1
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Liu X, Li K, Yang Y, Cao D, Xu X, He Z, Wu W. Gut resistome profiling reveals high diversity and fluctuations in pancreatic cancer cohorts. Front Cell Infect Microbiol 2024; 14:1354234. [PMID: 38384305 PMCID: PMC10879602 DOI: 10.3389/fcimb.2024.1354234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Background Pancreatic cancer is one of the deadliest cancer, with a 5-year overall survival rate of 11%. Unfortunately, most patients are diagnosed with advanced stage by the time they present with symptoms. In the past decade, microbiome studies have explored the association of pancreatic cancer with the human oral and gut microbiomes. However, the gut microbial antibiotic resistance genes profiling of pancreatic cancer patients was never reported compared to that of the healthy cohort. Results In this study, we addressed the gut microbial antibiotic resistance genes profile using the metagenomic data from two online public pancreatic cancer cohorts. We found a high degree of data concordance between the two cohorts, which can therefore be used for cross-sectional comparisons. Meanwhile, we used two strategies to predict antibiotic resistance genes and compared the advantages and disadvantages of these two approaches. We also constructed microbe-antibiotic resistance gene networks and found that most of the hub nodes in the networks were antibiotic resistance genes. Conclusions In summary, we describe the panorama of antibiotic resistance genes in the gut microbes of patients with pancreatic cancer. We hope that our study will provide new perspectives on treatment options for the disease.
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Affiliation(s)
- Xudong Liu
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Kexin Li
- School of Engineering Medicine, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany
| | - Yun Yang
- School of Engineering Medicine, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China
| | - Dingyan Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xinjie Xu
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Zilong He
- School of Engineering Medicine, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China
| | - Wenming Wu
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
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2
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Bashiardes S, Christodoulou C. Orally Administered Drugs and Their Complicated Relationship with Our Gastrointestinal Tract. Microorganisms 2024; 12:242. [PMID: 38399646 PMCID: PMC10893523 DOI: 10.3390/microorganisms12020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Orally administered compounds represent the great majority of all pharmaceutical compounds produced for human use and are the most popular among patients since they are practical and easy to self-administer. Following ingestion, orally administered drugs begin a "perilous" journey down the gastrointestinal tract and their bioavailability is modulated by numerous factors. The gastrointestinal (GI) tract anatomy can modulate drug bioavailability and accounts for interpatient drug response heterogeneity. Furthermore, host genetics is a contributor to drug bioavailability modulation. Importantly, a component of the GI tract that has been gaining notoriety with regard to drug treatment interactions is the gut microbiota, which shares a two-way interaction with pharmaceutical compounds in that they can be influenced by and are able to influence administered drugs. Overall, orally administered drugs are a patient-friendly treatment option. However, during their journey down the GI tract, there are numerous host factors that can modulate drug bioavailability in a patient-specific manner.
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Affiliation(s)
- Stavros Bashiardes
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Nicosia 2371, Cyprus;
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3
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Joyce SA, Clarke DJ. Microbial metabolites as modulators of host physiology. Adv Microb Physiol 2024; 84:83-133. [PMID: 38821635 DOI: 10.1016/bs.ampbs.2023.12.001] [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] [Indexed: 06/02/2024]
Abstract
The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.
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Affiliation(s)
- Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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4
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Martinelli F, Thiele I. Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities. Gut Microbes 2024; 16:2387400. [PMID: 39150897 PMCID: PMC11332652 DOI: 10.1080/19490976.2024.2387400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/18/2024] Open
Abstract
This comprehensive review elucidates the pivotal role of microbes in drug metabolism, synthesizing insights from an exhaustive analysis of over two hundred papers. Employing a structural classification system grounded in drug atom involvement, the review categorizes the microbiome-mediated drug-metabolizing capabilities of over 80 drugs. Additionally, it compiles pharmacodynamic and enzymatic details related to these reactions, striving to include information on encoding genes and specific involved microorganisms. Bridging biochemistry, pharmacology, genetics, and microbiology, this review not only serves to consolidate diverse research fields but also highlights the potential impact of microbial drug metabolism on future drug design and in silico studies. With a visionary outlook, it also lays the groundwork for personalized medicine interventions, emphasizing the importance of interdisciplinary collaboration for advancing drug development and enhancing therapeutic strategies.
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Affiliation(s)
- Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- Digital Metabolic Twin Centre, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland
- Digital Metabolic Twin Centre, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
- School of Microbiology, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
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5
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Kolodnitsky AS, Ionov NS, Rudik AV, Filimonov DA, Poroikov VV. HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database. J Chem Inf Model 2023; 63:6463-6468. [PMID: 37871298 DOI: 10.1021/acs.jcim.3c00837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The metagenome of bacteria colonizing the human intestine is a set of genes that is almost 150 times greater than the set of host genes. Some of these genes encode enzymes whose functioning significantly expands the number of potential pathways for xenobiotic metabolism. The resulting metabolites can exhibit activity different from that of the parent compound. This can decrease the efficacy of pharmacotherapy as well as induce undesirable and potentially life-threatening side effects. Thus, analysis of the biotransformation of small drug-like compounds mediated by the gut microbiota is an important step in the development of new pharmaceutical agents and repurposing of the approved drugs. In vitro research, the interaction of drug-like compounds with the gut microbiota is a multistep and time-consuming process. Systematic testing of large sets of chemical structures is associated with a number of challenges, including the lack of standardized techniques and significant financial costs to identify the structure of the final metabolites. Estimation of the compounds' ability to be biotransformed by the gut microbiota and prediction of the structures of their metabolites are possible in silico. However, the development of computational approaches is limited by the lack of information about chemical structures metabolized by microbiota enzymes. The aim of this study is to create a database containing information on the metabolism of drug-like compounds by the gut microbiota. We created the data set containing information about 368 structures metabolized and 310 structures not metabolized by the human gut microbiota. The HGMMX database is freely available at https://www.way2drug.com/hgmmx. The information presented will be useful in the development of computational approaches for analyzing the impact of the human microbiota on metabolism of drug-like molecules.
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Affiliation(s)
- Anton S Kolodnitsky
- Institute of Biomedical Chemistry (IBMC), 10 Bldg. 8, Pogodinskaya Str., Moscow, 119121, Russia
| | - Nikita S Ionov
- Institute of Biomedical Chemistry (IBMC), 10 Bldg. 8, Pogodinskaya Str., Moscow, 119121, Russia
| | - Anastasia V Rudik
- Institute of Biomedical Chemistry (IBMC), 10 Bldg. 8, Pogodinskaya Str., Moscow, 119121, Russia
| | - Dmitry A Filimonov
- Institute of Biomedical Chemistry (IBMC), 10 Bldg. 8, Pogodinskaya Str., Moscow, 119121, Russia
| | - Vladimir V Poroikov
- Institute of Biomedical Chemistry (IBMC), 10 Bldg. 8, Pogodinskaya Str., Moscow, 119121, Russia
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6
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Su HH, Huang YH, Lien Y, Yang PC, Huang CY. Crystal Structure of DNA Replication Protein SsbA Complexed with the Anticancer Drug 5-Fluorouracil. Int J Mol Sci 2023; 24:14899. [PMID: 37834349 PMCID: PMC10573954 DOI: 10.3390/ijms241914899] [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: 08/31/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play a crucial role in DNA metabolism by binding and stabilizing single-stranded DNA (ssDNA) intermediates. Through their multifaceted roles in DNA replication, recombination, repair, replication restart, and other cellular processes, SSB emerges as a central player in maintaining genomic integrity. These attributes collectively position SSBs as essential guardians of genomic integrity, establishing interactions with an array of distinct proteins. Unlike Escherichia coli, which contains only one type of SSB, some bacteria have two paralogous SSBs, referred to as SsbA and SsbB. In this study, we identified Staphylococcus aureus SsbA (SaSsbA) as a fresh addition to the roster of the anticancer drug 5-fluorouracil (5-FU) binding proteins, thereby expanding the ambit of the 5-FU interactome to encompass this DNA replication protein. To investigate the binding mode, we solved the complexed crystal structure with 5-FU at 2.3 Å (PDB ID 7YM1). The structure of glycerol-bound SaSsbA was also determined at 1.8 Å (PDB ID 8GW5). The interaction between 5-FU and SaSsbA was found to involve R18, P21, V52, F54, Q78, R80, E94, and V96. Based on the collective results from mutational and structural analyses, it became evident that SaSsbA's mode of binding with 5-FU diverges from that of SaSsbB. This complexed structure also holds the potential to furnish valuable comprehension regarding how 5-FU might bind to and impede analogous proteins in humans, particularly within cancer-related signaling pathways. Leveraging the information furnished by the glycerol and 5-FU binding sites, the complexed structures of SaSsbA bring to the forefront the potential viability of several interactive residues as potential targets for therapeutic interventions aimed at curtailing SaSsbA activity. Acknowledging the capacity of microbiota to influence the host's response to 5-FU, there emerges a pressing need for further research to revisit the roles that bacterial and human SSBs play in the realm of anticancer therapy.
