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Ermolenko E, Baryshnikova N, Alekhina G, Zakharenko A, Ten O, Kashchenko V, Novikova N, Gushchina O, Ovchinnikov T, Morozova A, Ilina A, Karaseva A, Tsapieva A, Gladyshev N, Dmitriev A, Suvorov A. Autoprobiotics in the Treatment of Patients with Colorectal Cancer in the Early Postoperative Period. Microorganisms 2024; 12:980. [PMID: 38792809 PMCID: PMC11124500 DOI: 10.3390/microorganisms12050980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Despite great advances in the treatment of oncological diseases, the development of medical technologies to prevent or reduce complications of therapy, in particular, those associated with surgery and the introduction of antibiotics, remains relevant. The aim of this study is to evaluate the effectiveness of the use of autoprobiotics based on indigenous non-pathogenic strains of Enterococcus faecium and Enterococcus hirae as a personalized functional food product (PFFP) in the complex therapy of colorectal cancer (CRC) in the early postoperative period. A total of 36 patients diagnosed with CRC were enrolled in the study. Study group A comprised 24 CRC patients who received autoprobiotic therapy in the early postoperative period, while the control group C included 12 CRC patients without autoprobiotic therapy. Prior to surgery and between days 14 and 16 post-surgery, comprehensive evaluations were conducted on all patients, encompassing the following: stool and gastroenterological complaints analysis, examination of the gut microbiota (bacteriological study, quantitative polymerase chain reaction, metagenome analysis), and analysis of interleukins in the serum. Results: The use of autoprobiotics led to a decrease in dyspeptic complaints after surgery. It was also associated with the absence of postoperative complications, did not cause any side effects, and led to a decrease in the level of pro-inflammatory cytokines (IL-6 and IL-18) in the blood serum. The use of autoprobiotics led to positive changes in the structure of escherichia and enterococci populations, the elimination of Parvomonas micra and Fusobacterium nucleatum, and a decrease in the quantitative content of Clostridium perfringens and Akkermansia muciniphila. Metagenomic analysis (16S rRNA) revealed an increase in alpha diversity. Conclusion: The introduction of autoprobiotics in the postoperative period is a highly effective and safe approach in the complex treatment of CRC. Future studies will allow the discovery of additional fine mechanisms of autoprobiotic therapy and its impact on the digestive, immune, endocrine, and neural systems.
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Affiliation(s)
- Elena Ermolenko
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
| | - Natalia Baryshnikova
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
- Department of Internal Disease of Stomatology Faculty, Pavlov First St-Petersburg State Medical University, 197022 St-Petersburg, Russia
- Laboratory of Medico-Social Problems of Pediatry, St-Petersburg State Pediatric Medical University, 194100 St-Petersburg, Russia
| | - Galina Alekhina
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
| | - Alexander Zakharenko
- Oncology Department, Pavlov First St-Petersburg State Medical University, 197022 St-Petersburg, Russia;
| | - Oleg Ten
- North-Western District Scientific and Clinical Center Named after L. G. Sokolov, 194291 St-Petersburg, Russia (O.G.)
| | - Victor Kashchenko
- Department of Faculty Surgery, St-Petersburg State University, 199034 St-Petersburg, Russia;
- Beloostrov High Technology Clinic (MMC VT LLC), 188652 Leningrad Region, Russia
| | - Nadezhda Novikova
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
| | - Olga Gushchina
- North-Western District Scientific and Clinical Center Named after L. G. Sokolov, 194291 St-Petersburg, Russia (O.G.)
| | - Timofey Ovchinnikov
- North-Western District Scientific and Clinical Center Named after L. G. Sokolov, 194291 St-Petersburg, Russia (O.G.)
| | - Anastasia Morozova
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
| | - Anastasia Ilina
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
| | - Alena Karaseva
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
- Microbiology Department, St-Petersburg State University, 199034 St-Petersburg, Russia
| | - Anna Tsapieva
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
| | - Nikita Gladyshev
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
| | - Alexander Dmitriev
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
- Department of Molecular Biotechnology, Saint-Petersburg State Institute of Technology, 190013 St-Petersburg, Russia
| | - Alexander Suvorov
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human”, World-Class Research Center “Center for Personalized Medicine”, Institute of Experimental Medicine, 197376 St-Petersburg, Russia; (E.E.); (A.M.); (A.T.); (N.G.)
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2
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Aitmanaitė L, Širmonaitis K, Russo G. Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap. Int J Mol Sci 2023; 24:13786. [PMID: 37762088 PMCID: PMC10531294 DOI: 10.3390/ijms241813786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The interaction between the microbial communities in the human body and the onset and progression of cancer has not been investigated until recently. The vast majority of the metagenomics research in this area has concentrated on the composition of microbiomes, attempting to link the overabundance or depletion of certain microorganisms to cancer proliferation, metastatic behaviour, and its resistance to therapies. However, studies elucidating the functional implications of the microbiome activity in cancer patients are still scarce; in particular, there is an overwhelming lack of studies assessing such implications directly, through analysis of the transcriptome of the bacterial community. This review summarises the contributions of metagenomics and metatranscriptomics to the knowledge of the microbial environment associated with several cancers; most importantly, it highlights all the advantages that metatranscriptomics has over metagenomics and suggests how such an approach can be leveraged to advance the knowledge of the cancer bacterial environment.
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Affiliation(s)
| | | | - Giancarlo Russo
- EMBL Partnership Institute for Gene Editing, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (L.A.); (K.Š.)
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3
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Wang AJ, Song D, Hong YM, Liu NN. Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the "microworld" age. Mol Omics 2023; 19:283-296. [PMID: 36916422 DOI: 10.1039/d2mo00288d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.
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Affiliation(s)
- An-Jun Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Dingka Song
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Yue-Mei Hong
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Ning-Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
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4
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Zhang H, Zhang H, Jiang Q. Progress in research of gut microbiota in colorectal cancer. Shijie Huaren Xiaohua Zazhi 2023; 31:138-142. [DOI: 10.11569/wcjd.v31.i4.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The human gut microbiota is a large and complex microbial community that is linked to human health and disease. Intestinal homeostasis is dependent on the tight interplay between the host and gut microbiota. Moreover, the gut microbiota plays an important role in digestion and metabolism. In recent years, the gut microbiota is still the most studied topic, and numerous studies have shown that the gut microbiota is closely related to colorectal cancer. In this paper, we will review the relationship between the gut microbiota and colorectal cancer pathogenesis, prevention, and treatment, with an aim to provide some new ideas for the research of colorectal cancer.
