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Gene function prediction

Yufeng Lv, Wenhao Wei, Zhong Huang, Zhichao Chen, Yuan Fang, Lili Pan, Xueqiong Han, Zihai Xu
PURPOSE: The aim of this study was to develop a novel long non-coding RNA (lncRNA) expression signature to accurately predict early recurrence for patients with hepatocellular carcinoma (HCC) after curative resection. PATIENTS AND METHODS: Using expression profiles downloaded from The Cancer Genome Atlas database, we identified multiple lncRNAs with differential expression between early recurrence (ER) group and non-early recurrence (non-ER) group of HCC. Least absolute shrinkage and selection operator (LASSO) for logistic regression models were used to develop a lncRNA-based classifier for predicting ER in the training set...
June 20, 2018: Hepatology Research: the Official Journal of the Japan Society of Hepatology
Sylvie Oddou-Muratorio, Julie Gauzere, Aurore Bontemps, Jean-François Rey, Etienne K Klein
Inter-individual variation in fecundities has major consequences on population evolutionary potential, through genetic drift and selection. Using two spatially explicit mating models that analyze the genotypes of seeds and seedlings, we investigated the variation of male and female fecundities within and among three European beech (Fagus sylvatica) stands situated along an altitudinal gradient. Female and male individual fecundity distributions were both skewed in this monoecious species, and we found a higher variance in female as compared to male fecundities...
June 20, 2018: Molecular Ecology
Michael B Burns, Emmanuel Montassier, Juan Abrahante, Sambhawa Priya, David E Niccum, Alexander Khoruts, Timothy K Starr, Dan Knights, Ran Blekhman
Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues...
June 20, 2018: PLoS Genetics
Jongmin Sim, Yeseul Kim, Hyunsung Kim, Su-Jin Shin, Dong-Hoon Kim, Seung Sam Paik, Kiseok Jang
Lung cancer is the most common cause of cancer-associated death worldwide. Postoperative relapse and subsequent metastasis result in a high mortality rate, even in early stage lung cancer. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level and are frequently dysregulated in various cancers. The aim of this study was to identify recurrence-associated miRNAs in early stage lung cancer. To screen for differentially expressed miRNAs related to postoperative recurrence, miRNA microarray data derived from stage I lung adenocarcinoma formalin-fixed paraffin-embedded (FFPE) tissue samples (n = 6) and publically available the Cancer Genome Atlas (TCGA) data were analyzed...
June 2018: Medicine (Baltimore)
Leda Coelewij, David Curtis
A number of important findings have recently emerged relevant to identifying genetic risk factors for schizophrenia. Findings using common variants point towards gene sets of interest and also demonstrate an overlap with other psychiatric and nonpsychiatric disorders. Imputation of variants of the gene for complement component 4 (C4) from GWAS data has shown that the predicted expression of the C4A product is associated with schizophrenia risk. Very rare variants disrupting SETD1A, RBM12 or NRXN1 have a large effect on risk...
June 20, 2018: Annals of Human Genetics
Yingcheng Wu, Jinhuan Wei, Yue Ming, Zhanghao Chen, Jinzhong Yu, Renfang Mao, Hao Chen, Guoxiong Zhou, Yihui Fan
The low survival of patients with pancreatic ductal adenocarcinoma (PDAC) makes the treatment of this disease one of the most challenging task in modern medicine. Here, by mining a large-scale cancer genome atlas data set of pancreatic cancer tissues, we identified 21 long noncoding RNAs (lncRNAs) that significantly associated with overall survival in patients with PDAC (P < .01). Further analysis revealed that 8 lncRNAs turned out to be independently correlated with patients' overall survival, and the risk score could be calculated based on their expression...
June 20, 2018: Journal of Cellular Biochemistry
Ru Yang, Suxuan Liu, Jian Wen, Leixi Xue, Yi Zhang, Dong Yan, Guokun Wang, Zhichun Liu
Acute kidney injury (AKI) results in retention of waste products and dysregulation of extracellular volume and electrolytes, thus leading to a variety of complications. Recent advances in long noncoding RNAs suggested their close relationship with disease progression. In the current study, we investigated the role and mechanism of maternally expressed gene 3 (MEG3) on AKI pathogenesis. Real-time polymerase chain reaction found that the expression of MEG3 was significantly increased in both kidney tissues and TKPTS cells induced by lipopolysaccharide (LPS)...
June 20, 2018: Journal of Cellular Biochemistry
Alcy Torres, Catherine A Brownstein, Sahil K Tembulkar, Kelsey Graber, Casie Genetti, Robin J Kleiman, Kathleen J Sweadner, Chrystal Mavros, Kevin X Liu, Niklas Smedemark-Margulies, Kiran Maski, Edward Yang, Pankaj B Agrawal, Jiahai Shi, Alan H Beggs, Eugene D'Angelo, Sarah Hope Lincoln, Devon Carroll, Fatma Dedeoglu, William A Gahl, Catherine M Biggs, Kathryn J Swoboda, Gerard T Berry, Joseph Gonzalez-Heydrich
Complex phenotypes may represent novel syndromes that are the composite interaction of several genetic and environmental factors. We describe an 9-year old male with high functioning autism spectrum disorder and Muckle-Wells syndrome who at age 5  years of age manifested perseverations that interfered with his functioning at home and at school. After age 6, he developed intermittent episodes of fatigue and somnolence lasting from hours to weeks that evolved over the course of months to more chronic hypersomnia...