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Affiliation(s)
- Hsin-Hui Su
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City 717, Taiwan
| | - Yen-Hua Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Yi Lien
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Po-Chun Yang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung City 402, Taiwan
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7
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Cai J, Auster A, Cho S, Lai Z. Dissecting the human gut microbiome to better decipher drug liability: A once-forgotten organ takes center stage. J Adv Res 2023; 52:171-201. [PMID: 37419381 PMCID: PMC10555929 DOI: 10.1016/j.jare.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND The gut microbiome is a diverse system within the gastrointestinal tract composed of trillions of microorganisms (gut microbiota), along with their genomes. Accumulated evidence has revealed the significance of the gut microbiome in human health and disease. Due to its ability to alter drug/xenobiotic pharmacokinetics and therapeutic outcomes, this once-forgotten "metabolic organ" is receiving increasing attention. In parallel with the growing microbiome-driven studies, traditional analytical techniques and technologies have also evolved, allowing researchers to gain a deeper understanding of the functional and mechanistic effects of gut microbiome. AIM OF REVIEW From a drug development perspective, microbial drug metabolism is becoming increasingly critical as new modalities (e.g., degradation peptides) with potential microbial metabolism implications emerge. The pharmaceutical industry thus has a pressing need to stay up-to-date with, and continue pursuing, research efforts investigating clinical impact of the gut microbiome on drug actions whilst integrating advances in analytical technology and gut microbiome models. Our review aims to practically address this need by comprehensively introducing the latest innovations in microbial drug metabolism research- including strengths and limitations, to aid in mechanistically dissecting the impact of the gut microbiome on drug metabolism and therapeutic impact, and to develop informed strategies to address microbiome-related drug liability and minimize clinical risk. KEY SCIENTIFIC CONCEPTS OF REVIEW We present comprehensive mechanisms and co-contributing factors by which the gut microbiome influences drug therapeutic outcomes. We highlight in vitro, in vivo, and in silico models for elucidating the mechanistic role and clinical impact of the gut microbiome on drugs in combination with high-throughput, functionally oriented, and physiologically relevant techniques. Integrating pharmaceutical knowledge and insight, we provide practical suggestions to pharmaceutical scientists for when, why, how, and what is next in microbial studies for improved drug efficacy and safety, and ultimately, support precision medicine formulation for personalized and efficacious therapies.
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Affiliation(s)
- Jingwei Cai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA.
| | - Alexis Auster
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Sungjoon Cho
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Zijuan Lai
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
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8
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Gnatzy L, Ismailos G, Vertzoni M, Reppas C. Managing the clinical effects of drug-induced intestinal dysbiosis with a focus to antibiotics: Challenges and opportunities. Eur J Pharm Sci 2023; 188:106510. [PMID: 37380062 DOI: 10.1016/j.ejps.2023.106510] [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: 04/03/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 06/30/2023]
Abstract
The term "intestinal dysbiosis" is used for indicating change(s) of the intestinal microbiota which have been associated with the development of diseases and the deterioration of disease treatments in humans. In this review, documented clinical effects of drug-induced intestinal dysbiosis are briefly presented, and methodologies which could be considered for the management of drug-induced intestinal dysbiosis based on clinical data are critically reviewed. Until relevant methodologies are optimized and/or their effectiveness to the general population is confirmed, and, since drug-induced intestinal dysbiosis refers predominantly to antibiotic-specific intestinal dysbiosis, a pharmacokinetically-based approach for mitigating the impact of antimicrobial therapy on intestinal dysbiosis is proposed.
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Affiliation(s)
- Lea Gnatzy
- Department of Pharmacy, National and Kapodistrian University of Athens, Zografou, Greece
| | - George Ismailos
- Experimental, Research and Training Center ELPEN, ELPEN Pharmaceuticals, Pikermi, Greece; National Antimicrobial Testing Committee, Athens, Greece
| | - Maria Vertzoni
- Department of Pharmacy, National and Kapodistrian University of Athens, Zografou, Greece
| | - Christos Reppas
- Department of Pharmacy, National and Kapodistrian University of Athens, Zografou, Greece.
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9
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Shamsuzzaman M, Ahsan T, Rahman H, Das KC, Salimullah. Integration of pharmacogenomic and pharmacomicrobiomic data for personalized medicine. PRECISION MEDICAL SCIENCES 2023. [DOI: 10.1002/prm2.12095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Affiliation(s)
- Muhammad Shamsuzzaman
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Tamim Ahsan
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Hadisur Rahman
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Salimullah
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
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10
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Lin ES, Huang YH, Yang PC, Peng WF, Huang CY. Complexed Crystal Structure of the Dihydroorotase Domain of Human CAD Protein with the Anticancer Drug 5-Fluorouracil. Biomolecules 2023; 13:149. [PMID: 36671534 PMCID: PMC9856072 DOI: 10.3390/biom13010149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Dihydroorotase (DHOase) is the third enzyme in the pathway used for the biosynthesis of pyrimidine nucleotides. In mammals, DHOase is active in a trifunctional enzyme, CAD, which also carries out the activities of carbamoyl phosphate synthetase and aspartate transcarbamoylase. Prior to this study, it was unknown whether the FDA-approved clinical drug 5-fluorouracil (5-FU), which is used as an anticancer therapy, could bind to the DHOase domain of human CAD (huDHOase). Here, we identified huDHOase as a new 5-FU binding protein, thereby extending the 5-FU interactome to this human enzyme. In order to investigate where 5-FU binds to huDHOase, we solved the complexed crystal structure at 1.97 Å (PDB ID 8GVZ). The structure of huDHOase complexed with malate was also determined for the sake of comparison (PDB ID 8GW0). These two nonsubstrate ligands were bound at the active site of huDHOase. It was previously established that the substrate N-carbamoyl-L-aspartate is either bound to or moves away from the active site, but it is the loop that is extended towards (loop-in mode) or moved away (loop-out mode) from the active site. DHOase also binds to nonsubstrate ligands via the loop-out mode. In contrast to the Escherichia coli DHOase model, our complexed structures revealed that huDHOase binds to either 5-FU or malate via the loop-in mode. We further characterized the binding of 5-FU to huDHOase using site-directed mutagenesis and the fluorescence quenching method. Considering the loop-in mode, the dynamic loop in huDHOase should be a suitable drug-targeting site for further designing inhibitors and clinical chemotherapies to suppress pyrimidine biosynthesis in cancer cell lines.
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Affiliation(s)
- En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, Taichung City 403, Taiwan
| | - Yen-Hua Huang
- Department of Beauty Science, National Taichung University of Science and Technology, Taichung City 403, Taiwan
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Po-Chun Yang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Wei-Feng Peng
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medicine, College of Medicine, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Pediatrics, National Taiwan University Children’s Hospital, Taipei 100, Taiwan
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung City 402, Taiwan
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Zhou J, Ouyang J, Gao Z, Qin H, Jun W, Shi T. MagMD: database summarizing the Metabolic action of gut Microbiota to Drugs. Comput Struct Biotechnol J 2022; 20:6427-6430. [DOI: 10.1016/j.csbj.2022.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
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12
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Gulnaz A, Chang JE, Maeng HJ, Shin KH, Lee KR, Chae YJ. A mechanism-based understanding of altered drug pharmacokinetics by gut microbiota. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2022. [DOI: 10.1007/s40005-022-00600-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Gamal A, Elshaer M, Alabdely M, Kadry A, McCormick TS, Ghannoum M. The Mycobiome: Cancer Pathogenesis, Diagnosis, and Therapy. Cancers (Basel) 2022; 14:2875. [PMID: 35740541 PMCID: PMC9221014 DOI: 10.3390/cancers14122875] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
Cancer is among the leading causes of death globally. Despite advances in cancer research, a full understanding of the exact cause has not been established. Recent data have shown that the microbiome has an important relationship with cancer on various levels, including cancer pathogenesis, diagnosis and prognosis, and treatment. Since most studies have focused only on the role of bacteria in this process, in this article we review the role of fungi-another important group of the microbiome, the totality of which is referred to as the "mycobiome"-in the development of cancer and how it can impact responses to anticancer medications. Furthermore, we provide recent evidence that shows how the different microbial communities interact and affect each other at gastrointestinal and non-gastrointestinal sites, including the skin, thereby emphasizing the importance of investigating the microbiome beyond bacteria.
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Affiliation(s)
- Ahmed Gamal
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
| | - Mohammed Elshaer
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Mayyadah Alabdely
- Department of Internal Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA;
| | - Ahmed Kadry
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Dermatology and Venereology, Al-Azhar University, Cairo 11651, Egypt
| | - Thomas S. McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
| | - Mahmoud Ghannoum
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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Dikeocha IJ, Al-Kabsi AM, Miftahussurur M, Alshawsh MA. Pharmacomicrobiomics: Influence of gut microbiota on drug and xenobiotic metabolism. FASEB J 2022; 36:e22350. [PMID: 35579628 DOI: 10.1096/fj.202101986r] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 11/11/2022]
Abstract
Gut microbiota is the most diverse and complex biological ecosystem, which is estimated to consist of greater than 5 million distinct genes and 100 trillion cells which are in constant communication with the host environment. The interaction between the gut microbiota and drugs and other xenobiotic compounds is bidirectional, quite complicated, and not fully understood yet. The impact of xenobiotics from pollution, manufacturing processes or from the environment is harmful to human health at varying degrees and this needs to be recognized and addressed. The gut microbiota is capable of biotransforming/metabolizing of various drugs and xenobiotic compounds as well as altering the activity and toxicity of these substances, thereby influencing how a host responds to drugs and xenobiotics and this emerging field is known as pharmacomicrobiomics. In this review, we discussed different mechanisms of drug-gut microbiota interaction and highlighted the influence of drug-gut microbiome interactions on the clinical response in humans.
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Affiliation(s)
| | | | - Muhammad Miftahussurur
- Helicobacter Pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, Indonesia
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15
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Piawah S, Walker EJ, Van Blarigan EL, Atreya CE. The Gut Microbiome in Colorectal Cancer. Hematol Oncol Clin North Am 2022; 36:491-506. [DOI: 10.1016/j.hoc.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Mehrotra T, Maulik SK. Hepatic drug metabolism and gut microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 191:207-228. [DOI: 10.1016/bs.pmbts.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Schupack DA, Mars RAT, Voelker DH, Abeykoon JP, Kashyap PC. The promise of the gut microbiome as part of individualized treatment strategies. Nat Rev Gastroenterol Hepatol 2022; 19:7-25. [PMID: 34453142 PMCID: PMC8712374 DOI: 10.1038/s41575-021-00499-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
Variability in disease presentation, progression and treatment response has been a central challenge in medicine. Although variability in host factors and genetics are important, it has become evident that the gut microbiome, with its vast genetic and metabolic diversity, must be considered in moving towards individualized treatment. In this Review, we discuss six broad disease groups: infectious disease, cancer, metabolic disease, cardiovascular disease, autoimmune or inflammatory disease, and allergic and atopic diseases. We highlight current knowledge on the gut microbiome in disease pathogenesis and prognosis, efficacy, and treatment-related adverse events and its promise for stratifying existing treatments and as a source of novel therapies. The Review is not meant to be comprehensive for each disease state but rather highlights the potential implications of the microbiome as a tool to individualize treatment strategies in clinical practice. Although early, the outlook is optimistic but challenges need to be overcome before clinical implementation, including improved understanding of underlying mechanisms, longitudinal studies with multiple data layers reflecting gut microbiome and host response, standardized approaches to testing and reporting, and validation in larger cohorts. Given progress in the microbiome field with concurrent basic and clinical studies, the microbiome will likely become an integral part of clinical care within the next decade.