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Affiliation(s)
- Hao Zhang
- Department of Laboratory Medicine, Chengbei District, Hangzhou First People's Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Hong Zhang
- Department of Laboratory Medicine, Chengbei District, Hangzhou First People's Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Qin Jiang
- Department of Laboratory Medicine, Chengbei District, Hangzhou First People's Hospital, Hangzhou 310022, Zhejiang Province, China
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5
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Pandey H, Tang DWT, Wong SH, Lal D. Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities. Cancers (Basel) 2023; 15:cancers15030866. [PMID: 36765824 PMCID: PMC9913759 DOI: 10.3390/cancers15030866] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.
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Affiliation(s)
- Himani Pandey
- Redcliffe Labs, Electronic City, Noida 201301, India
| | - Daryl W. T. Tang
- School of Biological Sciences, Nanyang Technological University, Singapore 308232, Singapore
| | - Sunny H. Wong
- Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Correspondence: (S.H.W.); (D.L.)
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
- Correspondence: (S.H.W.); (D.L.)
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6
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Saeed M, Shoaib A, Kandimalla R, Javed S, Almatroudi A, Gupta R, Aqil F. Microbe-based therapies for colorectal cancer: Advantages and limitations. Semin Cancer Biol 2022; 86:652-665. [PMID: 34020027 DOI: 10.1016/j.semcancer.2021.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/06/2021] [Accepted: 05/14/2021] [Indexed: 01/27/2023]
Abstract
Cancer is one of the leading global causes of death in both men and women. Colorectal cancer (CRC) alone accounts for ∼10 % of total new global cases and poses an over 4% lifetime risk of developing cancer. Recent advancements in the field of biotechnology and microbiology concocted novel microbe-based therapies to treat various cancers, including CRC. Microbes have been explored for human use since centuries, especially for the treatment of various ailments. The utility of microbes in cancer therapeutics is widely explored, and various bacteria, fungi, and viruses are currently in use for the development of cancer therapeutics. The human gut hosts about 100 trillion microbes that release their metabolites in active, inactive, or dead conditions. Microbial secondary metabolites, proteins, immunotoxins, and enzymes are used to target cancer cells to induce cell cycle arrest, apoptosis, and death. Various approaches, such as dietary interventions, the use of prebiotics and probiotics, and fecal microbiota transplantation have been used to modulate the gut microbiota in order to prevent or treat CRC pathogenesis. The present review highlights the role of the gut microbiota in CRC precipitation, the potential mechanisms and use of microorganisms as CRC biomarkers, and strategies to modulate microbiota for the prevention and treatment of CRC.
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Affiliation(s)
- Mohd Saeed
- Department of Biology, College of Sciences, University of Hail, Hail, Saudi Arabia
| | - Ambreen Shoaib
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Raghuram Kandimalla
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
| | - Shamama Javed
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim 51431, Saudi Arabia
| | - Ramesh Gupta
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
| | - Farrukh Aqil
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Medicine, University of Louisville, Louisville, KY 40202, USA.
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7
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Scott N, Whittle E, Jeraldo P, Chia N. A systemic review of the role of enterotoxic Bacteroides fragilis in colorectal cancer. Neoplasia 2022; 29:100797. [PMID: 35461079 PMCID: PMC9046963 DOI: 10.1016/j.neo.2022.100797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/25/2022] [Accepted: 04/01/2022] [Indexed: 12/13/2022]
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) has received significant attention for a possible association with, or causal role in, colorectal cancer (CRC). The goal of this review was to assess the status of the published evidence supporting (i) the association between ETBF and CRC and (ii) the causal role of ETBF in CRC. PubMed and Scopus searches were performed in August 2021 to identify human, animal, and cell studies pertaining to the role of ETBF in CRC. Inclusion criteria included the use of cell lines, mice, exposure to BFT or ETBF, and detection of bft. Review studies were excluded, and studies were limited to the English language. Quality of study design and risk of bias analysis was performed on the cell, animal, and human studies using ToxRTools, SYRCLE, and NOS, respectively. Ninety-five eligible studies were identified, this included 22 human studies, 24 animal studies, 43 cell studies, and 6 studies that included both cells and mice studies. We found that a large majority of studies supported an association or causal role of ETBF in CRC, as well as high levels of study bias was detected in the in vitro and in vivo studies. The high-level heterogeneity in study design and reporting made it difficult to synthesize these findings into a unified conclusion, suggesting that the need for future studies that include improved mechanistic models, longitudinal in vitro and in vivo evidence, and appropriate control of confounding factors will be required to confirm whether ETBF has a direct role in CRC etiopathogenesis.
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Affiliation(s)
- Nancy Scott
- Bioinformatics and Computational Biology, University of Minnesota, 111 South Broadway, Rochester, MN 55904, USA
| | - Emma Whittle
- Department of Surgery, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Patricio Jeraldo
- Department of Surgery, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.
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8
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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9
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Uriarte-Navarrete I, Hernández-Lemus E, de Anda-Jáuregui G. Gene-Microbiome Co-expression Networks in Colon Cancer. Front Genet 2021; 12:617505. [PMID: 33659025 PMCID: PMC7917223 DOI: 10.3389/fgene.2021.617505] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/22/2021] [Indexed: 12/27/2022] Open
Abstract
It is known that cancer onset and development arise from complex, multi-factorial phenomena spanning from the molecular, functional, micro-environmental, and cellular up to the tissular and organismal levels. Important advances have been made in the systematic analysis of the molecular (mostly genomic and transcriptomic) within large studies of high throughput data such as The Cancer Genome Atlas collaboration. However, the role of the microbiome in the induction of biological changes needed to reach these pathological states remains to be explored, largely because of scarce experimental data. In recent work a non-standard bioinformatics strategy was used to indirectly quantify microbial abundance from TCGA RNA-seq data, allowing the evaluation of the microbiome in well-characterized cancer patients, thus opening the way to studies incorporating the molecular and microbiome dimensions altogether. In this work, we used such recently described approaches for the quantification of microbial species alongside with gene expression. With this, we will reconstruct bipartite networks linking microbial abundance and gene expression in the context of colon cancer, by resorting to network reconstruction based on measures from information theory. The rationale is that microbial communities may induce biological changes important for the cancerous state. We analyzed changes in microbiome-gene interactions in the context of early (stages I and II) and late (stages III and IV) colon cancer, studied changes in network descriptors, and identify key discriminating features for early and late stage colon cancer. We found that early stage bipartite network is associated with the establishment of structural features in the tumor cells, whereas late stage is related to more advance signaling and metabolic features. This functional divergence thus arise as a consequence of changes in the organization of the corresponding gene-microorganism co-expression networks.
