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Metagenomics cancer

Jing Zuo, Dahu Wang, Haitao Shen, Fengling Liu, Jing Han, Xianghong Zhang
One of the important mediators of Epithelial to mesenchymal transition (EMT) is the Snail1 protein (encoded by SNAI1) which facilitates transition to mesenchymal state by transcriptionally repressing the epithelial cell marker E-cadherin. Given its central role in EMT and tumor metastasis, the cell has evolved multiple levels of regulatory mechanism at transcriptional, post-transcriptional, and post-translational level to regulate SNAI1 expression. Recently, miR-153 has been shown to regulate SNAI1 expression in hepatocellular carcinoma...
October 13, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
Jessie Qy Liang, Jonathan Chiu, Yingxuan Chen, Yanqin Huang, Akira Higashimori, Jing-Yuan Fang, Hassan Brim, Hassan Ashktorab, Siew Chien Ng, Simon Sm Ng, Shu Zheng, Francis Kl Chan, Joseph Jy Sung, Jun Yu
PURPOSE: Gut microbiota have been implicated in the development of colorectal cancer (CRC). We evaluated the utility of fecal bacterial marker candidates identified by our metagenome sequencing analysis for CRC diagnosis. EXPERIMENTAL DESIGN: 439 subjects (203 CRC and 236 healthy subjects) from two independent Asian cohorts were included. Probe-based duplex quantitative PCR (qPCR) assays were established for quantification of bacterial marker candidates. RESULTS: Candidates identified by metagenome sequencing, including Fusobacterium nucleatum (Fn), Bacteroides clarus (Bc), Roseburia intestinalis (Ri), Clostridium hathewayi (Ch), and one undefined species (labeled as m7), were examined in fecal samples of 203 CRC patients and 236 healthy controls by duplex-qPCR...
October 3, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Jindong Li, Qingchuan Feng, Xudong Wei, Yongkui Yu
Lung cancer remains a leading cause of cancer-related mortality, with metastatic progression remaining the single largest cause of lung cancer mortality. Hence, it is imperative to determine reliable biomarkers of lung cancer prognosis. MicroRNA-490-3p has been previously reported to be a positive prognostic biomarker for hepatocellular cancer. However, its role in human lung cancer has not yet been elucidated. Here, we report that hsa-miR-490-3p expression is significantly higher in human lung cancer tissue specimens and cell line...
September 28, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
Sachin Goyal, Pratima Nangia-Makker, Lulu Farhana, Yingjie Yu, Adhip Pn Majumdar
Over the past two decades there has been remarkable progress in cancer diagnosis, treatment and screening. The basic mechanisms leading to pathogenesis of various types of cancers are also understood better and some patients, if diagnosed at a particular stage go on to lead a normal pre-diagnosis life. Despite these achievements, racial disparity in some cancers remains a mystery. The higher incidence, aggressiveness and mortality of breast, prostate and colorectal cancers (CRCs) in African-Americans as compared to Caucasian-Americans are now well documented...
September 26, 2016: World Journal of Stem Cells
Manosha Perera, Nezar Noor Al-Hebshi, David J Speicher, Irosha Perera, Newell W Johnson
Oral cancer, primarily oral squamous cell carcinoma (OSCC), continues to be a major global health problem with high incidence and low survival rates. While the major risk factors for this malignancy, mostly lifestyle related, have been identified, around 15% of oral cancer cases remain unexplained. In light of evidence implicating bacteria in the aetiology of some cancer types, several epidemiological studies have been conducted in the last decade, employing methodologies ranging from traditional culture techniques to 16S rRNA metagenomics, to assess the possible role of bacteria in OSCC...
2016: Journal of Oral Microbiology
Thierry Pédron, Giulia Nigro, Philippe J Sansonetti
Metagenomic analysis of the human intestinal microbiome has provided a wealth of information that allowed an exceptionally detailed description of its microbial content and physiological potential. It also set the basis for studies allowing correlation of alterations in the balance of this microbiota and the occurrence of a certain number of emerging diseases, such as inflammatory bowel diseases, obesity and diabetes, and possibly colorectal cancer. The time has come to give the intestinal microbiota in symbiosis with its host an experimental dimension...
