1
|
Schneider KM, Kummen M, Trivedi PJ, Hov JR. Role of microbiome in autoimmune liver diseases. Hepatology 2024; 80:965-987. [PMID: 37369002 PMCID: PMC11407779 DOI: 10.1097/hep.0000000000000506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/25/2023] [Indexed: 06/29/2023]
Abstract
The microbiome plays a crucial role in integrating environmental influences into host physiology, potentially linking it to autoimmune liver diseases, such as autoimmune hepatitis, primary biliary cholangitis, and primary sclerosing cholangitis. All autoimmune liver diseases are associated with reduced diversity of the gut microbiome and altered abundance of certain bacteria. However, the relationship between the microbiome and liver diseases is bidirectional and varies over the course of the disease. This makes it challenging to dissect whether such changes in the microbiome are initiating or driving factors in autoimmune liver diseases, secondary consequences of disease and/or pharmacological intervention, or alterations that modify the clinical course that patients experience. Potential mechanisms include the presence of pathobionts, disease-modifying microbial metabolites, and more nonspecific reduced gut barrier function, and it is highly likely that the effect of these change during the progression of the disease. Recurrent disease after liver transplantation is a major clinical challenge and a common denominator in these conditions, which could also represent a window to disease mechanisms of the gut-liver axis. Herein, we propose future research priorities, which should involve clinical trials, extensive molecular phenotyping at high resolution, and experimental studies in model systems. Overall, autoimmune liver diseases are characterized by an altered microbiome, and interventions targeting these changes hold promise for improving clinical care based on the emerging field of microbiota medicine.
Collapse
Affiliation(s)
| | - Martin Kummen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Palak J Trivedi
- National Institute for Health and Care Research Birmingham Biomedical Research Centre, Centre for Liver and Gastroenterology Research, University of Birmingham, UK
- Liver Unit, University Hospitals Birmingham Queen Elizabeth, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, UK
- Institute of Applied Health Research, University of Birmingham, UK
| | - Johannes R Hov
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| |
Collapse
|
2
|
Shi Z, Li Z, Zhang M. Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies. J Transl Med 2024; 22:837. [PMID: 39261861 PMCID: PMC11391643 DOI: 10.1186/s12967-024-05640-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024] Open
Abstract
The intricate interplay between the host and its microbiota has garnered increasing attention in the past decade. Specifically, the emerging recognition of microorganisms within diverse cancer tissues, previously presumed sterile, has ignited a resurgence of enthusiasm and research endeavors. Four potential migratory routes have been identified as the sources of intratumoral microbial "dark matter," including direct invasion of mucosal barriers, spreading from normal adjacent tissue, hematogenous spread, and lymphatic drainage, which contribute to the highly heterogeneous features of intratumor microbiota. Importantly, multitudes of studies delineated the roles of intratumor microbiota in cancer initiation and progression, elucidating underlying mechanisms such as genetic alterations, epigenetic modifications, immune dysfunctions, activating oncogenic pathways, and inducing metastasis. With the deepening understanding of intratumoral microbial composition, novel microbiota-based strategies for early cancer diagnosis and prognostic stratification continue to emerge. Furthermore, intratumor microbiota exerts significant influence on the efficacy of cancer therapeutics, particularly immunotherapy, making it an enticing target for intervention in cancer treatment. In this review, we present a comprehensive discussion of the current understanding pertaining to the developmental history, heterogeneous profiles, underlying originations, and carcinogenic mechanisms of intratumor microbiota, and uncover its potential predictive and intervention values, as well as several inevitable challenges as a target for personalized cancer management strategies.
Collapse
Affiliation(s)
- Zhuangzhuang Shi
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, 450000, China
| | - Zhaoming Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, 450000, China.
| | - Mingzhi Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, 450000, China.
| |
Collapse
|
3
|
Xiao Q, Chen WJ, Wu F, Zhang XY, Li X, Wei J, Chen TT, Liu ZX. Individuality and generality of intratumoral microbiome in the three most prevalent gynecological malignancies: an observational study. Microbiol Spectr 2024; 12:e0100424. [PMID: 39101825 PMCID: PMC11370256 DOI: 10.1128/spectrum.01004-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/22/2024] [Indexed: 08/06/2024] Open
Abstract
Growing evidence have indicated the crucial role of intratumor microbiome in a variety of solid tumor. However, the intratumoral microbiome in gynecological malignancies is largely unknown. In the present study, a total of 90 Han patients, including 30 patients with cancer in cervix, ovary, and endometrium each were enrolled, the composition of intratumoral microbiome was assessed by 16S rDNA amplicon high throughput sequencing. We found that the diversity and metabolic potential of intratumoral microbiome in all three cancer types were very similar. Furthermore, all three cancer types shared a few taxa that collectively take up high relative abundance and positive rate, including Pseudomonas sp., Comamonadaceae gen. sp., Bradyrhizobium sp., Saccharomonospora sp., Cutibacterium acnes, Rubrobacter sp., Dialister micraerophilus, and Escherichia coli. Additionally, Haemophilus parainfluenzae and Paracoccus sp. in cervical cancer, Pelomonas sp. in ovarian cancer, and Enterococcus faecalis in endometrial cancer were identified by LDA to be a representative bacterial strain. In addition, in cervical cancer patients, alpha-fetoprotein (AFP) (correlation coefficient = -0.3714) was negatively correlated (r = 0.4, 95% CI: 0.03 to 0.7) with Rubrobacter sp. and CA199 (correlation coefficient = 0.3955) was positively associated (r = 0.4, 95% CI: 0.03 to 0.7) with Saccharomonospora sp.. In ovarian cancer patients, CA125 (correlation coefficient = -0.4451) was negatively correlated (r = -0.4, 95% CI: -0.7 to -0.09) with Porphyromonas sp.. In endometrial cancer patients, CEA (correlation coefficient = -0.3868) was negatively correlated (r = -0.4, 95% CI: -0.7 to -0.02) with Cutibacterium acnes. This study promoted our understanding of the intratumoral microbiome in gynecological malignancies.IMPORTANCEIn this study, we found the compositional spectrum of tumor microbes among gynecological malignancies were largely similar by sharing a few taxa and differentiated by substantial species owned uniquely. Certain species, mostly unreported, were identified to be associated with clinical characteristics. This study prompted our understanding of gynecological malignancies and offered evidence for tumor microbes affecting tumor biology among cancers in the female reproductive system.
Collapse
Affiliation(s)
- Qin Xiao
- Departments of Reproductive Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Wen-jie Chen
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, China
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institution of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Fei Wu
- Departments of Reproductive Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xin-yi Zhang
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xia Li
- Department of Assisted Reproduction, Maternity and Child Health Hospital of Jiujiang, Jiujiang, Jiangxi, China
| | - Jing Wei
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institution of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Ting-tao Chen
- Departments of Reproductive Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institution of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zhao-xia Liu
- Departments of Reproductive Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| |
Collapse
|
4
|
Li M, Liu N, Zhu J, Wu Y, Niu L, Liu Y, Chen L, Bai B, Miao Y, Yang Y, Chen Q. Engineered probiotics with sustained release of interleukin-2 for the treatment of inflammatory bowel disease after oral delivery. Biomaterials 2024; 309:122584. [PMID: 38735180 DOI: 10.1016/j.biomaterials.2024.122584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
Inflammatory bowel disease (IBD) is a kind of auto-immune disease characterized by disrupted intestinal barrier and mucosal epithelium, imbalanced gut microbiome and deregulated immune responses. Therefore, the restoration of immune equilibrium and gut microbiota could potentially serve as a hopeful approach for treating IBD. Herein, the oral probiotic Escherichia coli Nissle 1917 (ECN) was genetically engineered to express secretable interleukin-2 (IL-2), a kind of immunomodulatory agent, for the treatment of IBD. In our design, probiotic itself has the ability to regulate the gut microenvironment and IL-2 at low dose could selectively promote the generation of regulatory T cells to elicit tolerogenic immune responses. To improve the bioavailability of ECN expressing IL-2 (ECN-IL2) in the gastrointestinal tract, enteric coating Eudragit L100-55 was used to coat ECN-IL2, achieving significantly enhanced accumulation of engineered probiotics in the intestine. More importantly, L100-55 coated ECN-IL2 could effectively activated Treg cells to regulate innate immune responses and gut microbiota, thereby relieve inflammation and repair the colon epithelial barrier in dextran sodium sulfate (DSS) induced IBD. Therefore, genetically and chemically modified probiotics with excellent biocompatibility and efficiency in regulating intestinal microflora and intestinal inflammation show great potential for IBD treatment in the future.
Collapse
Affiliation(s)
- Maoyi Li
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Nanhui Liu
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Jiafei Zhu
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Yumin Wu
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Le Niu
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Yi Liu
- Department of Thoracic Surgery Shanghai Pulmonary Hospital School of Medicine Tong ji University, Shanghai, 200433, China
| | - Linfu Chen
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Boxiong Bai
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Yu Miao
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Yang Yang
- Department of Thoracic Surgery Shanghai Pulmonary Hospital School of Medicine Tong ji University, Shanghai, 200433, China
| | - Qian Chen
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China.
| |
Collapse
|
5
|
Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. Repair of genomic interstrand crosslinks. DNA Repair (Amst) 2024; 141:103739. [PMID: 39106540 PMCID: PMC11423799 DOI: 10.1016/j.dnarep.2024.103739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/11/2024] [Accepted: 07/25/2024] [Indexed: 08/09/2024]
Abstract
Genomic interstrand crosslinks (ICLs) are formed by reactive species generated during normal cellular metabolism, produced by the microbiome, and employed in cancer chemotherapy. While there are multiple options for replication dependent and independent ICL repair, the crucial step for each is unhooking one DNA strand from the other. Much of our insight into mechanisms of unhooking comes from powerful model systems based on plasmids with defined ICLs introduced into cells or cell free extracts. Here we describe the properties of exogenous and endogenous ICL forming compounds and provide an historical perspective on early work on ICL repair. We discuss the modes of unhooking elucidated in the model systems, the concordance or lack thereof in drug resistant tumors, and the evolving view of DNA adducts, including ICLs, formed by metabolic aldehydes.
