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https://www.readbyqxmd.com/read/28542458/a-pilot-study-using-metagenomic-sequencing-of-the-sputum-microbiome-suggests-potential-bacterial-biomarkers-for-lung-cancer
#1
Simon J S Cameron, Keir E Lewis, Sharon A Huws, Matthew J Hegarty, Paul D Lewis, Justin A Pachebat, Luis A J Mur
Lung cancer (LC) is the most prevalent cancer worldwide, and responsible for over 1.3 million deaths each year. Currently, LC has a low five year survival rates relative to other cancers, and thus, novel methods to screen for and diagnose malignancies are necessary to improve patient outcomes. Here, we report on a pilot-sized study to evaluate the potential of the sputum microbiome as a source of non-invasive bacterial biomarkers for lung cancer status and stage. Spontaneous sputum samples were collected from ten patients referred with possible LC, of which four were eventually diagnosed with LC (LC+), and six had no LC after one year (LC-)...
2017: PloS One
https://www.readbyqxmd.com/read/28525602/aloin-a-component-of-the-aloe-vera-plant-leaf-induces-pathological-changes-and-modulates-the-composition-of-microbiota-in-the-large-intestine-of-f344-n-male-rats
#2
Mary D Boudreau, Greg R Olson, Volodymyr P Tryndyak, Matthew S Bryant, Robert P Felton, Frederick A Beland
In a previous study, the oral administration of an Aloe vera whole leaf extract induced dose-related mucosal and goblet cell hyperplasia in the rat colon after 13-weeks and colon cancer after two years. The primary goal of this study was to determine whether or not the administration of aloin, a component of the Aloe vera plant leaf, would replicate the pathophysiological effects that were observed in rats in the previous study with an Aloe vera whole leaf extract. Groups of 10 male F344/N rats were administered aloin at 0, 6...
May 19, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28496197/helicobacter-pylori-derived-extracellular-vesicles-increased-in-the-gastric-juices-of-gastric-adenocarcinoma-patients-and-induced-inflammation-mainly-via-specific-targeting-of-gastric-epithelial-cells
#3
Hyun-Il Choi, Jun-Pyo Choi, Jiwon Seo, Beom Jin Kim, Mina Rho, Jin Kwan Han, Jae Gyu Kim
Evidence indicates that Helicobacter pylori is the causative agent of chronic gastritis and perhaps gastric malignancy. Extracellular vesicles (EVs) play an important role in the evolutional process of malignancy due to their genetic material cargo. We aimed to evaluate the clinical significance and biological mechanism of H. pylori EVs on the pathogenesis of gastric malignancy. We performed 16S rDNA-based metagenomic analysis of gastric juices either from endoscopic or surgical patients. From each sample of gastric juices, the bacteria and EVs were isolated...
May 12, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28481406/the-role-of-the-microbiome-in-cancer-development-and-therapy
#4
REVIEW
Aadra P Bhatt, Matthew R Redinbo, Scott J Bultman
Answer questions and earn CME/CNE The human body harbors enormous numbers of microbiota that influence cancer susceptibility, in part through their prodigious metabolic capacity and their profound influence on immune cell function. Microbial pathogens drive tumorigenesis in 15% to 20% of cancer cases. Even larger numbers of malignancies are associated with an altered composition of commensal microbiota (dysbiosis) based on microbiome studies using metagenomic sequencing. Although association studies cannot distinguish whether changes in microbiota are causes or effects of cancer, a causative role is supported by rigorously controlled preclinical studies using gnotobiotic mouse models colonized with one or more specific bacteria...
