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https://www.readbyqxmd.com/read/28427191/down-regulation-of-long-non-coding-rna-rp11-708h21-4-is-associated-with-poor-prognosis-for-colorectal-cancer-and-promotes-tumorigenesis-through-regulating-akt-mtor-pathway
#1
Longci Sun, Chunhui Jiang, Chunjie Xu, Hanbing Xue, Hong Zhou, Lei Gu, Ye Liu, Qing Xu
Long non-coding RNAs (lncRNAs) serve critical roles in cancer development and progression. Herein, through next generation RNA sequencing and experimental validations, we determined the expression status of RP11-708H21.4 in colorectal cancer (CRC) and explored its clinical significance and biological functions in CRC. Differentially expressed lncRNAs from CRC samples and corresponding normal mucosa tissues was screened through RNA sequencing, and RP11-708H21.4 was selected for further experimental validation...
March 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419837/identification-and-molecular-cloning-of-novel-transcripts-of-the-human-kallikrein-related-peptidase-10-klk10-gene-using-next-generation-sequencing
#2
Panagiotis G Adamopoulos, Christos K Kontos, Andreas Scorilas
Kallikreins (KLKs) form the largest group of serine proteases in the human genome sharing many structural and functional characteristics. Multiple alternative transcripts have been reported for most human KLKs, while many of them have been found aberrantly expressed in various human malignancies, thus possessing significant prognostic or/and diagnostic value. Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity, as it affects cell cycle control, proliferation, apoptosis, invasion, and metastasis...
April 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28404879/developmental-transcriptome-profiling-of-bovine-muscle-tissue-reveals-an-abundant-gosb-that-regulates-myoblast-proliferation-and-apoptosis
#3
Hui Li, Xuefeng Wei, Jiameng Yang, Dong Dong, Yongzhen Huang, Xianyong Lan, Martin Plath, Chuzhao Lei, Xinglei Qi, Yueyu Bai, Hong Chen
The formation of bovine skeletal muscle involves complex developmental and physiological processes that play a vital role in determining the quality of beef; however, the regulatory mechanisms underlying differences in meat quality are largely unknown. We conducted transcriptome analysis of bovine muscle tissues to compare gene expression profiles between embryonic and adult stages. Total RNAs from skeletal muscle of Qinchuan cattle at fetal and adult stages were used to construct libraries for Illumina next-generation sequencing using the Ribo-Zero RNA sequencing (RNA-Seq) method...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28365443/genetic-alterations-as-esophageal-tissues-from-squamous-dysplasia-to-carcinoma
#4
Xi Liu, Min Zhang, Songmin Ying, Chong Zhang, Runhua Lin, Jiaxuan Zheng, Guohong Zhang, Dongping Tian, Yi Guo, Caiwen Du, Yuping Chen, Shaobin Chen, Xue Su, Juan Ji, Wanting Deng, Xiang Li, Shiyue Qiu, Ruijing Yan, Zexin Xu, Yuan Wang, Yuanning Guo, Jiancheng Cui, Shanshan Zhuang, Huan Yu, Qi Zheng, Moshe Marom, Sitong Sheng, Guoqiang Zhang, Songnian Hu, Ruiqiang Li, Min Su
BACKGROUND & AIMS: Esophageal squamous cell carcinoma (ESCC) is most common subtype of esophageal cancer. Little is known about the genetic changes that occur in esophageal cells during development of ESCC. We performed next-generation sequence analyses of esophageal non-tumor, intraepithelial neoplasia (IEN), and ESCC tissues from the same patients to track genetic changes during tumor development. METHODS: We performed whole-genome, exome, or targeted sequence analyses of 227 esophageal tissue samples from 70 patients with ESCC undergoing resection at Shantou University Medical College in China from 2012 through 2015 (no patients had received chemotherapy or radiation therapy); we analyzed normal tissue, tissue with simple hyperplasia, dysplastic tissue (intraepithelial neoplasia, IEN), and ESCC tissues collected from different regions of the esophagus at the same time...
March 29, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28347747/molecular-characterization-of-human-osteoblast-derived-extracellular-vesicle-mrna-using-next-generation-sequencing
#5
Jess Morhayim, Jeroen van de Peppel, Amel Dudakovic, Hideki Chiba, Andre J van Wijnen, Johannes P van Leeuwen
Extracellular vesicles (EVs) are membrane-bound intercellular communication vehicles that transport proteins, lipids and nucleic acids with regulatory capacity between cells. RNA profiling using microarrays and sequencing technologies has revolutionized the discovery of EV-RNA content, which is crucial to understand the molecular mechanism of EV function. Recent studies have indicated that EVs are enriched with specific RNAs compared to the originating cells suggestive of an active sorting mechanism. Here, we present the comparative transcriptome analysis of human osteoblasts and their corresponding EVs using next-generation sequencing...