Collapse
Affiliation(s)
- Marina A Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Althaf Shaik
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ishani Majumdar
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Chen Ling
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| |
Collapse
|
6
|
Lutsiv T, Hussan H, Thompson HJ. Ecosystemic Approach to Understanding Gut Microbiome-Mediated Prevention of Colorectal Cancer. Cancer J 2024; 30:329-344. [PMID: 39312453 DOI: 10.1097/ppo.0000000000000743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Humans and their associated microorganisms coexist in complex symbiotic relationships. Continuously advancing research is demonstrating the crucial role of host-associated microbiota in the pathophysiology and etiology of disease and in mediating the prevention thereof. As an exemplar, the gut microbiota, especially colonic bacteria, have been extensively studied in colorectal cancer (CRC), and the growing body of evidence establishes new oncomicrobes and their oncometabolites associated with the initiation and promotion of carcinogenesis. Herein, we discuss the importance of approaching the gut microbiome as an ecosystem rather than an assortment of individual factors, especially in the context of cancer prevention. Furthermore, we argue that a dietary pattern effectively drives multiple nodes of the gut microbial ecosystem toward disease- or health-promoting qualities. In the modern circumstances of excessive consumption of ultraprocessed and animal-based foods and concomitant escalation of chronic disease burden worldwide, we focus on whole food-derived dietary fiber as a key to establishing a health-promoting eubiosis in the gut.
Collapse
|
7
|
Jin DM, Morton JT, Bonneau R. Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. mSystems 2024; 9:e0029524. [PMID: 39078158 PMCID: PMC11334437 DOI: 10.1128/msystems.00295-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/08/2024] [Indexed: 07/31/2024] Open
Abstract
Microbiome studies have revealed gut microbiota's potential impact on complex diseases. However, many studies often focus on one disease per cohort. We developed a meta-analysis workflow for gut microbiome profiles and analyzed shotgun metagenomic data covering 11 diseases. Using interpretable machine learning and differential abundance analysis, our findings reinforce the generalization of binary classifiers for Crohn's disease (CD) and colorectal cancer (CRC) to hold-out cohorts and highlight the key microbes driving these classifications. We identified high microbial similarity in disease pairs like CD vs ulcerative colitis (UC), CD vs CRC, Parkinson's disease vs type 2 diabetes (T2D), and schizophrenia vs T2D. We also found strong inverse correlations in Alzheimer's disease vs CD and UC. These findings, detected by our pipeline, provide valuable insights into these diseases. IMPORTANCE Assessing disease similarity is an essential initial step preceding a disease-based approach for drug repositioning. Our study provides a modest first step in underscoring the potential of integrating microbiome insights into the disease similarity assessment. Recent microbiome research has predominantly focused on analyzing individual diseases to understand their unique characteristics, which by design excludes comorbidities in individuals. We analyzed shotgun metagenomic data from existing studies and identified previously unknown similarities between diseases. Our research represents a pioneering effort that utilizes both interpretable machine learning and differential abundance analysis to assess microbial similarity between diseases.
Collapse
Affiliation(s)
- Dong-Min Jin
- Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - James T. Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Richard Bonneau
- Center for Genomics and Systems Biology, New York University, New York, New York, USA
- Genentech, New York, New York, USA
| |
Collapse
|
8
|
Hamamah S, Lobiuc A, Covasa M. Antioxidant Role of Probiotics in Inflammation-Induced Colorectal Cancer. Int J Mol Sci 2024; 25:9026. [PMID: 39201713 PMCID: PMC11354872 DOI: 10.3390/ijms25169026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
Colorectal cancer (CRC) continues to be a significant contributor to global morbidity and mortality. Emerging evidence indicates that disturbances in gut microbial composition, the formation of reactive oxygen species (ROS), and the resulting inflammation can lead to DNA damage, driving the pathogenesis and progression of CRC. Notably, bacterial metabolites can either protect against or contribute to oxidative stress by modulating the activity of antioxidant enzymes and influencing signaling pathways that govern ROS-induced inflammation. Additionally, microbiota byproducts, when supplemented through probiotics, can affect tumor microenvironments to enhance treatment efficacy and selectively mediate the ROS-induced destruction of CRC cells. This review aims to discuss the mechanisms by which taxonomical shifts in gut microbiota and related metabolites such as short-chain fatty acids, secondary bile acids, and trimethylamine-N-oxide influence ROS concentrations to safeguard or promote the onset of inflammation-mediated CRC. Additionally, we focus on the role of probiotic species in modulating ROS-mediated signaling pathways that influence both oxidative status and inflammation, such as Nrf2-Keap1, NF-κB, and NLRP3 to mitigate carcinogenesis. Overall, a deeper understanding of the role of gut microbiota on oxidative stress may aid in delaying or preventing the onset of CRC and offer new avenues for adjunct, CRC-specific therapeutic interventions such as cancer immunotherapy.
Collapse
Affiliation(s)
- Sevag Hamamah
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA 91766, USA;
- Department of Internal Medicine, Scripps Mercy Hospital, San Diego, CA 92103, USA
| | - Andrei Lobiuc
- Department of Medicine and Biomedical Sciences, College of Medicine and Biological Science, University of Suceava, 7200229 Suceava, Romania;
| | - Mihai Covasa
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA 91766, USA;
- Department of Medicine and Biomedical Sciences, College of Medicine and Biological Science, University of Suceava, 7200229 Suceava, Romania;
| |
Collapse
|
9
|
Dudkina N, Park HB, Song D, Jain A, Khan SA, Flavell RA, Johnson CH, Palm NW, Crawford JM. Human AKR1C3 binds agonists of GPR84 and participates in an expanded polyamine pathway. Cell Chem Biol 2024:S2451-9456(24)00313-1. [PMID: 39163853 DOI: 10.1016/j.chembiol.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/15/2024] [Accepted: 07/22/2024] [Indexed: 08/22/2024]
Abstract
Altered human aldo-keto reductase family 1 member C3 (AKR1C3) expression has been associated with poor prognosis in diverse cancers, ferroptosis resistance, and metabolic diseases. Despite its clinical significance, the endogenous biochemical roles of AKR1C3 remain incompletely defined. Using untargeted metabolomics, we identified a major transformation mediated by AKR1C3, in which a spermine oxidation product "sperminal" is reduced to "sperminol." Sperminal causes DNA damage and activates the DNA double-strand break response, whereas sperminol induces autophagy in vitro. AKR1C3 also pulls down acyl-pyrones and pyrone-211 inhibits AKR1C3 activity. Through G protein-coupled receptor ligand screening, we determined that pyrone-211 is also a potent agonist of the semi-orphan receptor GPR84. Strikingly, mammalian fatty acid synthase produces acyl-pyrones in vitro, and this production is modulated by NADPH. Taken together, our studies support a regulatory role of AKR1C3 in an expanded polyamine pathway and a model linking fatty acid synthesis and NADPH levels to GPR84 signaling.
Collapse
Affiliation(s)
- Natavan Dudkina
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT 06516, USA
| | - Hyun Bong Park
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT 06516, USA; Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Deguang Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06536, USA
| | - Abhishek Jain
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06536, USA
| | - Sajid A Khan
- Department of Surgery, Division of Surgical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06536, USA; Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06536, USA
| | - Caroline H Johnson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06536, USA.
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06536, USA.
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA.
| |
Collapse
|
10
|
Lewis K, Lee RE, Brötz-Oesterhelt H, Hiller S, Rodnina MV, Schneider T, Weingarth M, Wohlgemuth I. Sophisticated natural products as antibiotics. Nature 2024; 632:39-49. [PMID: 39085542 DOI: 10.1038/s41586-024-07530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/07/2024] [Indexed: 08/02/2024]
Abstract
In this Review, we explore natural product antibiotics that do more than simply inhibit an active site of an essential enzyme. We review these compounds to provide inspiration for the design of much-needed new antibacterial agents, and examine the complex mechanisms that have evolved to effectively target bacteria, including covalent binders, inhibitors of resistance, compounds that utilize self-promoted entry, those that evade resistance, prodrugs, target corrupters, inhibitors of 'undruggable' targets, compounds that form supramolecular complexes, and selective membrane-acting agents. These are exemplified by β-lactams that bind covalently to inhibit transpeptidases and β-lactamases, siderophore chimeras that hijack import mechanisms to smuggle antibiotics into the cell, compounds that are activated by bacterial enzymes to produce reactive molecules, and antibiotics such as aminoglycosides that corrupt, rather than merely inhibit, their targets. Some of these mechanisms are highly sophisticated, such as the preformed β-strands of darobactins that target the undruggable β-barrel chaperone BamA, or teixobactin, which binds to a precursor of peptidoglycan and then forms a supramolecular structure that damages the membrane, impeding the emergence of resistance. Many of the compounds exhibit more than one notable feature, such as resistance evasion and target corruption. Understanding the surprising complexity of the best antimicrobial compounds provides a roadmap for developing novel compounds to address the antimicrobial resistance crisis by mining for new natural products and inspiring us to design similarly sophisticated antibiotics.
Collapse
Affiliation(s)
- Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Boston, MA, USA.
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Tubingen, Germany
- Controlling Microbes to Fight Infection-Cluster of Excellence, Tubingen, Germany
| | | | - Marina V Rodnina
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
| | - Markus Weingarth
- Chemistry Department, Utrecht University, Utrecht, the Netherlands
| | - Ingo Wohlgemuth
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| |
Collapse
|
11
|
Schneider E, O'Riordan KJ, Clarke G, Cryan JF. Feeding gut microbes to nourish the brain: unravelling the diet-microbiota-gut-brain axis. Nat Metab 2024; 6:1454-1478. [PMID: 39174768 DOI: 10.1038/s42255-024-01108-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 07/15/2024] [Indexed: 08/24/2024]
Abstract
The prevalence of brain disorders, including stress-related neuropsychiatric disorders and conditions with cognitive dysfunction, is rising. Poor dietary habits contribute substantially to this accelerating trend. Conversely, healthy dietary intake supports mood and cognitive performance. Recently, the communication between the microorganisms within the gastrointestinal tract and the brain along the gut-brain axis has gained prominence as a potential tractable target to modulate brain health. The composition and function of the gut microbiota is robustly influenced by dietary factors to alter gut-brain signalling. To reflect this interconnection between diet, gut microbiota and brain functioning, we propose that a diet-microbiota-gut-brain axis exists that underpins health and well-being. In this Review, we provide a comprehensive overview of the interplay between diet and gut microbiota composition and function and the implications for cognition and emotional functioning. Important diet-induced effects on the gut microbiota for the development, prevention and maintenance of neuropsychiatric disorders are described. The diet-microbiota-gut-brain axis represents an uncharted frontier for brain health diagnostics and therapeutics across the lifespan.