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Affiliation(s)
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Conacyt Research Chairs, National Council on Science and Technology, Mexico City, Mexico
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10
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Vernia F, Longo S, Stefanelli G, Viscido A, Latella G. Dietary Factors Modulating Colorectal Carcinogenesis. Nutrients 2021; 13:nu13010143. [PMID: 33401525 PMCID: PMC7824178 DOI: 10.3390/nu13010143] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
The development of colorectal cancer, responsible for 9% of cancer-related deaths, is favored by a combination of genetic and environmental factors. The modification of diet and lifestyle may modify the risk of colorectal cancer (CRC) and prevent neoplasia in up to 50% of cases. The Western diet, characterized by a high intake of fat, red meat and processed meat has emerged as an important contributor. Conversely, a high intake of dietary fiber partially counteracts the unfavorable effects of meat through multiple mechanisms, including reduced intestinal transit time and dilution of carcinogenic compounds. Providing antioxidants (e.g., vitamins C and E) and leading to increased intraluminal production of protective fermentation products, like butyrate, represent other beneficial and useful effects of a fiber-rich diet. Protective effects on the risk of developing colorectal cancer have been also advocated for some specific micronutrients like vitamin D, selenium, and calcium. Diet-induced modifications of the gut microbiota modulate colonic epithelial cell homeostasis and carcinogenesis. This can have, under different conditions, opposite effects on the risk of CRC, through the production of mutagenic and carcinogenic agents or, conversely, of protective compounds. The aim of this review is to summarize the most recent evidence on the role of diet as a potential risk factor for the development of colorectal malignancies, as well as providing possible prevention dietary strategies.
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11
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Mohseni AH, Taghinezhad-S S, Fu X. Gut microbiota-derived metabolites and colorectal cancer: New insights and updates. Microb Pathog 2020; 149:104569. [DOI: 10.1016/j.micpath.2020.104569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/04/2020] [Accepted: 10/12/2020] [Indexed: 12/16/2022]
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12
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Dalal N, Jalandra R, Sharma M, Prakash H, Makharia GK, Solanki PR, Singh R, Kumar A. Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives. Biomed Pharmacother 2020; 131:110648. [PMID: 33152902 DOI: 10.1016/j.biopha.2020.110648] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) ranks third among the most commonly occurring cancers worldwide, and it causes half a million deaths annually. Alongside mechanistic study for CRC detection and treatment by conventional techniques, new technologies have been developed to study CRC. These technologies include genomics, transcriptomics, proteomics, and metabolomics which elucidate DNA markers, RNA transcripts, protein and, metabolites produced inside the colon and rectum part of the gut. All these approaches form the omics arena, which presents a remarkable opportunity for the discovery of novel prognostic, diagnostic and therapeutic biomarkers and also delineate the underlying mechanism of CRC causation, which may further help in devising treatment strategies. This review also mentions the latest developments in metagenomics and culturomics as emerging evidence suggests that metagenomics of gut microbiota has profound implications in the causation, prognosis, and treatment of CRC. A majority of bacteria cannot be studied as they remain unculturable, so culturomics has also been strengthened to develop culture conditions suitable for the growth of unculturable bacteria and identify unknown bacteria. The overall purpose of this review is to succinctly evaluate the application of omics technologies in colorectal cancer research for improving the diagnosis and treatment strategies.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India
| | - Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Hridayesh Prakash
- Amity Institute of Virology and Immunology, Amity University, Sector 125, Noida 201313, Uttar Pradesh, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajeev Singh
- Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India.
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India.
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13
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Gut Microbiota and Colon Cancer: A Role for Bacterial Protein Toxins? Int J Mol Sci 2020; 21:ijms21176201. [PMID: 32867331 PMCID: PMC7504354 DOI: 10.3390/ijms21176201] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence indicates that the human intestinal microbiota can contribute to the etiology of colorectal cancer. Triggering factors, including inflammation and bacterial infections, may favor the shift of the gut microbiota from a mutualistic to a pro-carcinogenic configuration. In this context, certain bacterial pathogens can exert a pro-tumoral activity by producing enzymatically-active protein toxins that either directly induce host cell DNA damage or interfere with essential host cell signaling pathways involved in cell proliferation, apoptosis, and inflammation. This review is focused on those toxins that, by mimicking carcinogens and cancer promoters, could represent a paradigm for bacterially induced carcinogenesis.
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14
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Shelton CD, Byndloss MX. Gut Epithelial Metabolism as a Key Driver of Intestinal Dysbiosis Associated with Noncommunicable Diseases. Infect Immun 2020; 88:e00939-19. [PMID: 32122941 PMCID: PMC7309626 DOI: 10.1128/iai.00939-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In high-income countries, the leading causes of death are noncommunicable diseases (NCDs), such as obesity, cancer, and cardiovascular disease. An important feature of most NCDs is inflammation-induced gut dysbiosis characterized by a shift in the microbial community structure from obligate to facultative anaerobes such as Proteobacteria This microbial imbalance can contribute to disease pathogenesis by either a depletion in or the production of microbiota-derived metabolites. However, little is known about the mechanism by which inflammation-mediated changes in host physiology disrupt the microbial ecosystem in our large intestine leading to disease. Recent work by our group suggests that during gut homeostasis, epithelial hypoxia derived from peroxisome proliferator-activated receptor γ (PPAR-γ)-dependent β-oxidation of microbiota-derived short-chain fatty acids limits oxygen availability in the colon, thereby maintaining a balanced microbial community. During inflammation, disruption in gut anaerobiosis drives expansion of facultative anaerobic Enterobacteriaceae, regardless of their pathogenic potential. Therefore, our research group is currently exploring the concept that dysbiosis-associated expansion of Enterobacteriaceae can be viewed as a microbial signature of epithelial dysfunction and may play a greater role in different models of NCDs, including diet-induced obesity, atherosclerosis, and inflammation-associated colorectal cancer.