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Affiliation(s)
- Daniel A Schupack
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Dayne H Voelker
- Division of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jithma P Abeykoon
- Division of Hematology and Oncology, Mayo Clinic, Rochester, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.
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18
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Kumar R, Sood U, Kaur J, Anand S, Gupta V, Patil KS, Lal R. The rising dominance of microbiology: what to expect in the next 15 years? Microb Biotechnol 2022; 15:110-128. [PMID: 34713975 PMCID: PMC8719816 DOI: 10.1111/1751-7915.13953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 01/10/2023] Open
Abstract
What microbiology beholds after a decade and a half in the future requires a vision based on the facts and ongoing trends in research and technological advancements. While the latter, assisted by microbial dark matter, presents a greater potential of creating an upsurge in in-situ and ex-situ rapid microbial detection techniques, this anticipated change will also set forth a revolution in microbial cultivation and diversity analyses. The availability of a microbial genetic toolbox at the expanse will help complement the current understanding of the microbiome and assist in real-time monitoring of the dynamics for detecting the health status of the host with utmost precision. Alongside, in light of the emerging infectious diseases, antimicrobial resistance (AMR) and social demands for safer and better health care alternatives, microbiology laboratories are prospected to drift in terms of the volume and nature of research and outcomes. With today's microbiological lens, one can predict with certainty that in the years to come, microbes will play a significant role in therapeutic treatment and the designing of novel diagnostic techniques. Another area where the scope of microbial application seems to be promising is the use of novel probiotics as a method to offer health benefits whilst promoting metabolic outputs specific for microbiome replenishment. Nonetheless, the evolution of extraterrestrial microbes or the adaptation of earth microbes as extraterrestrial residents are also yet another prominent microbial event one may witness in the upcoming years. But like the two sides of the coin, there is also an urgent need to dampen the bloom of urbanization, overpopulation and global trade and adopting sustainable approaches to control the recurrence of epidemics and pandemics.
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Affiliation(s)
- Roshan Kumar
- Post‐Graduate Department of ZoologyMagadh UniversityBodh GayaBihar824234India
| | - Utkarsh Sood
- The Energy and Resources InstituteDarbari Seth Block, IHC Complex, Lodhi RoadNew Delhi110003India
| | - Jasvinder Kaur
- Department of ZoologyGargi CollegeUniversity of DelhiSiri Fort RoadNew Delhi110049India
| | - Shailly Anand
- Department of ZoologyDeen Dayal Upadhyaya CollegeUniversity of DelhiDwarkaNew Delhi110078India
| | - Vipin Gupta
- Indira Paryavaran BhawanMinistry of Environment, Forest and Climate ChangeLodi ColonyNew Delhi110003India
| | - Kishor Sureshbhai Patil
- Department of Biological SciencesP. D. Patel Institute of Applied SciencesCharotar University of Science and Technology (CHARUSAT)ChangaGujarat388421India
| | - Rup Lal
- The Energy and Resources InstituteDarbari Seth Block, IHC Complex, Lodhi RoadNew Delhi110003India
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19
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Dhurjad P, Dhavaliker C, Gupta K, Sonti R. Exploring drug metabolism by the gut microbiota: modes of metabolism and experimental approaches. Drug Metab Dispos 2021; 50:224-234. [PMID: 34969660 DOI: 10.1124/dmd.121.000669] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Increasing evidence uncovers the involvement of gut microbiota in the metabolism of numerous pharmaceutical drugs. The human gut microbiome harbours 10-100 trillion symbiotic gut microbial bacteria that utilize drugs as substrates for enzymatic processes to alter host metabolism. Thus, microbiota-mediated drug metabolism can change the conventional drug action course and cause inter-individual differences in efficacy and toxicity, making it vital for drug discovery and development. This review focuses on drug biotransformation pathways and discusses different models for evaluating gut microbiota role in drug metabolism. Significance Statement This review emphasizes the importance of gut microbiota and different modes of drug metabolism mediated by them. It provides information on in vivo, in vitro, ex vivo, in silico and multi-omics approaches for identifying the role of gut microbiota in the metabolism. Further, it highlights the significance of gut microbiota mediated metabolism in the process of new drug discovery and development as a rationale for safe and efficacious drug therapy.
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Affiliation(s)
- Pooja Dhurjad
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Chinmayi Dhavaliker
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Kajal Gupta
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Rajesh Sonti
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
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20
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Mikrobiota jelitowa a leki. Interakcje wpływające na skuteczność i bezpieczeństwo farmakoterapii. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstrakt
Mikrobiota jelitowa stanowi nieodłączny element organizmu umożliwiający jego prawidłowe funkcjonowanie. Dzięki mikroorganizmom jelitowym możliwa jest stymulacja układu odpornościowego, synteza witamin czy poprawa wchłaniania składników odżywczych. Jednak jej aktywność może również niekorzystnie działać na organizm, m.in. z powodu przetwarzania treści jelitowej. Opisywana w artykule interakcja mikrobiota–lek uwzględnia pozytywny i negatywny wpływ mikroorganizmów jelitowych na farmakoterapię poprzez bezpośrednie i pośrednie oddziaływanie na lek w organizmie. Ze względu na to, że mikrobiom stanowi nieodłączny element organizmu, ingerencja nawet w jego niewielką część może doprowadzić do wystąpienia daleko idących, czasami niespodziewanych skutków. Stąd w celu poprawy skuteczności i bezpieczeństwa farmakoterapii konieczne jest wyjaśnienie mechanizmów oddziaływania mikrobioty na lek w organizmie.
W artykule podsumowano obecną wiedzę na temat biologicznej aktywności mikrobioty jelitowej, a zwłaszcza oddziaływań mikrobiota–leki determinujących skuteczność i bezpieczeństwo farmakoterapii. Wyszukiwanie przeprowadzono we wrześniu 2020 r. w bazach danych PubMed, Scopus, Web of Science, Cochrane Library i powszechnie dostępnej literaturze z użyciem terminów: „mikrobiota jelitowa”, „mikrobiom”, „metabolizm leku”, „interakcje mikrobiota–lek”. W artykule omówiono interakcje między mikrobiotą a lekami m.in. z grupy antybiotyków, inhibitorów pompy protonowej, sulfonamidów, pochodnych kwasu 5-aminosalicylowego, niesteroidowych leków przeciwzapalnych, przeciwnowotworowych, statyn czy metforminą.
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21
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Huang X, Li M, Hou S, Tian B. Role of the microbiome in systemic therapy for pancreatic ductal adenocarcinoma (Review). Int J Oncol 2021; 59:101. [PMID: 34738624 PMCID: PMC8577795 DOI: 10.3892/ijo.2021.5281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/18/2021] [Indexed: 02/05/2023] Open
Abstract
A large body of evidence has revealed that the microbiome serves a role in all aspects of cancer, particularly cancer treatment. To date, studies investigating the relationship between the microbiome and systemic therapy for pancreatic ductal adenocarcinoma (PDAC) are lacking. PDAC is a high‑mortality malignancy (5‑year survival rate; <9% for all stages). Systemic therapy is one of the most important treatment choices for all patients; however, resistance or toxicity can affect its efficacy. Studies have supported the hypothesis that the microbiome is closely associated with the response to systemic therapy in PDAC, including the induction of drug resistance, or toxicity and therapy‑related changes in microbiota composition. The present review comprehensively summarized the role of the microbiome in systemic therapy for PDAC and the associated molecular mechanisms in an attempt to provide a novel direction for the improvement of treatment response and proposed potential directions for in‑depth research.
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Affiliation(s)
| | | | - Shengzhong Hou
- Department of Pancreatic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Bole Tian
- Department of Pancreatic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China
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22
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Naik A, Misra SK. Modern Sensing Approaches for Predicting Toxicological Responses of Food- and Drug-Based Bioactives on Microbiomes of Gut Origin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6396-6413. [PMID: 34081444 DOI: 10.1021/acs.jafc.1c02736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent scientific findings have correlated the gut microbes with homeostasis of human health by delineating their role in pathogen resistance, bioactive metabolization, and immune responses. Foreign materials, like xenobiotics, that induce an altering effect to the human body also influence the gut microbiome to some extent and often limit their use as a result of significant side effects. Investigating the xenobiotic effect of new therapeutic material or edible could be quite painstaking and economically non-viable. Thus, the use of predictive toxicology methods can be an innovative strategy in the food, pharma, and agriculture industries. There are reported in silico, ex vivo, in vitro, and in vivo methods to evaluate such effects but with added drawbacks, such as lower predictability, physiological dissimilarities, and high cost of associated invasive procedures. This review highlights the current and future possibilities with newer modern sensing approaches of economic and time-scale advantages for predicting toxicological responses on gut microbiomes.
