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Behl T, Rachamalla M, Najda A, Sehgal A, Singh S, Sharma N, Bhatia S, Al-Harrasi A, Chigurupati S, Vargas-De-La-Cruz C, Hobani YH, Mohan S, Goyal A, Katyal T, Solarska E, Bungau S. Applications of Adductomics in Chemically Induced Adverse Outcomes and Major Emphasis on DNA Adductomics: A Pathbreaking Tool in Biomedical Research. Int J Mol Sci 2021; 22:10141. [PMID: 34576304 PMCID: PMC8467560 DOI: 10.3390/ijms221810141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/04/2021] [Accepted: 09/13/2021] [Indexed: 01/06/2023] Open
Abstract
Adductomics novel and emerging discipline in the toxicological research emphasizes on adducts formed by reactive chemical agents with biological molecules in living organisms. Development in analytical methods propelled the application and utility of adductomics in interdisciplinary sciences. This review endeavors to add a new dimension where comprehensive insights into diverse applications of adductomics in addressing some of society's pressing challenges are provided. Also focuses on diverse applications of adductomics include: forecasting risk of chronic diseases triggered by reactive agents and predicting carcinogenesis induced by tobacco smoking; assessing chemical agents' toxicity and supplementing genotoxicity studies; designing personalized medication and precision treatment in cancer chemotherapy; appraising environmental quality or extent of pollution using biological systems; crafting tools and techniques for diagnosis of diseases and detecting food contaminants; furnishing exposure profile of the individual to electrophiles; and assisting regulatory agencies in risk assessment of reactive chemical agents. Characterizing adducts that are present in extremely low concentrations is an exigent task and more over absence of dedicated database to identify adducts is further exacerbating the problem of adduct diagnosis. In addition, there is scope of improvement in sample preparation methods and data processing software and algorithms for accurate assessment of adducts.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; (T.B.); (A.S.); (S.S.); (N.S.)
| | - Mahesh Rachamalla
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada;
| | - Agnieszka Najda
- Department of Vegetable Crops and Medicinal Plants, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; (T.B.); (A.S.); (S.S.); (N.S.)
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; (T.B.); (A.S.); (S.S.); (N.S.)
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; (T.B.); (A.S.); (S.S.); (N.S.)
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa 33, Oman; (S.B.); (A.A.-H.)
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa 33, Oman; (S.B.); (A.A.-H.)
| | - Sridevi Chigurupati
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Celia Vargas-De-La-Cruz
- Faculty of Pharmacy and Biochemistry, Academic Department of Pharmacology, Bromatology and Toxicology, Centro Latinoamericano de Enseñanza e Investigación en Bacteriología Alimentaria, Universidad Nacional Mayor de San Marcos, Lima 15001, Peru;
- E-Health Research Center, Universidad de Ciencias y Humanidades, Lima 15001, Peru
| | - Yahya Hasan Hobani
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 114, Saudi Arabia;
| | - Syam Mohan
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan 114, Saudi Arabia;
| | - Amit Goyal
- GHG Khalsa College of Pharmacy, Gurusar Sadhar, Ludhiana 141104, India;
| | - Taruna Katyal
- RBMCH Division, ICMR Head Quarters, Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India;
| | - Ewa Solarska
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, 8 Skromna Street, 20-704 Lublin, Poland;
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania;
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202
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Abstract
Metagenomic analyses have revealed microbial dysbiosis in the gut of patients with colorectal cancer (CRC). The gut microbiota influences CRC via a variety of mechanisms, including microbial-derived factors such as metabolites or genotoxins. Pathogenic drivers and opportunistic passenger bacteria may underlie direct effect of the gut microbiota on carcinogenesis. We posit that metabolites generated by gut microbiota can influence CRC through a multitude of epigenetic or genetic effects on malignant transformation. A closer look at the cross talks between the commensals, epithelial cells, immune regulators etc., needs to be established with more substantiated studies. The recurrence of chemoresistant disease following therapy undoubtedly provides the impetus for morbidity and mortality; yet, the role of gut microbiome in drug resistance remains to be fully investigated. We review the current literature on microbial dysbiosis during CRC and discuss the mechanistic basis of CRC-associated bacteria in tumor initiation, progression and drug resistance.
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203
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Liu X, Cheng Y, Zang D, Zhang M, Li X, Liu D, Gao B, Zhou H, Sun J, Han X, Lin M, Chen J. The Role of Gut Microbiota in Lung Cancer: From Carcinogenesis to Immunotherapy. Front Oncol 2021; 11:720842. [PMID: 34490119 PMCID: PMC8417127 DOI: 10.3389/fonc.2021.720842] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022] Open
Abstract
The influence of microbiota on host health and disease has attracted adequate attention, and gut microbiota components and microbiota-derived metabolites affect host immune homeostasis locally and systematically. Some studies have found that gut dysbiosis, disturbance of the structure and function of the gut microbiome, disrupts pulmonary immune homeostasis, thus leading to increased disease susceptibility; the gut-lung axis is the primary cross-talk for this communication. Gut dysbiosis is involved in carcinogenesis and the progression of lung cancer through genotoxicity, systemic inflammation, and defective immunosurveillance. In addition, the gut microbiome harbors the potential to be a novel biomarker for predicting sensitivity and adverse reactions to immunotherapy in patients with lung cancer. Probiotics and fecal microbiota transplantation (FMT) can enhance the efficacy and depress the toxicity of immune checkpoint inhibitors by regulating the gut microbiota. Although current studies have found that gut microbiota closely participates in the development and immunotherapy of lung cancer, the mechanisms require further investigation. Therefore, this review aims to discuss the underlying mechanisms of gut microbiota influencing carcinogenesis and immunotherapy in lung cancer and to provide new strategies for governing gut microbiota to enhance the prevention and treatment of lung cancer.
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Affiliation(s)
- Xiangjun Liu
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Ye Cheng
- Department of Oncology, The Third Hospital of Dalian Medical University, Dalian, China
| | - Dan Zang
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Min Zhang
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Xiuhua Li
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Dan Liu
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Bing Gao
- Department of Oncology, The Third Hospital of Dalian Medical University, Dalian, China
| | - Huan Zhou
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Jinzhe Sun
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Xu Han
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Meixi Lin
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Jun Chen
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, China
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204
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Kim CS, Turocy T, Moon G, Shine EE, Crawford JM. Escherichia coli-Derived γ-Lactams and Structurally Related Metabolites Are Produced at the Intersection of Colibactin and Fatty Acid Biosynthesis. Org Lett 2021; 23:6895-6899. [PMID: 34406772 PMCID: PMC10577019 DOI: 10.1021/acs.orglett.1c02461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Colibactin is a genotoxic hybrid polyketide-nonribosomal peptide that drives colorectal cancer initiation. While clinical data suggest colibactin genotoxicity in vivo is largely caused by the major DNA-cross-linking metabolite, the colibactin locus produces a diverse collection of metabolites with mostly unknown biological activities. Here, we describe 10 new colibactin pathway metabolites (1-10) that are dependent on its α-aminomalonyl-carrier protein. The most abundant metabolites, 1 and 2, were isolated and structurally characterized mainly by nuclear magnetic resonance spectroscopy to be γ-lactam derivatives, and the remaining related structures were inferred via shared biosynthetic logic. Our proposed formation of 1-10, which is supported by stereochemical analysis, invokes cross-talk between colibactin and fatty acid biosynthesis, illuminating further the complexity of this diversity-oriented pathway.
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Affiliation(s)
- Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut 06516, United States
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Tayah Turocy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Gyuri Moon
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Emilee E. Shine
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, United States
- Present address: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, United States
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205
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Knippel RJ, Drewes JL, Sears CL. The Cancer Microbiome: Recent Highlights and Knowledge Gaps. Cancer Discov 2021; 11:2378-2395. [PMID: 34400408 DOI: 10.1158/2159-8290.cd-21-0324] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023]
Abstract
Knowledge of the human microbiome, which is likely a critical factor in the initiation, progression, and prognosis of multiple forms of cancer, is rapidly expanding. In this review, we focus on recent investigations to discern putative, causative microbial species and the microbiome composition and structure currently associated with procarcinogenesis and tumorigenesis at select body sites. We specifically highlight forms of cancer, gastrointestinal and nongastrointestinal, that have significant bacterial associations and well-defined experimental evidence with the aim of generating directions for future experimental and translational investigations to develop a clearer understanding of the multifaceted mechanisms by which microbiota affect cancer formation. SIGNIFICANCE: Emerging and, for some cancers, strong experimental and translational data support the contribution of the microbiome to cancer biology and disease progression. Disrupting microbiome features and pathways contributing to cancer may provide new approaches to improving cancer outcomes in patients.
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Affiliation(s)
- Reece J Knippel
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julia L Drewes
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cynthia L Sears
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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206
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Kouzu K, Tsujimoto H, Kishi Y, Ueno H, Shinomiya N. Role of Microbial Infection-Induced Inflammation in the Development of Gastrointestinal Cancers. MEDICINES 2021; 8:medicines8080045. [PMID: 34436224 PMCID: PMC8400127 DOI: 10.3390/medicines8080045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022]
Abstract
There has been increasing evidence that a local inflammatory response stimulates tumor cells to acquire metastatic potential, and the concept of inflammatory oncotaxis has been spreading in recent years. However, the interaction between microbial inflammation and the development of gastrointestinal cancer is still unclear. This review summarizes the present knowledge on the role of microbial inflammation in the development of gastrointestinal cancers from the perspective of molecular biological findings. Chronic inflammation caused by bacterial infection is known to induce cancers as exemplified by Helicobacter pylori, which is associated with the development of gastric cancer via the activation of the TLR4 pathway by bacterial lipopolysaccharide followed by cancer growth through CagA-MET signaling. In addition, the development of inflammatory bowel diseases has been known to become a risk factor for colorectal cancers, where inflammation caused by certain bacterial infections plays a key role. It is also known that the cancer microenvironment is associated with cancer growth. Moreover, infectious complication after surgery for gastrointestinal cancers may promote tumor progression via the stimulation of pathogen-associated molecular patterns and various inflammatory mediators secreted by immunocytes. Further research on the link between microbial inflammation and cancer progression is needed to drive a paradigm shift in cancer treatment.
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Affiliation(s)
- Keita Kouzu
- Department of Surgery, National Defense Medical College, Saitama 359-0042, Japan; (K.K.); (Y.K.); (H.U.)
| | - Hironori Tsujimoto
- Department of Surgery, National Defense Medical College, Saitama 359-0042, Japan; (K.K.); (Y.K.); (H.U.)
- Correspondence: ; Tel.: +81-4-2995-1637
| | - Yoji Kishi
- Department of Surgery, National Defense Medical College, Saitama 359-0042, Japan; (K.K.); (Y.K.); (H.U.)
| | - Hideki Ueno
- Department of Surgery, National Defense Medical College, Saitama 359-0042, Japan; (K.K.); (Y.K.); (H.U.)