Collapse
Affiliation(s)
| | | | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
| |
Collapse
|
12
|
Ding G, Yang X, Li Y, Wang Y, Du Y, Wang M, Ye R, Wang J, Zhang Y, Chen Y, Zhang Y. Gut microbiota regulates gut homeostasis, mucosal immunity and influences immune-related diseases. Mol Cell Biochem 2024:10.1007/s11010-024-05077-y. [PMID: 39060829 DOI: 10.1007/s11010-024-05077-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024]
Abstract
The intestinal microbiome constitutes a sophisticated and massive ecosystem pivotal for maintaining gastrointestinal equilibrium and mucosal immunity via diverse pathways. The gut microbiota is continuously reshaped by multiple environmental factors, thereby influencing overall wellbeing or predisposing individuals to disease state. Many observations reveal an altered microbiome composition in individuals with autoimmune conditions, coupled with shifts in metabolic profiles, which has spurred ongoing development of therapeutic interventions targeting the microbiome. This review delineates the microbial consortia of the intestine, their role in sustaining gastrointestinal stability, the association between the microbiome and immune-mediated pathologies, and therapeutic modalities focused on microbiome modulation. We emphasize the entire role of the intestinal microbiome in human health and recommend microbiome modulation as a viable strategy for disease prophylaxis and management. However, the application of gut microbiota modification for the treatment of immune-related diseases, such as fecal microbiota transplantation and probiotics, remain quite challenging. Therefore, more research is needed into the role and mechanisms of these therapeutics.
Collapse
Affiliation(s)
- Guoao Ding
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
- Department of Life Science, Anhui University, Hefei, 230061, China
| | - Xuezhi Yang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Ying Li
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
| | - Ying Wang
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
| | - Yujie Du
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
| | - Meng Wang
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
| | - Ruxin Ye
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
| | - Jingjing Wang
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
| | - Yongkang Zhang
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
| | - Yajun Chen
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China
| | - Yan Zhang
- School of Biological and Food Engineering, Hefei Normal University, Hefei, 230061, China.
- Department of Life Science, Anhui University, Hefei, 230061, China.
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Medical University, Hefei, 230032, China.
| |
Collapse
|
13
|
Sandys O, Stokkers PCF, Te Velde AA. DAMP-ing IBD: Extinguish the Fire and Prevent Smoldering. Dig Dis Sci 2024:10.1007/s10620-024-08523-5. [PMID: 38963463 DOI: 10.1007/s10620-024-08523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
In inflammatory bowel diseases (IBD), the most promising therapies targeting cytokines or immune cell trafficking demonstrate around 40% efficacy. As IBD is a multifactorial inflammation of the intestinal tract, a single-target approach is unlikely to solve this problem, necessitating an alternative strategy that addresses its variability. One approach often overlooked by the pharmaceutically driven therapeutic options is to address the impact of environmental factors. This is somewhat surprising considering that IBD is increasingly viewed as a condition heavily influenced by such factors, including diet, stress, and environmental pollution-often referred to as the "Western lifestyle". In IBD, intestinal responses result from a complex interplay among the genetic background of the patient, molecules, cells, and the local inflammatory microenvironment where danger- and microbe-associated molecular patterns (D/MAMPs) provide an adjuvant-rich environment. Through activating DAMP receptors, this array of pro-inflammatory factors can stimulate, for example, the NLRP3 inflammasome-a major amplifier of the inflammatory response in IBD, and various immune cells via non-specific bystander activation of myeloid cells (e.g., macrophages) and lymphocytes (e.g., tissue-resident memory T cells). Current single-target biological treatment approaches can dampen the immune response, but without reducing exposure to environmental factors of IBD, e.g., by changing diet (reducing ultra-processed foods), the adjuvant-rich landscape is never resolved and continues to drive intestinal mucosal dysregulation. Thus, such treatment approaches are not enough to put out the inflammatory fire. The resultant smoldering, low-grade inflammation diminishes physiological resilience of the intestinal (micro)environment, perpetuating the state of chronic disease. Therefore, our hypothesis posits that successful interventions for IBD must address the complexity of the disease by simultaneously targeting all modifiable aspects: innate immunity cytokines and microbiota, adaptive immunity cells and cytokines, and factors that relate to the (micro)environment. Thus the disease can be comprehensively treated across the nano-, meso-, and microscales, rather than with a focus on single targets. A broader perspective on IBD treatment that also includes options to adapt the DAMPing (micro)environment is warranted.
Collapse
Affiliation(s)
- Oliver Sandys
- Tytgat Institute for Liver and Intestinal Research, AmsterdamUMC, AGEM, University of Amsterdam, Amsterdam, The Netherlands
| | - Pieter C F Stokkers
- Department of Gastroenterology and Hepatology, OLVG West, Amsterdam, The Netherlands
| | - Anje A Te Velde
- Tytgat Institute for Liver and Intestinal Research, AmsterdamUMC, AGEM, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
14
|
Mehra P, Kumar A. Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology. Cell Biochem Funct 2024; 42:e4063. [PMID: 38961596 DOI: 10.1002/cbf.4063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 07/05/2024]
Abstract
The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.
Collapse
Affiliation(s)
- Parul Mehra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| |
Collapse
|
15
|
Nakatsu G, Andreeva N, MacDonald MH, Garrett WS. Interactions between diet and gut microbiota in cancer. Nat Microbiol 2024; 9:1644-1654. [PMID: 38907007 DOI: 10.1038/s41564-024-01736-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/20/2024] [Indexed: 06/23/2024]
Abstract
Dietary patterns and specific dietary components, in concert with the gut microbiota, can jointly shape susceptibility, resistance and therapeutic response to cancer. Which diet-microbial interactions contribute to or mitigate carcinogenesis and how they work are important questions in this growing field. Here we interpret studies of diet-microbial interactions to assess dietary determinants of intestinal colonization by opportunistic and oncogenic bacteria. We explore how diet-induced expansion of specific gut bacteria might drive colonic epithelial tumorigenesis or create immuno-permissive tumour milieus and introduce recent findings that provide insight into these processes. Additionally, we describe available preclinical models that are widely used to study diet, microbiome and cancer interactions. Given the rising clinical interest in dietary modulations in cancer treatment, we highlight promising clinical trials that describe the effects of different dietary alterations on the microbiome and cancer outcomes.
Collapse
Affiliation(s)
- Geicho Nakatsu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Natalia Andreeva
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Meghan H MacDonald
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Harvard Chan Microbiome in Public Health Center, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
16
|
Holbrook-Smith D, Trouillon J, Sauer U. Metabolomics and Microbial Metabolism: Toward a Systematic Understanding. Annu Rev Biophys 2024; 53:41-64. [PMID: 38109374 DOI: 10.1146/annurev-biophys-030722-021957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Over the past decades, our understanding of microbial metabolism has increased dramatically. Metabolomics, a family of techniques that are used to measure the quantities of small molecules in biological samples, has been central to these efforts. Advances in analytical chemistry have made it possible to measure the relative and absolute concentrations of more and more compounds with increasing levels of certainty. In this review, we highlight how metabolomics has contributed to understanding microbial metabolism and in what ways it can still be deployed to expand our systematic understanding of metabolism. To that end, we explain how metabolomics was used to (a) characterize network topologies of metabolism and its regulation networks, (b) elucidate the control of metabolic function, and (c) understand the molecular basis of higher-order phenomena. We also discuss areas of inquiry where technological advances should continue to increase the impact of metabolomics, as well as areas where our understanding is bottlenecked by other factors such as the availability of statistical and modeling frameworks that can extract biological meaning from metabolomics data.
Collapse
Affiliation(s)
| | - Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
| |
Collapse
|
17
|
Mager LF, Krause T, McCoy KD. Interaction of microbiota, mucosal malignancies, and immunotherapy-Mechanistic insights. Mucosal Immunol 2024; 17:402-415. [PMID: 38521413 DOI: 10.1016/j.mucimm.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
The microbiome has emerged as a crucial modulator of host-immune interactions and clearly impacts tumor development and therapy efficacy. The microbiome is a double-edged sword in cancer development and therapy as both pro-tumorigenic and anti-tumorigenic bacterial taxa have been identified. The staggering number of association-based studies in various tumor types has led to an enormous amount of data that makes it difficult to identify bacteria that promote tumor development or modulate therapy efficacy from bystander bacteria. Here we aim to comprehensively summarize the current knowledge of microbiome-host immunity interactions and cancer therapy in various mucosal tissues to find commonalities and thus identify potential functionally relevant bacterial taxa. Moreover, we also review recent studies identifying specific bacteria and mechanisms through which the microbiome modulates cancer development and therapy efficacy.