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Affiliation(s)
- Aishwarya Naik
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
| | - Santosh K Misra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kalyanpur, Uttar Pradesh 208016, India
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23
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Wang Z, Hopson LM, Singleton SS, Yang X, Jogunoori W, Mazumder R, Obias V, Lin P, Nguyen BN, Yao M, Miller L, White J, Rao S, Mishra L. Mice with dysfunctional TGF-β signaling develop altered intestinal microbiome and colorectal cancer resistant to 5FU. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166179. [PMID: 34082069 DOI: 10.1016/j.bbadis.2021.166179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
Emerging data show a rise in colorectal cancer (CRC) incidence in young men and women that is often chemoresistant. One potential risk factor is an alteration in the microbiome. Here, we investigated the role of TGF-β signaling on the intestinal microbiome and the efficacy of chemotherapy for CRC induced by azoxymethane and dextran sodium sulfate in mice. We used two genotypes of TGF-β-signaling-deficient mice (Smad4+/- and Smad4+/-Sptbn1+/-), which developed CRC with similar phenotypes and had similar alterations in the intestinal microbiome. Using these mice, we evaluated the intestinal microbiome and determined the effect of dysfunctional TGF-β signaling on the response to the chemotherapeutic agent 5-Fluoro-uracil (5FU) after induction of CRC. Using shotgun metagenomic sequencing, we determined gut microbiota composition in mice with CRC and found reduced amounts of beneficial species of Bacteroides and Parabacteroides in the mutants compared to the wild-type (WT) mice. Furthermore, the mutant mice with CRC were resistant to 5FU. Whereas the abundances of E. boltae, B.dorei, Lachnoclostridium sp., and Mordavella sp. were significantly reduced in mice with CRC, these species only recovered to basal amounts after 5FU treatment in WT mice, suggesting that the alterations in the intestinal microbiome resulting from compromised TGF-β signaling impaired the response to 5FU. These findings could have implications for inhibiting the TGF-β pathway in the treatment of CRC or other cancers.
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Affiliation(s)
- Zhuanhuai Wang
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA; Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lindsay M Hopson
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Stephanie S Singleton
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Xiaochun Yang
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA; The Institute for Bioelectronic Medicine, Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory, Department of Medicine, Division of Gastroenterology and Hepatology, Northwell Health, NY, USA
| | - Wilma Jogunoori
- Research and Development, Veterans Affairs Medical Center, Washington, DC, USA
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Vincent Obias
- Department of Surgery, The George Washington University, Washington, DC, USA
| | - Paul Lin
- Department of Surgery, The George Washington University, Washington, DC, USA
| | - Bao-Ngoc Nguyen
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA
| | - Michael Yao
- Department of Gastroenterology, Veterans Affairs Medical Center, Washington, DC, USA
| | - Larry Miller
- Department of Medicine, Division of Gastroenterology, Zucker School of Medicine at Hofstra/Northwell Health System, New Hyde Park, NY, USA
| | - Jon White
- Department of Surgery, The George Washington University, Washington, DC, USA
| | - Shuyun Rao
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA; The Institute for Bioelectronic Medicine, Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory, Department of Medicine, Division of Gastroenterology and Hepatology, Northwell Health, NY, USA.
| | - Lopa Mishra
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA; The Institute for Bioelectronic Medicine, Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory, Department of Medicine, Division of Gastroenterology and Hepatology, Northwell Health, NY, USA.
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24
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Drug Response Diversity: A Hidden Bacterium? J Pers Med 2021; 11:jpm11050345. [PMID: 33922920 PMCID: PMC8146020 DOI: 10.3390/jpm11050345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 11/27/2022] Open
Abstract
Interindividual heterogeneity in response to treatment is a real public health problem. It is a factor that can be responsible not only for ineffectiveness or fatal toxicity but also for hospitalization due to iatrogenic effects, thus increasing the cost of patient care. Several research teams have been interested in what may be at the origin of these phenomena, particularly at the genetic level and the basal activity of organs dedicated to the inactivation and elimination of drug molecules. Today, a new branch is being set up, explaining the enigmatic part that could not be explained before. Pharmacomicrobiomics attempts to investigate the interactions between bacteria, especially those in the gut, and drug response. In this review, we provide a state of the art on what this field has brought as new information and discuss the challenges that lie ahead to see the real application in clinical practice.
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25
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Luo Y, Zhou T. Connecting the dots: Targeting the microbiome in drug toxicity. Med Res Rev 2021; 42:83-111. [PMID: 33856076 DOI: 10.1002/med.21805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/22/2021] [Accepted: 03/31/2021] [Indexed: 12/13/2022]
Abstract
The gut microbiota has a vast influence on human health and its role in initiating, aggravating, or ameliorating diseases is beginning to emerge. Recently, its contribution to heterogeneous toxicological responses is also gaining attention, especially in drug-induced toxicity. Whether they are orally administered or not, drugs may interact with the gut microbiota directly or indirectly, which leads to altered toxicity. Present studies focus more on the unidirectional influence of how xenobiotics disturb intestinal microbial composition and functions, and thus induce altered homeostasis. However, interactions between the gut microbiota and xenobiotics are bidirectional and the impact of the gut microbiota on xenobiotics, especially on drugs, should not be neglected. Thus, in this review, we focus on how the gut microbiota modulates drug toxicity by highlighting the microbiome, microbial enzyme, and microbial metabolites. We connect the dots between drugs, the microbiome, microbial enzymes or metabolites, drug metabolites, and host toxicological responses to facilitate the discovery of microbial targets and mechanisms associated with drug toxicity. Besides this, current mainstream strategies to manipulate drug toxicity by targeting the microbiome are summarized and discussed. The review provides technical reference for the evaluation of medicinal properties in the research and development of innovative drugs, and for the future exploitation of strategies to reduce drug toxicity by targeting the microbiome.
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Affiliation(s)
- Yusha Luo
- Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Tingting Zhou
- Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, China
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26
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Li W, Deng X, Chen T. Exploring the Modulatory Effects of Gut Microbiota in Anti-Cancer Therapy. Front Oncol 2021; 11:644454. [PMID: 33928033 PMCID: PMC8076595 DOI: 10.3389/fonc.2021.644454] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/18/2021] [Indexed: 12/16/2022] Open
Abstract
In the recent decade, gut microbiota has received growing interest due to its role in human health and disease. On the one hand, by utilizing the signaling pathways of the host and interacting with the immune system, the gut microbiota is able to maintain the homeostasis in human body. This important role is mainly modulated by the composition of microbiota, as a normal microbiota composition is responsible for maintaining the homeostasis of human body, while an altered microbiota profile could contribute to several pathogenic conditions and may further lead to oncogenesis and tumor progression. Moreover, recent insights have especially focused on the important role of gut microbiota in current anticancer therapies, including chemotherapy, radiotherapy, immunotherapy and surgery. Research findings have indicated a bidirectional interplay between gut microbiota and these therapeutic methods, in which the implementation of different therapeutic methods could lead to different alterations in gut microbiota, and the presence of gut microbiota could in turn contribute to different therapeutic responses. As a result, manipulating the gut microbiota to reduce the therapy-induced toxicity may provide an adjuvant therapy to achieve a better therapeutic outcome. Given the complex role of gut microbiota in cancer treatment, this review summarizes the interactions between gut microbiota and anticancer therapies, and demonstrates the current strategies for reshaping gut microbiota community, aiming to provide possibilities for finding an alternative approach to lower the damage and improve the efficacy of cancer therapy.
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Affiliation(s)
- Wenyu Li
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Queen Mary School, Nanchang University, Nanchang, China
| | - Xiaorong Deng
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tingtao Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, The First Affiliated Hospital, Nanchang University, Nanchang, China
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27
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Zimmermann M, Patil KR, Typas A, Maier L. Towards a mechanistic understanding of reciprocal drug-microbiome interactions. Mol Syst Biol 2021; 17:e10116. [PMID: 33734582 PMCID: PMC7970330 DOI: 10.15252/msb.202010116] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Broad-spectrum antibiotics target multiple gram-positive and gram-negative bacteria, and can collaterally damage the gut microbiota. Yet, our knowledge of the extent of damage, the antibiotic activity spectra, and the resistance mechanisms of gut microbes is sparse. This limits our ability to mitigate microbiome-facilitated spread of antibiotic resistance. In addition to antibiotics, non-antibiotic drugs affect the human microbiome, as shown by metagenomics as well as in vitro studies. Microbiome-drug interactions are bidirectional, as microbes can also modulate drugs. Chemical modifications of antibiotics mostly function as antimicrobial resistance mechanisms, while metabolism of non-antibiotics can also change the drugs' pharmacodynamic, pharmacokinetic, and toxic properties. Recent studies have started to unravel the extensive capacity of gut microbes to metabolize drugs, the mechanisms, and the relevance of such events for drug treatment. These findings raise the question whether and to which degree these reciprocal drug-microbiome interactions will differ across individuals, and how to take them into account in drug discovery and precision medicine. This review describes recent developments in the field and discusses future study areas that will benefit from systems biology approaches to better understand the mechanistic role of the human gut microbiota in drug actions.
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Affiliation(s)
- Michael Zimmermann
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Kiran Raosaheb Patil
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- The Medical Research Council Toxicology UnitUniversity of CambridgeCambridgeUK
| | - Athanasios Typas
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’University of TübingenTübingenGermany
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28
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He Y, Liu QW, Liao HX, Xu WW. Microbiota in cancer chemoradiotherapy resistance. Clin Transl Med 2020; 11:e250. [PMID: 33463064 PMCID: PMC7774460 DOI: 10.1002/ctm2.250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 11/10/2022] Open
Affiliation(s)
- Yan He
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qin Wen Liu
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Hua Xin Liao
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Wen Wen Xu
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
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29
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Garajová I, Balsano R, Wang H, Leonardi F, Giovannetti E, Deng D, Peters GJ. The role of the microbiome in drug resistance in gastrointestinal cancers. Expert Rev Anticancer Ther 2020; 21:165-176. [PMID: 33115280 DOI: 10.1080/14737140.2021.1844007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: The microbiota is recognized for its impact on both human health and disease. The human microbiota is made up of trillions of cells, including bacteria, viruses, and fungi. The largest population of microbes reside in the gut, prompting research for better understanding of the impact of gastrointestinal microbiota in different diseases. Evidence from numerous studies has pointed out the role of commensal microbes as key determinants of cancer pathogenesis. Moreover, gut microbiota may play an important role in chemoresistance; consequently, this knowledge might be important for novel strategies to improve anticancer treatment efficacy.Areas covered: We describe the role of microbiota in different gastrointestinal cancer types (esophageal, gastric, colorectal, hepatocellular and pancreatic-biliary tract cancers). Moreover, we analyzed the impact of the microbiota on resistance to anticancer therapies, and, lastly, we focused on possibilities of microbiota modulation to enhance anticancer therapy efficacy.Expert opinion: Increasing evidence shows that gut microbiota might influence resistance to anticancer treatment, including conventional chemotherapy, immunotherapy, radiotherapy, and surgery. Therefore, a better knowledge of gut microbiota and its interactions with anticancer drugs will enable us to develop novel anticancer treatment strategies and subsequently improve the cancer patients' outcome.