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207
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Association of Polygenic Risk Score and Bacterial Toxins at Screening Colonoscopy with Colorectal Cancer Progression: A Multicenter Case-Control Study. Toxins (Basel) 2021; 13:toxins13080569. [PMID: 34437440 PMCID: PMC8402601 DOI: 10.3390/toxins13080569] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer death worldwide, and its incidence is correlated with infections, chronic inflammation, diet, and genetic factors. An emerging aspect is that microbial dysbiosis and chronic infections triggered by certain bacteria can be risk factors for tumor progression. Recent data suggest that certain bacterial toxins implicated in DNA attack or in proliferation, replication, and death can be risk factors for insurgence and progression of CRC. In this study, we recruited more than 300 biopsy specimens from people undergoing colonoscopy, and we analyzed to determine whether a correlation exists between the presence of bacterial genes coding for toxins possibly involved in CRC onset and progression and the different stages of CRC. We also analyzed to determine whether CRC-predisposing genetic factors could contribute to bacterial toxins response. Our results showed that CIF toxin is associated with polyps or adenomas, whereas pks+ seems to be a predisposing factor for CRC. Toxins from Escherichia coli as a whole have a higher incidence rate in adenocarcinoma patients compared to controls, whereas Bacteroides fragilis toxin does not seem to be associated with pre-cancerous nor with cancerous lesions. These results have been obtained irrespectively of the presence of CRC-risk loci.
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208
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Abstract
The probiotic Escherichia coli strain Nissle 1917 (DSM 6601, Mutaflor), generally considered beneficial and safe, has been used for a century to treat various intestinal diseases. However, Nissle 1917 hosts in its genome the pks pathogenicity island that codes for the biosynthesis of the genotoxin colibactin. Colibactin is a potent DNA alkylator, suspected to play a role in colorectal cancer development. We show in this study that Nissle 1917 is functionally capable of producing colibactin and inducing interstrand cross-links in the genomic DNA of epithelial cells exposed to the probiotic. This toxicity was even exacerbated with lower doses of the probiotic, when the exposed cells started to divide again but exhibited aberrant anaphases and increased gene mutation frequency. DNA damage was confirmed in vivo in mouse models of intestinal colonization, demonstrating that Nissle 1917 produces the genotoxin in the gut lumen. Although it is possible that daily treatment of adult humans with their microbiota does not produce the same effects, administration of Nissle 1917 as a probiotic or as a chassis to deliver therapeutics might exert long-term adverse effects and thus should be considered in a risk-versus-benefit evaluation. IMPORTANCE Nissle 1917 is sold as a probiotic and considered safe even though it has been known since 2006 that it harbors the genes for colibactin synthesis. Colibactin is a potent genotoxin that is now linked to causative mutations found in human colorectal cancer. Many papers concerning the use of this strain in clinical applications ignore or elude this fact or misleadingly suggest that Nissle 1917 does not induce DNA damage. Here, we demonstrate that Nissle 1917 produces colibactin in vitro and in vivo and induces mutagenic DNA damage. This is a serious safety concern that must not be ignored in the interests of patients, the general public, health care professionals, and ethical probiotic manufacturers.
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209
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Lee MH. Harness the functions of gut microbiome in tumorigenesis for cancer treatment. Cancer Commun (Lond) 2021; 41:937-967. [PMID: 34355542 PMCID: PMC8504147 DOI: 10.1002/cac2.12200] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/16/2021] [Indexed: 11/08/2022] Open
Abstract
It has been shown that gut microbiota dysbiosis leads to physiological changes and links to a number of diseases, including cancers. Thus, many cancer categories and treatment regimens should be investigated in the context of the microbiome. Owing to the availability of metagenome sequencing and multiomics studies, analyses of species characterization, host genetic changes, and metabolic profile of gut microbiota have become feasible, which has facilitated an exponential knowledge gain about microbiota composition, taxonomic alterations, and host interactions during tumorigenesis. However, the complexity of the gut microbiota, with a plethora of uncharacterized host‐microbe, microbe‐microbe, and environmental interactions, still contributes to the challenge of advancing our knowledge of the microbiota‐cancer interactions. These interactions manifest in signaling relay, metabolism, immunity, tumor development, genetic instability, sensitivity to cancer chemotherapy and immunotherapy. This review summarizes current studies/molecular mechanisms regarding the association between the gut microbiota and the development of cancers, which provides insights into the therapeutic strategies that could be harnessed for cancer diagnosis, treatment, or prevention.
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Affiliation(s)
- Mong-Hong Lee
- Research Institute of Gastroenterology, Sun Yat-sen University, Guangzhou, Guangdong, 510020, P. R. China.,Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510020, P. R. China
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210
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Oncogenic gene fusions in nonneoplastic precursors as evidence that bacterial infection can initiate prostate cancer. Proc Natl Acad Sci U S A 2021; 118:2018976118. [PMID: 34341114 DOI: 10.1073/pnas.2018976118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Prostate adenocarcinoma is the second most commonly diagnosed cancer in men worldwide, and the initiating factors are unknown. Oncogenic TMPRSS2:ERG (ERG+) gene fusions are facilitated by DNA breaks and occur in up to 50% of prostate cancers. Infection-driven inflammation is implicated in the formation of ERG+ fusions, and we hypothesized that these fusions initiate in early inflammation-associated prostate cancer precursor lesions, such as proliferative inflammatory atrophy (PIA), prior to cancer development. We investigated whether bacterial prostatitis is associated with ERG+ precancerous lesions in unique cases with active bacterial infections at the time of radical prostatectomy. We identified a high frequency of ERG+ non-neoplastic-appearing glands in these cases, including ERG+ PIA transitioning to early invasive cancer. These lesions were positive for ERG protein by immunohistochemistry and ERG messenger RNA by in situ hybridization. We additionally verified TMPRSS2:ERG genomic rearrangements in precursor lesions using tricolor fluorescence in situ hybridization. Identification of rearrangement patterns combined with whole-prostate mapping in three dimensions confirmed multiple (up to eight) distinct ERG+ precancerous lesions in infected cases. We further identified the pathogen-derived genotoxin colibactin as a potential source of DNA breaks in clinical cases as well as cultured prostate cells. Overall, we provide evidence that bacterial infections can initiate driver gene alterations in prostate cancer. In addition, our observations indicate that infection-induced ERG+ fusions are an early alteration in the carcinogenic process and that PIA may serve as a direct precursor to prostate cancer.
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211
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Bondarenko O, Mortimer M, Kahru A, Feliu N, Javed I, Kakinen A, Lin S, Xia T, Song Y, Davis TP, Lynch I, Parak WJ, Leong DT, Ke PC, Chen C, Zhao Y. Nanotoxicology and Nanomedicine: The Yin and Yang of Nano-Bio Interactions for the New Decade. NANO TODAY 2021; 39:101184. [PMID: 36937379 PMCID: PMC10018814 DOI: 10.1016/j.nantod.2021.101184] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nanotoxicology and nanomedicine are two sub-disciplines of nanotechnology focusing on the phenomena, mechanisms, and engineering at the nano-bio interface. For the better part of the past three decades, these two disciplines have been largely developing independently of each other. Yet recent breakthroughs in microbiome research and the current COVID-19 pandemic demonstrate that holistic approaches are crucial for solving grand challenges in global health. Here we show the Yin and Yang relationship between the two fields by highlighting their shared goals of making safer nanomaterials, improved cellular and organism models, as well as advanced methodologies. We focus on the transferable knowledge between the two fields as nanotoxicological research is moving from pristine to functional nanomaterials, while inorganic nanomaterials - the main subjects of nanotoxicology - have become an emerging source for the development of nanomedicines. We call for a close partnership between the two fields in the new decade, to harness the full potential of nanotechnology for benefiting human health and environmental safety.
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Affiliation(s)
- Olesja Bondarenko
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5d, 00790 Helsinki, Finland
| | - Monika Mortimer
- Institute of Environmental and Health Sciences, College of Quality and Safety Engineering, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Anne Kahru
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia
| | - Neus Feliu
- Fachbereich Physik und Chemie, Universität Hamburg, 22607 Hamburg, Germany
| | - Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
| | - Sijie Lin
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Tian Xia
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Division of NanoMedicine, Department of Medicine, University of California Los Angeles (UCLA), 570 Westwood Plaza, CNSI 6511, Los Angeles, CA 90095, United States
| | - Yang Song
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing, 400715, China
| | - Thomas P. Davis
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Iseult Lynch
- School of Geography Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Wolfgang J. Parak
- Fachbereich Physik und Chemie, Universität Hamburg, 22607 Hamburg, Germany
- Department of Instrument Science and Engineering, Institute of Nano Biomedicine and Engineering, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- Address correspondence to: Pu Chun Ke, ; Chunying Chen, ; Yuliang Zhao,
| | - Chunying Chen
- CAS Center for Excellence in Nanoscience and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
- Address correspondence to: Pu Chun Ke, ; Chunying Chen, ; Yuliang Zhao,
| | - Yuliang Zhao
- CAS Center for Excellence in Nanoscience and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
- Address correspondence to: Pu Chun Ke, ; Chunying Chen, ; Yuliang Zhao,
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212
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Sayed IM, Ramadan HKA, El-Mokhtar MA, Abdel-Wahid L. Microbiome and gastrointestinal malignancies. CURRENT OPINION IN PHYSIOLOGY 2021. [DOI: 10.1016/j.cophys.2021.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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213
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Knippel RJ, Sears CL. The Microbiome Colorectal Cancer Puzzle: Initiator, Propagator, and Avenue for Treatment and Research. J Natl Compr Canc Netw 2021; 19:986-992. [PMID: 34416704 DOI: 10.6004/jnccn.2021.7062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/19/2021] [Indexed: 11/17/2022]
Abstract
The human gut microbiome has an ever-increasing role in the instigation and progression of colorectal cancer (CRC). Recent investigations have focused on identifying the key causative bacterial species and the composition and structure of the microbiome as a whole that ultimately lead to tumorigenesis in the colon. Understanding the bacterial mechanisms that promote CRC provides a rich area for the development of new screening modalities and therapeutics that may improve patient outcomes. This article reviews the various mechanisms that bacteria in the gut use to induce and/or promote tumor formation, discusses the application of the microbiome in the prevention and therapy of CRC, and provides directions for future research endeavors aiming to develop a more complete understanding of this complex phenomenon.
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Affiliation(s)
| | - Cynthia L Sears
- Division of Infectious Diseases.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, and.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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214
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Bouferraa Y, Chedid A, Amhaz G, El Lakkiss A, Mukherji D, Temraz S, Shamseddine A. The Role of Gut Microbiota in Overcoming Resistance to Checkpoint Inhibitors in Cancer Patients: Mechanisms and Challenges. Int J Mol Sci 2021; 22:ijms22158036. [PMID: 34360802 PMCID: PMC8347208 DOI: 10.3390/ijms22158036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
The introduction of immune checkpoint inhibitors has constituted a major revolution in the treatment of patients with cancer. In contrast with the traditional cytotoxic therapies that directly kill tumor cells, this treatment modality enhances the ability of the host’s immune system to recognize and target cancerous cells. While immune checkpoint inhibitors have been effective across multiple cancer types, overcoming resistance remains a key area of ongoing research. The gut microbiota and its role in cancer immunosurveillance have recently become a major field of study. Gut microbiota has been shown to have direct and systemic effects on cancer pathogenesis and hosts anti-tumor immune response. Many studies have also shown that the host microbiota profile plays an essential role in the response to immunotherapy, especially immune checkpoint inhibitors. As such, modulating this microbial environment has offered a potential path to overcome the resistance to immune checkpoint inhibitors. In this review, we will talk about the role of microbiota in cancer pathogenesis and immune-system activity. We will also discuss preclinical and clinical studies that have increased our understanding about the roles and the mechanisms through which microbiota influences the response to treatment with immune checkpoint inhibitors.
