28000891/expression-of-mir%C3%A2-26a-exhibits-a-negative-correlation-with-hmga1-and-regulates-cancer-progression-by-targeting-hmga1-in-lung-adenocarcinoma-cells
#8
Noboru Sekimoto, Ayako Suzuki, Yutaka Suzuki, Sumio Sugano
Lung cancer is the most common cause of cancer‑associated mortality worldwide, and the number of cases is increasing annually. Several studies have shown that microRNAs (miRNAs) control proliferation, differentiation, and apoptosis in various cell types, and increasing evidence indicates the presence of aberrant miRNA expression profiles and unique miRNA signaling pathways in several types of cancer. The present study aimed to identify miRNAs, which correlated specifically with the progression of lung cancer through the analysis of 57,100 transcripts and 1,341 small RNA expression profiles in 26 lung adenocarcinoma cell lines using next‑generation sequencing...
February 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27981244/evaluating-side-effects-of-nanoparticle-mediated-sirna-delivery-to-mesenchymal-stem-cells-using-next-generation-sequencing-and-enrichment-analysis
#9
Dominic W Malcolm, Janet E Sorrells, Daniel Van Twisk, Juilee Thakar, Danielle S W Benoit
RNA interference has immense potential to modulate cell functions. However, effective delivery of small interfering RNA (siRNA) while avoiding deleterious side effects has proven challenging. This study investigates both intended and unintended effects of diblock copolymer nanoparticle (NP) delivery of siRNA delivery to human mesenchymal stem cells (hMSC). Specifically, siRNA delivery was investigated at a range of NP-siRNA:hMSC ratios with a focus on the effects of NP-siRNA treatment on hMSC functions. Additionally, next generation RNA sequencing (RNAseq) was used with enrichment analysis to observe side effects in hMSC gene expression...
June 2016: Bioeng Transl Med
https://www.readbyqxmd.com/read/27957330/evidence-of-perturbed-germinal-center-dynamics-but-preserved-antibody-diversity-in-end-stage-renal-disease
#10
Kristian Assing, Christian Nielsen, Marianne Jakobsen, Alexandra Scholze, Mads Nybo, Grete Soerensen, Sussie Mortensen, Knud Vejen, Torben Barington, Claus Bistrup
INTRODUCTION: End-stage renal disease (ESRD) is associated with increased infectious susceptibility and with reduced vaccine responses consistent with compromised humoral immunity. Whether the compromised humoral immunity is due to reduced antibody diversity (reduced somatic hypermutation [SHM]) or altered germinal center (GC) dynamics is not known. The GC-derived chemokine CXCL13 as well as peripheral T follicular helper cells (pTFH) reflect GC dynamics, but have, similar to SHM, never been characterized in relation to ESRD...
June 2016: Immunity, Inflammation and Disease
https://www.readbyqxmd.com/read/27932991/cannabidiol-modulates-the-immunophenotype-and-inhibits-the-activation-of-the-inflammasome-in-human-gingival-mesenchymal-stem-cells
#11
Rosaliana Libro, Domenico Scionti, Francesca Diomede, Marco Marchisio, Gianpaolo Grassi, Federica Pollastro, Adriano Piattelli, Placido Bramanti, Emanuela Mazzon, Oriana Trubiani
Human Gingival Mesenchymal Stem Cells (hGMSCs) are multipotential cells that can expand and differentiate in culture under specific and standardized conditions. In the present study, we have investigated whether in vitro pre-treatment of hGMSCs with Cannabidiol (CBD) can influence their expression profile, improving the therapeutic potential of this cell culture. Following CBD treatment (5 μM) for 24 h, gene expression analysis through Next Generation Sequencing (NGS) has revealed several genes differentially expressed between CBD-treated hGMSCs (CBD-hGMSCs) and control cells (CTR-hGMSCs) that were linked to inflammation and apoptosis...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27918106/cannabidiol-activates-neuronal-precursor-genes-in-human-gingival-mesenchymal-stromal-cells
#12
Thangavelu Soundara Rajan, Sabrina Giacoppo, Domenico Scionti, Francesca Diomede, Gianpaolo Grassi, Federica Pollastro, Adriano Piattelli, Placido Bramanti, Emanuela Mazzon, Oriana Trubiani
In the last years, mesenchymal stromal cells (MSCs) from oral tissues have received considerable interest in regenerative medicine since they can be obtained with minimal invasive procedure and exhibit immunomodulatory properties. This study was aimed to investigate whether in vitro pre-treatment of MSCs obtained from human gingiva (hGMSCs) with Cannabidiol (CBD), a cannabinoid component produced by the plant Cannabis sativa, may promote human gingiva derived MSCs to differentiate toward neuronal precursor cells...
December 5, 2016: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/27826100/mutation-analysis-of-trps1-gene-including-core-promoter-5-utr-and-3-utr-regulatory-sequences-with-insight-into-their-organization
#13
Roman Solc, Michaela Klugerova, Josef Vcelak, Alice Baxova, Miloslav Kuklik, Jan Vseticka, Rastislav Beharka, Katerina Hirschfeldova
The TRPS1 protein is a potent regulator of proliferation, differentiation, and apoptosis. The TRPS1 gene aberrations are strongly associated with rare trichorhinophalangeal syndrome (TRPS) development. We have conducted MLPA analysis to capture deletion within the crucial 8q24.1 chromosomal region in combination with mutation analysis of TRPS1 gene including core promoter, 5'UTR, and 3'UTR sequences in nine TRPS patients. Low complexity or extent of untranslated regulatory sequences avoided them from analysis in previous studies...
