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Xueying Zhang, Ying Xu, Lulu Fu, Dandan Li, Xiaowei Dai, Lianlian Liu, Jingshun Zhang, Lianwen Zheng, Manhua Cui
BACKGROUND: Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine disorder in women of reproductive age and is commonly complicated by adverse endometrial outcomes. Long non-coding RNAs (lncRNAs) are a class of non-protein-coding transcripts that are more than 200 nucleotides in length. Accumulating evidence indicates that lncRNAs are involved in the development of various human diseases. Among these lncRNAs, lncRNA CD36-005 (CD36-005) is indicated to be associated with the pathogenesis of PCOS...
October 15, 2018: Reproductive Biology and Endocrinology: RB&E
Aldo H De-La-Cruz-Montoya, Eric G Ramírez-Salazar, Mayeli M Martínez-Aguilar, Pablo M González-de-la-Rosa, Manuel Quiterio, Cei Abreu-Goodger, Jorge Salmerón, Rafael Velázquez-Cruz
Osteoporosis is the most frequent disorder of bone metabolism, owing to an alteration between osteoclast and osteoblast activity, which results from the interaction of genetic, environmental, and epigenetic factors. microRNAs, small non-coding RNAs of around 22 nucleotides with important regulatory roles in gene regulation, that target mRNAs for post-transcriptional destabilization have been suggested as biomarkers in several disorders. In this work, we used small RNA sequencing to identify microRNAs from peripheral blood monocytes that were differentially expressed between non-osteoporotic and osteoporotic Mexican postmenopausal women, to elucidate the potential role of microRNAs as non-invasive marker candidates in osteoporosis...
October 15, 2018: Experimental Biology and Medicine
Changqing Ma, Bowen Liang, Bo Chang, Li Liu, Jiuying Yan, Yazhou Yang, Zhengyang Zhao
The red color of apples ( Malus domestica ) is an attractive trait for consumers. The green skinned "Granny Smith" cultivar develops red pigmentation after bagging treatment. DNA methylation plays an important role in various developmental processes in plants. To explore the possible functions of DNA methylation in the pigmentation of bagged "Granny Smith" apples, we first analyzed the anthocyanin content of fruit skin following treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC)...
October 12, 2018: International Journal of Molecular Sciences
Yun-Hu Zhao, Xiao-Lin Qin, Jie-Yi Yang, Yi-Wen Liao, Xing-Zhong Wu, He-Ping Zheng
OBJECTIVES: The aim of the present study was to identify the ceftriaxone resistance-related genes of N. gonorrhoeae. METHODS: We compared the differences in gene expression between the susceptibility (MIC=0.002-0.004μg/ml) and decreased susceptibility (MIC=0.125-0.5μg/ml) of isolates to ceftriaxone using RNA sequencing (RNA-Seq). RESULTS: The total RNAs of 10 clinical isolates were used to make libraries and generated an average of 24.07 Mb reads per sample; these were assembled into 1871 mRNA genes...
October 12, 2018: Journal of Global Antimicrobial Resistance
Zhong-Yang Xu, Chao Zhou, Ke-Feng Zhang, Yan-Ping Zheng
Ankylosing spondylitis (AS) is a common form of seronegative spondyloarthritis. We had identified differentially expressed genes (DEGs) in AS based on our previous RNA-sequencing results. Our study aimed to identify key genes in AS by integrated microarray analysis. In this present study, we identified 1328 DEGs between AS and normal control by using integrated analysis of two datasets derived from the Gene Expression Omnibus (GEO) database. Functional annotation of DEGs were performed. Pathways in cancer, Pancreatic cancer and Natural killer cell mediated cytotoxicity were significantly enriched pathways for DEGs...
October 12, 2018: Immunology Letters
Nathan P Cramer, Alexandru Korotcov, Asamoah Bosomtwi, Xiufen Xu, Derek Holman, Kathleen Whiting, Scott Jones, Andrew Hoy, Bernard J Dardzinski, Zygmunt Galdzicki
We sought to understand the mechanisms underlying cognitive deficits that are reported to affect non-native subjects following their prolonged stay and/or work at high altitude (HA). We found that mice exposed to a simulated environment of 5000 m exhibit deficits in hippocampal learning and memory accompanied by abnormalities in brain MR imaging. Exposure (1-8 months) to HA led to an increase in brain ventricular volume, a reduction in relative cerebral blood flow and changes in diffusion tensor imaging (DTI) derived parameters within the hippocampus and corpus callosum...
October 12, 2018: Experimental Neurology
Aaron S Mendez, Carolin Vogt, Jens Bohne, Britt A Glaunsinger
A number of viruses remodel the cellular gene expression landscape by globally accelerating messenger RNA (mRNA) degradation. Unlike the mammalian basal mRNA decay enzymes, which largely target mRNA from the 5' and 3' end, viruses instead use endonucleases that cleave their targets internally. This is hypothesized to more rapidly inactivate mRNA while maintaining selective power, potentially though the use of a targeting motif(s). Yet, how mRNA endonuclease specificity is achieved in mammalian cells remains largely unresolved...