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215
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Sadecki PW, Balboa SJ, Lopez LR, Kedziora KM, Arthur JC, Hicks LM. Evolution of Polymyxin Resistance Regulates Colibactin Production in Escherichia coli. ACS Chem Biol 2021; 16:1243-1254. [PMID: 34232632 PMCID: PMC8601121 DOI: 10.1021/acschembio.1c00322] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The complex reservoir of metabolite-producing bacteria in the gastrointestinal tract contributes tremendously to human health and disease. Bacterial composition, and by extension gut metabolomic composition, is undoubtably influenced by the use of modern antibiotics. Herein, we demonstrate that polymyxin B, a last resort antibiotic, influences the production of the genotoxic metabolite colibactin from adherent-invasive Escherichia coli (AIEC) NC101. Colibactin can promote colorectal cancer through DNA double stranded breaks and interstrand cross-links. While the structure and biosynthesis of colibactin have been elucidated, chemical-induced regulation of its biosynthetic gene cluster and subsequent production of the genotoxin by E. coli are largely unexplored. Using a multiomic approach, we identified that polymyxin B stress enhances the abundance of colibactin biosynthesis proteins (Clb's) in multiple pks+ E. coli strains, including pro-carcinogenic AIEC, NC101; the probiotic strain, Nissle 1917; and the antibiotic testing strain, ATCC 25922. Expression analysis via qPCR revealed that increased transcription of clb genes likely contributes to elevated Clb protein levels in NC101. Enhanced production of Clb's by NC101 under polymyxin stress matched an increased production of the colibactin prodrug motif, a proxy for the mature genotoxic metabolite. Furthermore, E. coli with a heightened tolerance for polymyxin induced greater mammalian DNA damage, assessed by quantification of γH2AX staining in cultured intestinal epithelial cells. This study establishes a key link between the polymyxin B stress response and colibactin production in pks+ E. coli. Ultimately, our findings will inform future studies investigating colibactin regulation and the ability of seemingly innocuous commensal microbes to induce host disease.
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Affiliation(s)
- Patric W. Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samantha J. Balboa
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lacey R. Lopez
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Katarzyna M. Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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216
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Pultar F, Hansen ME, Wolfrum S, Böselt L, Fróis-Martins R, Bloch S, Kravina AG, Pehlivanoglu D, Schäffer C, LeibundGut-Landmann S, Riniker S, Carreira EM. Mutanobactin D from the Human Microbiome: Total Synthesis, Configurational Assignment, and Biological Evaluation. J Am Chem Soc 2021; 143:10389-10402. [PMID: 34212720 DOI: 10.1021/jacs.1c04825] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutanobactin D is a non-ribosomal, cyclic peptide isolated from Streptococcus mutans and shows activity reducing yeast-to-hyphae transition as well as biofilm formation of the pathogenic yeast Candida albicans. We report the first total synthesis of this natural product, which relies on enantioselective, zinc-mediated 1,3-dipolar cycloaddition and a sequence of cascading reactions, providing the key lipidated γ-amino acid found in mutanobactin D. The synthesis enables configurational assignment, determination of the dominant solution-state structure, and studies to assess the stability of the lipopeptide substructure found in the natural product. The information stored in the fingerprint region of the IR spectra in combination with quantum chemical calculations proved key to distinguishing between epimers of the α-substituted β-keto amide. Synthetic mutanobactin D drives discovery and analysis of its effect on growth of other members of the human oral consortium. Our results showcase how total synthesis is central for elucidating the complex network of interspecies communications of human colonizers.
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Affiliation(s)
- Felix Pultar
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Moritz E Hansen
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Susanne Wolfrum
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Lennard Böselt
- Laboratorium für Physikalische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Ricardo Fróis-Martins
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland.,Institute of Experimental Immunology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Susanne Bloch
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Alberto G Kravina
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Deren Pehlivanoglu
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Salomé LeibundGut-Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland.,Institute of Experimental Immunology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Erick M Carreira
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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217
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Abstract
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The genomic era has dramatically changed how we discover and investigate
microbial biochemistry. In particular, the exponential expansion in
the number of sequenced microbial genomes provides investigators with
a vast wealth of sequence data to exploit for the discovery of biochemical
functions and mechanisms, as well as novel enzymes and metabolites.
In contrast to early biochemical work, which was largely characterized
by “forward” approaches that proceed from biomass to
enzyme to gene, the availability of genome sequences enables the discovery
of new microbial metabolic activities, enzymes, and metabolites by
“reverse” approaches that originate with genetic information
or by approaches that incorporate features of both forward and reverse
methodologies. In the genomic era, the canonical organization of microbial
genomes into gene clusters presents a singular opportunity for the
utilization of genomic data. Specifically, genomic context (information
gleaned from the genes surrounding a gene of interest in the chromosome)
is a powerful tool for chemical discovery in microbial systems because
of the functional and/or physiological relationship that usually exists
between genes found within a gene cluster. This means that the investigator
can use this inferred link to generate hypotheses about the functions
of individual genes in the cluster or even the function of the entire
cluster itself. Here, we discuss how analysis of genomic context in
combination with a mechanistic understanding of enzymes can facilitate
numerous facets of microbial biochemical research including the identification
of biosynthetic gene clusters, the discovery of important and novel
enzymes, the elucidation of natural product structures, and the identification
of new metabolic pathways. We highlight work from our laboratory using
genomic context to discover and study biosynthetic pathways that produce
natural products, including the cylindrocyclophanes, nitrogen–nitrogen
bond-containing metabolites, and the gut microbial genotoxin colibactin.
Although use of genomic context is most commonly associated with studies
of natural product biosynthesis, we also show that it can be applied
to the study of primary metabolism. We illustrate this with examples
from our work studying the members of the glycyl radical enzyme superfamily
involved in choline and 4-hydroxyproline degradation in the human
gut. Looking forward, we envision increased opportunities to use such
information, with the combination of biochemical knowledge and computational
tools poised to fuel a new revolution in our ability to connect genes
and their biochemical functions. In particular, we note a need for
methods that computationally formalize the functional association
between genes when such associations are not obvious from manual gene
annotations. Such tools will drastically augment the feasibility and
scope of gene cluster analysis and accelerate the discovery of new
microbial enzymes, metabolites, and metabolic processes.
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Affiliation(s)
- Duncan J. Kountz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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218
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Shen W, Tang D, Deng Y, Li H, Wang T, Wan P, Liu R. Association of gut microbiomes with lung and esophageal cancer: a pilot study. World J Microbiol Biotechnol 2021; 37:128. [PMID: 34212246 DOI: 10.1007/s11274-021-03086-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 06/02/2021] [Indexed: 12/16/2022]
Abstract
Gut microbiota, especially human pathogens, has been shown to be involved in the occurrence and development of cancer. Esophageal squamous cell carcinoma and lung cancer are two malignant cancers, and their relationship with gut microbiota is still unclear. Virulence factor database (VFDB) is an integrated and comprehensive online resource for curating information about human pathogens. Here, based on VFDB database, we analyzed the differences of bacteria at genus level in the gut of patients with esophageal squamous cell carcinoma, lung cancer, and healthy controls. We proposed the possible cancer-associated bacteria in gut and put forward their possible effects. Apart from this, principal coordinate analysis (PCoA) and analysis of similarities (ANSOIM) suggested that some bacteria in the gut can be used as potential biomarkers to screen esophageal squamous cell carcinoma and lung cancer, and their effectiveness was preliminary verified. The relative abundance of Klebsiella and Streptococcus can be used to distinguish patients with esophageal squamous cell carcinoma and lung cancer from healthy controls. The absolute abundance of Klebsiella can further distinguish patients with esophageal squamous cell carcinoma from patients with lung cancer. In particular, the relative abundance of Fusobacterium can directly distinguish between patients with esophageal squamous cell carcinoma and healthy controls. Additionally, the absolute abundance of Haemophilus can distinguish lung cancer from healthy controls. Our study provided a new way based on VFDB database to explore the relationship between gut microbiota and cancer, and initially proposed a feasible cancer screening method.
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Affiliation(s)
- Weitao Shen
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Derong Tang
- Department of Thoracic Surgery, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, 223300, Jiangsu, China
| | - Yali Deng
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Huilin Li
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Tian Wang
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Ping Wan
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Ran Liu
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
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219
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Watanabe D, Murakami H, Ohno H, Tanisawa K, Konishi K, Todoroki-Mori K, Tsunematsu Y, Sato M, Ogata Y, Miyoshi N, Kubota N, Kunisawa J, Wakabayashi K, Kubota T, Watanabe K, Miyachi M. Stool pattern is associated with not only the prevalence of tumorigenic bacteria isolated from fecal matter but also plasma and fecal fatty acids in healthy Japanese adults. BMC Microbiol 2021; 21:196. [PMID: 34182940 PMCID: PMC8240356 DOI: 10.1186/s12866-021-02255-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Colibactin-producing Escherichia coli containing polyketide synthase (pks+ E. coli) has been shown to be involved in colorectal cancer (CRC) development through gut microbiota analysis in animal models. Stool status has been associated with potentially adverse gut microbiome profiles from fecal analysis in adults. We examined the association between stool patterns and the prevalence of pks+ E. coli isolated from microbiota in fecal samples of 224 healthy Japanese individuals. RESULTS Stool patterns were determined through factorial analysis using a previously validated questionnaire that included stool frequency, volume, color, shape, and odor. Factor scores were classified into tertiles. The prevalence of pks+ E. coli was determined by using specific primers for pks+ E. coli in fecal samples. Plasma and fecal fatty acids were measured via gas chromatography-mass spectrometry. The prevalence of pks+ E. coli was 26.8%. Three stool patterns identified by factorial analysis accounted for 70.1% of all patterns seen (factor 1: lower frequency, darker color, and harder shape; factor 2: higher volume and softer shape; and factor 3: darker color and stronger odor). Multivariable-adjusted odds ratios (95% confidence intervals) of the prevalence of pks+ E. coli for the highest versus the lowest third of the factor 1 score was 3.16 (1.38 to 7.24; P for trend = 0.006). This stool pattern exhibited a significant positive correlation with fecal isobutyrate, isovalerate, valerate, and hexanoate but showed a significant negative correlation with plasma eicosenoic acid and α-linoleic acid, as well as fecal propionate and succinate. No other stool patterns were significant. CONCLUSIONS These results suggest that stool patterns may be useful in the evaluation of the presence of tumorigenic bacteria and fecal fatty acids through self-monitoring of stool status without the requirement for specialist technology or skill. Furthermore, it may provide valuable insight about effective strategies for the early discovery of CRC.
