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Metagenomics cancer

Teruaki Nakatsuji, Tiffany H Chen, Anna M Butcher, Lynnie L Trzoss, Sang-Jip Nam, Karina T Shirakawa, Wei Zhou, Julia Oh, Michael Otto, William Fenical, Richard L Gallo
We report the discovery that strains of Staphylococcus epidermidis produce 6- N -hydroxyaminopurine (6-HAP), a molecule that inhibits DNA polymerase activity. In culture, 6-HAP selectively inhibited proliferation of tumor lines but did not inhibit primary keratinocytes. Resistance to 6-HAP was associated with the expression of mitochondrial amidoxime reducing components, enzymes that were not observed in cells sensitive to this compound. Intravenous injection of 6-HAP in mice suppressed the growth of B16F10 melanoma without evidence of systemic toxicity...
February 2018: Science Advances
Javier Fernández, Lorena García, Joaquín Monte, Claudio J Villar, Felipe Lombó
Colorectal cancer is the fourth most common neoplasia in Europe, where it accounts for 28.2 new cases per 100,000 inhabitants. In an effort to decrease the incidence of this disease, various prevention measures are being studied, one of which are anthocyanin-rich foods. Anthocyanins are potent antioxidant flavonoids mainly found in flowers and colorful fruits and vegetables. These nutraceuticals have diverse biological functions once ingested, including immunomodulatory, anti-inflammatory and antitumor functions...
March 1, 2018: Genes
Audrey Humphries, Adil Daud
Although immunotherapy has been remarkably effective across multiple cancer types, there continues to be a significant number of non-responding patients. A possible factor proposed to influence the efficacy of immunotherapies is the gut microbiome. We discuss the results and implications of recent research on the relationship between the gut microbiome, our immune systems, and immune checkpoint inhibitor therapies including anti-CTLA-4 Ab and anti-PD-1 Ab. While the investigations all exhibit interesting results and conclusions, we find little congruence in the specific bacteria that were found favorable for antitumor responses...
March 1, 2018: Human Vaccines & Immunotherapeutics
Shaomin Zou, Lekun Fang, Mong-Hong Lee
Gastrointestinal microbiome, containing at least 100 trillion bacteria, resides in the mucosal surface of human intestine. Recent studies show that perturbations in the microbiota may influence physiology and link to a number of diseases, including colon tumorigenesis. Colorectal cancer (CRC), the third most common cancer, is the disease resulting from multi-genes and multi-factors, but the mechanistic details between gut microenvironment and CRC remain poorly characterized. Thanks to new technologies such as metagenome sequencing, progress in large-scale analysis of the genetic and metabolic profile of gut microbial has been possible, which has facilitated studies about microbiota composition, taxonomic alterations and host interactions...
February 2018: Gastroenterology Report
Jincheng Wang, Lili Tang, Hongyuan Zhou, Jun Zhou, Travis C Glenn, Chwan-Li Shen, Jia-Sheng Wang
Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0...
January 31, 2018: Journal of Nutritional Biochemistry
Meenakshi Rajpoot, Anil K Sharma, Anil Sharma, Girish Kumar Gupta
The human body is a home to more than 1 trillion microbes with a diverse variety of commensal microbes that play a crucial role towards the health of the individual. These microbes occupy different habitats such as gut, skin, vagina, oral etc. Not only the types and abundance of microbes are different in different organs, but also these may differ in different individuals. The genome of these microbiota and their ecosystem constitute to form a microbiome. Factors such as diet, environment, host genetics etc...
February 6, 2018: Seminars in Cancer Biology
Dolores Corella, Oscar Coltell, Fernando Macian, José M Ordovás
Increasingly, studies showing the protective effects of the Mediterranean diet (MedDiet) on different diseases (cardiovascular, diabetes, some cancers, and even total mortality and aging indicators) are being published. The scientific evidence level for each outcome is variable, and new studies are needed to better understand the molecular mechanisms whereby the MedDiet may exercise its effects. Here, we present recent advances in understanding the molecular basis of MedDiet effects, mainly focusing on cardiovascular diseases but also discussing other related diseases...
