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Metagenomics cancer

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https://www.readbyqxmd.com/read/29313867/hpv-chlamydia-trachomatis-co-infection-metagenomic-analysis-of-cervical-microbiota-in-asymptomatic-women
#1
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
https://www.readbyqxmd.com/read/29302014/the-commensal-microbiome-is-associated-with-anti-pd-1-efficacy-in-metastatic-melanoma-patients
#2
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 16S ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria...
January 5, 2018: Science
https://www.readbyqxmd.com/read/29285293/two-new-species-of-betatorqueviruses-identified-in-a-human-melanoma-that-metastasized-to-the-brain
#3
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
https://www.readbyqxmd.com/read/29247187/alterations-in-oral-bacterial-communities-are-associated-with-risk-factors-for-oral-and-oropharyngeal-cancer
#4
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
https://www.readbyqxmd.com/read/29247170/harnessing-the-microbiomes-of-brassica-vegetables-for-health-issues
#5
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
https://www.readbyqxmd.com/read/29235578/are-we-any-closer-to-screening-for-colorectal-cancer-using-microbial-markers-a-critical-review
#6
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 13, 2017: Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia
https://www.readbyqxmd.com/read/29233840/microbiome-in-pten-hamartoma-tumor-syndrome
#7
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
https://www.readbyqxmd.com/read/29228570/keratin-8-reduces-colonic-permeability-and-maintains-gut-microbiota-homeostasis-protecting-against-colitis-and-colitis-associated-tumorigenesis
#8
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
https://www.readbyqxmd.com/read/29196415/oral-microbiome-composition-reflects-prospective-risk-for-esophageal-cancers
#9
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
https://www.readbyqxmd.com/read/29126050/metagenomic-analysis-of-the-bacterial-communities-and-their-functional-profiles-in-water-and-sediments-of-the-apies-river-south-africa-as-a-function-of-land-use
#10
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
https://www.readbyqxmd.com/read/29122821/metagenomic-deep-sequencing-of-aqueous-fluid-detects-intraocular-lymphomas
#11
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...
November 9, 2017: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/29120399/a-microbiomic-analysis-in-african-americans-with-colonic-lesions-reveals-streptococcus-sp-vt162-as-a-marker-of-neoplastic-transformation
#12
Hassan Brim, Shibu Yooseph, Edward Lee, Zaki Sherif, Muneer Abbas, Adeyinka O Laiyemo, Sudhir Varma, Manolito Torralba, Scot E Dowd, Karen E Nelson, Wimal Pathmasiri, Susan Sumner, Willem de Vos, Qiaoyi Liang, Jun Yu, Erwin Zoetendal, Hassan Ashktorab
Increasing evidence suggests a role of the gut microbiota in colorectal carcinogenesis (CRC). To detect bacterial markers of colorectal cancer in African Americans a metabolomic analysis was performed on fecal water extracts. DNA from stool samples of adenoma and healthy subjects and from colon cancer and matched normal tissues was analyzed to determine the microbiota composition (using 16S rDNA) and genomic content (metagenomics). Metagenomic functions with discriminative power between healthy and neoplastic specimens were established...
November 9, 2017: Genes
https://www.readbyqxmd.com/read/29113654/the-role-of-intestinal-bacteria-in-the-development-and-progression-of-gastrointestinal-tract-neoplasms
#13
REVIEW
Kosuke Mima, Shuji Ogino, Shigeki Nakagawa, Hiroshi Sawayama, Koichi Kinoshita, Ryuichi Krashima, Takatsugu Ishimoto, Katsunori Imai, Masaaki Iwatsuki, Daisuke Hashimoto, Yoshifumi Baba, Yasuo Sakamoto, Yo-Ichi Yamashita, Naoya Yoshida, Akira Chikamoto, Takatoshi Ishiko, Hideo Baba
More than 100 trillion microorganisms inhabit the human intestinal tract and play important roles in health conditions and diseases, including cancer. Accumulating evidence demonstrates that specific bacteria and bacterial dysbiosis in the gastrointestinal tract can potentiate the development and progression of gastrointestinal tract neoplasms by damaging DNA, activating oncogenic signaling pathways, producing tumor-promoting metabolites such as secondary bile acids, and suppressing antitumor immunity. Other bacterial species have been shown to produce short-chain fatty acids such as butyrate, which can suppress inflammation and carcinogenesis in the gastrointestinal tract...