September 2018: Molecular Genetics and Metabolism Reports
Meiwei Zhang, Yangfan Wang, Yangping Li, Wanru Li, Ruojiao Li, Xinran Xie, Shi Wang, Xiaoli Hu, Lingling Zhang, Zhenmin Bao
Neuropeptides play essential roles in regulation of reproduction and growth in marine molluscs. But their function in marine bivalves - a group of animals of commercial importance - is largely unexplored due to the lack of systematic identification of these molecules. In this study, we sequenced and analyzed the transcriptome of nerve ganglia of Yesso scallop Patinopecten yessoensis , from which 63 neuropeptide genes were identified based on BLAST and de novo prediction approaches, and 31 were confirmed by proteomic analysis using the liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
2018: Frontiers in Genetics
Federica Del Chierico, Francesca Abbatini, Alessandra Russo, Andrea Quagliariello, Sofia Reddel, Danila Capoccia, Romina Caccamo, Stefano Ginanni Corradini, Valerio Nobili, Francesco De Peppo, Bruno Dallapiccola, Frida Leonetti, Gianfranco Silecchia, Lorenza Putignani
Obesity levels, especially in children, have dramatically increased over the last few decades. Recently, several studies highlighted the involvement of gut microbiota in the pathophysiology of obesity. We investigated the composition of gut microbiota in obese adolescents and adults compared to age-matched normal weight (NW) volunteers in order to assemble age- and obesity-related microbiota profiles. The composition of gut microbiota was analyzed by 16S rRNA-based metagenomics. Ecological representations of microbial communities were computed, and univariate, multivariate, and correlation analyses performed on bacterial profiles...
2018: Frontiers in Microbiology
Annegret Lucke, Josef Böhm, Qendrim Zebeli, Barbara U Metzler-Zebeli
Dietary deoxynivalenol (DON) impairs the intestinal functions and performance in broiler chickens, whereas little is known about the effect of DON on the gastrointestinal microbiota. This study evaluated the impact of graded levels of dietary DON contamination on the cecal bacterial microbiota, their predicted metabolic abilities and short-chain fatty acid (SCFA) profiles in chickens. In using a single oral lipopolysaccharide (LPS) challenge we further assessed whether an additional intestinal stressor would potentiate DON-related effects on the cecal microbiota...
2018: Frontiers in Microbiology
Feng Shao, Mei Huang, Futao Meng, Qiang Huang
Gemcitabine resistance is currently the main problem of chemotherapy for advanced pancreatic cancer patients. The resistance is thought to be caused by altered drug metabolism or reduced apoptosis of cancer cells. However, the underlying mechanism of Gemcitabine resistance in pancreatic cancer remains unclear. In this study, we established Gemcitabine resistant PANC-1 (PANC-1-GR) cell lines and compared the circular RNAs (circRNAs) profiles between PANC-1 cells and PANC-1-GR cells by RNA sequencing. Differentially expressed circRNAs were demonstrated using scatter plot and cluster heatmap analysis...
2018: Frontiers in Pharmacology
Matthew L Holding, Mark J Margres, Andrew J Mason, Christopher L Parkinson, Darin R Rokyta
Venom-gland transcriptomics is a key tool in the study of the evolution, ecology, function, and pharmacology of animal venoms. In particular, gene-expression variation and coding sequences gained through transcriptomics provide key information for explaining functional venom variation over both ecological and evolutionary timescales. The accuracy and usefulness of inferences made through transcriptomics, however, is limited by the accuracy of the transcriptome assembly, which is a bioinformatic problem with several possible solutions...
June 19, 2018: Toxins
Sara Donzelli, Elisa Milano, Magdalena Pruszko, Andrea Sacconi, Silvia Masciarelli, Ilaria Iosue, Elisa Melucci, Enzo Gallo, Irene Terrenato, Marcella Mottolese, Maciej Zylicz, Alicja Zylicz, Francesco Fazi, Giovanni Blandino, Giulia Fontemaggi
BACKGROUND: As crucial regulators of the immune response against pathogens, macrophages have been extensively shown also to be important players in several diseases, including cancer. Specifically, breast cancer macrophages tightly control the angiogenic switch and progression to malignancy. ID4, a member of the ID (inhibitors of differentiation) family of proteins, is associated with a stem-like phenotype and poor prognosis in basal-like breast cancer. Moreover, ID4 favours angiogenesis by enhancing the expression of pro-angiogenic cytokines interleukin-8, CXCL1 and vascular endothelial growth factor...