May 8, 2017: CA: a Cancer Journal for Clinicians
https://www.readbyqxmd.com/read/28345673/sex-dependent-effects-on-gut-microbiota-regulate-hepatic-carcinogenic-outcomes
#5
Guoxiang Xie, Xiaoning Wang, Aihua Zhao, Jingyu Yan, Wenlian Chen, Runqiu Jiang, Junfang Ji, Fengjie Huang, Yunjing Zhang, Sha Lei, Kun Ge, Xiaojiao Zheng, Cynthia Rajani, Rosanna A Alegado, Jiajian Liu, Ping Liu, Jeremy Nicholson, Wei Jia
Emerging evidence points to a strong association between sex and gut microbiota, bile acids (BAs), and gastrointestinal cancers. Here, we investigated the mechanistic link between microbiota and hepatocellular carcinogenesis using a streptozotocin-high fat diet (STZ-HFD) induced nonalcoholic steatohepatitis-hepatocellular carcinoma (NASH-HCC) murine model and compared results for both sexes. STZ-HFD feeding induced a much higher incidence of HCC in male mice with substantially increased intrahepatic retention of hydrophobic BAs and decreased hepatic expression of tumor-suppressive microRNAs...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#6
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28288568/deep-sequencing-of-hpv-e6-e7-genes-reveals-loss-of-genotypic-diversity-and-gain-of-clonal-dominance-in-high-grade-intraepithelial-lesions-of-the-cervix
#7
Jane Shen-Gunther, Yufeng Wang, Zhao Lai, Graham M Poage, Luis Perez, Tim H M Huang
BACKGROUND: Human papillomavirus (HPV) is the carcinogen of almost all invasive cervical cancer and a major cause of oral and other anogenital malignancies. HPV genotyping by dideoxy (Sanger) sequencing is currently the reference method of choice for clinical diagnostics. However, for samples with multiple HPV infections, genotype identification is singular and occasionally imprecise or indeterminable due to overlapping chromatograms. Our aim was to explore and compare HPV metagenomes in abnormal cervical cytology by deep sequencing for correlation with disease states...
March 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28287094/enlightening-discriminative-network-functional-modules-behind-principal-component-analysis-separation-in-differential-omic-science-studies
#8
Sara Ciucci, Yan Ge, Claudio Durán, Alessandra Palladini, Víctor Jiménez-Jiménez, Luisa María Martínez-Sánchez, Yuting Wang, Susanne Sales, Andrej Shevchenko, Steven W Poser, Maik Herbig, Oliver Otto, Andreas Androutsellis-Theotokis, Jochen Guck, Mathias J Gerl, Carlo Vittorio Cannistraci
Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28174737/metagenomic-characterization-of-microbial-communities-in-situ-within-the-deeper-layers-of-the-ileum-in-crohn-s-disease
#9
Chandra Sekhar Pedamallu, Ami S Bhatt, Susan Bullman, Sharyle Fowler, Samuel S Freeman, Jacqueline Durand, Joonil Jung, Fujiko Duke, Veronica Manzo, Diana Cai, Ashwin Ananthakrishnan, Akinyemi I Ojesina, Aruna Ramachandran, Dirk Gevers, Ramnik J Xavier, Atul K Bhan, Matthew Meyerson, Vijay Yajnik
BACKGROUND & AIMS: Microbial dysbiosis and aberrant host-microbe interactions in the gut are believed to contribute to the development and progression of Crohn's disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS: Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease-free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28126350/peptostreptococcus-anaerobius-induces-intracellular-cholesterol-biosynthesis-in-colon-cells-to-induce-proliferation-and-causes-dysplasia-in-mice
#10
Ho Tsoi, Eagle S H Chu, Xiang Zhang, Jianqiu Sheng, Daniel Nakatsu, Siew C Ng, Anthony W H Chan, Francis K L Chan, Joseph J Y Sung, Jun Yu
BACKGROUND & AIMS: Stool samples from patients with colorectal cancer (CRC) have a higher abundance of Peptostreptococcus anaerobius than stool from individuals without CRC, based on metagenome sequencing. We investigated whether P anaerobius contributes to colon tumor formation in mice and its possible mechanisms of carcinogenesis. METHODS: We performed quantitative polymerase chain reaction analyses to measure P anaerobius in 112 stool samples and 255 colon biopsies from patients with CRC or advanced adenoma and from healthy individuals (controls) undergoing colonoscopy examination at hospitals in Hong Kong and Beijing...
January 23, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28125788/inference-of-environmental-factor-microbe-and-microbe-microbe-associations-from-metagenomic-data-using-a-hierarchical-bayesian-statistical-model
#11
Yuqing Yang, Ning Chen, Ting Chen
The inference of associations between environmental factors and microbes and among microbes is critical to interpreting metagenomic data, but compositional bias, indirect associations resulting from common factors, and variance within metagenomic sequencing data limit the discovery of associations. To account for these problems, we propose metagenomic Lognormal-Dirichlet-Multinomial (mLDM), a hierarchical Bayesian model with sparsity constraints, to estimate absolute microbial abundance and simultaneously infer both conditionally dependent associations among microbes and direct associations between microbes and environmental factors...