January 26, 2018: Annual Review of Food Science and Technology
Liqiang Liu, Xiaowei Zhang, Chengrui Nan, Zongmao Zhao, Shucheng Ma, Wenhua Li, Hongchao Hu, Zhaohui Liang
Glioblastoma (GBM) is an incurable cancer, with mean post-diagnosis survival time of 14-16 months. Metagenomic analysis by The Cancer Genome Atlas (TCGA) program has identified microRNA-182-5p (miR-182-5p or miR-182) as the only miRNA associated with favorable disease prognosis and temozolomide (TMZ) susceptibility. Previous reports have indicated that miR-182 down regulates expression of BCL2L12, c-MET, and HIF2A. However, other messenger RNA (mRNA) targets of miR-182 have not been validated which would explain its association with a favorable disease prognosis...
December 29, 2017: Oncotarget
Christian Schönbach, Jinyan Li, Lan Ma, Paul Horton, Muhammad Farhan Sjaugi, Shoba Ranganathan
The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics...
January 19, 2018: BMC Genomics
Marisa Di Pietro, Simone Filardo, Maria Grazia Porpora, Nadia Recine, Maria Agnese Latino, Rosa Sessa
HPV and Chlamydia trachomatis are the most common causes of sexually transmitted diseases worldwide. Most infections are asymptomatic and left untreated lead to severe reproductive tract sequelae such as cervical cancer and infertility. Interestingly, C. trachomatis may also increase the susceptibility to HPV infection as well as contribute to viral persistence. Recently, a growing body of evidence has suggested that the composition of the cervico-vaginal microbiota plays a key role in the susceptibility and outcome of genital infections caused by several pathogens, including HPV and C...
January 9, 2018: New Microbiologica
Vyara Matson, Jessica Fessler, Riyue Bao, Tara Chongsuwat, Yuanyuan Zha, Maria-Luisa Alegre, Jason J Luke, Thomas F Gajewski
Anti-PD-1-based immunotherapy has had a major impact on cancer treatment but has only benefited a subset of patients. Among the variables that could contribute to interpatient heterogeneity is differential composition of the patients' microbiome, which has been shown to affect antitumor immunity and immunotherapy efficacy in preclinical mouse models. We analyzed baseline stool samples from metastatic melanoma patients before immunotherapy treatment, through an integration of 16 S ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria...
January 5, 2018: Science
Terry Fei Fan Ng, Jennifer A Dill, Alvin C Camus, Eric Delwart, Erwin G Van Meir
The role of viral infections in the etiology of brain cancer remains uncertain. Prior studies mostly focused on transcriptome or viral DNA integrated in tumor cells. To investigate for the presence of viral particles, we performed metagenomics sequencing on viral capsid-protected nucleic acids from 12 primary and 8 metastatic human brain tumors. One brain tumor metastasized from a skin melanoma harbored two new human anellovirus species, Torque teno mini virus Emory1 (TTMV Emory1) and Emory2 (TTMV Emory2), while the remaining 19 samples did not reveal any exogenous viral sequences...
December 1, 2017: Oncotarget
Daniela Börnigen, Boyu Ren, Robert Pickard, Jingfeng Li, Enver Ozer, Erica M Hartmann, Weihong Xiao, Timothy Tickle, Jennifer Rider, Dirk Gevers, Eric A Franzosa, Mary Ellen Davey, Maura L Gillison, Curtis Huttenhower
Oral squamous cell carcinomas are a major cause of morbidity and mortality, and tobacco usage, alcohol consumption, and poor oral hygiene are established risk factors. To date, no large-scale case-control studies have considered the effects of these risk factors on the composition of the oral microbiome, nor microbial community associations with oral cancer. We compared the composition, diversity, and function of the oral microbiomes of 121 oral cancer patients to 242 age- and gender-matched controls using a metagenomic multivariate analysis pipeline...
December 15, 2017: Scientific Reports
Birgit Wassermann, Daria Rybakova, Christina Müller, Gabriele Berg
Plant health is strongly connected with plants´ microbiome. In case of raw-eaten plants, the microbiome can also affect human health. To study potential impacts on health issues of both hosts, the microbiome composition of seven different Brassica vegetables, originating from different food processing pathways, was analyzed by a combined approach of amplicon sequencing, metagenomic mining and cultivation. All Brassica vegetables harbored a highly diverse microbiota as identified by 16S rRNA gene amplicon sequencing...