June 19, 2018: Breast Cancer Research: BCR
Ting Li, Xujie Gao, Lei Han, Jinpu Yu, Hui Li
BACKGROUND: Gastric cancer (GC) is a prevalent malignant cancer of digestive system. To identify key genes in GC, mRNA microarray GSE27342, GSE29272, and GSE33335 were downloaded from GEO database. METHODS: Differentially expressed genes (DEGs) were obtained using GEO2R. DAVID database was used to analyze function and pathways enrichment of DEGs. Protein-protein interaction (PPI) network was established by STRING and visualized by Cytoscape software. Then, the influence of hub genes on overall survival (OS) was performed by the Kaplan-Meier plotter online tool...
June 19, 2018: World Journal of Surgical Oncology
Yi-Ming Ren, Yuan-Hui Duan, Yun-Bo Sun, Tao Yang, Wen-Jun Zhao, Dong-Liang Zhang, Zheng-Wei Tian, Meng-Qiang Tian
BACKGROUND: Human osteosarcoma (OS) is one of the most common primary bone sarcoma, because of early metastasis and few treatment strategies. It has been reported that the tumorigenicity and self-renewal capacity of side population (SP) cells play roles in human OS via regulating of target genes. This study aims to complement the differentially expressed genes (DEGs) that regulated between the SP cells and the non-SP cells from primary human OS and identify their functions and molecular pathways associated with OS...
June 19, 2018: Journal of Orthopaedic Surgery and Research
John Richard Lee, Matthew Magruder, Lisa Zhang, Lars F Westblade, Michael J Satlin, Amy Robertson, Emmanuel Edusei, Carl Crawford, Lilan Ling, Ying Taur, Jonas Schlueter, Michelle Lubetzky, Darshana Dadhania, Eric Pamer, Manikkam Suthanthiran
Post-transplant diarrhea is associated with kidney allograft failure and death but its etiology remains unknown in the majority of cases. Because altered gut microbial ecology is a potential basis for diarrhea, we investigated whether post-transplant diarrhea is associated with gut dysbiosis. We enrolled 71 kidney allograft recipients for serial fecal specimen collections in the first 3 months of transplantation and profiled the gut microbiota using 16S rRNA gene V4-V5 deep sequencing. The Shannon diversity index was significantly lower in 28 diarrheal fecal specimens from 25 recipients with post-transplant diarrhea than in 112 fecal specimens from 46 recipients without post-transplant diarrhea...
June 19, 2018: American Journal of Transplantation
Yanhan Deng, Zongzhe Li, Juan Liu, Zheng Wang, Yanyan Cao, Yong Mou, Bohua Fu, Biwen Mo, Jianghong Wei, Zhenshun Cheng, Liman Luo, Jingping Li, Ying Shu, Xiaomei Wang, Guangwei Luo, Shuo Yang, Yingnan Wang, Jing Zhu, Jingping Yang, Ming Wu, Xuyan Xu, Renying Ge, Xueqin Chen, Qingzhen Peng, Guang Wei, Yaqing Li, Hua Yang, Shirong Fang, Xiaoju Zhang, Weining Xiong
Idiopathic pulmonary fibrosis (IPF) is a genetic heterogeneous disease with high mortality and poor prognosis. However, a large fraction of genetic cause remains unexplained, especially in sporadic IPF (∼80% IPF). By systemically reviewing related literature and potential pathogenic pathways, 92 potentially IPF-related genes were selected and sequenced in genomic DNAs from 253 sporadic IPF patients and 125 matched health controls using targeted massively parallel next-generation sequencing. The identified risk variants were confirmed by Sanger sequencing...
June 19, 2018: Human Mutation
Daniel R Calabrese, Rebecca Florez, Katherine Dewey, Christine Hui, Dara Torgerson, Tiffany Chong, Hilary Faust, Raja Rajalingam, Steven R Hays, Jeff A Golden, Jasleen Kukreja, Jonathan P Singer, John R Greenland
Most lung transplantation immunosuppression regimens include tacrolimus. Single nucleotide polymorphisms (SNPs) in genes important to tacrolimus bioavailability and clearance (ABCB1, CYP3A4 and CYP3A5) are associated with differences in tacrolimus pharmacokinetics. We hypothesized that polymorphisms in these genes would impact immunosuppression-related outcomes. We categorized ABCB1, CYP3A4, and CYP3A5 SNPs for 321 lung allograft recipients. Genotype effects on time to therapeutic tacrolimus level, interactions with antifungal medications, concentration to dose (C0 /D), acute kidney injury, and rejection were assessed using linear models adjusted for subject characteristics and repeat measures...
June 19, 2018: Clinical Transplantation
Julie C Krzykwa, Alexis Olivas, Marlo K Sellin Jeffries
The fathead minnow fish embryo toxicity (FET) test has been proposed as a more humane alternative to current toxicity testing methods, as younger organisms are thought to experience less distress during toxicant exposure. However, the FET test protocol does not include endpoints that allow for the prediction of sublethal adverse outcomes, limiting its utility relative to other test types. Researchers have proposed the development of sublethal endpoints for the FET test to increase its utility. The present study 1) developed methods for previously unmeasured sublethal metrics in fathead minnows (i...
June 19, 2018: Environmental Toxicology and Chemistry
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