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Affiliation(s)
- Catherine D Shelton
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mariana X Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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15
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Rasmussen TS, Koefoed AK, Jakobsen RR, Deng L, Castro-Mejía JL, Brunse A, Neve H, Vogensen FK, Nielsen DS. Bacteriophage-mediated manipulation of the gut microbiome – promises and presents limitations. FEMS Microbiol Rev 2020; 44:507-521. [DOI: 10.1093/femsre/fuaa020] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/02/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Anna Kirstine Koefoed
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Rasmus Riemer Jakobsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Ling Deng
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Josué L Castro-Mejía
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9, 2nd floor - 1870, Frederiksberg, Denmark
| | - Horst Neve
- Institute of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1 - 24103, Kiel, Germany
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
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16
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Metaproteomics characterizes human gut microbiome function in colorectal cancer. NPJ Biofilms Microbiomes 2020; 6:14. [PMID: 32210237 PMCID: PMC7093434 DOI: 10.1038/s41522-020-0123-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/26/2020] [Indexed: 02/08/2023] Open
Abstract
Pathogenesis of colorectal cancer (CRC) is associated with alterations in gut microbiome. Previous studies have focused on the changes of taxonomic abundances by metagenomics. Variations of the function of intestinal bacteria in CRC patients compared to healthy crowds remain largely unknown. Here we collected fecal samples from CRC patients and healthy volunteers and characterized their microbiome using quantitative metaproteomic method. We have identified and quantified 91,902 peptides, 30,062 gut microbial protein groups, and 195 genera of microbes. Among the proteins, 341 were found significantly different in abundance between the CRC patients and the healthy volunteers. Microbial proteins related to iron intake/transport; oxidative stress; and DNA replication, recombination, and repair were significantly alternated in abundance as a result of high local concentration of iron and high oxidative stress in the large intestine of CRC patients. Our study shows that metaproteomics can provide functional information on intestinal microflora that is of great value for pathogenesis research, and can help guide clinical diagnosis in the future.
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17
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Zhu W, Miyata N, Winter MG, Arenales A, Hughes ER, Spiga L, Kim J, Sifuentes-Dominguez L, Starokadomskyy P, Gopal P, Byndloss MX, Santos RL, Burstein E, Winter SE. Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer. J Exp Med 2019; 216:2378-2393. [PMID: 31358565 PMCID: PMC6781011 DOI: 10.1084/jem.20181939] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/28/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
Enterobacteriaceae family members such as E. coli exacerbate development of intestinal malignancy. Zhu et al. report that targeting the metabolism of protumoral Enterobacteriaceae by tungstate prevents tumor development in murine models of colitis-associated colorectal cancer. Chronic inflammation and gut microbiota dysbiosis, in particular the bloom of genotoxin-producing E. coli strains, are risk factors for the development of colorectal cancer. Here, we sought to determine whether precision editing of gut microbiota metabolism and composition could decrease the risk for tumor development in mouse models of colitis-associated colorectal cancer (CAC). Expansion of experimentally introduced E. coli strains in the azoxymethane/dextran sulfate sodium colitis model was driven by molybdoenzyme-dependent metabolic pathways. Oral administration of sodium tungstate inhibited E. coli molybdoenzymes and selectively decreased gut colonization with genotoxin-producing E. coli and other Enterobacteriaceae. Restricting the bloom of Enterobacteriaceae decreased intestinal inflammation and reduced the incidence of colonic tumors in two models of CAC, the azoxymethane/dextran sulfate sodium colitis model and azoxymethane-treated, Il10-deficient mice. We conclude that metabolic targeting of protumoral Enterobacteriaceae during chronic inflammation is a suitable strategy to prevent the development of malignancies arising from gut microbiota dysbiosis.
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Affiliation(s)
- Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Naoteru Miyata
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX.,Digestive Disease Center, International University of Health and Welfare, Mita Hospital, Japan
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Alexandre Arenales
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elizabeth R Hughes
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiwoong Kim
- Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Purva Gopal
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Mariana X Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Renato L Santos
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX .,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
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18
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Tunsjø HS, Gundersen G, Rangnes F, Noone JC, Endres A, Bemanian V. Detection of Fusobacterium nucleatum in stool and colonic tissues from Norwegian colorectal cancer patients. Eur J Clin Microbiol Infect Dis 2019; 38:1367-1376. [PMID: 31025134 DOI: 10.1007/s10096-019-03562-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/09/2019] [Indexed: 02/06/2023]
Abstract
Norway has one of the world's highest incidences of colorectal cancer (CRC). Accumulating research suggests that the intestinal microbiota may have an important role in initiation and progression of colorectal cancer. In order to evaluate microbiome-based biomarkers for non-invasive detection of CRC, the levels of Fusobacterium nucleatum and selected Escherichia coli toxin genes in stool and mucosa from a small cohort of Norwegian patients were investigated. The study cohort included 72 patients scheduled for colonoscopy. The patients were divided into three groups upon their examinations: cancer, polyp, and control groups. Levels of F. nucleatum in stool samples were significantly higher in the cancer group compared with the control group and the polyp group. High levels of F. nucleatum in stool reflected detection of F. nucleatum in the tumor tissues of colorectal cancer patients. However, no difference in the levels of E. coli toxin genes in neither stool nor biopsy samples between the patient groups was observed. This study suggests that a quantitative PCR assay targeting F. nucleatum in stool samples has the potential to be included in a larger panel of biomarkers for non-invasive testing for colorectal cancer.
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Affiliation(s)
- Hege Smith Tunsjø
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway.