November 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Ian J Miller, Niti Vanee, Stephen S Fong, Grace E Lim-Fong, Jason C Kwan
: The uncultured bacterial symbiont "Candidatus Endobugula sertula" is known to produce cytotoxic compounds called bryostatins, which protect the larvae of its host, Bugula neritina The symbiont has never been successfully cultured and it was thought that its genome might be significantly reduced. Here, we took a shotgun metagenomics and metatranscriptomics approach to assemble and characterize the genome of "Ca. E. sertula". We found that it had specific metabolic deficiencies in the biosynthesis of certain amino acids, but few other signs of genome degradation such as small size, abundant pseudogenes or low coding density...
September 2, 2016: Applied and Environmental Microbiology
Mehrbod Estaki, Jason Pither, Peter Baumeister, Jonathan P Little, Sandeep K Gill, Sanjoy Ghosh, Zahra Ahmadi-Vand, Katelyn R Marsden, Deanna L Gibson
BACKGROUND: Reduced microbial diversity in human intestines has been implicated in various conditions such as diabetes, colorectal cancer, and inflammatory bowel disease. The role of physical fitness in the context of human intestinal microbiota is currently not known. We used high-throughput sequencing to analyze fecal microbiota of 39 healthy participants with similar age, BMI, and diets but with varying cardiorespiratory fitness levels. Fecal short-chain fatty acids were analyzed using gas chromatography...
2016: Microbiome
Zhijian Liu, Shixing Yang, Yan Wang, Quan Shen, Yan Yang, Xutao Deng, Wen Zhang, Eric Delwart
BACKGROUND: The number of members in the genus Gammapapillomavirus of Family Papillomaviridae has recently been expanding most rapidly. The aim of this study was to characterize a novel human gammapapillomavirus type identified in a vaginal swab from a 25-year-old pregnant woman suffering from vaginitis. METHODS: Viral metagenomics method was used to detect the viral sequences in 88 vaginal swab samples collected from 88 pregnant women with vaginitis. A novel papillomavirus, named HPV-ZJ01 (GenBank no...
2016: Virology Journal
Jun Wang, Huijue Jia
Metagenome-wide association studies (MWAS) have enabled the high-resolution investigation of associations between the human microbiome and several complex diseases, including type 2 diabetes, obesity, liver cirrhosis, colorectal cancer and rheumatoid arthritis. The associations that can be identified by MWAS are not limited to the identification of taxa that are more or less abundant, as is the case with taxonomic approaches, but additionally include the identification of microbial functions that are enriched or depleted...
August 2016: Nature Reviews. Microbiology
Patricio Jeraldo, Alvaro Hernandez, Henrik B Nielsen, Xianfeng Chen, Bryan A White, Nigel Goldenfeld, Heidi Nelson, David Alhquist, Lisa Boardman, Nicholas Chia
The role of the microbiome in health and disease is attracting great attention, yet we still know little about some of the most prevalent microorganisms inside our bodies. Several years ago, Human Microbiome Project (HMP) researchers generated a list of "most wanted" taxa: bacteria both prevalent among healthy volunteers and distantly related to any sequenced organisms. Unfortunately, the challenge of assembling high-quality genomes from a tangle of metagenomic reads has slowed progress in learning about these uncultured bacteria...
2016: Frontiers in Microbiology
Emily Vogtmann, Xing Hua, Georg Zeller, Shinichi Sunagawa, Anita Y Voigt, Rajna Hercog, James J Goedert, Jianxin Shi, Peer Bork, Rashmi Sinha
Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population...
2016: PloS One
Trupti Patel, Priyanjali Bhattacharya, Suvrajit Das
PURPOSE: Gut microbiota is predicted to play a key role in manifestation of gastrointestinal tract cancers. The human gastrointestinal tract is a complex and abundant network of microbial community. Gut microbiota depicts the microbe population living in our intestine. Humans harbour more than 10(14) microbes in the gut, and the diversity and densities of the microbiota increase from stomach to colon. METHODS: The beneficial relationship between endogenous microbiota and the eukaryotic hosts helps in maintaining various metabolic activities of the body as well as temperature and pH balance...