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Affiliation(s)
- Ingrid Garajová
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Rita Balsano
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Heling Wang
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | | | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienz, Pisa, Italy
| | - Dongmei Deng
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Godefridus J Peters
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
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Sampsell K, Hao D, Reimer RA. The Gut Microbiota: A Potential Gateway to Improved Health Outcomes in Breast Cancer Treatment and Survivorship. Int J Mol Sci 2020; 21:E9239. [PMID: 33287442 PMCID: PMC7731103 DOI: 10.3390/ijms21239239] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is the most frequently diagnosed cancer in women worldwide. The disease and its treatments exert profound effects on an individual's physical and mental health. There are many factors that impact an individual's risk of developing breast cancer, their response to treatments, and their risk of recurrence. The community of microorganisms inhabiting the gastrointestinal tract, the gut microbiota, affects human health through metabolic, neural, and endocrine signaling, and immune activity. It is through these mechanisms that the gut microbiota appears to influence breast cancer risk, response to treatment, and recurrence. A disrupted gut microbiota or state of 'dysbiosis' can contribute to a biological environment associated with higher risk for cancer development as well as contribute to negative treatment side-effects. Many cancer treatments have been shown to shift the gut microbiota toward dysbiosis; however, the microbiota can also be positively manipulated through diet, prebiotic and probiotic supplementation, and exercise. The objective of this review is to provide an overview of the current understanding of the relationship between the gut microbiota and breast cancer and to highlight potential strategies for modulation of the gut microbiota that could lead to improved clinical outcomes and overall health in this population.
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Affiliation(s)
- Kara Sampsell
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada;
| | - Desirée Hao
- Department of Medical Oncology, Tom Baker Cancer Centre and Cumming School of Medicine, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;
| | - Raylene A. Reimer
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada;
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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Innao V, Allegra AG, Musolino C, Allegra A. New Frontiers about the Role of Human Microbiota in Immunotherapy: The Immune Checkpoint Inhibitors and CAR T-Cell Therapy Era. Int J Mol Sci 2020; 21:ijms21238902. [PMID: 33255336 PMCID: PMC7727716 DOI: 10.3390/ijms21238902] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Microbiota is considered an independent organ with the capability to modulate tumor growth and response to therapies. In the chemo-free era, the use of new immunotherapies, more selective and effective and less toxic, led to the extension of overall survival of patients, subject to their ability to not stop treatment. This has focused scientists’ attention to optimize responses by understanding and changing microbiota composition. While we have obtained abundant data from studies in oncologic and hematologic patients receiving conventional chemotherapy, we have less data about alterations in intestinal flora in those undergoing immunotherapy, especially based on Chimeric Antigen Receptor (CAR) T-cells. Actually, we know that the efficacy of Programmed Cell Death 1 (PD-1), PD-1 ligand, and Cytotoxic T lymphocyte-associated protein 4 (CTLA-4) is improved by probiotics rich in Bifidobacterium spp., while compounds of Bacteroidales and Burkholderiales protect from the development of the anti-CTLA-4-induced colitis in mouse models. CAR T-cell therapy seems to not be interfering with microbiota; however, the numerous previous therapies may have caused permanent damage, thus obscuring the data we might have obtained. Therefore, this review opens a new chapter to transfer known acquisitions to a typology of patients destined to grow.
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Affiliation(s)
- Vanessa Innao
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood, University of Messina, 98122 Messina, Italy;
- Correspondence: (V.I.); (A.A.)
| | - Andrea Gaetano Allegra
- Radiation Oncology Unit, Department of Biomedical, Experimental, and Clinical Sciences “Mario Serio”, Azienda Ospedaliero-Universitaria Careggi, University of Florence, 50100 Florence, Italy;
| | - Caterina Musolino
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood, University of Messina, 98122 Messina, Italy;
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood, University of Messina, 98122 Messina, Italy;
- Correspondence: (V.I.); (A.A.)
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Tao G, Huang J, Moorthy B, Wang C, Hu M, Gao S, Ghose R. Potential role of drug metabolizing enzymes in chemotherapy-induced gastrointestinal toxicity and hepatotoxicity. Expert Opin Drug Metab Toxicol 2020; 16:1109-1124. [PMID: 32841068 PMCID: PMC8059872 DOI: 10.1080/17425255.2020.1815705] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Toxicity of chemotherapy drugs is the leading cause of poor therapeutic outcome in many cancer patients. Gastrointestinal (GI) toxicity and hepatotoxicity are among the most common side effects of current chemotherapies. Emerging studies indicate that many chemotherapy-induced toxicities are driven by drug metabolism, but very few reviews summarize the role of drug metabolism in chemotherapy-induced GI toxicity and hepatotoxicity. In this review, we highlighted the importance of drug metabolizing enzymes (DMEs) in chemotherapy toxicity. AREAS COVERED Our review demonstrated that altered activity of DMEs play important role in chemotherapy-induced GI toxicity and hepatotoxicity. Besides direct changes in catalytic activities, the transcription of DMEs is also affected by inflammation, cell-signaling pathways, and/or by drugs in cancer patients due to the disease etiology. EXPERT OPINION More studies should focus on how DMEs are altered during chemotherapy treatment, and how such changes affect the metabolism of chemotherapy drug itself. This mutual interaction between chemotherapies and DMEs can lead to excessive exposure of parent drug or toxic metabolites which ultimately cause GI adverse effect.
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Affiliation(s)
- Gabriel Tao
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston TX, U.S
| | - Junqing Huang
- Formula-pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China
| | | | - Cathryn Wang
- Department of Pharmacy Practice and Translational Research, College of Pharmacy, University of Houston, Houston TX, U.S
| | - Ming Hu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston TX, U.S
| | - Song Gao
- Department of Pharmaceutical and Environmental Health Sciences, Texas Southern University, Houston TX, U.S
| | - Romi Ghose
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston TX, U.S
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Feng W, Liu J, Ao H, Yue S, Peng C. Targeting gut microbiota for precision medicine: Focusing on the efficacy and toxicity of drugs. Theranostics 2020; 10:11278-11301. [PMID: 33042283 PMCID: PMC7532689 DOI: 10.7150/thno.47289] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Intra- and interindividual variation in drug responses is one major reason for the failure of drug therapy, drug toxicity, and even the death of patients. Precision medicine, or personalized medicine, is a field of medicine that customizes an individual's medical diagnosis and treatment based on his/her genes, microbiomes, environments, etc. Over the past decade, a large number of studies have demonstrated that gut microbiota can modify the efficacy and toxicity of drugs, and the extent of the modification varies greatly from person to person because of the variability of the gut microbiota. Personalized manipulation of gut microbiota is an important approach to rectify the abnormal drug response. In this review, we aim to improve drug efficacy and reduce drug toxicity by combining precision medicine and gut microbiota. After describing the interactions between gut microbiota and xenobiotics, we discuss (1) the effects of gut microbiota on drug efficacy and toxicity and the corresponding mechanisms, (2) the variability of gut microbiota, which leads to variation in drug responses, (3) the biomarkers used for the patient stratification and treatment decisions before the use of drugs, and (4) the methods used for the personalized manipulation of gut microbiota to improve drug outcomes. Overall, we hope to improve the drug response by incorporating the knowledge of gut microbiota into clinical practice.
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Affiliation(s)
- Wuwen Feng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Juan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hui Ao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shijun Yue
- Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Cheng Peng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Jarmusch AK, Vrbanac A, Momper JD, Ma JD, Alhaja M, Liyanage M, Knight R, Dorrestein PC, Tsunoda SM. Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study. Clin Transl Sci 2020; 13:972-984. [PMID: 32216086 PMCID: PMC7485946 DOI: 10.1111/cts.12785] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/22/2020] [Indexed: 12/22/2022] Open
Abstract
Determining factors that contribute to interindividual and intra-individual variability in pharmacokinetics (PKs) and drug metabolism is essential for the optimal use of drugs in humans. Intestinal microbes are important contributors to variability; however, such gut microbe-drug interactions and the clinical significance of these interactions are still being elucidated. Traditional PKs can be complemented by untargeted mass spectrometry coupled with molecular networking to study the intricacies of drug metabolism. To show the utility of molecular networking on metabolism we investigated the impact of a 7-day course of cefprozil on cytochrome P450 (CYP) activity using a modified Cooperstown cocktail and assessed plasma, urine, and fecal data by targeted and untargeted metabolomics and molecular networking in healthy volunteers. This prospective study revealed that cefprozil decreased the activities of CYP1A2, CYP2C19, and CYP3A, decreased alpha diversity and increased interindividual microbiome variability. We further demonstrate a relationship between the loss of microbiome alpha diversity caused by cefprozil and increased drug and metabolite formation in fecal samples. Untargeted metabolomics/molecular networking revealed several omeprazole metabolites that we hypothesize may be metabolized by both CYP2C19 and bacteria from the gut microbiome. Our observations are consistent with the hypothesis that factors that perturb the gut microbiome, such as antibiotics, alter drug metabolism and ultimately drug efficacy and toxicity but that these effects are most strongly revealed on a per individual basis.