Collapse
Affiliation(s)
- Lukas F Mager
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada; Department of Internal Medicine I, Faculty of Medicine, University of Tübingen, Germany; M3 Research Center for Malignom, Metabolome and Microbiome, Faculty of Medicine University Tübingen, Germany
| | - Tim Krause
- Department of Internal Medicine I, Faculty of Medicine, University of Tübingen, Germany; M3 Research Center for Malignom, Metabolome and Microbiome, Faculty of Medicine University Tübingen, Germany
| | - Kathy D McCoy
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada.
| |
Collapse
|
18
|
Wang P, You Q, Liu Y, Miao H, Dong WF, Li L. Combating infections from drug-resistant bacteria: Unleashing synergistic broad-spectrum antibacterial power with high-entropy MXene/CDs. Colloids Surf B Biointerfaces 2024; 238:113874. [PMID: 38581833 DOI: 10.1016/j.colsurfb.2024.113874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024]
Abstract
The growing resistance of bacteria to antibiotics has posed challenges in treating associated bacterial infections, while the development of multi-model antibacterial strategies could efficient sterilization to prevent drug resistance. High-entropy MXene has emerged as a promising candidate for antibacterial synergy with inherent photothermal and photodynamic properties. Herein, a high-entropy nanomaterial of MXene/CDs was synthesized to amplify oxidative stress under near-infrared laser irradiation. Well-exfoliated MXene nanosheets have proven to show an excellent photothermal effect for sterilization. The incorporation of CDs could provide photo-generated electrons for MXene nanosheets to generate ROS, meanwhile reducing the recombination of electron-hole pairs to further accelerate the generation of photo-generated electrons. The MXene/CDs material demonstrates outstanding synergistic photothermal and photodynamic effects, possesses excellent biocompatibility and successfully eliminates drug-resistant bacteria as well as inhibits biofilm formation. While attaining a remarkable killing efficiency of up to 99.99% against drug-resistant Escherichia coli and Staphylococcus aureus, it also demonstrates outstanding antibacterial effects against four additional bacterial strains. This work not only establishes a synthesis precedent for preparing high-entropy MXene materials with CDs but also provides a potential approach for addressing the issue of drug-resistant bacterial infections.
Collapse
Affiliation(s)
- Panyong Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
| | - Qiannan You
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China.
| | - Yulu Liu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
| | - Huimin Miao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China
| | - Wen-Fei Dong
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China.
| | - Li Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; CAS Key Laboratory of Biomedical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), Suzhou 215163, China.
| |
Collapse
|
19
|
Wang Z, Chang Y, Sun H, Li Y, Tang T. Advances in molecular mechanisms of inflammatory bowel disease‑associated colorectal cancer (Review). Oncol Lett 2024; 27:257. [PMID: 38646499 PMCID: PMC11027113 DOI: 10.3892/ol.2024.14390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/15/2024] [Indexed: 04/23/2024] Open
Abstract
The link between inflammation and cancer is well documented and colonic inflammation caused by inflammatory bowel disease (IBD) is thought to be a high-risk factor for the development of colorectal cancer (CRC). The complex crosstalk between epithelial and inflammatory cells is thought to underlie the progression from inflammation to cancer. The present review collates and summarises recent advances in the understanding of the pathogenesis of IBD-associated CRC (IBD-CRC), including the oncogenic mechanisms of the main inflammatory signalling pathways and genetic alterations induced by oxidative stress during colonic inflammation, and discusses the crosstalk between the tumour microenvironment, intestinal flora and host immune factors during inflammatory oncogenesis in colitis-associated CRC. In addition, the therapeutic implications of anti-inflammatory therapy for IBD-CRC were discussed, intending to provide new insight into improve clinical practice.
Collapse
Affiliation(s)
- Zhi Wang
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Yu Chang
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Haibo Sun
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Yuqin Li
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Tongyu Tang
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| |
Collapse
|
20
|
Hohmann M, Brunner V, Johannes W, Schum D, Carroll LM, Liu T, Sasaki D, Bosch J, Clavel T, Sieber SA, Zeller G, Tschurtschenthaler M, Janßen KP, Gulder TAM. Bacillamide D produced by Bacillus cereus from the mouse intestinal bacterial collection (miBC) is a potent cytotoxin in vitro. Commun Biol 2024; 7:655. [PMID: 38806706 PMCID: PMC11133360 DOI: 10.1038/s42003-024-06208-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/17/2024] [Indexed: 05/30/2024] Open
Abstract
The gut microbiota influences human health and the development of chronic diseases. However, our understanding of potentially protective or harmful microbe-host interactions at the molecular level is still in its infancy. To gain further insights into the hidden gut metabolome and its impact, we identified a cryptic non-ribosomal peptide BGC in the genome of Bacillus cereus DSM 28590 from the mouse intestine ( www.dsmz.de/miBC ), which was predicted to encode a thiazol(in)e substructure. Cloning and heterologous expression of this BGC revealed that it produces bacillamide D. In-depth functional evaluation showed potent cytotoxicity and inhibition of cell migration using the human cell lines HCT116 and HEK293, which was validated using primary mouse organoids. This work establishes the bacillamides as selective cytotoxins from a bacterial gut isolate that affect mammalian cells. Our targeted structure-function-predictive approach is demonstrated to be a streamlined method to discover deleterious gut microbial metabolites with potential effects on human health.
Collapse
Affiliation(s)
- Maximilian Hohmann
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Valentina Brunner
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Division of Translational Cancer Research German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Widya Johannes
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
| | - Dominik Schum
- Department of Bioscience, Center for Functional Protein Assemblies, Technical University of Munich, 85748, Garching bei München, Germany
| | - Laura M Carroll
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 61997, Heidelberg, Germany
| | - Tianzhe Liu
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Daisuke Sasaki
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Research and Development Headquarters, Nitto Boseki Co., Ltd., 102-8489, Tokyo, Japan
| | - Johanna Bosch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, 52074, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, 52074, Aachen, Germany
| | - Stephan A Sieber
- Department of Bioscience, Center for Functional Protein Assemblies, Technical University of Munich, 85748, Garching bei München, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 61997, Heidelberg, Germany
| | - Markus Tschurtschenthaler
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
- Division of Translational Cancer Research German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
| | - Klaus-Peter Janßen
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Natural Product Biotechnology, Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.
| |
Collapse
|
21
|
Sayed IM, Vo DT, Alcantara J, Inouye KM, Pranadinata RF, Luo L, Boland CR, Goyal NP, Kuo DJ, Huang SC, Sahoo D, Ghosh P, Das S. Molecular Signatures for Microbe-Associated Colorectal Cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595902. [PMID: 38853996 PMCID: PMC11160670 DOI: 10.1101/2024.05.26.595902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Genetic factors and microbial imbalances play crucial roles in colorectal cancers (CRCs), yet the impact of infections on cancer initiation remains poorly understood. While bioinformatic approaches offer valuable insights, the rising incidence of CRCs creates a pressing need to precisely identify early CRC events. We constructed a network model to identify continuum states during CRC initiation spanning normal colonic tissue to pre-cancer lesions (adenomatous polyps) and examined the influence of microbes and host genetics. Methods A Boolean network was built using a publicly available transcriptomic dataset from healthy and adenoma affected patients to identify an invariant Microbe-Associated Colorectal Cancer Signature (MACS). We focused on Fusobacterium nucleatum ( Fn ), a CRC-associated microbe, as a model bacterium. MACS-associated genes and proteins were validated by RT-qPCR, RNA seq, ELISA, IF and IHCs in tissues and colon-derived organoids from genetically predisposed mice ( CPC-APC Min+/- ) and patients (FAP, Lynch Syndrome, PJS, and JPS). Results The MACS that is upregulated in adenomas consists of four core genes/proteins: CLDN2/Claudin-2 (leakiness), LGR5/leucine-rich repeat-containing receptor (stemness), CEMIP/cell migration-inducing and hyaluronan-binding protein (epithelial-mesenchymal transition) and IL8/Interleukin-8 (inflammation). MACS was induced upon Fn infection, but not in response to infection with other enteric bacteria or probiotics. MACS induction upon Fn infection was higher in CPC-APC Min+/- organoids compared to WT controls. The degree of MACS expression in the patient-derived organoids (PDOs) generally corresponded with the known lifetime risk of CRCs. Conclusions Computational prediction followed by validation in the organoid-based disease model identified the early events in CRC initiation. MACS reveals that the CRC-associated microbes induce a greater risk in the genetically predisposed hosts, suggesting its potential use for risk prediction and targeted cancer prevention.
Collapse
|
22
|
Wu S, Zhou H, Chen D, Lu Y, Li Y, Qiao J. Multi-omic analysis tools for microbial metabolites prediction. Brief Bioinform 2024; 25:bbae264. [PMID: 38859767 PMCID: PMC11165163 DOI: 10.1093/bib/bbae264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/08/2024] [Indexed: 06/12/2024] Open
Abstract
How to resolve the metabolic dark matter of microorganisms has long been a challenging problem in discovering active molecules. Diverse omics tools have been developed to guide the discovery and characterization of various microbial metabolites, which make it gradually possible to predict the overall metabolites for individual strains. The combinations of multi-omic analysis tools effectively compensates for the shortcomings of current studies that focus only on single omics or a broad class of metabolites. In this review, we systematically update, categorize and sort out different analysis tools for microbial metabolites prediction in the last five years to appeal for the multi-omic combination on the understanding of the metabolic nature of microbes. First, we provide the general survey on different updated prediction databases, webservers, or software that based on genomics, transcriptomics, proteomics, and metabolomics, respectively. Then, we discuss the essentiality on the integration of multi-omics data to predict metabolites of different microbial strains and communities, as well as stressing the combination of other techniques, such as systems biology methods and data-driven algorithms. Finally, we identify key challenges and trends in developing multi-omic analysis tools for more comprehensive prediction on diverse microbial metabolites that contribute to human health and disease treatment.
Collapse
Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Haonan Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Danlei Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Yutong Lu
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Yanni Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| |
Collapse
|
23
|
Wang Y, Quan J, Cheng X, Li C, Yuan Z. Relationship of black soldier fly larvae (BSFL) gut microbiota and bioconversion efficiency with properties of substrates. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 180:106-114. [PMID: 38564911 DOI: 10.1016/j.wasman.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Treating food waste using black soldier fly larvae (BSFL) is widely regarded as a promising nature-based measure. This study explored the influence of food waste particle sizes on substrate properties and its subsequent effects on bioconversion efficiency and gut microbiota. The results indicated that particle sizes mainly ranging from 4 mm to 10 mm (T1) significantly increased the weight loss rate of food waste by 35 % and larval biomass by 38 % compared to those in T4 (particle sizes mostly less than 2 mm) and promoted the bioconversion of carbon and nitrogen into larvae and gases. Investigation of substrates properties indicated that the final pH value of T1 was 7.79 ± 0.10, with Anaerococcus as the predominant substrate microorganism (relative abundance: 57.4 %), while T4 exhibited a final pH value of 5.71 ± 0.24, with Lactobacillus as the dominant microorganism (relative abundance: 95.2 %). Correlation analysis between substrate chemical properties and microbial community structure unveiled a strong relationship between substrate pH and the relative abundance of Anaerococcus and Lactobacillus. Furthermore, beneficial microorganisms such as Lactobacillus and Enterococcus colonized the BSFL gut of T1, while pathogenic bacterium Morganella, detrimental to BSFL gut function, was enriched in T4 (relative abundance: 60.9 %). Nevertheless, PCA analysis indicated that alterations in the gut microbial community structure may not be attributed to the substrate microorganisms. This study establishes particle size as a crucial parameter for BSFL bioconversion and advances understanding of the relationship between gut microbiota and substrate microbiota.