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
| | - Gro Gundersen
- Department of Multidisciplinary Laboratory Science and Medical Biochemistry, Genetic Unit, Akershus University Hospital, Lørenskog, Norway
| | - Fredrik Rangnes
- Department of Multidisciplinary Laboratory Science and Medical Biochemistry, Genetic Unit, Akershus University Hospital, Lørenskog, Norway
| | - John Christopher Noone
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Alexander Endres
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Vahid Bemanian
- Department of Multidisciplinary Laboratory Science and Medical Biochemistry, Genetic Unit, Akershus University Hospital, Lørenskog, Norway
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19
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Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat Med 2019; 25:679-689. [PMID: 30936547 PMCID: PMC7984229 DOI: 10.1038/s41591-019-0406-6] [Citation(s) in RCA: 613] [Impact Index Per Article: 122.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/20/2019] [Indexed: 02/07/2023]
Abstract
Association studies have linked microbiome alterations with many human diseases. However, they have not always reported consistent results, thereby necessitating cross-study comparisons. Here, a meta-analysis of eight geographically and technically diverse fecal shotgun metagenomic studies of colorectal cancer (CRC, n = 768), which was controlled for several confounders, identified a core set of 29 species significantly enriched in CRC metagenomes (false discovery rate (FDR) < 1 × 10-5). CRC signatures derived from single studies maintained their accuracy in other studies. By training on multiple studies, we improved detection accuracy and disease specificity for CRC. Functional analysis of CRC metagenomes revealed enriched protein and mucin catabolism genes and depleted carbohydrate degradation genes. Moreover, we inferred elevated production of secondary bile acids from CRC metagenomes, suggesting a metabolic link between cancer-associated gut microbes and a fat- and meat-rich diet. Through extensive validations, this meta-analysis firmly establishes globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics.
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Affiliation(s)
- Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paul Theodor Pyl
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine, University of Copenhagen, Copenhagen, Denmark.,Division of Surgery, Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Ece Kartal
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Konrad Zych
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alireza Kashani
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Alessio Milanese
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas S Fleck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anita Y Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Albert Palleja
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ruby Ponnudurai
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Luis Pedro Coelho
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nina Habermann
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Emma Niméus
- Division of Surgery, Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.,Division of Surgery, Department of Clinical Sciences Lund, Faculty of Medicine, Skane University Hospital, Lund, Sweden
| | - Andrew M Thomas
- Department CIBIO, University of Trento, Trento, Italy.,Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, Brazil
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Sara Gandini
- IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Sayaka Mizutani
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hirotsugu Shiroma
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Satoshi Shiba
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shinichi Yachida
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.,Department of Cancer Genome Informatics, Graduate School of Medicine/Faculty of Medicine, Osaka University, Osaka, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Levi Waldron
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA.,Institute for Implementation Science in Population Health, City University of New York, New York, NY, USA
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Hermann Brenner
- Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany.,Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany.,German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine, University of Copenhagen, Copenhagen, Denmark. .,Faculty of Healthy Sciences, University of Southern Denmark, Odense, Denmark.
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Molecular Medicine Partnership Unit, Heidelberg, Germany. .,Max Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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20
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Heintz-Buschart A, Wilmes P. Human Gut Microbiome: Function Matters. Trends Microbiol 2018; 26:563-574. [DOI: 10.1016/j.tim.2017.11.002] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/29/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022]
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21
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Zhou Y, He H, Xu H, Li Y, Li Z, Du Y, He J, Zhou Y, Wang H, Nie Y. Association of oncogenic bacteria with colorectal cancer in South China. Oncotarget 2018; 7:80794-80802. [PMID: 27821805 PMCID: PMC5348355 DOI: 10.18632/oncotarget.13094] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/28/2016] [Indexed: 12/15/2022] Open
Abstract
To quantify Fusobacterium spp., Enterococcus faecalis (E.faecalis), Enterotoxigenic Bacteroides fragilis (ETBF), and Enteropathogenic Escherichia coli in colorectal cancer (CRC) patients and their possible association with CRC clinicopathogical features, we collected the resected tumors and adjacent normal tissues (N) from 97 CRC patients. 48 age- and sex-matched healthy controls (HC) were also recruited. Real-time PCR was used for bacterial quantification. The median abundance ofFusobacterium spp.(p < 0.001, vs. N; p < 0.01,vs. HC), E.faecalis (p < 0.05, vs. N; p < 0.01, vs. HC) and ETBF (p < 0.001, vs. N; p < 0.05,vs. HC) in tumor tissues was significantly higher than that detected in normal tissue and HC. E.faecalis was detected in 95.88% of tumors and 93.81% of adjacent tissues. Fusobacterium spp. was detected in 72.16% of tumors and 67.01% of adjacent tissues. The combined E.faecalis and Fusobacterium spp. were detected in 70.10% of tumors and 36.08% of adjacent normal tissues. All four bacteria were detected in 33.72% and 22.09% of paired tumor and adjacent normal tissues, respectively. E.faecalis and Fusobacterium spp. are enriched in both tumor and adjacent tissue of CRC patients when compared to HC, suggesting that it is possible to be previously undetected changes in the pathohistologically normal colon tissue in the proximity of the tumor.
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Affiliation(s)
- Youlian Zhou
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Hanchang He
- The First People's Foshan Hospital, Chancheng District, Foshan, 528000, Guangdong, China
| | - Haoming Xu
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yingfei Li
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Zhiming Li
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yanlei Du
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Jie He
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yongjian Zhou
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Hong Wang
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yuqiang Nie
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
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22
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Espinoza JL, Minami M. Sensing Bacterial-Induced DNA Damaging Effects via Natural Killer Group 2 Member D Immune Receptor: From Dysbiosis to Autoimmunity and Carcinogenesis. Front Immunol 2018; 9:52. [PMID: 29422899 PMCID: PMC5788971 DOI: 10.3389/fimmu.2018.00052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/09/2018] [Indexed: 12/23/2022] Open
Abstract
The human genome is constantly exposed to exogenous and endogenous DNA damaging factors that frequently cause DNA damages. Unless repaired, damaged DNA can result in deleterious mutations capable of causing malignant transformation. Accordingly, cells have developed an advanced and effective surveillance system, the DNA damage response (DDR) pathway, which maintains genetic integrity. In addition to well-defined outcomes, such as cell cycle arrest, apoptosis, and senescence, another consequence of DDR activation is the induction of natural killer group 2 member D ligands (NKG2D-Ls) on the surface of stressed cells. Consequently, NKG2D-Ls-expressing cells are recognized and eliminated by NKG2D receptor-expressing immune cells, including NK cells, and various subsets of T-cells. Recent pieces of evidence indicate that commensal microbial imbalance (known as dysbiosis) can trigger DDR activation in host cells, which may result in sustained inflammatory responses. Therefore, dysbiosis can be seen as an important source of DNA damage agents that may be partially responsible for the overexpression of NKG2D-Ls on intestinal epithelial cells that is frequently observed in patients with inflammatory bowel disease and other disorders associated with altered human microbiota, including the development of colorectal cancer. In this article, we discuss recent evidence that appears to link an altered human microbiota with autoimmunity and carcinogenesis via the activation of DDR signals and the induction of NKG2D-Ls in stressed cells.