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Affiliation(s)
- Alan K. Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation CenterUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Alison Vrbanac
- Department of PediatricsUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Jeremiah D. Momper
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Joseph D. Ma
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Maher Alhaja
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Marlon Liyanage
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Rob Knight
- Department of PediatricsUniversity of California, San DiegoLa JollaCaliforniaUSA
- Center for Microbiome InnovationUniversity of California, San DiegoLa JollaCaliforniaUSA
- Department of Computer Science and EngineeringUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Collaborative Mass Spectrometry Innovation CenterUniversity of California, San DiegoLa JollaCaliforniaUSA
- Department of PediatricsUniversity of California, San DiegoLa JollaCaliforniaUSA
- Center for Microbiome InnovationUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Shirley M. Tsunoda
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
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35
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Peiffer DS. Modulation of the host microbiome by black raspberries or their components and the therapeutic implications in cancer. FOOD FRONTIERS 2020. [DOI: 10.1002/fft2.40] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Daniel S Peiffer
- Health Sciences Division Loyola University Chicago Maywood Illinois
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36
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Singh A, Nayak N, Rathi P, Verma D, Sharma R, Chaudhary A, Agarwal A, Tripathi YB, Garg N. Microbiome and host crosstalk: A new paradigm to cancer therapy. Semin Cancer Biol 2020; 70:71-84. [PMID: 32479952 DOI: 10.1016/j.semcancer.2020.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 12/17/2022]
Abstract
The commensal microbiome of humans has co-evolved for thousands of years. The microbiome regulates human health and is also linked to several diseases, including cancer. The advances in next-generation sequencing have significantly contributed to our understanding of the microbiome and its association with cancer and cancer therapy. Recent studies have highlighted a close relationship of the microbiome to the pharmacological effect of chemotherapy and immunotherapy. The chemo-drugs usually interfere with the host immune system and reduces the microbiome diversity inside the body, which in turn leads to decreased efficacy of these drugs. The human microbiome, specifically the gut microbiome, increases the potency of chemo-drugs through metabolism, enzymatic degradation, ecological differences, and immunomodulation. Recent research exploits the involvement of microbiome to shape the efficacy and decrease the toxicity of these chemo-drugs. In this review, we have highlighted the recent development in understanding the relationship of the human microbiome with cancer and also emphasize on various roles of the microbiome in the modulation of cancer therapy. Additionally, we also summarize the ongoing research focussed on the improved efficacy of chemotherapy and immunotherapy using the host microbiome.
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Affiliation(s)
- Ashutosh Singh
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi 175005, Himachal Pradesh, India
| | - Namyashree Nayak
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi 175005, Himachal Pradesh, India
| | - Preeti Rathi
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi 175005, Himachal Pradesh, India
| | - Deepanshu Verma
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi 175005, Himachal Pradesh, India
| | - Rohit Sharma
- Department of Rasashastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, BHU, Varanasi 221005, Uttar Pradesh, India
| | - Ashun Chaudhary
- Central University of Himachal Pradesh, Shahpur, Dist. Kangra, Himachal Pradesh 176206, India
| | - Alka Agarwal
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, BHU, Varanasi 221005, Uttar Pradesh, India
| | - Yamini Bhushan Tripathi
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, BHU, Varanasi 221005, Uttar Pradesh, India
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, BHU, Varanasi 221005, Uttar Pradesh, India.
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37
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Ke W, Saba JA, Yao CH, Hilzendeger MA, Drangowska-Way A, Joshi C, Mony VK, Benjamin SB, Zhang S, Locasale J, Patti GJ, Lewis N, O'Rourke EJ. Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion. Nat Commun 2020; 11:2587. [PMID: 32444616 PMCID: PMC7244588 DOI: 10.1038/s41467-020-16220-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota metabolizes drugs and alters their efficacy and toxicity. Diet alters drugs, the metabolism of the microbiota, and the host. However, whether diet-triggered metabolic changes in the microbiota can alter drug responses in the host has been largely unexplored. Here we show that dietary thymidine and serine enhance 5-fluoro 2'deoxyuridine (FUdR) toxicity in C. elegans through different microbial mechanisms. Thymidine promotes microbial conversion of the prodrug FUdR into toxic 5-fluorouridine-5'-monophosphate (FUMP), leading to enhanced host death associated with mitochondrial RNA and DNA depletion, and lethal activation of autophagy. By contrast, serine does not alter FUdR metabolism. Instead, serine alters E. coli's 1C-metabolism, reduces the provision of nucleotides to the host, and exacerbates DNA toxicity and host death without mitochondrial RNA or DNA depletion; moreover, autophagy promotes survival in this condition. This work implies that diet-microbe interactions can alter the host response to drugs without altering the drug or the host.
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Affiliation(s)
- Wenfan Ke
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA, USA
| | - James A Saba
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA, USA
| | - Cong-Hui Yao
- Department of Chemistry, Washington University, St. Louis, MO, USA
| | - Michael A Hilzendeger
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA, USA
| | - Anna Drangowska-Way
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA, USA
| | - Chintan Joshi
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Vinod K Mony
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA, USA
| | - Shawna B Benjamin
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sisi Zhang
- Department of Chemistry, Washington University, St. Louis, MO, USA
| | - Jason Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Gary J Patti
- Department of Chemistry, Washington University, St. Louis, MO, USA
| | - Nathan Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Eyleen J O'Rourke
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA, USA.
- Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA.
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Abstract
Increasing evidence suggests a role of the gut microbiota in patients' response to medicinal drugs. In our recent study, we combined genomics of human gut commensals and gnotobiotic animal experiments to quantify microbiota and host contributions to drug metabolism. Informed by experimental data, we built a physiology-based pharmacokinetic model of drug metabolism that includes intestinal compartments with microbiome drug-metabolizing activity. This model successfully predicted serum levels of metabolites of three different drugs, quantified microbial contribution to systemic drug metabolite exposure, and simulated the effect of different parameters on host and microbiota drug metabolism. In this addendum, we expand these simulations to assess the effect of microbiota on the systemic drug and metabolite levels under conditions of altered host physiology, microbiota drug-metabolizing activity or physico-chemical properties of drugs. This work illustrates how and under which circumstances the gut microbiome may influence drug pharmacokinetics, and discusses broader implications of expanded pharmacokinetic models.
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Affiliation(s)
- Maria Zimmermann-Kogadeeva
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Michael Zimmermann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L. Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA,CONTACT Andrew L. Goodman Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
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Scher JU, Nayak RR, Ubeda C, Turnbaugh PJ, Abramson SB. Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response. Nat Rev Rheumatol 2020; 16:282-292. [PMID: 32157196 PMCID: PMC11221369 DOI: 10.1038/s41584-020-0395-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Abstract
In the past three decades, extraordinary advances have been made in the understanding of the pathogenesis of, and treatment options for, inflammatory arthritides, including rheumatoid arthritis and spondyloarthritis. The use of methotrexate and subsequently biologic therapies (such as TNF inhibitors, among others) and oral small molecules have substantially improved clinical outcomes for many patients with inflammatory arthritis; for others, however, these agents do not substantially improve their symptoms. The emerging field of pharmacomicrobiomics, which investigates the effect of variations within the human gut microbiome on drugs, has already provided important insights into these therapeutics. Pharmacomicrobiomic studies have demonstrated that human gut microorganisms and their enzymatic products can affect the bioavailability, clinical efficacy and toxicity of a wide array of drugs through direct and indirect mechanisms. This discipline promises to facilitate the advent of microbiome-based precision medicine approaches in inflammatory arthritis, including strategies for predicting response to treatment and for modulating the microbiome to improve response to therapy or reduce drug toxicity.
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Affiliation(s)
- Jose U Scher
- Department of Medicine, Division of Rheumatology, New York University Langone Health, New York, NY, USA.
| | - Renuka R Nayak
- Rheumatology Division, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA
| | - Carles Ubeda
- Centro Superior de Investigacion en Salud Publica - FISABIO, Valencia, Spain
- CIBER en Epidemiologia y Salud Publica, Madrid, Spain
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Steven B Abramson
- Department of Medicine, Division of Rheumatology, New York University Langone Health, New York, NY, USA
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40
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Azevedo MM, Pina-Vaz C, Baltazar F. Microbes and Cancer: Friends or Faux? Int J Mol Sci 2020; 21:ijms21093115. [PMID: 32354115 PMCID: PMC7247677 DOI: 10.3390/ijms21093115] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/23/2020] [Accepted: 04/26/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer is one of the most aggressive and deadly diseases in the world, representing the second leading cause of death. It is a multifactorial disease, in which genetic alterations play a key role, but several environmental factors also contribute to its development and progression. Infections induced by certain viruses, bacteria, fungi and parasites constitute risk factors for cancer, being chronic infection associated to the development of certain types of cancer. On the other hand, susceptibility to infectious diseases is higher in cancer patients. The state of the host immune system plays a crucial role in the susceptibility to both infection and cancer. Importantly, immunosuppressive cancer treatments increase the risk of infection, by decreasing the host defenses. Furthermore, alterations in the host microbiota is also a key factor in the susceptibility to develop cancer. More recently, the identification of a tumor microbiota, in which bacteria establish a symbiotic relationship with cancer cells, opened a new area of research. There is evidence demonstrating that the interaction between bacteria and cancer cells can modulate the anticancer drug response and toxicity. The present review focuses on the interaction between microbes and cancer, specifically aiming to: (1) review the main infectious agents associated with development of cancer and the role of microbiota in cancer susceptibility; (2) highlight the higher vulnerability of cancer patients to acquire infectious diseases; (3) document the relationship between cancer cells and tissue microbiota; (4) describe the role of intratumoral bacteria in the response and toxicity to cancer therapy.