October 13, 2018: Nucleic Acids Research
Kaushik Chanda, Srijit Das, Joyeeta Chakraborty, Sudha Bucha, Arindam Maitra, Raghunath Chatterjee, Debashis Mukhopadhyay, Nitai P Bhattacharyya
Altered expression levels of protein-coding genes and microRNAs have been implicated in the pathogenesis of Huntington's disease (HD). The involvement of other ncRNAs, especially long ncRNAs (lncRNA), is being realized recently and the related knowledge is still rudimentary. Using small RNA sequencing and PCR arrays we observed perturbations in the levels of 12 ncRNAs in HD mouse brain, eight of which had human homologs. Of these, Meg3, Neat1, and Xist showed a consistent and significant increase in HD cell and animal models...
October 15, 2018: RNA Biology
Zheying Zhang, Na Song, Yongxia Wang, Jiateng Zhong, Tengteng Gu, Liping Yang, Xianfeng Shen, Yuelin Li, Xin Yang, Xiangyu Liu, Rui Yang, Haijun Wang
Circular RNAs (circRNAs) play an important regulatory role in tumorigenesis. The aim of the present study was to analyze the circRNA expression network and elucidate its potential implications in colorectal cancer (CRC). The circRNA expression profile was analyzed in CRC tissues by RNA sequencing, and the functions of differentially expressed genes were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The circRNA network was predicted with bioinformatics. On the basis of the results, we identified 23 differentially expressed circRNAs in CRC; GO and KEGG analyses demonstrated that the changes in circRNAs were mainly associated with regulation of biological and metabolic processes through binding to other molecules...
October 15, 2018: Journal of Cellular Biochemistry
Ishaan Gupta, Paul G Collier, Bettina Haase, Ahmed Mahfouz, Anoushka Joglekar, Taylor Floyd, Frank Koopmans, Ben Barres, August B Smit, Steven A Sloan, Wenjie Luo, Olivier Fedrigo, M Elizabeth Ross, Hagen U Tilgner
Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes, but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far. Although single splicing events have been described for ≤200 single cells with statistical confidence, full-length mRNA analyses for hundreds of cells have not been reported. Single-cell short-read 3' sequencing enables the identification of cellular subtypes, but full-length mRNA isoforms for these cell types cannot be profiled...
October 15, 2018: Nature Biotechnology
Lin-Chen Li, Xin-Xin Yu, Yu-Wei Zhang, Ye Feng, Wei-Lin Qiu, Cheng-Ran Xu
Pancreatic endocrine cells, which are clustered in islets, regulate blood glucose stability and energy metabolism. The distinct cell types in islets, including insulin-secreting β cells, are differentiated from common endocrine progenitors during the embryonic stage. Immature endocrine cells expand via cell proliferation and mature during a long postnatal developmental period. However, the mechanisms underlying these processes are not clearly defined. Single-cell RNA-sequencing is a promising approach for the characterization of distinct cell populations and tracing cell lineage differentiation pathways...
September 30, 2018: Journal of Visualized Experiments: JoVE
Min Li, Jian Wang, Dewu Liu, Heping Huang
Growing evidence suggests that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are involved in the occurrence and development of tumors and fibrotic diseases. However, the integrated analysis of lncRNA and circRNA expression, alongside associated co‑expression and competing endogenous RNA (ceRNA) networks, has not yet been performed in human hypertrophic scars (HS). The present study compared the expression levels of lncRNAs, circRNAs and mRNAs in human HS and normal skin tissues by high‑throughput RNA sequencing...
October 15, 2018: Molecular Medicine Reports
Jingsheng Yuan, Lulu Tan, Zhijie Yin, Kaixiong Tao, Guobing Wang, Wenjia Shi, Jinbo Gao
Gastric cancer is currently the fourth most common cancer and the third leading cause of cancer‑associated mortality worldwide. Studies have identified that certain biomarkers contribute to the prognosis, diagnosis and treatment of gastric cancer. However, the biomarkers of gastric cancer are rarely used clinically. Therefore, it is imperative to define novel molecular networks and key genes to guide the further study and clinical treatment of gastric cancer. In the present study, raw RNA sequencing data and clinicopathological information on patients with gastric cancer were downloaded from The Cancer Genome Atlas, and a weighted gene co‑expression network analysis was conducted...
October 15, 2018: Oncology Reports
Sarah J Quillin, Adam J Hockenberry, Michael C Jewett, H Steven Seifert
Neisseria gonorrhoeae mounts a substantial transcriptional program in response to hydrogen peroxide (HP), a prominent reactive oxygen species (ROS) encountered during infection. We tested which strain FA1090 genes show differential transcript abundance in response to sublethal amounts of HP to differentiate HP-responsive signaling from widespread cellular death and dysregulation. RNA sequencing (RNA-Seq) revealed that 150 genes were significantly upregulated and 143 genes downregulated following HP exposure...