December 15, 2017: Scientific Reports
Lubomir Stary, Kristyna Mezerova, Pavel Skalicky, Pavel Zboril, Vladislav Raclavsky
The role of gut microbiota in the development of sporadic colorectal cancer (CRC) is supported by a number of studies, however, the conclusiveness of published metagenomic studies is questioned by technical pitfalls and limited by small cohort sizes. In this review, we evaluate the current knowledge critically and outline practical solutions. We also list candidate CRC risk markers that are - in our opinion - well supported by available data and thus deserve clinical validation. Last but not least, we summarise available knowledge useful for improving care for patients immediately...
December 2017: Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia
Victoria Byrd, Ted M Getz, Roshan Padmanabhan, Hans Arora, Charis Eng
Germline PTEN mutations defining PTEN hamartoma tumor syndrome [PHTS] confer heritable predisposition to breast, endometrial, thyroid, and other cancers with known age-related risks, but it remains impossible to predict if any individual will develop cancer. In the general population, gut microbial dysbiosis has been linked to cancer, yet is unclear whether these are associated in PHTS patients. In this pilot study, we aimed to characterize microbial composition of stool, urine, and oral wash from 32 PTEN mutation-positive individuals using 16S rRNA-gene sequencing...
December 12, 2017: Endocrine-related Cancer
Chao Liu, En-Dong Liu, Yun-Xiao Meng, Xiao-Ming Dong, Ya-Lan Bi, Huan-Wen Wu, Yan-Chao Jin, Ke Zhao, Jian-Jie Li, Miao Yu, Yi-Qun Zhan, Hui Chen, Chang-Hui Ge, Xiao-Ming Yang, Chang-Yan Li
Keratin 8 (CK8) is the major component of the intermediate filaments of simple or single-layered epithelia. Gene targeting mice model suggest that CK8 is involved in colonic active ion transport, colorectal hyperplasia and inflammation. In the present study, we found that CK8 is downregulated in the colon during DSS-induced colitis and AOM/DSS-induced colitis-associated colorectal cancer (CAC) development. In human patients with colon cancer, CK8 is downregulated. Using CK8 heterozygous knockout mice (CK8+/- ), we found that CK8+/- mice are highly susceptible to DSS-induced colitis and more prone to AOM/DSS-induced CAC than wild type (WT) mice...
November 14, 2017: Oncotarget
Brandilyn A Peters, Jing Wu, Zhiheng Pei, Liying Yang, Mark P Purdue, Neal D Freedman, Eric J Jacobs, Susan M Gapstur, Richard B Hayes, Jiyoung Ahn
Bacteria may play a role in esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), although evidence is limited to cross-sectional studies. In this study, we examined the relationship of oral microbiota with EAC and ESCC risk in a prospective study nested in two cohorts. Oral bacteria were assessed using 16S rRNA gene sequencing in prediagnostic mouthwash samples from n = 81/160 EAC and n = 25/50 ESCC cases/matched controls. Findings were largely consistent across both cohorts. Metagenome content was predicted using PiCRUST...
December 1, 2017: Cancer Research
Akebe Luther King Abia, Arghavan Alisoltani, Jitendra Keshri, Eunice Ubomba-Jaswa
Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations...
November 7, 2017: Science of the Total Environment
John Gonzales, Thuy Doan, Jessica G Shantha, Michele Bloomer, Michael R Wilson, Joseph L DeRisi, Nisha Acharya
INTRODUCTION: Currently, the detection of pathogens or mutations associated with intraocular lymphomas heavily relies on prespecified, directed PCRs. With metagenomic deep sequencing (MDS), an unbiased high-throughput sequencing approach, all pathogens as well as all mutations present in the host's genome can be detected in the same small amount of ocular fluid. METHODS: In this cross-sectional case series, aqueous fluid samples from two patients were submitted to MDS to identify pathogens as well as common and rare cancer mutations...
January 2018: British Journal of Ophthalmology
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