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Affiliation(s)
- Maria Manuel Azevedo
- Department of Microbiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- CINTESIS, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Agrupamento de Escolas D. Maria II, 4760-067 V.N. Famalicão, Portugal
- Correspondence: ; Tel.: +351-22-551-36
| | - Cidália Pina-Vaz
- Department of Microbiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- CINTESIS, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Fátima Baltazar
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, 4835-258 Guimarães, Portugal
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41
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Abdelsalam NA, Ramadan AT, ElRakaiby MT, Aziz RK. Toxicomicrobiomics: The Human Microbiome vs. Pharmaceutical, Dietary, and Environmental Xenobiotics. Front Pharmacol 2020; 11:390. [PMID: 32372951 PMCID: PMC7179069 DOI: 10.3389/fphar.2020.00390] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/16/2020] [Indexed: 12/13/2022] Open
Abstract
The harmful impact of xenobiotics on the environment and human health is being more widely recognized; yet, inter- and intraindividual genetic variations among humans modulate the extent of harm, mostly through modulating the outcome of xenobiotic metabolism and detoxification. As the Human Genome Project revealed that host genetic, epigenetic, and regulatory variations could not sufficiently explain the complexity of interindividual variability in xenobiotics metabolism, its sequel, the Human Microbiome Project, is investigating how this variability may be influenced by human-associated microbial communities. Xenobiotic-microbiome relationships are mutual and dynamic. Not only does the human microbiome have a direct metabolizing potential on xenobiotics, but it can also influence the expression of the host metabolizing genes and the activity of host enzymes. On the other hand, xenobiotics may alter the microbiome composition, leading to a state of dysbiosis, which is linked to multiple diseases and adverse health outcomes, including increased toxicity of some xenobiotics. Toxicomicrobiomics studies these mutual influences between the ever-changing microbiome cloud and xenobiotics of various origins, with emphasis on their fate and toxicity, as well the various classes of microbial xenobiotic-modifying enzymes. This review article discusses classic and recent findings in toxicomicrobiomics, with examples of interactions between gut, skin, urogenital, and oral microbiomes with pharmaceutical, food-derived, and environmental xenobiotics. The current state and future prospects of toxicomicrobiomic research are discussed, and the tools and strategies for performing such studies are thoroughly and critically compared.
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Affiliation(s)
| | - Ahmed Tarek Ramadan
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Marwa Tarek ElRakaiby
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ramy Karam Aziz
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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42
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Xie Y, Hu F, Xiang D, Lu H, Li W, Zhao A, Huang L, Wang R. The metabolic effect of gut microbiota on drugs. Drug Metab Rev 2020; 52:139-156. [PMID: 32116054 DOI: 10.1080/03602532.2020.1718691] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuan Xie
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Fangdi Hu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Dawei Xiang
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Hui Lu
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Wenbin Li
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Anpeng Zhao
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Longji Huang
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
| | - Rong Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
- Key Laboratory of the Plateau Medicial, The 940 Hospital of Joint Logistics Support, PLA, Lanzhou, China
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Chae S, Kim DJ, Cho JY. Complex influences of gut microbiome metabolism on various drug responses. Transl Clin Pharmacol 2020; 28:7-16. [PMID: 32274377 PMCID: PMC7136083 DOI: 10.12793/tcp.2020.28.e3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 01/04/2023] Open
Abstract
The gut microbiome closely interacts with the host, and it has a major influence on drug response. Many studies have reported the possible microbial influences on drugs and the possible influences of drugs on the microbiome. This knowledge has led to a better understanding of intra- and inter-individual variabilities in clinical pharmacology. For a more precise understanding of the complex correlation between the microbiome and drugs, in this review, we summarized the current knowledge on the interactions between the gut microbiome and drug response. Moreover, we suggest gut microbiome-derived metabolites as possible modulators of drug response and recommend metabolomics as a powerful tool to achieve such understanding.
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Affiliation(s)
- Sihyun Chae
- Department of Clinical Pharmacology and Therapeutics, Seoul National University, College of Medicine and Hospital, Seoul 03080, Korea
| | - Da Jung Kim
- Department of Clinical Pharmacology and Therapeutics, Seoul National University, College of Medicine and Hospital, Seoul 03080, Korea
| | - Joo-Youn Cho
- Department of Clinical Pharmacology and Therapeutics, Seoul National University, College of Medicine and Hospital, Seoul 03080, Korea
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44
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Collins SL, Patterson AD. The gut microbiome: an orchestrator of xenobiotic metabolism. Acta Pharm Sin B 2020; 10:19-32. [PMID: 31998605 PMCID: PMC6984741 DOI: 10.1016/j.apsb.2019.12.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/21/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Microbes inhabiting the intestinal tract of humans represent a site for xenobiotic metabolism. The gut microbiome, the collection of microorganisms in the gastrointestinal tract, can alter the metabolic outcome of pharmaceuticals, environmental toxicants, and heavy metals, thereby changing their pharmacokinetics. Direct chemical modification of xenobiotics by the gut microbiome, either through the intestinal tract or re-entering the gut via enterohepatic circulation, can lead to increased metabolism or bioactivation, depending on the enzymatic activity within the microbial niche. Unique enzymes encoded within the microbiome include those that reverse the modifications imparted by host detoxification pathways. Additionally, the microbiome can limit xenobiotic absorption in the small intestine by increasing the expression of cell-cell adhesion proteins, supporting the protective mucosal layer, and/or directly sequestering chemicals. Lastly, host gene expression is regulated by the microbiome, including CYP450s, multi-drug resistance proteins, and the transcription factors that regulate them. While the microbiome affects the host and pharmacokinetics of the xenobiotic, xenobiotics can also influence the viability and metabolism of the microbiome. Our understanding of the complex interconnectedness between host, microbiome, and metabolism will advance with new modeling systems, technology development and refinement, and mechanistic studies focused on the contribution of human and microbial metabolism.
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Key Words
- 5-ASA, 5-aminosalicylic acid
- 5-FU, 5-fluorouracil
- AHR, aryl Hydrocarbon Receptor
- ALDH, aldehyde dehydrogenase
- Absorption
- BDE, bromodiphenyl ether
- BRV, brivudine
- BVU, bromovinyluracil
- Bioactivation
- CAR, constitutive androgen receptor
- CV, conventional
- CYP, cytochrome P450
- ER, estrogen receptor
- Enterohepatic circulation
- FXR, farnesoid X receptor
- GF, germ-free
- GUDCA, glycoursodeoxycholic acid
- Gastrointestinal tract
- Gut microbiome
- NSAID, non-steroidal anti-inflammatory drug
- PABA, p-aminobenzenesulphonamide
- PAH, polycyclic aromatic hydrocarbon
- PCB, polychlorinated biphenyl
- PD, Parkinson's disease
- PFOS, perfluorooctanesulfonic acid
- PXR, pregnane X receptor
- Pharmacokinetics
- SCFA, short chain fatty acid
- SN-38G, SN-38 glucuronide
- SULT, sulfotransferase
- TCDF, 2,3,7,8-tetrachlorodibenzofuran
- TUDCA, tauroursodeoxycholic acid
- UGT, uracil diphosphate-glucuronosyltransferase
- Xenobiotic metabolism
- cgr, cytochrome glycoside reductase
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Affiliation(s)
- Stephanie L. Collins
- Department of Biochemistry, Microbiology, and Molecular Biology, the Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Science, the Pennsylvania State University, University Park, PA 16802, USA
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Gu S, Zaidi S, Hassan I, Mohammad T, Malta TM, Noushmehr H, Nguyen B, Crandall KA, Srivastav J, Obias V, Lin P, Nguyen BN, Yao M, Yao R, King CH, Mazumder R, Mishra B, Rao S, Mishra L. Mutated CEACAMs Disrupt Transforming Growth Factor Beta Signaling and Alter the Intestinal Microbiome to Promote Colorectal Carcinogenesis. Gastroenterology 2020; 158:238-252. [PMID: 31585122 PMCID: PMC7124154 DOI: 10.1053/j.gastro.2019.09.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS We studied interactions among proteins of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family, which interact with microbes, and transforming growth factor beta (TGFB) signaling pathway, which is often altered in colorectal cancer cells. We investigated mechanisms by which CEACAM proteins inhibit TGFB signaling and alter the intestinal microbiome to promote colorectal carcinogenesis. METHODS We collected data on DNA sequences, messenger RNA expression levels, and patient survival times from 456 colorectal adenocarcinoma cases, and a separate set of 594 samples of colorectal adenocarcinomas, in The Cancer Genome Atlas. We performed shotgun metagenomic sequencing analyses of feces from wild-type mice and mice with defects in TGFB signaling (Sptbn1+/- and Smad4+/-/Sptbn1+/-) to identify changes in microbiota composition before development of colon tumors. CEACAM protein and its mutants were overexpressed in SW480 and HCT116 colorectal cancer cell lines, which were analyzed by immunoblotting and proliferation and colony formation assays. RESULTS In colorectal adenocarcinomas, high expression levels of genes encoding CEACAM proteins, especially CEACAM5, were associated with reduced survival times of patients. There was an inverse correlation between expression of CEACAM genes and expression of TGFB pathway genes (TGFBR1, TGFBR2, and SMAD3). In colorectal adenocarcinomas, we also found an inverse correlation between expression of genes in the TGFB signaling pathway and genes that regulate stem cell features of cells. We found mutations encoding L640I and A643T in the B3 domain of human CEACAM5 in colorectal adenocarcinomas; structural studies indicated that these mutations would alter the interaction between CEACAM5 and TGFBR1. Overexpression of these mutants in SW480 and HCT116 colorectal cancer cell lines increased their anchorage-independent growth and inhibited TGFB signaling to a greater extent than overexpression of wild-type CEACAM5, indicating that they are gain-of-function mutations. Compared with feces from wild-type mice, feces from mice with defects in TGFB signaling had increased abundance of bacterial species that have been associated with the development of colon tumors, including Clostridium septicum, and decreased amounts of beneficial bacteria, such as Bacteroides vulgatus and Parabacteroides distasonis. CONCLUSION We found expression of CEACAMs and genes that regulate stem cell features of cells to be increased in colorectal adenocarcinomas and inversely correlated with expression of TGFB pathway genes. We found colorectal adenocarcinomas to express mutant forms of CEACAM5 that inhibit TGFB signaling and increase proliferation and colony formation. We propose that CEACAM proteins disrupt TGFB signaling, which alters the composition of the intestinal microbiome to promote colorectal carcinogenesis.