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Affiliation(s)
- Daiki Watanabe
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Haruka Murakami
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Harumi Ohno
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Kumpei Tanisawa
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Kana Konishi
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Kikue Todoroki-Mori
- Department of Clinical Nutrition, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Yuji Ogata
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Noriyuki Miyoshi
- School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Naoto Kubota
- Department of Clinical Nutrition, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Keiji Wakabayashi
- School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Tetsuya Kubota
- Department of Clinical Nutrition, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan.,Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kanagawa, 243-0435, Japan.,Division of Diabetes and Metabolism, The Institute for Medical Science, Asahi Life Foundation, Tokyo, 103-0002, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Motohiko Miyachi
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, 162-8636, Japan. .,Faculty of Sport Sciences, Waseda University, Saitama, 359-1192, Japan.
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220
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Biondi A, Basile F, Vacante M. Familial adenomatous polyposis and changes in the gut microbiota: New insights into colorectal cancer carcinogenesis. World J Gastrointest Oncol 2021; 13:495-508. [PMID: 34163569 PMCID: PMC8204352 DOI: 10.4251/wjgo.v13.i6.495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/15/2021] [Accepted: 05/08/2021] [Indexed: 02/06/2023] Open
Abstract
Patients with familial adenomatous polyposis (FAP), an autosomal dominant hereditary colorectal cancer syndrome, have a lifetime risk of developing cancer of nearly 100%. Recent studies have pointed out that the gut microbiota could play a crucial role in the development of colorectal adenomas and the consequent progression to colorectal cancer. Some gut bacteria, such as Fusobacterium nucleatum, Escherichia coli, Clostridium difficile, Peptostreptococcus, and enterotoxigenic Bacteroides fragilis, could be implicated in colorectal carcinogenesis through different mechanisms, including the maintenance of a chronic inflammatory state, production of bioactive tumorigenic metabolites, and DNA damage. Studies using the adenomatous polyposis coliMin/+ mouse model, which resembles FAP in most respects, have shown that specific changes in the intestinal microbial community could influence a multistep progression, the intestinal "adenoma-carcinoma sequence", which involves mucosal barrier injury, low-grade inflammation, activation of the Wnt pathway. Therefore, modulation of gut microbiota might represent a novel therapeutic target for patients with FAP. Administration of probiotics, prebiotics, antibiotics, and nonsteroidal anti-inflammatory drugs could potentially prevent the progression of the adenoma-carcinoma sequence in FAP. The aim of this review was to summarize the best available knowledge on the role of gut microbiota in colorectal carcinogenesis in patients with FAP.
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Affiliation(s)
- Antonio Biondi
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania 95123, Italy
- Multidisciplinary Research Center for Rare Diseases, University of Catania, Catania 95123, Italy
| | - Francesco Basile
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania 95123, Italy
- Multidisciplinary Research Center for Rare Diseases, University of Catania, Catania 95123, Italy
| | - Marco Vacante
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania 95123, Italy
- Multidisciplinary Research Center for Rare Diseases, University of Catania, Catania 95123, Italy
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221
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Wami H, Wallenstein A, Sauer D, Stoll M, von Bünau R, Oswald E, Müller R, Dobrindt U. Insights into evolution and coexistence of the colibactin- and yersiniabactin secondary metabolite determinants in enterobacterial populations. Microb Genom 2021; 7. [PMID: 34128785 PMCID: PMC8461471 DOI: 10.1099/mgen.0.000577] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial genotoxin colibactin interferes with the eukaryotic cell cycle by causing dsDNA breaks. It has been linked to bacterially induced colorectal cancer in humans. Colibactin is encoded by a 54 kb genomic region in Enterobacteriaceae. The colibactin genes commonly co-occur with the yersiniabactin biosynthetic determinant. Investigating the prevalence and sequence diversity of the colibactin determinant and its linkage to the yersiniabactin operon in prokaryotic genomes, we discovered mainly species-specific lineages of the colibactin determinant and classified three main structural settings of the colibactin–yersiniabactin genomic region in Enterobacteriaceae. The colibactin gene cluster has a similar but not identical evolutionary track to that of the yersiniabactin operon. Both determinants could have been acquired on several occasions and/or exchanged independently between enterobacteria by horizontal gene transfer. Integrative and conjugative elements play(ed) a central role in the evolution and structural diversity of the colibactin–yersiniabactin genomic region. Addition of an activating and regulating module (clbAR) to the biosynthesis and transport module (clbB-S) represents the most recent step in the evolution of the colibactin determinant. In a first attempt to correlate colibactin expression with individual lineages of colibactin determinants and different bacterial genetic backgrounds, we compared colibactin expression of selected enterobacterial isolates in vitro. Colibactin production in the tested Klebsiella species and Citrobacter koseri strains was more homogeneous and generally higher than that in most of the Escherichia coli isolates studied. Our results improve the understanding of the diversity of colibactin determinants and its expression level, and may contribute to risk assessment of colibactin-producing enterobacteria.
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Affiliation(s)
- Haleluya Wami
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | - Daniel Sauer
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, Campus E8 1, Saarbrücken, Germany
| | - Monika Stoll
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Münster, Germany
| | | | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, Campus E8 1, Saarbrücken, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
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222
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LaCourse KD, Johnston CD, Bullman S. The relationship between gastrointestinal cancers and the microbiota. Lancet Gastroenterol Hepatol 2021; 6:498-509. [PMID: 33743198 PMCID: PMC10773981 DOI: 10.1016/s2468-1253(20)30362-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023]
Abstract
The contribution of the microbiota to disease progression and treatment efficacy is often neglected when determining who is at the highest risk of developing gastrointestinal cancers or designing treatment strategies for patients. We reviewed the current literature on the effect of the human microbiota on cancer risk, prognosis, and treatment efficacy. We highlight emerging research that seeks to identify microbial signatures as biomarkers for various gastrointestinal cancers, and discuss how we could harness knowledge of the microbiome to detect, prevent, and treat these cancers. Finally, we outline further research needed in the field of gastrointestinal cancers and the microbiota, and describe the efforts required to increase the accuracy and reproducibility of data linking the microbiome to cancer.
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Affiliation(s)
- Kaitlyn D LaCourse
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher D Johnston
- Vaccine and Infection Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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223
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Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H. Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nat Commun 2021; 12:3225. [PMID: 34050176 PMCID: PMC8163882 DOI: 10.1038/s41467-021-23502-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.
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Affiliation(s)
- Bahar Behsaz
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Edna Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St Petersburg, Russia
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Florian Grundmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Deepa Acharya
- Tiny Earth Chemistry Hub, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Annabell Linck
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Changhui Guan
- The Jackson Laboratory of Medical Genomics, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory of Medical Genomics, Farmington, CT, USA
| | - Pieter C Dorrestein
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt & Senckenberg Research Institute, Frankfurt am Main, Germany.
- Max-Planck-Institute for Terrestrial Microbiology, Department for Natural Products in Organismic Interactions, Marburg, Germany.
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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Hibino S, Kawazoe T, Kasahara H, Itoh S, Ishimoto T, Sakata-Yanagimoto M, Taniguchi K. Inflammation-Induced Tumorigenesis and Metastasis. Int J Mol Sci 2021; 22:ijms22115421. [PMID: 34063828 PMCID: PMC8196678 DOI: 10.3390/ijms22115421] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammation, especially chronic inflammation, plays a pivotal role in tumorigenesis and metastasis through various mechanisms and is now recognized as a hallmark of cancer and an attractive therapeutic target in cancer. In this review, we discuss recent advances in molecular mechanisms of how inflammation promotes tumorigenesis and metastasis and suppresses anti-tumor immunity in various types of solid tumors, including esophageal, gastric, colorectal, liver, and pancreatic cancer as well as hematopoietic malignancies.
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Affiliation(s)
- Sana Hibino
- Research Center for Advanced Science and Technology, Department of Inflammology, The University of Tokyo, Tokyo 153-0041, Japan;
| | - Tetsuro Kawazoe
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan;
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan;
| | - Hidenori Kasahara
- National Center for Global Health and Medicine, Department of Stem Cell Biology, Research Institute, Tokyo 162-8655, Japan;
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Shinji Itoh
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan;
| | - Takatsugu Ishimoto
- Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan;
| | | | - Koji Taniguchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan;
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
- Correspondence: ; Tel.: +81-11-706-5050
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225
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Kent ML, Wall ES, Sichel S, Watral V, Stagaman K, Sharpton TJ, Guillemin K. Pseudocapillaria tomentosa, Mycoplasma spp., and Intestinal Lesions in Experimentally Infected Zebrafish Danio rerio. Zebrafish 2021; 18:207-220. [PMID: 33999743 DOI: 10.1089/zeb.2020.1955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Intestinal neoplasms and preneoplastic lesions are common in zebrafish research facilities. Previous studies have demonstrated that these neoplasms are caused by a transmissible agent, and two candidate agents have been implicated: a Mycoplasma sp. related to Mycoplasma penetrans and the intestinal parasitic nematode, Pseudocapillaria tomentosa, and both agents are common in zebrafish facilities. To elucidate the role of these two agents in the occurrence and severity of neoplasia and other intestinal lesions, we conducted two experimental inoculation studies. Exposed fish were examined at various time points over an 8-month period for intestinal histopathologic changes and the burden of Mycoplasma and nematodes. Fish exposed to Mycoplasma sp. isolated from zebrafish were associated with preneoplastic lesions. Fish exposed to the nematode alone or with the Mycoplasma isolate developed severe lesions and neoplasms. Both inflammation and neoplasm scores were associated with an increase in Mycoplasma burden. These results support the conclusions that P. tomentosa is a strong promoter of intestinal neoplasms in zebrafish and that Mycoplasma alone can also cause intestinal lesions and accelerate cancer development in the context of nematode infection.
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Affiliation(s)
- Michael L Kent
- Department of Microbiology and Oregon State University, Corvallis, Oregon, USA.,Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Elena S Wall
- Department of Biology and Institute of Molecular Biology, Eugene, University of Oregon, Eugene, Oregon, USA
| | - Sophie Sichel
- Department of Biology and Institute of Molecular Biology, Eugene, University of Oregon, Eugene, Oregon, USA
| | - Virginia Watral
- Department of Microbiology and Oregon State University, Corvallis, Oregon, USA
| | - Keaton Stagaman
- Department of Microbiology and Oregon State University, Corvallis, Oregon, USA
| | - Thomas J Sharpton
- Department of Microbiology and Oregon State University, Corvallis, Oregon, USA.,Department of Statistics, Oregon State University, Corvallis, Oregon, USA
| | - Karen Guillemin
- Department of Biology and Institute of Molecular Biology, Eugene, University of Oregon, Eugene, Oregon, USA.,Humans and the Microbiome Program, CIFAR, Toronto, Ontario, Canada
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226
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Dougherty MW, Jobin C. Shining a Light on Colibactin Biology. Toxins (Basel) 2021; 13:346. [PMID: 34065799 PMCID: PMC8151066 DOI: 10.3390/toxins13050346] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022] Open
Abstract
Colibactin is a secondary metabolite encoded by the pks gene island identified in several Enterobacteriaceae, including some pathogenic Escherichia coli (E. coli) commonly enriched in mucosal tissue collected from patients with inflammatory bowel disease and colorectal cancer. E. coli harboring this biosynthetic gene cluster cause DNA damage and tumorigenesis in cell lines and pre-clinical models, yet fundamental knowledge regarding colibactin function is lacking. To accurately assess the role of pks+ E. coli in cancer etiology, the biological mechanisms governing production and delivery of colibactin by these bacteria must be elucidated. In this review, we will focus on recent advances in our understanding of colibactin's structural mode-of-action and mutagenic potential with consideration for how this activity may be regulated by physiologic conditions within the intestine.