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Affiliation(s)
- J Luis Espinoza
- Department of Hematology and Rheumatology, Faculty of Medicine, Kindai University, Osakasayama, Japan
| | - Mika Minami
- Faculty of Medicine, Kindai University, Higashi-osaka, Japan
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23
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Zuñiga C, Zaramela L, Zengler K. Elucidation of complexity and prediction of interactions in microbial communities. Microb Biotechnol 2017; 10:1500-1522. [PMID: 28925555 PMCID: PMC5658597 DOI: 10.1111/1751-7915.12855] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ. Interpretation of these multi-omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. Here, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.
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Affiliation(s)
- Cristal Zuñiga
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Livia Zaramela
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Karsten Zengler
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
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24
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Zha L, Wilson MR, Brotherton CA, Balskus EP. Characterization of Polyketide Synthase Machinery from the pks Island Facilitates Isolation of a Candidate Precolibactin. ACS Chem Biol 2016; 11:1287-95. [PMID: 26890481 DOI: 10.1021/acschembio.6b00014] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Colibactin is a human gut bacterial genotoxin of unknown structure that has been linked to colon cancer. The biosynthesis of this elusive metabolite is directed by the pks gene cluster, which encodes a hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) assembly line that is hypothesized to use the unusual polyketide building block aminomalonate. This biosynthetic pathway is thought to initially produce an inactive intermediate (precolibactin) that is processed to the active toxin. Here, we report the first in vitro biochemical characterization of the PKS components of the pks enzymatic assembly line. We evaluate PKS extender unit utilization and show that ClbG, a freestanding acyltransferase (AT) from the pks gene cluster, recognizes aminomalonyl-acyl carrier protein (AM-ACP) and transfers this building block to multiple PKS modules, including a cis-AT PKS ClbI. We also use genetics to explore the in vivo role of ClbG in colibactin and precolibactin biosynthesis. Unexpectedly, production of previously identified pks-associated metabolites is dramatically increased in a ΔclbP/ΔclbG mutant strain, enabling the first structure elucidation of a bithiazole-containing candidate precolibactin. This work provides new insights into the unusual biosynthetic capabilities of the pks gene cluster, offers further support for the hypothesis that colibactin directly damages DNA, and suggests that additional, uncharacterized pks-derived metabolites containing aminomalonate play critical roles in genotoxicity.
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Affiliation(s)
- Li Zha
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew R. Wilson
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Carolyn A. Brotherton
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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25
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Gagnière J, Raisch J, Veziant J, Barnich N, Bonnet R, Buc E, Bringer MA, Pezet D, Bonnet M. Gut microbiota imbalance and colorectal cancer. World J Gastroenterol 2016; 22:501-518. [PMID: 26811603 PMCID: PMC4716055 DOI: 10.3748/wjg.v22.i2.501] [Citation(s) in RCA: 493] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/06/2015] [Accepted: 10/20/2015] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota acts as a real organ. The symbiotic interactions between resident micro-organisms and the digestive tract highly contribute to maintain the gut homeostasis. However, alterations to the microbiome caused by environmental changes (e.g., infection, diet and/or lifestyle) can disturb this symbiotic relationship and promote disease, such as inflammatory bowel diseases and cancer. Colorectal cancer is a complex association of tumoral cells, non-neoplastic cells and a large amount of micro-organisms, and the involvement of the microbiota in colorectal carcinogenesis is becoming increasingly clear. Indeed, many changes in the bacterial composition of the gut microbiota have been reported in colorectal cancer, suggesting a major role of dysbiosis in colorectal carcinogenesis. Some bacterial species have been identified and suspected to play a role in colorectal carcinogenesis, such as Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis, Enterococcus faecalis, Clostridium septicum, Fusobacterium spp. and Escherichia coli. The potential pro-carcinogenic effects of these bacteria are now better understood. In this review, we discuss the possible links between the bacterial microbiota and colorectal carcinogenesis, focusing on dysbiosis and the potential pro-carcinogenic properties of bacteria, such as genotoxicity and other virulence factors, inflammation, host defenses modulation, bacterial-derived metabolism, oxidative stress and anti-oxidative defenses modulation. We lastly describe how bacterial microbiota modifications could represent novel prognosis markers and/or targets for innovative therapeutic strategies.