December 2017: Surgical Oncology
https://www.readbyqxmd.com/read/29104759/human-microbiome-signatures-of-differential-colorectal-cancer-drug-metabolism
#14
Leah Guthrie, Sanchit Gupta, Johanna Daily, Libusha Kelly
It is well appreciated that microbial metabolism of drugs can influence treatment efficacy. Microbial β-glucuronidases in the gut can reactivate the excreted, inactive metabolite of irinotecan, a first-line chemotherapeutic for metastatic colorectal cancer. Reactivation causes adverse drug responses, including severe diarrhea. However, a direct connection between irinotecan metabolism and the composition of an individual's gut microbiota has not previously been made. Here, we report quantitative evidence of inter-individual variability in microbiome metabolism of the inactive metabolite of irinotecan to its active form...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29097494/gut-microbiome-influences-efficacy-of-pd-1-based-immunotherapy-against-epithelial-tumors
#15
Bertrand Routy, Emmanuelle Le Chatelier, Lisa Derosa, Connie P M Duong, Maryam Tidjani Alou, Romain Daillère, Aurélie Fluckiger, Meriem Messaoudene, Conrad Rauber, Maria P Roberti, Marine Fidelle, Caroline Flament, Vichnou Poirier-Colame, Paule Opolon, Christophe Klein, Kristina Iribarren, Laura Mondragón, Nicolas Jacquelot, Bo Qu, Gladys Ferrere, Céline Clémenson, Laura Mezquita, Jordi Remon Masip, Charles Naltet, Solenn Brosseau, Coureche Kaderbhai, Corentin Richard, Hira Rizvi, Florence Levenez, Nathalie Galleron, Benoit Quinquis, Nicolas Pons, Bernhard Ryffel, Véronique Minard-Colin, Patrick Gonin, Jean-Charles Soria, Eric Deutsch, Yohann Loriot, François Ghiringhelli, Gérard Zalcman, François Goldwasser, Bernard Escudier, Matthew D Hellmann, Alexander Eggermont, Didier Raoult, Laurence Albiges, Guido Kroemer, Laurence Zitvogel
Immune checkpoint inhibitors (ICIs) targeting the PD-1/PD-L1 axis induce sustained clinical responses in a sizable minority of cancer patients. We found that primary resistance to ICIs can be attributed to abnormal gut microbiome composition. Antibiotics inhibited the clinical benefit of ICIs in patients with advanced cancer. Fecal microbiota transplantation (FMT) from cancer patients who responded to ICIs into germ-free or antibiotic-treated mice ameliorated the antitumor effects of PD-1 blockade, whereas FMT from nonresponding patients failed to do so...
January 5, 2018: Science
https://www.readbyqxmd.com/read/29097493/gut-microbiome-modulates-response-to-anti-pd-1-immunotherapy-in-melanoma-patients
#16
V Gopalakrishnan, C N Spencer, L Nezi, A Reuben, M C Andrews, T V Karpinets, P A Prieto, D Vicente, K Hoffman, S C Wei, A P Cogdill, L Zhao, C W Hudgens, D S Hutchinson, T Manzo, M Petaccia de Macedo, T Cotechini, T Kumar, W S Chen, S M Reddy, R Szczepaniak Sloane, J Galloway-Pena, H Jiang, P L Chen, E J Shpall, K Rezvani, A M Alousi, R F Chemaly, S Shelburne, L M Vence, P C Okhuysen, V B Jensen, A G Swennes, F McAllister, E Marcelo Riquelme Sanchez, Y Zhang, E Le Chatelier, L Zitvogel, N Pons, J L Austin-Breneman, L E Haydu, E M Burton, J M Gardner, E Sirmans, J Hu, A J Lazar, T Tsujikawa, A Diab, H Tawbi, I C Glitza, W J Hwu, S P Patel, S E Woodman, R N Amaria, M A Davies, J E Gershenwald, P Hwu, J E Lee, J Zhang, L M Coussens, Z A Cooper, P A Futreal, C R Daniel, N J Ajami, J F Petrosino, M T Tetzlaff, P Sharma, J P Allison, R R Jenq, J A Wargo
Pre-clinical mouse models suggest that the gut microbiome modulates tumor response to checkpoint blockade immunotherapy; however, this has not been well-characterized in human cancer patients. Here we examined the oral and gut microbiome of melanoma patients undergoing anti-PD-1 immunotherapy (n=112). Significant differences were observed in the diversity and composition of the patient gut microbiome of responders (R) versus non-responders (NR). Analysis of patient fecal microbiome samples (n=43, 30R, 13NR) showed significantly higher alpha diversity (p<0...
November 2, 2017: Science
https://www.readbyqxmd.com/read/29077792/unsupervised-multiple-kernel-learning-for-heterogeneous-data-integration
#17
Jérôme Mariette, Nathalie Villa-Vialaneix
Motivation: Recent high-throughput sequencing advances have expanded the breadth of available omics datasets and the integrated analysis of multiple datasets obtained on the same samples has allowed to gain important insights in a wide range of applications. However, the integration of various sources of information remains a challenge for systems biology since produced datasets are often of heterogeneous types, with the need of developing generic methods to take their different specificities into account...
October 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29041989/links-of-gut-microbiota-composition-with-alcohol-dependence-syndrome-and-alcoholic-liver-disease
#18
Veronika B Dubinkina, Alexander V Tyakht, Vera Y Odintsova, Konstantin S Yarygin, Boris A Kovarsky, Alexander V Pavlenko, Dmitry S Ischenko, Anna S Popenko, Dmitry G Alexeev, Anastasiya Y Taraskina, Regina F Nasyrova, Evgeny M Krupitsky, Nino V Shalikiani, Igor G Bakulin, Petr L Shcherbakov, Lyubov O Skorodumova, Andrei K Larin, Elena S Kostryukova, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Sergey Y Malanin, Ruzilya K Ismagilova, Tatiana V Grigoryeva, Elena N Ilina, Vadim M Govorun
BACKGROUND: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29029730/assessing-the-diversity-of-rodent-borne-viruses-exploring-of-high-throughput-sequencing-and-classical-amplification-sequencing-approaches
#19
Stephan Drewes, Petra Straková, Jan F Drexler, Jens Jacob, Rainer G Ulrich
Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research...
2017: Advances in Virus Research
https://www.readbyqxmd.com/read/28983453/remote-sensing-between-liver-and-intestine-importance-of-microbial-metabolites
#20
Zidong Donna Fu, Julia Yue Cui
Recent technological advancements including metagenomics sequencing and metabolomics have allowed the discovery of critical functions of gut microbiota in obesity, malnutrition, neurological disorders, asthma, and xenobiotic metabolism. Classification of the human gut microbiome into distinct "enterotypes" has been proposed to serve as a new paradigm for understanding the interplay between microbial variation and human disease phenotypes, as many organs are affected by gut microbiota modifications during the pathogenesis of diseases...
June 2017: Current Pharmacology Reports
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