Collapse
Affiliation(s)
- Yu Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jiawei Quan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiang Cheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Chunxing Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Lishui Institute of Ecology and Environment, Nanjing University, Nanjing 212200, China
| | - Zengwei Yuan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Lishui Institute of Ecology and Environment, Nanjing University, Nanjing 212200, China; Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing 210023, China.
| |
Collapse
|
24
|
Goldman S, Xin J, Provenzano J, Coley CW. MIST-CF: Chemical Formula Inference from Tandem Mass Spectra. J Chem Inf Model 2024; 64:2421-2431. [PMID: 37725368 DOI: 10.1021/acs.jcim.3c01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step toward structurally elucidating unknown metabolites. While great strides have been made toward solving this problem, the current state-of-the-art method depends on time-intensive, proprietary, and expert-parametrized fragmentation tree construction and scoring. In this work, we extend our previous spectrum Transformer methodology into an energy-based modeling framework, MIST-CF: Metabolite Inference with Spectrum Transformers for Chemical Formula prediction, for learning to rank chemical formula and adduct assignments given an unannotated MS/MS spectrum. Importantly, MIST-CF learns in a data-dependent fashion using a Formula Transformer neural network architecture and circumvents the need for fragmentation tree construction. We train and evaluate our model on a large open-access database, showing an absolute improvement of 10% top 1 accuracy over other neural network architectures. We further validate our approach on the CASMI2022 challenge data set, achieving nearly equivalent performance to the winning entry within the positive mode category without any manual curation or postprocessing of our results. These results demonstrate an exciting strategy to more powerfully leverage MS2 fragment peaks for predicting MS1 precursor chemical formulas with data-driven learning.
Collapse
Affiliation(s)
- Samuel Goldman
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge 02139, Massachusetts, United States
| | - Jiayi Xin
- Statistics and Actuarial Science, The University of Hong Kong, Hong Kong 999077, China
| | - Joules Provenzano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02139, Massachusetts, United States
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02139, Massachusetts, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge 02139, Massachusetts, United States
| |
Collapse
|
25
|
Abstract
Colorectal cancer (CRC) is a substantial source of global morbidity and mortality in dire need of improved prevention and treatment strategies. As our understanding of CRC grows, it is becoming increasingly evident that the gut microbiota, consisting of trillions of microorganisms in direct interface with the colon, plays a substantial role in CRC development and progression. Understanding the roles that individual microorganisms and complex microbial communities play in CRC pathogenesis, along with their attendant mechanisms, will help yield novel preventive and therapeutic interventions for CRC. In this Review, we discuss recent evidence concerning global perturbations of the gut microbiota in CRC, associations of specific microorganisms with CRC, the underlying mechanisms by which microorganisms potentially drive CRC development and the roles of complex microbial communities in CRC pathogenesis. While our understanding of the relationship between the microbiota and CRC has improved in recent years, our findings highlight substantial gaps in current research that need to be filled before this knowledge can be used to the benefit of patients.
Collapse
Affiliation(s)
- Maxwell T White
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia L Sears
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
26
|
Jalandra R, Dalal N, Mohan A, Solanki PR, Kumar A. A novel method for enrichment of Morganella morganii in fecal samples using designed culture medium. Cell Biochem Funct 2024; 42:e4004. [PMID: 38583079 DOI: 10.1002/cbf.4004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
Morganella morganii is a gram negative, facultative anaerobic rod-shaped bacterium, commonly found in environment and in the intestine of human, mammals, and reptiles as a part of their gut microbiome. M. morganii can cause Gram-negative folliculitis, black nail infection, acute retiform purpura, fetal demise, and subdural empyema. The increasing frequency of M. morganii infections generate the need for efficient methods to enrich the presence of M. morganii in clinical samples to make its detection easier. Culturomics aims to grow and maximize the number of culturable bacteria. Different methods are followed to maximize the growth of minority population of bacteria by disrupting the growth of bacteria which are present in higher concentration. This article presents a method for selective enriching the M. morganii in human fecal samples. This method includes prior incubation of fecal microbiota in an anaerobic environment, adding supplement like fecal water to give dormant bacteria a break to become active to grow to threshold concentration, and an enrichment stage which provides the additional opportunity of growing to M. morganii on the selective medium. This method also provides an ingenuous way for augmenting the growth of fecal M. morganii species.
Collapse
Affiliation(s)
- Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
- Department of Zoology, Maharshi Dayanand University, Rohtak, India
| | - Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
- Azraeli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Anand Mohan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | | | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| |
Collapse
|
27
|
Liu Q, Yang Y, Pan M, Yang F, Yu Y, Qian Z. Role of the gut microbiota in tumorigenesis and treatment. Theranostics 2024; 14:2304-2328. [PMID: 38646653 PMCID: PMC11024857 DOI: 10.7150/thno.91700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/01/2024] [Indexed: 04/23/2024] Open
Abstract
The gut microbiota is a crucial component of the intricate microecosystem within the human body that engages in interactions with the host and influences various physiological processes and pathological conditions. In recent years, the association between dysbiosis of the gut microbiota and tumorigenesis has garnered increasing attention, as it is recognized as a hallmark of cancer within the scientific community. However, only a few microorganisms have been identified as potential drivers of tumorigenesis, and enhancing the molecular understanding of this process has substantial scientific importance and clinical relevance for cancer treatment. In this review, we delineate the impact of the gut microbiota on tumorigenesis and treatment in multiple types of cancer while also analyzing the associated molecular mechanisms. Moreover, we discuss the utility of gut microbiota data in cancer diagnosis and patient stratification. We further outline current research on harnessing microorganisms for cancer treatment while also analyzing the prospects and challenges associated with this approach.
Collapse
Affiliation(s)
- Qingya Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yun Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Meng Pan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Fan Yang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yan Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhiyong Qian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| |
Collapse
|
28
|
Zou Y, Wang S, Zhang H, Gu Y, Chen H, Huang Z, Yang F, Li W, Chen C, Men L, Tian Q, Xie T. The triangular relationship between traditional Chinese medicines, intestinal flora, and colorectal cancer. Med Res Rev 2024; 44:539-567. [PMID: 37661373 DOI: 10.1002/med.21989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/05/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023]
Abstract
Over the past decade, colorectal cancer has reported a higher incidence in younger adults and a lower mortality rate. Recently, the influence of the intestinal flora in the initiation, progression, and treatment of colorectal cancer has been extensively studied, as well as their positive therapeutic impact on inflammation and the cancer microenvironment. Historically, traditional Chinese medicine (TCM) has been widely used in the treatment of colorectal cancer via promoted cancer cell apoptosis, inhibited cancer metastasis, and reduced drug resistance and side effects. The present research is more on the effect of either herbal medicine or intestinal flora on colorectal cancer. The interactions between TCM and intestinal flora are bidirectional and the combined impacts of TCM and gut microbiota in the treatment of colon cancer should not be neglected. Therefore, this review discusses the role of intestinal bacteria in the progression and treatment of colorectal cancer by inhibiting carcinogenesis, participating in therapy, and assisting in healing. Then the complex anticolon cancer effects of different kinds of TCM monomers, TCM drug pairs, and traditional Chinese prescriptions embodied in apoptosis, metastasis, immune suppression, and drug resistance are summarized separately. In addition, the interaction between TCM and intestinal flora and the combined effect on cancer treatment were analyzed. This review provides a mechanistic reference for the application of TCM and intestinal flora in the clinical treatment of colorectal cancer and paves the way for the combined development and application of microbiome and TCM.
Collapse
Affiliation(s)
- Yuqing Zou
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Shuling Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Honghua Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yuxin Gu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Huijuan Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Zhihua Huang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Feifei Yang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Wenqi Li
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Cheng Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lianhui Men
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Qingchang Tian
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines; Engineering Laboratory of Development and Application of Traditional Chinese Medicines; Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| |
Collapse
|
29
|
Hu ZQ, Hung YM, Chen LH, Lai LC, Pan MH, Chuang EY, Tsai MH. NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:254-264. [PMID: 38568776 DOI: 10.1109/tcbb.2024.3349572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.
Collapse
|
30
|
Jin DM, Morton JT, Bonneau R. Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582333. [PMID: 38464323 PMCID: PMC10925178 DOI: 10.1101/2024.02.27.582333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Microbiome studies have revealed gut microbiota's potential impact on complex diseases. However, many studies often focus on one disease per cohort. We developed a meta-analysis workflow for gut microbiome profiles and analyzed shotgun metagenomic data covering 11 diseases. Using interpretable machine learning and differential abundance analysis, our findings reinforce the generalization of binary classifiers for Crohn's disease (CD) and colorectal cancer (CRC) to hold-out cohorts and highlight the key microbes driving these classifications. We identified high microbial similarity in disease pairs like CD vs ulcerative colitis (UC), CD vs CRC, Parkinson's disease vs type 2 diabetes (T2D), and schizophrenia vs T2D. We also found strong inverse correlations in Alzheimer's disease vs CD and UC. These findings detected by our pipeline provide valuable insights into these diseases.
Collapse
Affiliation(s)
- Dong-Min Jin
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - James T. Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Richard Bonneau
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Genentech, New York, NY, USA
| |
Collapse
|
31
|
Hernández-Castro C, Múnera Duque A, Hoyos Burgos JP, Toro Londoño MÁ, Agudelo López SDP, Carmena D, Sánchez S. Draft genome sequences of four Morganella morganii strains isolated from Colombian colorectal cancer patient stool specimens. Microbiol Resour Announc 2024; 13:e0107723. [PMID: 38265220 PMCID: PMC10868278 DOI: 10.1128/mra.01077-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
We report the draft genome sequences of four Morganella morganii strains isolated from the stools of four patients diagnosed with colorectal cancer (CRC) in Medellín, Colombia. These genomes represent an important addition to the limited number of genomes of M. morganii strains originating from CRC patients currently available.