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26
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Burns MB, Lynch J, Starr TK, Knights D, Blekhman R. Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment. Genome Med 2015; 7:55. [PMID: 26170900 PMCID: PMC4499914 DOI: 10.1186/s13073-015-0177-8] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background The human gut microbiome is associated with the development of colon cancer, and recent studies have found changes in the microbiome in cancer patients compared to healthy controls. Studying the microbial communities in the tumor microenvironment may shed light on the role of host–bacteria interactions in colorectal cancer. Here, we highlight the major shifts in the colorectal tumor microbiome relative to that of matched normal colon tissue from the same individual, allowing us to survey the microbial communities in the tumor microenvironment and providing intrinsic control for environmental and host genetic effects on the microbiome. Methods We sequenced the microbiome in 44 primary tumor and 44 patient-matched normal colon tissue samples to determine differentially abundant microbial taxa These data were also used to functionally characterize the microbiome of the cancer and normal sample pairs and identify functional pathways enriched in the tumor-associated microbiota. Results We find that tumors harbor distinct microbial communities compared to nearby healthy tissue. Our results show increased microbial diversity in the tumor microenvironment, with changes in the abundances of commensal and pathogenic bacterial taxa, including Fusobacterium and Providencia. While Fusobacterium has previously been implicated in colorectal cancer, Providencia is a novel tumor-associated agent which has not been identified in previous studies. Additionally, we identified a clear, significant enrichment of predicted virulence-associated genes in the colorectal cancer microenvironment, likely dependent upon the genomes of Fusobacterium and Providencia. Conclusions This work identifies bacterial taxa significantly correlated with colorectal cancer, including a novel finding of an elevated abundance of Providencia in the tumor microenvironment. We also describe the predicted metabolic pathways and enzymes differentially present in the tumor-associated microbiome, and show an enrichment of virulence-associated bacterial genes in the tumor microenvironment. This predicted virulence enrichment supports the hypothesis that the microbiome plays an active role in colorectal cancer development and/or progression. Our results provide a starting point for future prognostic and therapeutic research with the potential to improve patient outcomes. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0177-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael B Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
| | - Joshua Lynch
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
| | - Timothy K Starr
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ; Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN USA ; Biotechnology Institute, University of Minnesota, Minneapolis, MN USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
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27
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Allali I, Delgado S, Marron PI, Astudillo A, Yeh JJ, Ghazal H, Amzazi S, Keku T, Azcarate-Peril MA. Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain. Gut Microbes 2015; 6:161-72. [PMID: 25875428 PMCID: PMC4615176 DOI: 10.1080/19490976.2015.1039223] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer in the world and the second leading cause of cancer deaths in the US and Spain. The molecular mechanisms involved in the etiology of CRC are not yet elucidated due in part to the complexity of the human gut microbiota. In this study, we compared the microbiome composition of 90 tumor and matching adjacent tissue (adjacent) from cohorts from the US and Spain by 16S rRNA amplicon sequencing in order to determine the impact of the geographic origin on the CRC microbiome. Data showed a significantly (P < 0.05) higher Phylogenetic Diversity (PD) for the US (PD Adjacent = 26.3 ± 5.3, PD Tumor = 23.3 ± 6.2) compared to the Spanish cohort (PD Adjacent = 18.9 ± 5.9, PD Tumor = 18.7 ± 6.6) while no significant differences in bacterial diversity were observed between tumor and adjacent tissues for individuals from the same country. Adjacent tissues from the Spanish cohort were enriched in Firmicutes (SP = 43.9% and US = 22.2%, P = 0.0001) and Actinobacteria (SP = 1.6% and US = 0.5%, P = 0.0018) compared to US adjacent tissues, while adjacent tissues from the US had significantly higher abundances of Fusobacteria (US = 8.1% and SP = 1.5%, P = 0.0023) and Sinergistetes (US = 0.3% and SP = 0.1%, P = 0.0097). Comparisons between tumor and adjacent tissues in each cohort identified the genus Eikenella significantly over represented in US tumors (T = 0.024% and A = 0%, P = 0.03), and the genera Fusobacterium (T = 10.4% and A = 1.5%, P = <0.0001), Bulleida (T = 0.36% and A = 0.09%, P = 0.02), Gemella (T = 1.46% and A = 0.19%, P = 0.03), Parvimonas (T = 3.14% and A = 0.86%, P = 0.03), Campylobacter (T = 0.15% and A = 0.008%, P = 0.047), and Streptococcus (T = 2.84% and A = 2.19%, P = 0.05) significantly over represented in Spanish tumors. Predicted metagenome functional content from 16S rRNA surveys showed that bacterial motility proteins and proteins involved in flagellar assembly were over represented in adjacent tissues of both cohorts, while pathways involved in fatty acid biosynthesis, the MAPK signaling pathway, and bacterial toxins were over represented in tumors. Our study suggests that microbiome compositional and functional dissimilarities by geographic location should be taken in consideration when approaching CRC therapeutic options.
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Affiliation(s)
- Imane Allali
- Department of Cell Biology and Physiology, and Microbiome Core Facility; University of North Carolina School of Medicine; Chapel Hill, NC, USA,Laboratory of Biochemistry & Immunology; Faculty of Sciences; University Mohammed V; Rabat, Morocco,Laboratory of Genetics and Biotechnology; Faculty of Sciences of Oujda; University Mohammed Premier; Oujda, Morocco
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products; Instituto de Productos Lácteos de Asturias (IPLA-CSIC); Villaviciosa-Asturias, Spain
| | - Pablo Isidro Marron
- Instituto Universitario de Oncología del Principado de Asturias; Hospital Universitario Central de Asturias; Universidad de Oviedo; Asturias, Spain
| | - Aurora Astudillo
- Instituto Universitario de Oncología del Principado de Asturias; Hospital Universitario Central de Asturias; Universidad de Oviedo; Asturias, Spain
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center; Departments of Surgery and Pharmacology; University of North Carolina School of Medicine; Chapel Hill, NC, USA
| | - Hassan Ghazal
- Laboratory of Genetics and Biotechnology; Faculty of Sciences of Oujda; University Mohammed Premier; Oujda, Morocco,Polydisciplinary Faculty of Nador; University Mohammed Premier; Nador, Morocco
| | - Saaïd Amzazi
- Laboratory of Biochemistry & Immunology; Faculty of Sciences; University Mohammed V; Rabat, Morocco
| | - Temitope Keku
- Division of Gastroenterology & Hepatology; Department of Medicine; University of North Carolina School of Medicine; Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Cell Biology and Physiology, and Microbiome Core Facility; University of North Carolina School of Medicine; Chapel Hill, NC, USA,Correspondence to: M Andrea Azcarate-Peril
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28
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Viljoen KS, Dakshinamurthy A, Goldberg P, Blackburn JM. Quantitative profiling of colorectal cancer-associated bacteria reveals associations between fusobacterium spp., enterotoxigenic Bacteroides fragilis (ETBF) and clinicopathological features of colorectal cancer. PLoS One 2015; 10:e0119462. [PMID: 25751261 PMCID: PMC4353626 DOI: 10.1371/journal.pone.0119462] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/23/2015] [Indexed: 12/11/2022] Open
Abstract
Various studies have presented clinical or in vitro evidence linking bacteria to colorectal cancer, but these bacteria have not previously been concurrently quantified by qPCR in a single cohort. We quantify these bacteria (Fusobacterium spp., Streptococcus gallolyticus, Enterococcus faecalis, Enterotoxigenic Bacteroides fragilis (ETBF), Enteropathogenic Escherichia coli (EPEC), and afaC- or pks-positive E. coli) in paired tumour and normal tissue samples from 55 colorectal cancer patients. We further investigate the relationship between a) the presence and b) the level of colonisation of each bacterial species with site and stage of disease, age, gender, ethnicity and MSI-status. With the exception of S. gallolyticus, we detected all bacteria profiled here in both tumour and normal samples at varying frequencies. ETBF (FDR = 0.001 and 0.002 for normal and tumour samples) and afaC-positive E. coli (FDR = 0.03, normal samples) were significantly enriched in the colon compared to the rectum. ETBF (FDR = 0.04 and 0.002 for normal and tumour samples, respectively) and Fusobacterium spp. (FDR = 0.03 tumour samples) levels were significantly higher in late stage (III/IV) colorectal cancers. Fusobacterium was by far the most common bacteria detected, occurring in 82% and 81% of paired tumour and normal samples. Fusobacterium was also the only bacterium that was significantly higher in tumour compared to normal samples (p = 6e-5). We also identified significant associations between high-level colonisation by Fusobacterium and MSI-H (FDR = 0.05), age (FDR = 0.03) or pks-positive E. coli (FDR = 0.01). Furthermore, we exclusively identified atypical EPEC in our cohort, which has not been previously reported in association with colorectal cancer. By quantifying colorectal cancer-associated bacteria across a single cohort, we uncovered inter- and intra-individual patterns of colonization not previously recognized, as well as important associations with clinicopathological features, especially in the case of Fusobacterium and ETBF.