September 2018: MSystems
Zsolt Balázs, Dóra Tombácz, Attila Szűcs, Michael Snyder, Zsolt Boldogkői
No abstract text is available yet for this article.
2018: Frontiers in Genetics
Xin You, Yixin Zhao, Jing Sui, Xianbiao Shi, Yulu Sun, Jiahan Xu, Geyu Liang, Qingxiang Xu, Yongzhong Yao
Recent scientific evidence has suggested that long noncoding RNAs (lncRNAs) play an important part in tumorigenesis as an important member of competing endogenous RNAs (ceRNAs). Hundreds of RNA sequence data and relevant clinic information are freely accessible in The Cancer Genome Atlas (TCGA) datasets. However, the role of cancer-related lncRNAs in papillary thyroid cancer (PTC) is not fully understood yet. In this study, we identified 461 RNA sequencing data from TCGA. Subsequently, 45 lncRNAs, 21 miRNAs, and 78 mRNAs were chosen to construct a ceRNA network of PTC...
October 14, 2018: Cancer Medicine
Jean-David Fumet, Corentin Richard, Fanny Ledys, Quentin Klopfenstein, Philippe Joubert, Bertrand Routy, Caroline Truntzer, Andréanne Gagné, Marc-André Hamel, Camila Figueiredo Guimaraes, Bruno Coudert, Laurent Arnould, Laure Favier, Aurélie Lagrange, Sylvain Ladoire, Pierre Saintigny, Sandra Ortiz-Cuaran, Maurice Perol, Pascal Foucher, Paul Hofman, Marius Ilie, Sandy Chevrier, Romain Boidot, Valentin Derangere, François Ghiringhelli
BACKGROUND: No study has evaluated the predictive and prognostic role of CD8 and PD-L1 coexpression in non-small-cell lung cancer (NSCLC). METHODS: We analyzed RNA sequencing and/or immunohistochemistry staining in NSCLC patients from The Cancer Genome Atlas (n = 1016), and 34 metastatic NSCLC samples not treated by immunotherapy as prognostic cohorts. As predictive aspect of CD8 and PD-L1, we used 85 NSCLC patients treated with anti-PD-1. Two validation cohorts were used including 44 NSCLC patients treated with anti-PD-1 and an external cohort with different tumor types...
October 15, 2018: British Journal of Cancer
Laura Izquierdo, Laura Mateu, Juan José Lozano, Ruth Montalbo, Mercedes Ingelmo-Torres, Ascensión Gómez, Lluís Peri, Lourdes Mengual, Agustín Franco, Antonio Alcaraz
BACKGROUND: The pathogenesis of bladder pain syndrome (BPS) remains incompletely defined, and there is no standard treatment for BPS as yet. OBJECTIVE: To gain detailed insight into the disease pathobiology of BPS through comparative gene expression analysis of urine from BPS patients versus control individuals and, furthermore, to determine the efficacy of triamcinolone treatment in BPS patients in terms of the gene expression profiles in urine. DESIGN, SETTING, AND PARTICIPANTS: A prospective pilot study including 21 urine samples from patients with Hunner's lesions (n=6) and controls (n=9) between January and August 2017...
October 11, 2018: European Urology Focus
Jonathan D Mortison, Monica Schenone, Jacob A Myers, Ziyang Zhang, Linfeng Chen, Christie Ciarlo, Eamon Comer, S Kundhavai Natchiar, Steven A Carr, Bruno P Klaholz, Andrew G Myers
Apart from their antimicrobial properties, tetracyclines demonstrate clinically validated effects in the amelioration of pathological inflammation and human cancer. Delineation of the target(s) and mechanism(s) responsible for these effects, however, has remained elusive. Here, employing quantitative mass spectrometry-based proteomics, we identified human 80S ribosomes as targets of the tetracyclines Col-3 and doxycycline. We then developed in-cell click selective crosslinking with RNA sequence profiling (icCL-seq) to map binding sites for these tetracyclines on key human rRNA substructures at nucleotide resolution...
October 5, 2018: Cell Chemical Biology
Siavash Fazel Darbandi, Sarah E Robinson Schwartz, Qihao Qi, Rinaldo Catta-Preta, Emily Lin-Ling Pai, Jeffrey D Mandell, Amanda Everitt, Anna Rubin, Rebecca A Krasnoff, Sol Katzman, David Tastad, Alex S Nord, A Jeremy Willsey, Bin Chen, Matthew W State, Vikaas S Sohal, John L R Rubenstein
An understanding of how heterozygous loss-of-function mutations in autism spectrum disorder (ASD) risk genes, such as TBR1, contribute to ASD remains elusive. Conditional Tbr1 deletion during late mouse gestation in cortical layer 6 neurons (Tbr1layer6 mutants) provides novel insights into its function, including dendritic patterning, synaptogenesis, and cell-intrinsic physiology. These phenotypes occur in heterozygotes, providing insights into mechanisms that may underlie ASD pathophysiology. Restoring expression of Wnt7b largely rescues the synaptic deficit in Tbr1layer6 mutant neurons...
October 5, 2018: Neuron
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