Collapse
Affiliation(s)
- Carolina Hernández-Castro
- Parasitology Group, Faculty of Medicine, Academic Corporation for the Study of Tropical Pathologies, University of Antioquia, Medellín, Colombia
- Reference and Research Laboratory on Parasitology, Spanish National Centre for Microbiology, Health Institute Carlos III, Madrid, Spain
| | - Alejandro Múnera Duque
- Department of Surgery, Faculty of Medicine, University of Antioquia, Medellín, Colombia
- Hospital Alma Máter de Antioquia, Medellín, Colombia
| | | | - Miguel Ángel Toro Londoño
- Parasitology Group, Faculty of Medicine, Academic Corporation for the Study of Tropical Pathologies, University of Antioquia, Medellín, Colombia
| | - Sonia del Pilar Agudelo López
- Parasitology Group, Faculty of Medicine, Academic Corporation for the Study of Tropical Pathologies, University of Antioquia, Medellín, Colombia
| | - David Carmena
- Reference and Research Laboratory on Parasitology, Spanish National Centre for Microbiology, Health Institute Carlos III, Madrid, Spain
- CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain
| | - Sergio Sánchez
- Reference and Research Laboratory on Food and Waterborne Bacterial Infections, Spanish National Centre for Microbiology, Health Institute Carlos III, Madrid, Spain
| |
Collapse
|
32
|
Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 2024; 32:209-226.e7. [PMID: 38215740 PMCID: PMC10923022 DOI: 10.1016/j.chom.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.
Collapse
Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Martin Stražar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric M Brown
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Temple
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kerry Pierce
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shen Jin
- Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | - Marie-Madlen Pust
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Zach Costliow
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thomas Walters
- Division of Gastroenterology, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brendan M Boyle
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
33
|
Li X, Ji LJ, Feng KD, Huang H, Liang MR, Cheng SJ, Meng XD. Emerging role of exosomes in ulcerative colitis: Targeting NOD-like receptor family pyrin domain containing 3 inflammasome. World J Gastroenterol 2024; 30:527-541. [PMID: 38463022 PMCID: PMC10921143 DOI: 10.3748/wjg.v30.i6.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/21/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic recurrent inflammatory bowel disease. Despite ongoing advances in our understanding of UC, its pathogenesis is yet unelucidated, underscoring the urgent need for novel treatment strategies for patients with UC. Exosomes are nanoscale membrane particles that mediate intercellular communication by carrying various bioactive molecules, such as proteins, RNAs, DNA, and metabolites. The NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome is a cytosolic tripartite protein complex whose activation induces the maturation and secretion of proinflammatory cytokines interleukin-1β (IL-1β) and IL-18, triggering the inflammatory response to a pathogenic agent or injury. Growing evidence suggests that exosomes are new modulators of the NLRP3 inflammasome, with vital roles in the pathological process of UC. Here, recent evidence is reviewed on the role of exosomes and NLRP3 inflammasome in UC. First, the dual role of exosomes on NLRP3 inflammasome and the effect of NLRP3 inflammasome on exosome secretion are summarized. Finally, an outlook on the directions of exosome-NLRP3 inflammasome crosstalk research in the context of UC is proposed and areas of further research on this topic are highlighted.
Collapse
Affiliation(s)
- Xin Li
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou Province, China
| | - Li-Jiang Ji
- Department of Anorectal Surgery, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu 215500, Jiangsu Province, China
| | - Kai-Di Feng
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hua Huang
- Department of Anorectal Surgery, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu 215500, Jiangsu Province, China
| | - Mei-Rou Liang
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shi-Jin Cheng
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiu-Dong Meng
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou Province, China
| |
Collapse
|
34
|
Sun Y, Wang X, Li L, Zhong C, Zhang Y, Yang X, Li M, Yang C. The role of gut microbiota in intestinal disease: from an oxidative stress perspective. Front Microbiol 2024; 15:1328324. [PMID: 38419631 PMCID: PMC10899708 DOI: 10.3389/fmicb.2024.1328324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Recent studies have indicated that gut microbiota-mediated oxidative stress is significantly associated with intestinal diseases such as colorectal cancer, ulcerative colitis, and Crohn's disease. The level of reactive oxygen species (ROS) has been reported to increase when the gut microbiota is dysregulated, especially when several gut bacterial metabolites are present. Although healthy gut microbiota plays a vital role in defending against excessive oxidative stress, intestinal disease is significantly influenced by excessive ROS, and this process is controlled by gut microbiota-mediated immunological responses, DNA damage, and intestinal inflammation. In this review, we discuss the relationship between gut microbiota and intestinal disease from an oxidative stress perspective. In addition, we also provide a summary of the most recent therapeutic approaches for preventing or treating intestinal diseases by modifying gut microbiota.
Collapse
Affiliation(s)
- Yiqi Sun
- Surgery of Traditional Chinese Medicine Department, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xurui Wang
- Surgery of Traditional Chinese Medicine Department, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lei Li
- Department of Anorectal Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chao Zhong
- Traditional Chinese Medicine Department of Orthopaedic and Traumatic, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Zhang
- Colorectal and Anal Surgery, Chengdu Anorectal Hospital, Chengdu, China
| | - Xiangdong Yang
- Colorectal and Anal Surgery, Chengdu Anorectal Hospital, Chengdu, China
| | - Mingyue Li
- Special Needs Outpatient Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chao Yang
- Surgery of Traditional Chinese Medicine Department, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
35
|
El Tekle G, Andreeva N, Garrett WS. The Role of the Microbiome in the Etiopathogenesis of Colon Cancer. Annu Rev Physiol 2024; 86:453-478. [PMID: 38345904 DOI: 10.1146/annurev-physiol-042022-025619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Studies in preclinical models support that the gut microbiota play a critical role in the development and progression of colorectal cancer (CRC). Specific microbial species and their corresponding virulence factors or associated small molecules can contribute to CRC development and progression either via direct effects on the neoplastic transformation of epithelial cells or through interactions with the host immune system. Induction of DNA damage, activation of Wnt/β-catenin and NF-κB proinflammatory pathways, and alteration of the nutrient's availability and the metabolic activity of cancer cells are the main mechanisms by which the microbiota contribute to CRC. Within the tumor microenvironment, the gut microbiota alter the recruitment, activation, and function of various immune cells, such as T cells, macrophages, and dendritic cells. Additionally, the microbiota shape the function and composition of cancer-associated fibroblasts and extracellular matrix components, fashioning an immunosuppressive and pro-tumorigenic niche for CRC. Understanding the complex interplay between gut microbiota and tumorigenesis can provide therapeutic opportunities for the prevention and treatment of CRC.
Collapse
Affiliation(s)
- Geniver El Tekle
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA;
- The Harvard Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Natalia Andreeva
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA;
- The Harvard Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA;
- The Harvard Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| |
Collapse
|
36
|
Elmassry MM, Sugihara K, Chankhamjon P, Camacho FR, Wang S, Sugimoto Y, Chatterjee S, Chen LA, Kamada N, Donia MS. A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579278. [PMID: 38370680 PMCID: PMC10871352 DOI: 10.1101/2024.02.07.579278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Changes in the gut microbiome have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a multi-cohort analysis of small molecule biosynthetic gene clusters (BGCs) in 5,306 metagenomic samples of the gut microbiome from 2,033 Inflammatory Bowel Disease (IBD) patients and 833 matched healthy subjects and identified a group of Clostridia-derived BGCs that are significantly associated with IBD. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the IBD-enriched BGCs. Using two mouse models of colitis, we show that the discovered small molecules disrupt gut permeability and exacerbate inflammation in chemically and genetically susceptible mice. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of microbiome-host interactions in the context of microbiome-associated diseases.
Collapse
Affiliation(s)
- Moamen M Elmassry
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | | | - Francine R Camacho
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544, USA
| | - Shuo Wang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
| | - Yuki Sugimoto
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Seema Chatterjee
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Lea Ann Chen
- Department of Medicine, Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, 08901, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
- Lead Contact
| |
Collapse
|
37
|
Dai R, Kelly BN, Ike A, Berger D, Chan A, Drew DA, Ljungman D, Mutiibwa D, Ricciardi R, Tumusiime G, Cusack JC. The Impact of the Gut Microbiome, Environment, and Diet in Early-Onset Colorectal Cancer Development. Cancers (Basel) 2024; 16:676. [PMID: 38339427 PMCID: PMC10854951 DOI: 10.3390/cancers16030676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Traditionally considered a disease common in the older population, colorectal cancer is increasing in incidence among younger demographics. Evidence suggests that populational- and generational-level shifts in the composition of the human gut microbiome may be tied to the recent trends in gastrointestinal carcinogenesis. This review provides an overview of current research and putative mechanisms behind the rising incidence of colorectal cancer in the younger population, with insight into future interventions that may prevent or reverse the rate of early-onset colorectal carcinoma.
Collapse
Affiliation(s)
- Rui Dai
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Harvard University, Boston, MA 02115, USA; (D.B.); (A.C.); (D.A.D.); (R.R.)
| | - Bridget N. Kelly
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA (A.I.)
| | - Amarachi Ike
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA (A.I.)
| | - David Berger
- Harvard Medical School, Harvard University, Boston, MA 02115, USA; (D.B.); (A.C.); (D.A.D.); (R.R.)
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA (A.I.)
| | - Andrew Chan
- Harvard Medical School, Harvard University, Boston, MA 02115, USA; (D.B.); (A.C.); (D.A.D.); (R.R.)
- Department of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David A. Drew
- Harvard Medical School, Harvard University, Boston, MA 02115, USA; (D.B.); (A.C.); (D.A.D.); (R.R.)
- Department of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David Ljungman
- Sahlgrenska University Hospital, University of Gothenburg, 413 45 Gothenburg, Sweden;
| | - David Mutiibwa
- Department of Surgery, Mbarara University of Science and Technology, Mbarara P.O. Box 1410, Uganda;
| | - Rocco Ricciardi
- Harvard Medical School, Harvard University, Boston, MA 02115, USA; (D.B.); (A.C.); (D.A.D.); (R.R.)