January 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27793108/deep-multi-stage-transcriptome-of-the-schistosomiasis-vector-biomphalaria-glabrata-provides-platform-for-understanding-molluscan-disease-related-pathways
#14
Nathan J Kenny, Marta Truchado-García, Cristina Grande
BACKGROUND: The gastropod mollusc Biomphalaria glabrata is well known as a vector for the tropical disease schistosomiasis, which affects nearly 200 million people worldwide. Despite intensive study, our understanding of the genetic basis of B. glabrata development, growth and disease resistance is constrained by limited genetic resources, constraints for which next-generation sequencing methods provide a ready solution. METHODS: Illumina sequencing and de novo assembly using the Trinity program was used to generate a high-quality transcriptomic dataset spanning the entirety of in ovo development in schistosomiasis-free B...
October 28, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27775669/towards-stratified-medicine-in-plasma-cell-myeloma
#15
REVIEW
Philip Egan, Stephen Drain, Caroline Conway, Anthony J Bjourson, H Denis Alexander
Plasma cell myeloma is a clinically heterogeneous malignancy accounting for approximately one to 2% of newly diagnosed cases of cancer worldwide. Treatment options, in addition to long-established cytotoxic drugs, include autologous stem cell transplant, immune modulators, proteasome inhibitors and monoclonal antibodies, plus further targeted therapies currently in clinical trials. Whilst treatment decisions are mostly based on a patient's age, fitness, including the presence of co-morbidities, and tumour burden, significant scope exists for better risk stratification, sub-classification of disease, and predictors of response to specific therapies...
October 21, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27760824/rna-interference-directed-against-the-transglutaminase-gene-triggers-dysbiosis-of-gut-microbiota-in-drosophila
#16
Sanae Sekihara, Toshio Shibata, Mai Hyakkendani, Shun-Ichiro Kawabata
We recently reported that transglutaminase (TG) suppresses immune deficiency pathway-controlled antimicrobial peptides (IMD-AMPs), thereby conferring immune tolerance to gut microbes, and that RNAi of the TG gene in flies decreases the lifespan compared with non-TG-RNAi flies. Here, analysis of the bacterial composition of the Drosophila gut by next-generation sequencing revealed that gut microbiota comprising one dominant genus of Acetobacter in non-TG-RNAi flies was shifted to that comprising two dominant genera of Acetobacter and Providencia in TG-RNAi flies...
November 25, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27660025/enrichment-and-verification-of-differentially-expressed-mirnas-in-bursa-of-fabricius-in-two-breeds-of-duck
#17
Jun Luo, Junying Liu, Hehe Liu, Tao Zhang, Jiwen Wang, Hua He, Chunchun Han
The bursa of Fabricius (BF) is a central humoral immune organ belonging to avian specifically. Recent studies had suggested that miRNAs were active regulators involved in the immune processes. This study was to investigate the possible differences of the BF at miRNA level between two genetically disparate duck breeds. Using Illumina next-generation sequencing, the data showed that there were 66 differentially expressed miRNAs and 28 novel miRNAs in bursa. A set of abundant miRNAs (i.e., let-7, miR-146a-5p, miR-21-5p, miR-17~92) which involved in immunity and disease were detected and the predicted target genes of the novel miRNAs were associated with duck high anti-adversity ability...
September 16, 2016: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/27568792/micrornas-in-chronic-lymphocytic-leukemia-an-old-disease-with-new-genetic-insights
#18
Maria Ciccone, George A Calin
Chronic lymphocytic leukemia (CLL) is the most common leukemia among adult population in western country. In the last decade, several findings have substantially revolutionized the old concept that CLL is a disease originating from mature, not-dividing cell with indolent clinical course. Notably, next generation sequencing (NGS) has contributed to deepen the knowledge of the cellular networks that imply the onset and the progression of CLL. Among genetic aberrations that are recurrently observed in B-cells from patients with CLL, microRNA deregulation represented the first epigenetic mechanism that has been identified...
2016: MicroRNA
https://www.readbyqxmd.com/read/27551494/functional-characterization-of-the-ectopically-expressed-olfactory-receptor-2at4-in-human-myelogenous-leukemia
#19
S Manteniotis, S Wojcik, P Brauhoff, M Möllmann, L Petersen, J R Göthert, W Schmiegel, U Dührsen, G Gisselmann, H Hatt
The olfactory receptor (OR) family was found to be expressed mainly in the nasal epithelium. In the last two decades members of the OR family were detected to be functional expressed in different parts of the human body such as in liver, prostate or intestine cancer cells. Here, we detected the expression of several ORs in the human chronic myelogenous leukemia (CML) cell line K562 and in white blood cells of clinically diagnosed acute myeloid leukemia (AML) patients by RT-PCR and next-generation sequencing...
2016: Cell Death Discovery
https://www.readbyqxmd.com/read/27542260/role-of-high-expression-levels-of-stk39-in-the-growth-migration-and-invasion-of-non-small-cell-type-lung-cancer-cells
#20
Zhao Li, Wenzhuo Zhu, Liwen Xiong, Xiaobo Yu, Xi Chen, Qiang Lin
Non-small cell type lung cancer (NSCLC) is the most common malignancy and the leading cause of cancer related mortality. In this study, serine/threonine kinase 39 (STK39) was identified as an up-regulated gene in NSCLC tissues by next-generation RNA sequencing. Although STK39 gene polymorphisms may be prognostic of overall survival in patients with early stage NSCLC, the roles of STK39 in NSCLC cancer are poorly understood. In the current study, Genome Set Enrichment Analysis (GSEA) on the RNA-seq data of NSCLC specimens indicated that cancer-related process and pathways, including metastasis, cell cycle, apoptosis and p38 pathway, were significantly correlated with STK39 expression...
September 20, 2016: Oncotarget
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