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Affiliation(s)
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL 32610, USA;
- Department of Infectious Diseases and Inflammation, University of Florida, Gainesville, FL 32610, USA
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227
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Role of Gut Microbiota and Probiotics in Colorectal Cancer: Onset and Progression. Microorganisms 2021; 9:microorganisms9051021. [PMID: 34068653 PMCID: PMC8151957 DOI: 10.3390/microorganisms9051021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota plays an important role in maintaining homeostasis in the human body, and the disruption of these communities can lead to compromised host health and the onset of disease. Current research on probiotics is quite promising and, in particular, these microorganisms have demonstrated their potential for use as adjuvants for the treatment of colorectal cancer. This review addresses the possible applications of probiotics, postbiotics, synbiotics, and next-generation probiotics in colorectal cancer research.
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228
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Gut Microbiota as Potential Biomarker and/or Therapeutic Target to Improve the Management of Cancer: Focus on Colibactin-Producing Escherichia coli in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13092215. [PMID: 34063108 PMCID: PMC8124679 DOI: 10.3390/cancers13092215] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Gut microbiota is emerging as new diagnostic and prognostic marker and/or therapeutic target to improve the management of cancer. This review aims to summarize microbial signatures that have been associated with digestive and other cancers. We report the clinical relevance of these microbial markers to predict the response to cancer therapy. Among these biomarkers, colibactin-producing E. coli are prevalent in the colonic mucosa of patients with colorectal cancer and they promote colorectal carcinogenesis in several pre-clinical models. Here we discuss the promising use of colibactin-producing E. coli as a new predictive factor and a therapeutic target in colon cancer management. Abstract The gut microbiota is crucial for physiological development and immunological homeostasis. Alterations of this microbial community called dysbiosis, have been associated with cancers such colorectal cancers (CRC). The pro-carcinogenic potential of this dysbiotic microbiota has been demonstrated in the colon. Recently the role of the microbiota in the efficacy of anti-tumor therapeutic strategies has been described in digestive cancers and in other cancers (e.g., melanoma and sarcoma). Different bacterial species seem to be implicated in these mechanisms: F. nucleatum, B. fragilis, and colibactin-associated E. coli (CoPEC). CoPEC bacteria are prevalent in the colonic mucosa of patients with CRC and they promote colorectal carcinogenesis in susceptible mouse models of CRC. In this review, we report preclinical and clinical data that suggest that CoPEC could be a new factor predictive of poor outcomes that could be used to improve cancer management. Moreover, we describe the possibility of using these bacteria as new therapeutic targets.
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229
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Tripathi P, Bruner SD. Structural Basis for the Interactions of the Colibactin Resistance Gene Product ClbS with DNA. Biochemistry 2021; 60:1619-1625. [PMID: 33945270 DOI: 10.1021/acs.biochem.1c00201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The natural product colibactin, along with its associated biosynthetic gene cluster, is an example system for the role microbially derived small molecules play in the human microbiome. This is particularly relevant in the human gut, where host microbiota is involved in various disorders, including colorectal cancer pathogenesis. Bacteria harboring the colibactin gene cluster induce alkylation of nucleobases in host DNA, forming interstrand cross-links both in vivo and in vitro. These lesions can lead to deleterious double-strand breaks and have been identified as the primary mechanism of colibactin-induced cytotoxicity. The gene product ClbS is one of several mechanisms utilized by the producing bacteria to maintain genome integrity. ClbS catalyzes hydrolytic inactivation of colibactin and has been shown to bind DNA, incurring self-resistance. Presented is the molecular basis for ClbS bound to a DNA oligonucleotide. The structure shows the interaction of the protein with the ends of a DNA duplex with terminal nucleotides flipped to the enzyme active site. The structure suggests an additional function for ClbS, the binding to damaged DNA followed by repair. Additionally, our study provides general insight into the function of the widely distributed and largely uncharacterized DUF1706 protein family.
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Affiliation(s)
- Prabhanshu Tripathi
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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230
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Foegeding NJ, Jones ZS, Byndloss MX. Western lifestyle as a driver of dysbiosis in colorectal cancer. Dis Model Mech 2021; 14:dmm049051. [PMID: 34060626 PMCID: PMC8214737 DOI: 10.1242/dmm.049051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Landmark discoveries in the gut microbiome field have paved the way for new research aimed at illuminating the influence of microbiota in colorectal cancer. A major challenge is to account for the effect of inherently variable environmental factors on the host and the gut microbiome, while concurrently determining their contribution to carcinogenesis. Here, we briefly discuss the role of the gut microbial community in colorectal cancer and elaborate on the recent insight that environmental factors related to a Western diet and lifestyle may drive the bloom of tumorigenic members of the gut microbiota. We also discuss how future research focused on untangling host-microbe interactions in the colon may influence medical insights that relate to the prevention and treatment of colorectal cancer.
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Affiliation(s)
- Nora J. Foegeding
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Zachary S. Jones
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Mariana X. Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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231
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Rosendahl Huber A, Pleguezuelos-Manzano C, Puschhof J. A bacterial mutational footprint in colorectal cancer genomes. Br J Cancer 2021; 124:1751-1753. [PMID: 33742142 PMCID: PMC8144397 DOI: 10.1038/s41416-021-01273-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/18/2022] Open
Abstract
Changes in the microbiome are associated with the development of colorectal cancer, but causal explanations have been lacking. We recently demonstrated that pks+ Escherichia coli induce a specific mutational pattern using intestinal organoids and these mutations are present in the genomes of colorectal cancer. This finding warrants further studies on the microbial role in oncogenic mutation induction, cancer development and future preventive strategies.
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Affiliation(s)
- Axel Rosendahl Huber
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Hubrecht Institute, Utrecht, The Netherlands.
| | - Cayetano Pleguezuelos-Manzano
- Oncode Institute, Hubrecht Institute, Utrecht, The Netherlands.
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands.
| | - Jens Puschhof
- Oncode Institute, Hubrecht Institute, Utrecht, The Netherlands.
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands.
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232
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Zhu R, Lang T, Yan W, Zhu X, Huang X, Yin Q, Li Y. Gut Microbiota: Influence on Carcinogenesis and Modulation Strategies by Drug Delivery Systems to Improve Cancer Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003542. [PMID: 34026439 PMCID: PMC8132165 DOI: 10.1002/advs.202003542] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/05/2021] [Indexed: 05/05/2023]
Abstract
Gut microbiota have close interactions with the host. It can affect cancer progression and the outcomes of cancer therapy, including chemotherapy, immunotherapy, and radiotherapy. Therefore, approaches toward the modulation of gut microbiota will enhance cancer prevention and treatment. Modern drug delivery systems (DDS) are emerging as rational and promising tools for microbiota intervention. These delivery systems have compensated for the obstacles associated with traditional treatments. In this review, the essential roles of gut microbiota in carcinogenesis, cancer progression, and various cancer therapies are first introduced. Next, advances in DDS that are aimed at enhancing the efficacy of cancer therapy by modulating or engineering gut microbiota are highlighted. Finally, the challenges and opportunities associated with the application of DDS targeting gut microbiota for cancer prevention and treatment are briefly discussed.
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Affiliation(s)
- Runqi Zhu
- State Key Laboratory of Drug Research and Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of Sciences501 Haike RoadShanghai201203China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijing100049China
| | - Tianqun Lang
- State Key Laboratory of Drug Research and Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of Sciences501 Haike RoadShanghai201203China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijing100049China
- Yantai Key Laboratory of Nanomedicine and Advanced PreparationsYantai Institute of Materia MedicaYantai264000China
| | - Wenlu Yan
- State Key Laboratory of Drug Research and Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of Sciences501 Haike RoadShanghai201203China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xiao Zhu
- State Key Laboratory of Drug Research and Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of Sciences501 Haike RoadShanghai201203China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xin Huang
- State Key Laboratory of Drug Research and Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of Sciences501 Haike RoadShanghai201203China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijing100049China
| | - Qi Yin
- State Key Laboratory of Drug Research and Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of Sciences501 Haike RoadShanghai201203China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijing100049China
- Yantai Key Laboratory of Nanomedicine and Advanced PreparationsYantai Institute of Materia MedicaYantai264000China
| | - Yaping Li
- State Key Laboratory of Drug Research and Center of PharmaceuticsShanghai Institute of Materia MedicaChinese Academy of Sciences501 Haike RoadShanghai201203China
- School of PharmacyUniversity of Chinese Academy of SciencesBeijing100049China
- Yantai Key Laboratory of Nanomedicine and Advanced PreparationsYantai Institute of Materia MedicaYantai264000China
- School of PharmacyYantai UniversityYantai264005China
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233
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Strakova N, Korena K, Karpiskova R. Klebsiella pneumoniae producing bacterial toxin colibactin as a risk of colorectal cancer development - A systematic review. Toxicon 2021; 197:126-135. [PMID: 33901549 DOI: 10.1016/j.toxicon.2021.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/24/2021] [Accepted: 04/11/2021] [Indexed: 12/12/2022]
Abstract
Microbiota can significantly contribute to colorectal cancer initiation and development. It was described that E. coli harbouring polyketide synthase (pks) genes can synthetize bacterial toxin colibactin, which was first described by Nougayrede's group in 2006. E. coli positive for pks genes were overrepresented in colorectal cancer biopsies and, therefore, prevalence and the effect of pks positive bacteria as a risk factor in colorectal cancer development is in our interest. Interestingly, pks gene cluster in E. coli shares a striking 100% sequence identity with K. pneumoniae, suggesting that their function and regulation are conserved. Moreover, K. pneumoniae can express a variety of virulence factors, including capsules, siderophores, iron-scavenging systems, adhesins and endotoxins. It was reported that pks cluster and thereby colibactin is also related to the hypervirulence of K. pneumoniae. Acquisition of the pks locus is associated with K. pneumoniae gut colonisation and mucosal invasion. Colibactin also increases the likelihood of serious complications of bacterial infections, such as development of meningitis and potentially tumorigenesis. Even though K. pneumoniae is undoubtedly a gut colonizer, the role of pks positive K. pneumoniae in GIT has not yet been investigated. It seems that CRC-distinctive microbiota is already present in the early stages of cancer development and, therefore, microbiome analysis could help to discover the early stages of cancer, which are crucial for effectiveness of anticancer therapy. We hypothesize, that pks positive K. pneumoniae can be a potential biomarker of tumour prevalence and anticancer therapy response.