March 24, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28339495/microrna-expression-profiles-identify-disease-specific-alterations-in-systemic-lupus-erythematosus-and-primary-sj%C3%A3-gren-s-syndrome
#6
Ji-Qing Chen, Gábor Papp, Szilárd Póliska, Krisztina Szabó, Tünde Tarr, Bálint László Bálint, Péter Szodoray, Margit Zeher
The discovery of microRNAs (miRNAs) and their critical role in genetic control opened new avenues in understanding of various biological processes including immune cell lineage commitment, differentiation, proliferation and apoptosis. However, a given miRNA may have hundreds of different mRNA targets and a target might be regulated by multiple miRNAs, thus the characterisation of dysregulated miRNA expression profiles could give a better insight into the development of immunological disturbances in autoimmune diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28295289/long-non-coding-rna-neat1-is-a-transcriptional-target-of-p53-and-modulates-p53-induced-transactivation-and-tumor-suppressor-function
#7
Masashi Idogawa, Tomoko Ohashi, Yasushi Sasaki, Hiroshi Nakase, Takashi Tokino
p53 is one of the most important tumor suppressor genes, and the direct transcriptional targets of p53 must be explored to elucidate its functional mechanisms. Thus far, the p53 targets that have been primarily studied are protein-coding genes. Our previous study revealed that several long non-coding RNAs (lncRNAs) are direct transcriptional targets of p53, and knockdown of specific lncRNAs modulates p53-induced apoptosis. In this study, analysis of next-generation chromatin immunoprecipitation-sequencing (ChIP-seq) data for p53 revealed that the lncRNA NEAT1 is a direct transcriptional target of p53...
March 14, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28294689/genomics-signaling-and-treatment-of-waldenstr%C3%A3-m-macroglobulinemia
#8
Zachary R Hunter, Guang Yang, Lian Xu, Xia Liu, Jorge J Castillo, Steven P Treon
Next-generation sequencing has revealed recurring somatic mutations in Waldenström macroglobulinemia (WM). Commonly recurring mutations include MYD88 (95% to 97%), CXCR4 (30% to 40%), ARID1A (17%), and CD79B (8% to 15%). Diagnostic discrimination of WM from overlapping B-cell malignancies is aided by MYD88 mutation status. Transcription is affected by MYD88 and CXCR4 mutations and includes overexpression of genes involved in VDJ recombination, CXCR4 pathway signaling, and BCL2 family members. Among patients with MYD88 mutations, those with CXCR4 mutations show transcriptional silencing of tumor suppressors associated with acquisition of mutated MYD88...
February 13, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28246447/transcriptomic-comparison-of-primary-bovine-horn-core-carcinoma-culture-and-parental-tissue-at-early-stage
#9
Sharadindu Shil, R S Joshi, C G Joshi, A K Patel, Ravi K Shah, Namrata Patel, Subhash J Jakhesara, Sumana Kundu, Bhaskar Reddy, P G Koringa, D N Rank
AIM: Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn's SCC tissue and its early passage primary culture using next generation sequencing was the aim of this study. MATERIALS AND METHODS: Whole transcriptome sequencing of horn's SCC tissue and its early passage cells using Ion Torrent PGM were done...
January 2017: Veterinary World
https://www.readbyqxmd.com/read/28199989/presence-of-cancer-associated-mutations-in-exhaled-breath-condensates-of-healthy-individuals-by-next-generation-sequencing
#10
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...
March 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28183795/med12-is-recurrently-mutated-in-middle-eastern-colorectal-cancer
#11
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
#12
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...
April 1, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28143578/circular-rnas-in-human-cancer
#13
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
#14
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 Foà, 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. In this study, we aimed at tracking the basal DLBCL genetic profile and its modification upon treatment using plasma cfDNA. Ultra-deep targeted next generation sequencing of pretreatment plasma cfDNA from DLBCL patients correctly discovered DLBCL-associated mutations that were represented in >20% of the alleles of the tumor biopsy with >90% sensitivity and ∼100% specificity...
April 6, 2017: Blood
https://www.readbyqxmd.com/read/28008282/expression-and-functionality-of-trpv1-in-breast-cancer-cells
#15
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
#16
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
#17
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
#18
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: Bioengineering & Translational Medicine
https://www.readbyqxmd.com/read/27957330/evidence-of-perturbed-germinal-center-dynamics-but-preserved-antibody-diversity-in-end-stage-renal-disease
#19
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
#20
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
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