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Affiliation(s)
- Shoujun Gu
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA
| | - Sobia Zaidi
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Tathiane M. Malta
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
| | - Bryan Nguyen
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Keith A. Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | | | - Vincent Obias
- Department of Surgery, The George Washington University, Washington, DC, USA
| | - Paul Lin
- Department of Surgery, The George Washington University, Washington, DC, USA
| | - Bao-Ngoc Nguyen
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA
| | - Michael Yao
- Department of Gastroenterology, Veterans Affairs Medical Center, Washington DC, USA
| | - Ren Yao
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Charles Hadley King
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Bibhuti Mishra
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA
| | - Shuyun Rao
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA
| | - Lopa Mishra
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA
- Department of Gastroenterology, Veterans Affairs Medical Center, Washington DC, USA
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Sun C, Chen L, Shen Z. Mechanisms of gastrointestinal microflora on drug metabolism in clinical practice. Saudi Pharm J 2019; 27:1146-1156. [PMID: 31885474 PMCID: PMC6921184 DOI: 10.1016/j.jsps.2019.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 09/28/2019] [Indexed: 02/06/2023] Open
Abstract
Considered as an essential "metabolic organ", intestinal microbiota plays a key role in human health and the predisposition to diseases. It is an aggregate genome of trillions of microorganisms residing in the human gastrointestinal tract. Since the 20th century, researches have showed that intestinal microbiome possesses a variety of metabolic activities that are able to modulate the fate of more than 30 approved drugs and immune checkpoint inhibitors. These drugs are transformed to bioactive, inactive, or toxic metabolites by microbial direct action or host-microbial co-metabolism. These metabolites are responsible for therapeutic effects exerted by these drugs or side effects induced by these drugs, even for death. In view of the significant effect on the drugs metabolism by the gut microbiota, it is pivotal for personalized medicine to explore additional drugs affected by gut microbiota and their involved strains for further making mechanism clear through suitable animal models. This review mainly focus on specific mechanisms involved, with reference to the current literature about drugs metabolism by related bacteria or its enzymes available.
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Affiliation(s)
- Chaonan Sun
- Department of Dermatology, Institute of Dermatology and Venereology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, Sichuan, 610072, China
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Ling Chen
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, 410042, China
| | - Zhu Shen
- Department of Dermatology, Institute of Dermatology and Venereology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, Sichuan, 610072, China
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
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47
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Sharma A, Das P, Buschmann M, Gilbert JA. The Future of Microbiome-Based Therapeutics in Clinical Applications. Clin Pharmacol Ther 2019; 107:123-128. [PMID: 31617205 DOI: 10.1002/cpt.1677] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/02/2019] [Indexed: 12/24/2022]
Abstract
The microbiome, a collection of microorganisms, their genomes, and the surrounding environmental conditions, is akin to a human organ, and knowledge is emerging on its role in human health and diseases. The influence of the microbiome in drug response has only been investigated in detail for the last 10 years. The human microbiome is a complex and highly dynamic system, which varies dramatically between individuals, yet there exists a common core microbiome that is heritable and can be transmitted to progeny. Here, we review the role of the human microbiome, which is now widely accepted as a major factor that drives the interpersonal variation in therapeutic response. We describe examples in which the microbiome modifies drug action. Despite its complexity, the microbiome can be readily altered, with the potential to increase the benefits and reduce the toxicity and side effects associated with pharmaceutical drugs. The potential of new microbiome-based strategies, such as fecal microbiota transplant, probiotics, and phage therapy, as promising medical therapeutics are outlined. We also suggest a combination reductionist and system-level approaches that could be applied to further investigate the role of microbiota in drug metabolism modulation of drug response. Finally, we emphasize the importance of combining microbiome and pharmacology studies as a novel means to treat disease and reduce side effects.
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Affiliation(s)
- Anukriti Sharma
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, UCSD, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, UCSD, La Jolla, California, USA
| | - Mary Buschmann
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, UCSD, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, UCSD, La Jolla, California, USA
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48
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Villéger R, Lopès A, Carrier G, Veziant J, Billard E, Barnich N, Gagnière J, Vazeille E, Bonnet M. Intestinal Microbiota: A Novel Target to Improve Anti-Tumor Treatment? Int J Mol Sci 2019; 20:ijms20184584. [PMID: 31533218 PMCID: PMC6770123 DOI: 10.3390/ijms20184584] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022] Open
Abstract
Recently, preclinical and clinical studies targeting several types of cancer strongly supported the key role of the gut microbiota in the modulation of host response to anti-tumoral therapies such as chemotherapy, immunotherapy, radiotherapy and even surgery. Intestinal microbiome has been shown to participate in the resistance to a wide range of anticancer treatments by direct interaction with the treatment or by indirectly stimulating host response through immunomodulation. Interestingly, these effects were described on colorectal cancer but also in other types of malignancies. In addition to their role in therapy efficacy, gut microbiota could also impact side effects induced by anticancer treatments. In the first part of this review, we summarized the role of the gut microbiome on the efficacy and side effects of various anticancer treatments and underlying mechanisms. In the second part, we described the new microbiota-targeting strategies, such as probiotics and prebiotics, antibiotics, fecal microbiota transplantation and physical activity, which could be effective adjuvant therapies developed in order to improve anticancer therapeutic efficiency.
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Affiliation(s)
- Romain Villéger
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
| | - Amélie Lopès
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
- Biologics Research, Sanofi R&D, 94400 Vitry-Sur-Seine, France.
| | - Guillaume Carrier
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
- Surgical Oncology Department, Institut du Cancer de Montpellier (ICM), Univ Montpellier, 34298 Montpellier, France.
| | - Julie Veziant
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
- Service de Chirurgie Digestive, CHU Clermont-Ferrand, Inserm, Université Clermont Auvergne, 63003 Clermont-Ferrand, France.
- 3iHP, CHU Clermont-Ferrand, Inserm, Université Clermont Auvergne, 63003 Clermont-Ferrand, France.
| | - Elisabeth Billard
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
| | - Nicolas Barnich
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
| | - Johan Gagnière
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
- Service de Chirurgie Digestive, CHU Clermont-Ferrand, Inserm, Université Clermont Auvergne, 63003 Clermont-Ferrand, France.
- 3iHP, CHU Clermont-Ferrand, Inserm, Université Clermont Auvergne, 63003 Clermont-Ferrand, France.
| | - Emilie Vazeille
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
- 3iHP, CHU Clermont-Ferrand, Inserm, Université Clermont Auvergne, 63003 Clermont-Ferrand, France.
- Service d'Hépato-gastro-entérologie, CHU Clermont-Ferrand, Inserm, Université Clermont Auvergne, 63003 Clermont-Ferrand, France.
| | - Mathilde Bonnet
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH) UMR 1071 Inserm/Université Clermont Auvergne, USC-INRA 2018, CRNH Auvergne, F-63000 Clermont-Ferrand, France.
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Koontz JM, Dancy BCR, Horton CL, Stallings JD, DiVito VT, Lewis JA. The Role of the Human Microbiome in Chemical Toxicity. Int J Toxicol 2019; 38:251-264. [PMID: 31220972 DOI: 10.1177/1091581819849833] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is overwhelming evidence that the microbiome must be considered when evaluating the toxicity of chemicals. Disruption of the normal microbial flora is a known effect of toxic exposure, and these disruptions may lead to human health effects. In addition, the biotransformation of numerous compounds has been shown to be dependent on microbial enzymes, with the potential for different host health outcomes resulting from variations in the microbiome. Evidence suggests that such metabolism of environmental chemicals by enzymes from the host's microbiota can affect the toxicity of that chemical to the host. Chemical-microbial interactions can be categorized into two classes: Microbiome Modulation of Toxicity (MMT) and Toxicant Modulation of the Microbiome (TMM). MMT refers to transformation of a chemical by microbial enzymes or metabolites to modify the chemical in a way that makes it more or less toxic. TMM is a change in the microbiota that results from a chemical exposure. These changes span a large magnitude of effects and may vary from microbial gene regulation, to inhibition of a specific enzyme, to the death of the microbes. Certain microbiomes or microbiota may become associated with different health outcomes, such as resistance or susceptibility to exposure to certain toxic chemicals, the ability to recover following a chemical-induced injury, the presence of disease-associated phenotypes, and the effectiveness of immune responses. Future work in toxicology will require an understanding of how the microbiome interacts with toxicants to fully elucidate how a compound will affect a diverse, real-world population.
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Affiliation(s)
- Jason M Koontz
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | - Blair C R Dancy
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | | | | | - Valerie T DiVito
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
| | - John A Lewis
- 1 US Army Center for Environmental Health Research, Fort Detrick, MD, USA
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50
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Sharma A, Buschmann MM, Gilbert JA. Pharmacomicrobiomics: The Holy Grail to Variability in Drug Response? Clin Pharmacol Ther 2019; 106:317-328. [PMID: 30937887 DOI: 10.1002/cpt.1437] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/11/2019] [Indexed: 12/23/2022]
Abstract
The human body, with 3.0 × 1013 cells and more than 3.8 × 1013 microorganisms, has nearly a one-to-one ratio of resident microbes to human cells. Initiatives like the Human Microbiome Project, American Gut, and Flemish Gut have identified associations between microbial taxa and human health. The study of interactions between microbiome and pharmaceutical agents, i.e., pharmacomicrobiomics, has revealed an instrumental role of the microbiome in modulating drug response that alters the therapeutic outcomes. In this review, we present our current comprehension of the relationship of the microbiome, host biology, and pharmaceutical agents such as cardiovascular drugs, analgesics, and chemotherapeutic agents to human disease and treatment outcomes. We also discuss the significance of studying diet-gene-drug interactions and further address the key challenges associated with pharmacomicrobiomics. Finally, we examine proposed models employing systems biology for the application of pharmacomicrobiomics and other -omics data, and provide approaches to elucidate microbiome-drug interactions to improve future translation to personalized medicine.
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Affiliation(s)
- Anukriti Sharma
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA
| | | | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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