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Affiliation(s)
- Nicol Strakova
- Laboratory of Zoonoses and Antibiotic Resistance, Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Hudcova 296/70, Brno, Czech Republic.
| | - Kristyna Korena
- Laboratory of Zoonoses and Antibiotic Resistance, Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Hudcova 296/70, Brno, Czech Republic
| | - Renata Karpiskova
- Laboratory of Zoonoses and Antibiotic Resistance, Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Hudcova 296/70, Brno, Czech Republic
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Salesse L, Lucas C, Hoang MHT, Sauvanet P, Rezard A, Rosenstiel P, Damon-Soubeyrand C, Barnich N, Godfraind C, Dalmasso G, Nguyen HTT. Colibactin-Producing Escherichia coli Induce the Formation of Invasive Carcinomas in a Chronic Inflammation-Associated Mouse Model. Cancers (Basel) 2021; 13:cancers13092060. [PMID: 33923277 PMCID: PMC8123153 DOI: 10.3390/cancers13092060] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Changes in the composition of the intestinal flora have been reported in patients with colorectal cancer, the second leading cause of cancer death in the world, with an increase in so-called "harmful" bacteria. Among these, Escherichia coli producing colibactin, a toxin that causes DNA damage, has attracted the interest of many research groups. Here, we showed that infection of wild-type mice with a colibactin-producing E. coli (CoPEC) strain, isolated from a patient with colorectal cancer, combined with chronic inflammation induced the formation of invasive colonic tumors, i.e., tumors that spread beyond epithelial layer and grow into surrounding tissues. We also showed that autophagy, a cell defense process, is necessary to inhibit the tumorigenesis induced by CoPEC. Thus, this work highlights the role of CoPEC as a driver of colorectal cancer development, and suggests that targeting autophagy could be a promising strategy to inhibit the protumoral effects of these bacteria. Abstract Background: Escherichia coli producing the genotoxin colibactin (CoPEC or colibactin-producing E. coli) abnormally colonize the colonic mucosa of colorectal cancer (CRC) patients. We previously showed that deficiency of autophagy in intestinal epithelial cells (IECs) enhances CoPEC-induced colorectal carcinogenesis in ApcMin/+ mice. Here, we tested if CoPEC trigger tumorigenesis in a mouse model lacking genetic susceptibility or the use of carcinogen. Methods: Mice with autophagy deficiency in IECs (Atg16l1∆IEC) or wild-type mice (Atg16l1flox/flox) were infected with the CoPEC 11G5 strain or the mutant 11G5∆clbQ incapable of producing colibactin and subjected to 12 cycles of DSS treatment to induce chronic colitis. Mouse colons were used for histological assessment, immunohistochemical and immunoblot analyses for DNA damage marker. Results: 11G5 or 11G5∆clbQ infection increased clinical and histological inflammation scores, and these were further enhanced by IEC-specific autophagy deficiency. 11G5 infection, but not 11G5∆clbQ infection, triggered the formation of invasive carcinomas, and this was further increased by autophagy deficiency. The increase in invasive carcinomas was correlated with enhanced DNA damage and independent of inflammation. Conclusions: CoPEC induce colorectal carcinogenesis in a CRC mouse model lacking genetic susceptibility and carcinogen. This work highlights the role of (i) CoPEC as a driver of CRC development, and (ii) autophagy in inhibiting the carcinogenic properties of CoPEC.
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Affiliation(s)
- Laurène Salesse
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
| | - Cécily Lucas
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
| | - My Hanh Thi Hoang
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
- Department of Cell Biology, Faculty of Biology, University of Science, Vietnam National University (VNU), Hanoi 100000, Vietnam
| | - Pierre Sauvanet
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
- Department of Digestive and Hepatobiliary Surgery, CHU Estaing, 63001 Clermont-Ferrand, France
| | - Alexandra Rezard
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, 24148 Kiel, Germany;
| | | | - Nicolas Barnich
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
| | - Catherine Godfraind
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
- Department of Pathology, CHU Gabriel Montpied, 63001 Clermont-Ferrand, France
| | - Guillaume Dalmasso
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
| | - Hang Thi Thu Nguyen
- M2iSH, UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 2018, CRNH, 63001 Clermont-Ferrand, France; (L.S.); (C.L.); (M.H.T.H.); (P.S.); (A.R.); (N.B.); (C.G.); (G.D.)
- Correspondence: ; Tel.: +33-473178381; Fax: +33-473178371
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Abstract
DNA interstrand cross-links (ICLs) covalently connect the two strands of the double helix and are extremely cytotoxic. Defective ICL repair causes the bone marrow failure and cancer predisposition syndrome, Fanconi anemia, and upregulation of repair causes chemotherapy resistance in cancer. The central event in ICL repair involves resolving the cross-link (unhooking). In this review, we discuss the chemical diversity of ICLs generated by exogenous and endogenous agents. We then describe how proliferating and nonproliferating vertebrate cells unhook ICLs. We emphasize fundamentally new unhooking strategies, dramatic progress in the structural analysis of the Fanconi anemia pathway, and insights into how cells govern the choice between different ICL repair pathways. Throughout, we highlight the many gaps that remain in our knowledge of these fascinating DNA repair pathways.
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Affiliation(s)
- Daniel R Semlow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Current affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Zhou T, Hirayama Y, Tsunematsu Y, Suzuki N, Tanaka S, Uchiyama N, Goda Y, Yoshikawa Y, Iwashita Y, Sato M, Miyoshi N, Mutoh M, Ishikawa H, Sugimura H, Wakabayashi K, Watanabe K. Isolation of New Colibactin Metabolites from Wild-Type Escherichia coli and In Situ Trapping of a Mature Colibactin Derivative. J Am Chem Soc 2021; 143:5526-5533. [PMID: 33787233 DOI: 10.1021/jacs.1c01495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Colibactin is a polyketide-nonribosomal peptide hybrid secondary metabolite that can form interstrand cross-links in double-stranded DNA. Colibactin-producing Escherichia coli has also been linked to colorectal oncogenesis. Thus, there is a strong interest in understanding the role colibactin may play in oncogenesis. Here, using the high-colibactin-producing wild-type E. coli strain we isolated from a clinical sample with the activity-based fluorescent probe we developed earlier, we were able to identify colibactin 770, which was recently identified and proposed as the complete form of colibactin, along with colibactin 788, 406, 416, 420, and 430 derived from colibactin 770 through structural rearrangements and solvolysis. Furthermore, we were able to trap the degrading mature colibactin species by converting the diketone moiety into quinoxaline in situ in the crude culture extract to form colibactin 860 at milligram scale. This allowed us to determine the stereochemically complex structure of the rearranged form of an intact colibactin, colibactin 788, in detail. Furthermore, our study suggested that we were capturing only a few percent of the actual colibactin produced by the microbe, providing a crude quantitative insight into the inherent instability of this compound. Through the structural assignment of colibactins and their degradative products by the combination of LC-HRMS and NMR spectroscopies, we were able to elucidate further the fate of inherently unstable colibactin, which could help acquire a more complete picture of colibactin metabolism and identify key DNA adducts and biomarkers for diagnosing colorectal cancer.
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Affiliation(s)
- Tao Zhou
- Adenoprevent Co., Ltd., Shizuoka 422-8526, Japan
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yuichiro Hirayama
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Nanami Suzuki
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Seiji Tanaka
- National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Nahoko Uchiyama
- National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Yukihiro Goda
- National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Yuko Yoshikawa
- School of Veterinary Medicine, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo 180-8602, Japan
| | - Yuji Iwashita
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Noriyuki Miyoshi
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Michihiro Mutoh
- Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hideki Ishikawa
- Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Keiji Wakabayashi
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- Adenoprevent Co., Ltd., Shizuoka 422-8526, Japan
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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237
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Brennan CA, Nakatsu G, Gallini Comeau CA, Drew DA, Glickman JN, Schoen RE, Chan AT, Garrett WS. Aspirin Modulation of the Colorectal Cancer-Associated Microbe Fusobacterium nucleatum. mBio 2021; 12:e00547-21. [PMID: 33824205 PMCID: PMC8092249 DOI: 10.1128/mbio.00547-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Aspirin is a chemopreventive agent for colorectal adenoma and cancer (CRC) that, like many drugs inclusive of chemotherapeutics, has been investigated for its effects on bacterial growth and virulence gene expression. Given the evolving recognition of the roles for bacteria in CRC, in this work, we investigate the effects of aspirin with a focus on one oncomicrobe-Fusobacterium nucleatum We show that aspirin and its primary metabolite salicylic acid alter F. nucleatum strain Fn7-1 growth in culture and that aspirin can effectively kill both actively growing and stationary Fn7-1. We also demonstrate that, at levels that do not inhibit growth, aspirin influences Fn7-1 gene expression. To assess whether aspirin modulation of F. nucleatum may be relevant in vivo, we use the ApcMin/+ mouse intestinal tumor model in which Fn7-1 is orally inoculated daily to reveal that aspirin-supplemented chow is sufficient to inhibit F. nucleatum-potentiated colonic tumorigenesis. We expand our characterization of aspirin sensitivity across other F. nucleatum strains, including those isolated from human CRC tissues, as well as other CRC-associated microbes, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli Finally, we determine that individuals who use aspirin daily have lower fusobacterial abundance in colon adenoma tissues, as determined by quantitative PCR performed on adenoma DNA. Together, our data support that aspirin has direct antibiotic activity against F. nucleatum strains and suggest that consideration of the potential effects of aspirin on the microbiome holds promise in optimizing risk-benefit assessments for use of aspirin in CRC prevention and management.IMPORTANCE There is an increasing understanding of the clinical correlations and potential mechanistic roles of specific members of the gut and tumoral microbiota in colorectal cancer (CRC) initiation, progression, and survival. However, we have yet to parlay this knowledge into better CRC outcomes through microbially informed diagnostic, preventive, or therapeutic approaches. Here, we demonstrate that aspirin, an established CRC chemopreventive, exhibits specific effects on the CRC-associated Fusobacterium nucleatum in culture, an animal model of intestinal tumorigenesis, and in human colonic adenoma tissues. Our work proposes a potential role for aspirin in influencing CRC-associated bacteria to prevent colorectal adenomas and cancer, beyond aspirin's canonical anti-inflammatory role targeting host tissues. Future research, such as studies investigating the effects of aspirin on fusobacterial load in patients, will help further elucidate the prospect of using aspirin to modulate F. nucleatumin vivo for improving CRC outcomes.