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA (A.I.)
| | - Gerald Tumusiime
- School of Medicine, Uganda Christian University, Mukono P.O. Box 4, Uganda;
| | - James C. Cusack
- Harvard Medical School, Harvard University, Boston, MA 02115, USA; (D.B.); (A.C.); (D.A.D.); (R.R.)
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA (A.I.)
| |
Collapse
|
38
|
Liu Z, Ma Y, Ye J, Li G, Kang X, Xie W, Wang X. Drug delivery systems for enhanced tumour treatment by eliminating intra-tumoral bacteria. J Mater Chem B 2024; 12:1194-1207. [PMID: 38197141 DOI: 10.1039/d3tb02362a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Cancer remains one of the serious threats to human health. The relationship between bacteria and various tumours has been widely reported in recent years, and studies on intra-tumoral bacteria have become important as intra-tumoral bacteria directly affect the tumorigenesis, progression, immunity and metastatic processes. Therefore, eliminating these commensal intra-tumoral bacteria while treating tumour is expected to be a potential strategy to further enhance the clinical outcome of tumour therapy. Drug delivery systems (DDSs) are widely used to deliver antibiotics and chemotherapeutic drugs for antibacterial and anticancer applications, respectively. Thus, this review firstly provides a comprehensive summary of the association between intra-tumoral bacteria and a host of tumours, followed by a description of advanced DDSs for improving the therapeutic efficacy of cancer treatment through the elimination of intra-tumoral bacteria. It is hoped that this review will provide guidelines for the therapeutic and "synergistic antimicrobial and antitumour" drug delivery strategy.
Collapse
Affiliation(s)
- Ziyi Liu
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
- School of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yige Ma
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Jinxin Ye
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Guofeng Li
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xiaoxu Kang
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Wensheng Xie
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xing Wang
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
39
|
Altshuller M, He X, MacKrell EJ, Wernke KM, Wong JWH, Sellés-Baiget S, Wang TY, Chou TF, Duxin JP, Balskus EP, Herzon SB, Semlow DR. The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.576698. [PMID: 38352618 PMCID: PMC10862771 DOI: 10.1101/2024.01.30.576698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Colibactin is a secondary metabolite produced by bacteria present in the human gut and is implicated in the progression of colorectal cancer and inflammatory bowel disease. This genotoxin alkylates deoxyadenosines on opposite strands of host cell DNA to produce DNA interstrand cross-links (ICLs) that block DNA replication. While cells have evolved multiple mechanisms to resolve ("unhook") ICLs encountered by the replication machinery, little is known about which of these pathways promote resistance to colibactin-induced ICLs. Here, we use Xenopus egg extracts to investigate replication-coupled repair of plasmids engineered to contain site-specific colibactin-ICLs. We show that replication fork stalling at a colibactin-ICL leads to replisome disassembly and activation of the Fanconi anemia ICL repair pathway, which unhooks the colibactin-ICL through nucleolytic incisions. These incisions generate a DNA double-strand break intermediate in one sister chromatid, which can be repaired by homologous recombination, and a monoadduct ("ICL remnant") in the other. Our data indicate that translesion synthesis past the colibactin-ICL remnant depends on Polη and a Polκ-REV1-Polζ polymerase complex. Although translesion synthesis past colibactin-induced DNA damage is frequently error-free, it can introduce T>N point mutations that partially recapitulate the mutation signature associated with colibactin exposure in vivo. Taken together, our work provides a biochemical framework for understanding how cells tolerate a naturally-occurring and clinically-relevant ICL.
Collapse
Affiliation(s)
- Maria Altshuller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xu He
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Elliot J. MacKrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kevin M. Wernke
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Joel W. H. Wong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Selene Sellés-Baiget
- TheNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Julien P. Duxin
- TheNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Daniel R. Semlow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| |
Collapse
|
40
|
Wetzel S, Müller A, Kohnert E, Mehrbarzin N, Huber R, Häcker G, Kreutz C, Lederer AK, Badr MT. Longitudinal dynamics of gut bacteriome and mycobiome interactions pre- and post-visceral surgery in Crohn's disease. Front Cell Infect Microbiol 2024; 13:1275405. [PMID: 38287975 PMCID: PMC10822897 DOI: 10.3389/fcimb.2023.1275405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/12/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Alterations of the gut microbiome are involved in the pathogenesis of Crohn's disease (CD). The role of fungi in this context is unclear. This study aimed to determine postoperative changes in the bacterial and fungal gut communities of CD patients undergoing intestinal resection, and to evaluate interactions between the bacteriome and mycobiome and their impact on the patients' outcome. Methods We report a subgroup analysis of a prospective cohort study, focusing on 10 CD patients whose fecal samples were collected for bacterial 16S rRNA and fungal ITS2 genes next-generation sequencing the day before surgery and on the 5th or 6th postoperative day. Results No significant differences in bacterial and fungal diversity were observed between preoperative and postoperative stool samples. By in-depth analysis, significant postoperative abundance changes of bacteria and fungi and 17 interkingdom correlations were detected. Network analysis identified 13 microbial clusters in the perioperative gut communities, revealing symbiotic and competitive interactions. Relevant factors were gender, age, BMI, lifestyle habits (smoking, alcohol consumption) and surgical technique. Postoperative abundance changes and identified clusters were associated with clinical outcomes (length of hospital stay, complications) and levels of inflammatory markers. Conclusions Our findings highlight the importance of dissecting the interactions of gut bacterial and fungal communities in CD patients and their potential influence on postoperative and disease outcomes.
Collapse
Affiliation(s)
- Simon Wetzel
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexander Müller
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva Kohnert
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Negin Mehrbarzin
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roman Huber
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Ann-Kathrin Lederer
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of General, Visceral and Transplant Surgery, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Aufdecken gemeinsamer Prinzipien immunvermittelter Erkrankungen: von der Grundlagenwissenschaft zu neuen Therapien (IMM-PACT)-Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
41
|
Kandalai S, Li H, Zhang N, Peng H, Zheng Q. The human microbiome and cancer: a diagnostic and therapeutic perspective. Cancer Biol Ther 2023; 24:2240084. [PMID: 37498047 PMCID: PMC10376920 DOI: 10.1080/15384047.2023.2240084] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/09/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Recent evidence has shown that the human microbiome is associated with various diseases, including cancer. The salivary microbiome, fecal microbiome, and circulating microbial DNA in blood plasma have all been used experimentally as diagnostic biomarkers for many types of cancer. The microbiomes present within local tissue, other regions, and tumors themselves have been shown to promote and restrict the development and progression of cancer, most often by affecting cancer cells or the host immune system. These microbes have also been shown to impact the efficacy of various cancer therapies, including radiation, chemotherapy, and immunotherapy. Here, we review the research advances focused on how microbes impact these different facets and why they are important to the clinical care of cancer. It is only by better understanding the roles these microbes play in the diagnosis, development, progression, and treatment of cancer, that we will be able to catch and treat cancer early.
Collapse
Affiliation(s)
- Shruthi Kandalai
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Huapeng Li
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Nan Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Haidong Peng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
42
|
Wang S, Xu B, Zhang Y, Chen G, Zhao P, Gao Q, Yuan L. The role of intestinal flora on tumorigenesis, progression, and the efficacy of PD-1/PD-L1 antibodies in colorectal cancer. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0376. [PMID: 38148328 PMCID: PMC10875280 DOI: 10.20892/j.issn.2095-3941.2023.0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
Intestinal flora affects the maturation of the host immune system, serves as a biomarker and efficacy predictor in the immunotherapy of several cancers, and has an important role in the development of colorectal cancer (CRC). Anti-PD-1/PD-L1 antibodies have shown satisfactory results in MSI-H/dMMR CRC but performed poorly in patients with MSS/pMMR CRC. In recent years an increasing number of studies have shown that intestinal flora has an important impact on anti-PD-1/PD-L1 antibody efficacy in CRC patients. Preclinical and clinical evidence have suggested that anti-PD-1/PD-L1 antibody efficacy can be improved by altering the composition of the intestinal flora in CRC. Herein, we summarize the studies related to the influence of intestinal flora on anti-PD-1/PD-L1 antibody efficacy in CRC and discuss the potential underlying mechanism(s). We have focused on the impact of the intestinal flora on the efficacy and safety of anti-PD-1/PD-L1 antibodies in CRC and how to better utilize the intestinal flora as an adjuvant to improve the efficacy of anti-PD-1/PD-L1 antibodies. In addition, we have provided a basis for the potential of the intestinal flora as a new treatment modality and indicator for determining patient prognosis.
Collapse
Affiliation(s)
- Sen Wang
- Department of Gastrointestinal Surgery, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Benling Xu
- Department of Immunotherapy, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Yangyang Zhang
- Department of Gastrointestinal Surgery, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Guangyu Chen
- Department of Immunotherapy, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Peng Zhao
- Department of Gastrointestinal Surgery, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Quanli Gao
- Department of Immunotherapy, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Long Yuan
- Department of Gastrointestinal Surgery, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450003, China
| |
Collapse
|
43
|
Thomas SC, Miller G, Li X, Saxena D. Getting off tract: contributions of intraorgan microbiota to cancer in extraintestinal organs. Gut 2023; 73:175-185. [PMID: 37918889 PMCID: PMC10842768 DOI: 10.1136/gutjnl-2022-328834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The gastrointestinal ecosystem has received the most attention when examining the contributions of the human microbiome to health and disease. This concentration of effort is logical due to the overwhelming abundance of microbes in the gut coupled with the relative ease of sampling compared with other organs. However, the intestines are intimately connected to multiple extraintestinal organs, providing an opportunity for homeostatic microbial colonisation and pathogenesis in organs traditionally thought to be sterile or only transiently harbouring microbiota. These habitats are challenging to sample, and their low microbial biomass among large amounts of host tissue can make study challenging. Nevertheless, recent findings have shown that many extraintestinal organs that are intimately linked to the gut harbour stable microbiomes, which are colonised from the gut in selective manners and have highlighted not just the influence of the bacteriome but that of the mycobiome and virome on oncogenesis and health.