September 2016: Journal of Gastrointestinal Cancer
Chan Hyuk Park, Dong Soo Han, Young-Ha Oh, A-Reum Lee, Yu-Ra Lee, Chang Soo Eun
Fusobacteria are associated with colorectal cancer (CRC) and are amplified during colorectal carcinogenesis. Compared to the adenoma-carcinoma sequence of carcinogenesis, serrated neoplasm has distinct clinical features and a different molecular background. We aimed to compare the gut microbiome between tubular adenoma (TA) and sessile serrated adenoma/polyp (SSA/P). Patients with TA, SSA/P, or CRC were recruited. Three pieces of colorectal mucosal tissue were obtained from each patient by endoscopic biopsy...
2016: Scientific Reports
Vitaly Smelov, Davit Bzhalava, Laila Sara Arroyo Mühr, Carina Eklund, Boris Komyakov, Andrey Gorelov, Joakim Dillner, Emilie Hultin
We tested prostatic secretions from men with and without prostate cancer (13 cases and 13 matched controls) or prostatitis (18 cases and 18 matched controls) with metagenomic sequencing. A large number (>200) of viral reads was only detected among four prostate cancer cases (1 patient each positive for Merkel cell polyomavirus, JC polyomavirus and Human Papillomavirus types 89 or 40, respectively). Lower numbers of reads from a large variety of viruses were detected in all patient groups. Our knowledge of the biology of the prostate may be furthered by the fact that DNA viruses are commonly shed from the prostate and can be readily detected by metagenomic sequencing of expressed prostate secretions...
2016: Scientific Reports
Maryann Kwa, Claudia S Plottel, Martin J Blaser, Sylvia Adams
The huge communities of residential microbes, including bacteria, viruses, Archaea, and Eukaryotes, that colonize humans are increasingly recognized as playing important roles in health and disease. A complex populous ecosystem, the human gastrointestinal (GI) tract harbors up to 10(11) bacterial cells per gram of luminal content, whose collective genome, the gut metagenome, contains a vastly greater number of individual genes than the human genome. In health, the function of the microbiome might be considered to be in dynamic equilibrium with the host, exerting both local and distant effects...
August 2016: Journal of the National Cancer Institute
Cyrielle Gasc, Eric Peyretaillade, Pierre Peyret
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures...
June 2, 2016: Nucleic Acids Research
Xu Xin, He Junzhi, Zhou Xuedong
A human oral microbiota is the ecological community of commensal, symbiotic, and pathogenic microorganisms found in human oral cavity. Oral microbiota exists mostly in the form of a biofilm and maintains a dynamic ecological equilibrium with the host body. However, the disturbance of this ecological balance inevitably causes oral infectious diseases, such as dental caries, apical periodontitis, periodontal diseases, pericoronitis, and craniofacial bone osteomyelitis. Oral microbiota is also correlated with many systemic diseases, including cancer, diabetes mellitus, rheumatoid arthritis, cardiovascular diseases, and preterm birth...
December 2015: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
The large amount of short read data that has to be assembled in future applications, such as in metagenomics or cancer genomics, strongly motivates the investigation of disk-based approaches to index next-generation sequencing (NGS) data. Positive results in this direction stimulate the investigation of efficient external memory algorithms for de novo assembly from NGS data. Our article is also motivated by the open problem of designing a space-efficient algorithm to compute a string graph using an indexing procedure based on the Burrows-Wheeler transform (BWT)...
March 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Shuji Ogino, Reiko Nishihara, Tyler J VanderWeele, Molin Wang, Akihiro Nishi, Paul Lochhead, Zhi Rong Qian, Xuehong Zhang, Kana Wu, Hongmei Nan, Kazuki Yoshida, Danny A Milner, Andrew T Chan, Alison E Field, Carlos A Camargo, Michelle A Williams, Edward L Giovannucci
Molecular pathology diagnostics to subclassify diseases based on pathogenesis are increasingly common in clinical translational medicine. Molecular pathological epidemiology (MPE) is an integrative transdisciplinary science based on the unique disease principle and the disease continuum theory. While it has been most commonly applied to research on breast, lung, and colorectal cancers, MPE can investigate etiologic heterogeneity in non-neoplastic diseases, such as cardiovascular diseases, obesity, diabetes mellitus, drug toxicity, and immunity-related and infectious diseases...
July 2016: Epidemiology
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