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Affiliation(s)
- Caitlin A Brennan
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T. H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
| | - Geicho Nakatsu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T. H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
| | - Carey Ann Gallini Comeau
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan N Glickman
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Robert E Schoen
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Andrew T Chan
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T. H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T. H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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238
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Murray KJ, Carlson ES, Stornetta A, Balskus EP, Villalta PW, Balbo S. Extension of Diagnostic Fragmentation Filtering for Automated Discovery in DNA Adductomics. Anal Chem 2021; 93:5754-5762. [PMID: 33797876 DOI: 10.1021/acs.analchem.0c04895] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Development of high-resolution/accurate mass liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) methodology enables the characterization of covalently modified DNA induced by interaction with genotoxic agents in complex biological samples. Constant neutral loss monitoring of 2'-deoxyribose or the nucleobases using data-dependent acquisition represents a powerful approach for the unbiased detection of DNA modifications (adducts). The lack of available bioinformatics tools necessitates manual processing of acquired spectral data and hampers high throughput application of these techniques. To address this limitation, we present an automated workflow for the detection and curation of putative DNA adducts by using diagnostic fragmentation filtering of LC-MS/MS experiments within the open-source software MZmine. The workflow utilizes a new feature detection algorithm, DFBuilder, which employs diagnostic fragmentation filtering using a user-defined list of fragmentation patterns to reproducibly generate feature lists for precursor ions of interest. The DFBuilder feature detection approach readily fits into a complete small-molecule discovery workflow and drastically reduces the processing time associated with analyzing DNA adductomics results. We validate our workflow using a mixture of authentic DNA adduct standards and demonstrate the effectiveness of our approach by reproducing and expanding the results of a previously published study of colibactin-induced DNA adducts. The reported workflow serves as a technique to assess the diagnostic potential of novel fragmentation pattern combinations for the unbiased detection of chemical classes of interest.
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Affiliation(s)
- Kevin J Murray
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, Minnesota 55455, United States
| | - Erik S Carlson
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Alessia Stornetta
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, Minnesota 55455, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, Minnesota 55455, United States.,Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, United States
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239
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Wang M, Ateia M, Awfa D, Yoshimura C. Regrowth of bacteria after light-based disinfection - What we know and where we go from here. CHEMOSPHERE 2021; 268:128850. [PMID: 33187648 DOI: 10.1016/j.chemosphere.2020.128850] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
Regrowth of bacteria after water/wastewater disinfection is a serious risk to public health, particularly when such pathogens carry antibiotic resistance genes. Despite increasing interest in light-based disinfection using ultraviolet or solar radiation, the mechanism of bacterial regrowth and their concentration upon light exposure (i.e., during storage, or after discharge into rivers or lakes) remain poorly understood. Therefore, we present a focused critical review to 1) elucidate regrowth mechanisms, 2) summarize the pros and cons of available experimental designs and detection techniques for regrowth evaluation, and 3) provide an outlook of key research directions for further investigations of post-disinfection bacterial regrowth. Bacterial regrowth can occur through reactivation from a viable but non-culturable state, repair of photo-induced DNA damage, and reproduction of bacteria surviving disinfection. Many studies have underestimated the degree of actual regrowth because of the use of simple experimental designs and plate count methods, which cannot quantify actual abundance of viable bacteria. Further research should investigate the effects of various factors on bacterial regrowth in realistic conditions in regrowth tests and adopt multiplex detection methods that combine culture-based and culture-independent approaches. An accurate understanding of the mechanisms involved in bacterial regrowth following disinfection is critical for safeguarding public health and aquatic environments.
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Affiliation(s)
- Manna Wang
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan
| | - Mohamed Ateia
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
| | - Dion Awfa
- Water and Wastewater Engineering Research Group, Faculty of Civil and Environmental Engineering, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia
| | - Chihiro Yoshimura
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan
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240
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Díaz-Gay M, Alexandrov LB. Unraveling the genomic landscape of colorectal cancer through mutational signatures. Adv Cancer Res 2021; 151:385-424. [PMID: 34148618 DOI: 10.1016/bs.acr.2021.03.003] [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] [Indexed: 12/14/2022]
Abstract
Colorectal cancer, along with most other cancer types, is driven by somatic mutations. Characteristic patterns of somatic mutations, known as mutational signatures, arise as a result of the activities of different mutational processes. Mutational signatures have diverse origins, including exogenous and endogenous sources. In the case of colorectal cancer, the analysis of mutational signatures has elucidated specific signatures for classically associated DNA repair deficiencies, namely mismatch repair (leading to microsatellite instability), base excision repair (due to MUTYH or NTHL1 mutations), and polymerase proofreading (due to POLE and POLD1 exonuclease domain mutations). Additional signatures also play a role in colorectal cancer, including those related to normal aging and those associated with gut microbiota, as well as a number of signatures with unknown etiologies. This chapter provides an overview of the current knowledge of mutational signatures, with a focus on colorectal cancer and on the recently reported signatures in physiologically normal and inflammatory bowel disease-affected somatic colon tissues.
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Affiliation(s)
- Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, United States; Department of Bioengineering, UC San Diego, La Jolla, CA, United States; Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, United States; Department of Bioengineering, UC San Diego, La Jolla, CA, United States; Moores Cancer Center, UC San Diego, La Jolla, CA, United States.
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241
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Abstract
The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses.
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Affiliation(s)
- Emilee E Shine
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Current affiliation: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jason M Crawford
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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242
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Abstract
Microbial roles in cancer formation, diagnosis, prognosis, and treatment have been disputed for centuries. Recent studies have provocatively claimed that bacteria, viruses, and/or fungi are pervasive among cancers, key actors in cancer immunotherapy, and engineerable to treat metastases. Despite these findings, the number of microbes known to directly cause carcinogenesis remains small. Critically evaluating and building frameworks for such evidence in light of modern cancer biology is an important task. In this Review, we delineate between causal and complicit roles of microbes in cancer and trace common themes of their influence through the host's immune system, herein defined as the immuno-oncology-microbiome axis. We further review evidence for intratumoral microbes and approaches that manipulate the host's gut or tumor microbiome while projecting the next phase of experimental discovery.
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Affiliation(s)
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Institut National de la Santé et de la Recherche Medicale (INSERM) U1015, Villejuif, France
- Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jeff Hasty
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA
- Molecular Biology Section, Division of Biological Science, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
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243
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Rozelle AL, Cheun Y, Vilas CK, Koag MC, Lee S. DNA interstrand cross-links induced by the major oxidative adenine lesion 7,8-dihydro-8-oxoadenine. Nat Commun 2021; 12:1897. [PMID: 33772030 PMCID: PMC7997976 DOI: 10.1038/s41467-021-22273-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/11/2021] [Indexed: 12/21/2022] Open
Abstract
Oxidative damage to DNA generates 7,8-dihydro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as two major lesions. Despite the comparable prevalence of these lesions, the biological effects of oxoA remain poorly characterized. Here we report the discovery of a class of DNA interstrand cross-links (ICLs) involving oxidized nucleobases. Under oxidative conditions, oxoA, but not oxoG, readily reacts with an opposite base to produce ICLs, highlighting a latent alkylating nature of oxoA. Reactive halogen species, one-electron oxidants, and the myeloperoxidase/H2O2/Cl− system induce oxoA ICLs, suggesting that oxoA-mediated cross-links may arise endogenously. Nucleobase analog studies suggest C2-oxoA is covalently linked to N2-guanine and N3-adenine for the oxoA-G and oxoA-A ICLs, respectively. The oxoA ICLs presumably form via the oxidative activation of oxoA followed by the nucleophilic attack by an opposite base. Our findings provide insights into oxoA-mediated mutagenesis and contribute towards investigations of oxidative stress-induced ICLs and oxoA-based latent alkylating agents. 7,8-dihydro-8-oxoguanine and 7,8-dihydro-8-oxoadenine (oxoA) are generated upon oxidative damage to DNA, but the biological effects of oxoA are not well known. Here, the authors report that only oxoA forms DNA interstrand crosslinks (ICLs) upon secondary oxidation and that these ICLs can be induced by reactive halogen species, one-electron oxidants and the myeloperoxidase/H2O2/Cl- system.
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Affiliation(s)
- Aaron L Rozelle
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.,McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Young Cheun
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Caroline K Vilas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Myong-Chul Koag
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Seongmin Lee
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.
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244
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Li Y, Hecht SS. Identification of an N'-Nitrosonornicotine-Specific Deoxyadenosine Adduct in Rat Liver and Lung DNA. Chem Res Toxicol 2021; 34:992-1003. [PMID: 33705110 DOI: 10.1021/acs.chemrestox.1c00013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tobacco-specific nitrosamines N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) are considered to be two of the most important carcinogens in unburned tobacco and its smoke. They readily cause tumors in laboratory animals and are classified as "carcinogenic to humans" by the International Agency for Research on Cancer. DNA adduct formation by these two carcinogens is believed to play a critical role in tobacco carcinogenesis. Among all the DNA adducts formed by NNN and NNK, 2'-deoxyadenosine (dAdo)-derived adducts have not been fully characterized. In the study reported here, we characterized the formation of N6-[4-(3-pyridyl)-4-oxo-1-butyl]-2'-deoxyadenosine (N6-POB-dAdo) and its reduced form N6-PHB-dAdo formed by NNN 2'-hydroxylation in rat liver and lung DNA. More importantly, we characterized a new dAdo adduct N6-[4-hydroxy-1-(pyridine-3-yl)butyl]-2'-deoxyadenosine (N6-HPB-dAdo) formed after NaBH3CN or NaBH4 reduction both in vitro in calf thymus DNA reacted with 5'-acetoxy-N'-nitrosonornicotine and in vivo in rat liver and lung upon treatment with NNN. This adduct was specifically formed by NNN 5'-hydroxylation. Chemical standards of N6-HPB-dAdo and the corresponding isotopically labeled internal standard [pyridine-d4]N6-HPB-dAdo were synthesized using a four-step method. Both NMR and high-resolution mass spectrometry data agreed well with the proposed structure of N6-HPB-dAdo. The new adduct coeluted with the synthesized internal standard under various LC conditions. Its product ion patterns of MS2 and MS3 transitions were also consistent with the proposed fragmentation patterns. Chromatographic resolution of the two diastereomers of N6-HPB-dAdo was successfully achieved. Quantitation suggested a dose-dependent response of the levels of this new adduct in the liver and lung of rats treated with NNN. However, its level was lower than that of 2-[2-(3-pyridyl)-N-pyrrolidinyl]-2'-deoxyinosine, a previously reported dGuo adduct that is also formed from NNN 5'-hydroxylation. The identification of N6-HPB-dAdo in this study leads to new insights pertinent to the mechanism of carcinogenesis by NNN and to the development of biomarkers of NNN metabolic activation.