January 25, 2017: Cell Systems
https://www.readbyqxmd.com/read/28096237/the-human-microbiome-and-cancer
#12
REVIEW
Seesandra V Rajagopala, Sanjay Vashee, Lauren M Oldfield, Yo Suzuki, J Craig Venter, Amalio Telenti, Karen E Nelson
Recent scientific advances have significantly contributed to our understanding of the complex connection between the microbiome and cancer. Our bodies are continuously exposed to microbial cells, both resident and transient, as well as their byproducts, including toxic metabolites. Circulation of toxic metabolites may contribute to cancer onset or progression at locations distant from where a particular microbe resides. Moreover, microbes may migrate to other locations in the human body and become associated with tumor development...
January 17, 2017: Cancer Prevention Research
https://www.readbyqxmd.com/read/28004480/a-metagenomic-study-of-the-preventive-effect-of-lactobacillus-rhamnosus-gg-on-intestinal-polyp-formation-in-apc-min-mice
#13
Y Ni, V H Y Wong, W C S Tai, J Li, W Y Wong, M M L Lee, F L Y Fong, H El-Nezami, G Panagiotou
AIMS: To investigate the in vivo effects of Lactobacillus rhamnosus GG (LGG) on intestinal polyp development and the interaction between this single-organism probiotic and the gut microbiota therein. METHODS AND RESULTS: The Apc(Min/+) mouse model was used to study the potential preventive effect of LGG on intestinal polyposis, while shotgun metagenomic sequencing was employed to characterize both taxonomic and functional changes within the gut microbial community...
December 22, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27821485/dietary-emulsifier-induced-low-grade-inflammation-promotes-colon-carcinogenesis
#14
Emilie Viennois, Didier Merlin, Andrew T Gewirtz, Benoit Chassaing
The increased risks conferred by inflammatory bowel disease (IBD) to the development of colorectal cancer gave rise to the term "colitis-associated cancer" and the concept that inflammation promotes colon tumorigenesis. A condition more common than IBD is low-grade inflammation, which correlates with altered gut microbiota composition and metabolic syndrome, both present in many cases of colorectal cancer. Recent findings suggest that low-grade inflammation in the intestine is promoted by consumption of dietary emulsifiers, a ubiquitous component of processed foods, which alter the composition of gut microbiota...
January 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/27739030/microrna-153-inhibits-tumor-progression-in-esophageal-squamous-cell-carcinoma-by-targeting-snai1
#15
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
https://www.readbyqxmd.com/read/27697996/fecal-bacteria-act-as-novel-biomarkers-for-noninvasive-diagnosis-of-colorectal-cancer
#16
Qiaoyi Liang, Jonathan Chiu, Yingxuan Chen, Yanqin Huang, Akira Higashimori, Jingyuan Fang, Hassan Brim, Hassan Ashktorab, Siew Chien Ng, Simon Siu Man Ng, Shu Zheng, Francis Ka Leung Chan, Joseph Jao Yiu Sung, Jun Yu
PURPOSE: Gut microbiota have been implicated in the development of colorectal cancer. We evaluated the utility of fecal bacterial marker candidates identified by our metagenome sequencing analysis for colorectal cancer diagnosis. EXPERIMENTAL DESIGN: Subjects (total 439; 203 colorectal cancer and 236 healthy subjects) from two independent Asian cohorts were included. Probe-based duplex quantitative PCR (qPCR) assays were established for the quantification of bacterial marker candidates...
October 3, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27683057/microrna-490-regulates-lung-cancer-metastasis-by-targeting-poly-r-c-binding-protein-1
#17
COMPARATIVE STUDY
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...
November 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/27679684/racial-disparity-in-colorectal-cancer-gut-microbiome-and-cancer-stem-cells
#18
REVIEW
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
https://www.readbyqxmd.com/read/27677454/emerging-role-of-bacteria-in-oral-carcinogenesis-a-review-with-special-reference-to-perio-pathogenic-bacteria
#19
REVIEW
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
https://www.readbyqxmd.com/read/27672151/from-homeostasis-to-pathology-decrypting-microbe-host-symbiotic-signals-in-the-intestinal-crypt
#20
REVIEW
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
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