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Affiliation(s)
- Katie S. Viljoen
- Institute of Infectious Disease & Molecular Medicine, Division of Medical Biochemistry, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Amirtha Dakshinamurthy
- Institute of Infectious Disease & Molecular Medicine, Division of Medical Biochemistry, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Paul Goldberg
- Surgical Gastroenterology Unit, Department of Surgery, Groote Schuur Hospital, Cape Town, South Africa
| | - Jonathan M. Blackburn
- Institute of Infectious Disease & Molecular Medicine, Division of Medical Biochemistry, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
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29
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Abstract
This highlight reviews recent studies of colibactin, a structurally uncharacterized genotoxin synthesized by members of the human gut microbiota.
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Affiliation(s)
- Emily P. Balskus
- Department of Chemistry and Chemical Biology
- Harvard University
- Cambridge
- USA
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30
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Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol 2014; 10:766. [PMID: 25432777 PMCID: PMC4299606 DOI: 10.15252/msb.20145645] [Citation(s) in RCA: 746] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism.
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Affiliation(s)
- Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julien Tap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Anita Y Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aurélien Amiot
- Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Jürgen Böhm
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francesco Brunetti
- Department of Surgery, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Nina Habermann
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rajna Hercog
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Moritz Koch
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Alain Luciani
- Department of Radiology, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Daniel R Mende
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin A Schneider
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christophe Tournigand
- Department of Medical Oncology, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Jeanne Tran Van Nhieu
- Department of Pathology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Takuji Yamada
- Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Jürgen Zimmermann
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Cornelia M Ulrich
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Iradj Sobhani
- Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany
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ElRakaiby M, Dutilh BE, Rizkallah MR, Boleij A, Cole JN, Aziz RK. Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:402-14. [PMID: 24785449 DOI: 10.1089/omi.2014.0018] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug-microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.
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Affiliation(s)
- Marwa ElRakaiby
- 1 Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University , Cairo, Egypt
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32
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Hagland HR, Søreide K. Cellular metabolism in colorectal carcinogenesis: Influence of lifestyle, gut microbiome and metabolic pathways. Cancer Lett 2014; 356:273-80. [PMID: 24614287 DOI: 10.1016/j.canlet.2014.02.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 02/05/2014] [Accepted: 02/28/2014] [Indexed: 02/07/2023]
Abstract
The interconnectivity between diet, gut microbiota and cell molecular responses is well known; however, only recently has technology allowed the identification of strains of microorganisms harbored in the gastrointestinal tract that may increase susceptibility to cancer. The colonic environment appears to play a role in the development of colon cancer, which is influenced by the human metabolic lifestyle and changes in the gut microbiome. Studying metabolic changes at the cellular level in cancer be useful for developing novel improved preventative measures, such as screening through metabolic breath-tests or treatment options that directly affect the metabolic pathways responsible for the carcinogenicity.
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Affiliation(s)
- Hanne R Hagland
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway; Gastrointestinal Translational Research Unit, Molecular Lab, Stavanger University Hospital, Stavanger, Norway
| | - Kjetil Søreide
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway; Gastrointestinal Translational Research Unit, Molecular Lab, Stavanger University Hospital, Stavanger, Norway; Department of Clinical Medicine, University of Bergen, Bergen, Norway.
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33
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Liu NQ, Meng SN, Liu Y. Clinical significance of microRNA-625 expression in colorectal cancer. Shijie Huaren Xiaohua Zazhi 2013; 21:3158-3162. [DOI: 10.11569/wcjd.v21.i29.3158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To analyze the association of expression of microRNA-625 (miR-625) with clinicopathological characteristics and survival in patients with colorectal cancer (CRC).
METHODS: The expression level of miR-625 was determined by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) in 78 human colorectal cancer tissue specimens and matched tumor-adjacent colorectal tissue specimens. The association of miR-625 expression with clinicopathological characteristics and survival in CRC patients was then analyzed.
RESULTS: Compared with tumor-adjacent normal mucosal specimens, miR-625 was significantly down-regulated in CRC tissue specimens (2.748 vs 0.769, P = 0.021). MiR-625 expression was decreased in CRC cell lines HCT116 and SW480 compared with Caco-2 cell line, which has a lower metastatic potential (0.634, 0.941 vs 2.048, both P < 0.05). Lower expression of miR-625 was positively associated with advanced lymph node metastasis, liver metastasis and overall survival (all P < 0.05).
CONCLUSION: Our results suggest that miR-625 may serve as an efficient clinical biomarker and a potential therapeutic target for the inhibition of metastasis in CRC.
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