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Affiliation(s)
- Yupeng Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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245
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The CDT of Helicobacter hepaticus induces pro-survival autophagy and nucleoplasmic reticulum formation concentrating the RNA binding proteins UNR/CSDE1 and P62/SQSTM1. PLoS Pathog 2021; 17:e1009320. [PMID: 33662035 PMCID: PMC7963068 DOI: 10.1371/journal.ppat.1009320] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/16/2021] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Humans are frequently exposed to bacterial genotoxins of the gut microbiota, such as colibactin and cytolethal distending toxin (CDT). In the present study, whole genome microarray-based identification of differentially expressed genes was performed in vitro on HT29 intestinal cells while following the ectopic expression of the active CdtB subunit of Helicobacter hepaticus CDT. Microarray data showed a CdtB-dependent upregulation of transcripts involved in positive regulation of autophagy concomitant with the downregulation of transcripts involved in negative regulation of autophagy. CdtB promotes the activation of autophagy in intestinal and hepatic cell lines. Experiments with cells lacking autophagy related genes, ATG5 and ATG7 infected with CDT- and colibactin-producing bacteria revealed that autophagy protects cells against the genotoxin-induced apoptotic cell death. Autophagy induction could also be associated with nucleoplasmic reticulum (NR) formation following DNA damage induced by these bacterial genotoxins. In addition, both genotoxins promote the accumulation of the autophagic receptor P62/SQSTM1 aggregates, which colocalized with foci concentrating the RNA binding protein UNR/CSDE1. Some of these aggregates were deeply invaginated in NR in distended nuclei together or in the vicinity of UNR-rich foci. Interestingly, micronuclei-like structures and some vesicles containing chromatin and γH2AX foci were found surrounded with P62/SQSTM1 and/or the autophagosome marker LC3. This study suggests that autophagy and P62/SQSTM1 regulate the abundance of micronuclei-like structures and are involved in cell survival following the DNA damage induced by CDT and colibactin. Similar effects were observed in response to DNA damaging chemotherapeutic agents, offering new insights into the context of resistance of cancer cells to therapies inducing DNA damage.
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246
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Miller AL, Bessho S, Grando K, Tükel Ç. Microbiome or Infections: Amyloid-Containing Biofilms as a Trigger for Complex Human Diseases. Front Immunol 2021; 12:638867. [PMID: 33717189 PMCID: PMC7952436 DOI: 10.3389/fimmu.2021.638867] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
The human microbiota is the community of microorganisms that live upon or within their human host. The microbiota consists of various microorganisms including bacteria, fungi, viruses, and archaea; the gut microbiota is comprised mostly of bacteria. Many bacterial species within the gut microbiome grow as biofilms, which are multicellular communities embedded in an extracellular matrix. Studies have shown that the relative abundances of bacterial species, and therefore biofilms and bacterial byproducts, change during progression of a variety of human diseases including gastrointestinal, autoimmune, neurodegenerative, and cancer. Studies have shown the location and proximity of the biofilms within the gastrointestinal tract might impact disease outcome. Gram-negative enteric bacteria secrete the amyloid curli, which makes up as much as 85% of the extracellular matrix of enteric biofilms. Curli mediates cell-cell attachment and attachment to various surfaces including extracellular matrix components such as fibronectin and laminin. Structurally, curli is strikingly similar to pathological and immunomodulatory human amyloids such as amyloid-β, which has been implicated in Alzheimer's disease, α-synuclein, which is involved in Parkinson's disease, and serum amyloid A, which is secreted during the acute phase of inflammation. The immune system recognizes both bacterial amyloid curli and human amyloids utilizing the same receptors, so curli also induces inflammation. Moreover, recent work indicates that curli can participate in the self-assembly process of pathological human amyloids. Curli is found within biofilms of commensal enteric bacteria as well as invasive pathogens; therefore, evidence suggests that curli contributes to complex human diseases. In this review, we summarize the recent findings on how bacterial biofilms containing curli participate in the pathological and immunological processes in gastrointestinal diseases, systemic autoimmune diseases, and neurodegenerative diseases.
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Affiliation(s)
- Amanda L Miller
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Shingo Bessho
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Kaitlyn Grando
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Çagla Tükel
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
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247
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Jain T, Sharma P, Are AC, Vickers SM, Dudeja V. New Insights Into the Cancer-Microbiome-Immune Axis: Decrypting a Decade of Discoveries. Front Immunol 2021; 12:622064. [PMID: 33708214 PMCID: PMC7940198 DOI: 10.3389/fimmu.2021.622064] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
The past decade has witnessed groundbreaking advances in the field of microbiome research. An area where immense implications of the microbiome have been demonstrated is tumor biology. The microbiome affects tumor initiation and progression through direct effects on the tumor cells and indirectly through manipulation of the immune system. It can also determine response to cancer therapies and predict disease progression and survival. Modulation of the microbiome can be harnessed to potentiate the efficacy of immunotherapies and decrease their toxicity. In this review, we comprehensively dissect recent evidence regarding the interaction of the microbiome and anti-tumor immune machinery and outline the critical questions which need to be addressed as we further explore this dynamic colloquy.
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Affiliation(s)
| | | | | | - Selwyn M. Vickers
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Vikas Dudeja
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
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248
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Two Polyketides Intertwined in Complex Regulation: Posttranscriptional CsrA-Mediated Control of Colibactin and Yersiniabactin Synthesis in Escherichia coli. mBio 2021; 13:e0381421. [PMID: 35100864 PMCID: PMC8805033 DOI: 10.1128/mbio.03814-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Bacteria have to process several levels of gene regulation and coordination of interconnected regulatory networks to ensure the most adequate cellular response to specific growth conditions. Especially, expression of complex and costly fitness and pathogenicity-associated traits is coordinated and tightly regulated at multiple levels. We studied the interconnected regulation of the expression of the colibactin and yersiniabactin polyketide biosynthesis machineries, which are encoded by two pathogenicity islands found in many phylogroup B2 Escherichia coli isolates. Comparative phenotypic and genotypic analyses identified the BarA-UvrY two-component system as an important regulatory element involved in colibactin and yersiniabactin expression. The carbon storage regulator (Csr) system controls the expression of a wide range of central metabolic and virulence-associated traits. The availability of CsrA, the key translational regulator of the Csr system, depends on BarA-UvrY activity. We employed reporter gene fusions to demonstrate UvrY- and CsrA-dependent expression of the colibactin and yersiniabactin determinants and confirmed a direct interaction of CsrA with the 5' untranslated leader transcripts of representative genes of the colibactin and yersiniabactin operons by RNA electrophoretic mobility shift assays. This posttranscriptional regulation adds an additional level of complexity to control mechanisms of polyketide expression, which is also orchestrated at the level of ferric uptake regulator (Fur)-dependent regulation of transcription and phosphopantetheinyl transferase-dependent activation of polyketide biosynthesis. Our results emphasize the interconnection of iron- and primary metabolism-responsive regulation of colibactin and yersiniabactin expression by the fine-tuned action of different regulatory mechanisms in response to variable environmental signals as a prerequisite for bacterial adaptability, fitness, and pathogenicity in different habitats. IMPORTANCE Secondary metabolite expression is a widespread strategy among bacteria to improve their fitness in habitats where they constantly compete for resources with other bacteria. The production of secondary metabolites is associated with a metabolic and energetic burden. Colibactin and yersiniabactin are two polyketides, which are expressed in concert and promote the virulence of different enterobacterial pathogens. To maximize fitness, they should be expressed only in microenvironments in which they are required. Accordingly, precise regulation of colibactin and yersiniabactin expression is crucial. We show that the expression of these two polyketides is also interconnected via primary metabolism-responsive regulation at the posttranscriptional level by the CsrA RNA-binding protein. Our findings may help to optimize (over-)expression and further functional characterization of the polyketide colibactin. Additionally, this new aspect of concerted colibactin and yersiniabactin expression extends our knowledge of conditions that favor the expression of these virulence- and fitness-associated factors in different Enterobacterales members.
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249
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Iftekhar A, Berger H, Bouznad N, Heuberger J, Boccellato F, Dobrindt U, Hermeking H, Sigal M, Meyer TF. Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells. Nat Commun 2021; 12:1003. [PMID: 33579932 PMCID: PMC7881031 DOI: 10.1038/s41467-021-21162-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/13/2021] [Indexed: 02/07/2023] Open
Abstract
Genotoxic colibactin-producing pks+ Escherichia coli induce DNA double-strand breaks, mutations, and promote tumor development in mouse models of colorectal cancer (CRC). Colibactin's distinct mutational signature is reflected in human CRC, suggesting a causal link. Here, we investigate its transformation potential using organoids from primary murine colon epithelial cells. Organoids recovered from short-term infection with pks+ E. coli show characteristics of CRC cells, e.g., enhanced proliferation, Wnt-independence, and impaired differentiation. Sequence analysis of Wnt-independent organoids reveals an enhanced mutational burden, including chromosomal aberrations typical of genomic instability. Although we do not find classic Wnt-signaling mutations, we identify several mutations in genes related to p53-signaling, including miR-34a. Knockout of Trp53 or miR-34 in organoids results in Wnt-independence, corroborating a functional interplay between the p53 and Wnt pathways. We propose larger chromosomal alterations and aneuploidy as the basis of transformation in these organoids, consistent with the early appearance of chromosomal instability in CRC.
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Affiliation(s)
- Amina Iftekhar
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Hilmar Berger
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel and University Hospital Schleswig Holstein - Campus Kiel, Kiel, Germany.,Department of Internal Medicine, Gastroenterology and Hepatology, Charité University Medicine, Berlin, Germany
| | - Nassim Bouznad
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig Maximilians University, München, Germany
| | - Julian Heuberger
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Department of Internal Medicine, Gastroenterology and Hepatology, Charité University Medicine, Berlin, Germany
| | - Francesco Boccellato
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Heiko Hermeking
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig Maximilians University, München, Germany.,German Cancer Consortium (DKTK), Partner Site München, München, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Sigal
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany. .,Department of Internal Medicine, Gastroenterology and Hepatology, Charité University Medicine, Berlin, Germany. .,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany. .,Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel and University Hospital Schleswig Holstein - Campus Kiel, Kiel, Germany.
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250
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Chagneau CV, Massip C, Bossuet-Greif N, Fremez C, Motta JP, Shima A, Besson C, Le Faouder P, Cénac N, Roth MP, Coppin H, Fontanié M, Martin P, Nougayrède JP, Oswald E. Uropathogenic E. coli induces DNA damage in the bladder. PLoS Pathog 2021; 17:e1009310. [PMID: 33630958 PMCID: PMC7906301 DOI: 10.1371/journal.ppat.1009310] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/13/2021] [Indexed: 01/19/2023] Open
Abstract
Urinary tract infections (UTIs) are among the most common outpatient infections, with a lifetime incidence of around 60% in women. We analysed urine samples from 223 patients with community-acquired UTIs and report the presence of the cleavage product released during the synthesis of colibactin, a bacterial genotoxin, in 55 of the samples examined. Uropathogenic Escherichia coli strains isolated from these patients, as well as the archetypal E. coli strain UTI89, were found to produce colibactin. In a murine model of UTI, the machinery producing colibactin was expressed during the early hours of the infection, when intracellular bacterial communities form. We observed extensive DNA damage both in umbrella and bladder progenitor cells. To the best of our knowledge this is the first report of colibactin production in UTIs in humans and its genotoxicity in bladder cells.
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Affiliation(s)
| | - Clémence Massip
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | | | | | - Jean-Paul Motta
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Ayaka Shima
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Céline Besson
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | | | - Nicolas Cénac
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Marie-Paule Roth
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Hélène Coppin
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | | | - Patricia Martin
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- VibioSphen, Prologue Biotech, Labège, France
| | | | - Eric Oswald
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
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