Collapse
Affiliation(s)
- Scott C Thomas
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
| | - George Miller
- Cancer Center, Holy Name Medical Center, Teaneck, NJ, USA
| | - Xin Li
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
- Perlmutter Cancer Institute, New York University Langone Medical Center, New York, NY, USA
- Department of Urology, New York University Grossman School of Medicine, New York, NY, USA
| | - Deepak Saxena
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, USA
- Perlmutter Cancer Institute, New York University Langone Medical Center, New York, NY, USA
- Department of Surgery, New York University Grossman School of Medicine, New York, NY, USA
| |
Collapse
|
44
|
Anderson SM, Sears CL. The Role of the Gut Microbiome in Cancer: A Review, With Special Focus on Colorectal Neoplasia and Clostridioides difficile. Clin Infect Dis 2023; 77:S471-S478. [PMID: 38051969 PMCID: PMC10697667 DOI: 10.1093/cid/ciad640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Indexed: 12/07/2023] Open
Abstract
The gut microbiome has coevolved with humans to aid in physiologic functions and prevent disease. An increasing prevalence of gut dysbiosis in modern society exists and has strong linkages to multiple disease processes common in the developed world. Mechanisms for microbiome-human interactions that impact host homeostasis include bacterial metabolite/toxin production, biofilm formation with mucous layer infiltration, and host immune system modulation. Most of this crosstalk occurs at the epithelial layer of the gut, and as such the role of these interactions in the induction of colorectal cancer-a highly prevalent disease globally and one undergoing significant epidemiologic shifts-is under increasing scrutiny. Although multiple individual gut bacteria have been hypothesized as possible driver organisms in the oncogenic process, no bacterium has been definitively identified as a causal agent of colorectal cancer, suggesting that host lifestyle factors, microbiome community interactions, and the mucosal and/or systemic immune response may play a critical role in the process. Recent evidence has emerged implicating the ubiquitous human pathogen Clostridioides difficile as a possible promoter of colorectal cancer through chronic toxin-mediated cellular changes. Although much remains to be defined regarding the natural history of infections caused by this pathogen and its potential for oncogenesis, it provides a strong model for the role of both individual bacteria and of the gut microbial community as a whole in the development of colorectal cancer.
Collapse
Affiliation(s)
- Sean M Anderson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Cynthia L Sears
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
45
|
Cao B, Zeng MN, Hao FX, Hao ZY, Zhang ZK, Liang XW, Wu YY, Zhang YH, Feng WS, Zheng XK. P-coumaric acid ameliorates Aβ 25-35-induced brain damage in mice by modulating gut microbiota and serum metabolites. Biomed Pharmacother 2023; 168:115825. [PMID: 37924791 DOI: 10.1016/j.biopha.2023.115825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/19/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease for which there is a lack of effective therapeutic drugs. There is great potential for natural products to be used in the development of anti-AD drugs. P-coumaric acid (PCA), a small molecule phenolic acid widely distributed in the plant kingdom, has pharmacological effects such as neuroprotection, but its anti-AD mechanism has not been fully elucidated. In the current study, we investigated the mechanism of PCA intervention in the Aβ25-35-induced AD model using gut microbiomics and serum metabolomics combined with in vitro and in vivo pharmacological experiments. PCA was found to ameliorate cognitive dysfunction and neuronal cell damage in Aβ25-35-injected mice as measured by behavioral, pathological and biochemical indicators. 16S rDNA sequencing and serum metabolomics showed that PCA reduced the abundance of pro-inflammatory-associated microbiota (morganella, holdemanella, fusicatenibacter and serratia) in the gut, which were closely associated with metabolites of the glucose metabolism, arachidonic acid metabolism, tyrosine metabolism and phospholipid metabolism pathways in serum. Next, in vivo and in vitro pharmacological investigations revealed that PCA regulated Aβ25-35-induced disruption of glucose metabolism through activation of PI3K/AKT/Glut1 signaling. Additionally, PCA ameliorated Aβ25-35-induced neuroinflammation by inhibiting nuclear translocation of NF-κB and by modulating upstream MAPK signaling. In conclusion, PCA ameliorated cognitive deficits in Aβ25-35-induced AD mice by regulating glucose metabolism and neuroinflammation, and the mechanism is related not only to restoring homeostasis of gut microbiota and serum metabolites, but also to PI3K/AKT/Glut1 and MAPK/NF-κB signaling.
Collapse
Affiliation(s)
- Bing Cao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Meng-Nan Zeng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Feng-Xiao Hao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Zhi-You Hao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Zhen-Kai Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Xi-Wen Liang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Yuan-Yuan Wu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Yu-Han Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Wei-Sheng Feng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China; Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of PR China, China.
| | - Xiao-Ke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China; Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of PR China, China.
| |
Collapse
|
46
|
Chen Z, Guan D, Wang Z, Li X, Dong S, Huang J, Zhou W. Microbiota in cancer: molecular mechanisms and therapeutic interventions. MedComm (Beijing) 2023; 4:e417. [PMID: 37937304 PMCID: PMC10626288 DOI: 10.1002/mco2.417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023] Open
Abstract
The diverse bacterial populations within the symbiotic microbiota play a pivotal role in both health and disease. Microbiota modulates critical aspects of tumor biology including cell proliferation, invasion, and metastasis. This regulation occurs through mechanisms like enhancing genomic damage, hindering gene repair, activating aberrant cell signaling pathways, influencing tumor cell metabolism, promoting revascularization, and remodeling the tumor immune microenvironment. These microbiota-mediated effects significantly impact overall survival and the recurrence of tumors after surgery by affecting the efficacy of chemoradiotherapy. Moreover, leveraging the microbiota for the development of biovectors, probiotics, prebiotics, and synbiotics, in addition to utilizing antibiotics, dietary adjustments, defensins, oncolytic virotherapy, and fecal microbiota transplantation, offers promising alternatives for cancer treatment. Nonetheless, due to the extensive and diverse nature of the microbiota, along with tumor heterogeneity, the molecular mechanisms underlying the role of microbiota in cancer remain a subject of intense debate. In this context, we refocus on various cancers, delving into the molecular signaling pathways associated with the microbiota and its derivatives, the reshaping of the tumor microenvironmental matrix, and the impact on tolerance to tumor treatments such as chemotherapy and radiotherapy. This exploration aims to shed light on novel perspectives and potential applications in the field.
Collapse
Affiliation(s)
- Zhou Chen
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Defeng Guan
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Zhengfeng Wang
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Xin Li
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
| | - Shi Dong
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
| | - Junjun Huang
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Wence Zhou
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
| |
Collapse
|
47
|
Kalayci FNC, Ozen S. Possible Role of Dysbiosis of the Gut Microbiome in SLE. Curr Rheumatol Rep 2023; 25:247-258. [PMID: 37737528 DOI: 10.1007/s11926-023-01115-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
PURPOSE OF REVIEW The resident gut microbiota serves as a double-edged sword that aids the host in multiple ways to preserve a healthy equilibrium and serve as early companions and boosters for the gradual evolution of our immune defensive layers; nevertheless, the perturbation of the symbiotic resident intestinal communities has a profound impact on autoimmunity induction, particularly in systemic lupus erythematosus (SLE). Herein, we seek to critically evaluate the microbiome research in SLE with a focus on intestinal dysbiosis. RECENT FINDINGS SLE is a complex and heterogeneous disorder with self-attack due to loss of tolerance, and there is aberrant excessive immune system activation. There is mounting evidence suggesting that intestinal flora disturbances may accelerate the formation and progression of SLE, presumably through a variety of mechanisms, including intestinal barrier dysfunction and leaky gut, molecular mimicry, bystander activation, epitope spreading, gender bias, and biofilms. Gut microbiome plays a critical role in SLE pathogenesis, and additional studies are warranted to properly define the impact of gut microbiome in SLE, which can eventually lead to new and potentially safer management approaches for this debilitating disease.
Collapse
Affiliation(s)
| | - Seza Ozen
- Department of Paediatric Rheumatology, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
| |
Collapse
|
48
|
Tang JL, Zhao MC, Chen H, Zhao BE, Wang YY, Guo YC, Wang TT, Cheng X, Ruan HR, Zhang JT, Wang HB. Lactiplantibacillus plantarum GL001 alleviates jejunal oxidative damage induced by intestinal ischemia-reperfusion injury by influencing jejunal tissue metabolism through the improvement of jejunal microbial composition. Life Sci 2023; 334:122234. [PMID: 37931744 DOI: 10.1016/j.lfs.2023.122234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
Intestinal ischemia-reperfusion (IIR) injury is associated with inflammation and oxidative stress, yet its precise mechanisms remain not fully understood. IIR injury is closely linked to the gut microbiota and its metabolites. The anti-inflammatory and antioxidant effects of Lactiplantibacillus plantarum are specific to IIR. In our study, we conducted a 30-day pre-treatment of SD rats with both a standard strain of Lactiplantibacillus plantarum and Lactiplantibacillus plantarum GL001. After a 7-day cessation of treatment, we induced an IIR injury model to investigate the mechanisms by which Lactiplantibacillus plantarum alleviates IIR damage. The results demonstrate that Lactiplantibacillus plantarum effectively mitigates the inflammatory and oxidative stress damage induced by IIR. Lactiplantibacillus plantarum GL001 can improve the gut microbiota by reducing the abundance of harmful bacteria and increasing the abundance of beneficial bacteria. In IIR intestinal tissue, the levels of secondary bile acids are elevated. The content of the bacterial metabolite Calcimycin increases. Annotations of metabolic pathways suggest that Lactiplantibacillus plantarum GL001 can alleviate IIR damage by modulating calcium-phosphorus homeostasis through the regulation of parathyroid hormone synthesis, secretion, and action. Microbiota-metabolite correlation analysis reveals a significant negative correlation between calcimycin and Lactonacillus and a significant positive correlation between calcimycin and Shigella. There is also a significant positive correlation between calcimycin and secondary bile acids. Lactiplantibacillus plantarum GL001 can alleviate oxidative damage induced by IIR through improvements in gut microbiota and intestinal tissue metabolism.
Collapse
Affiliation(s)
- Ji-Lang Tang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Ming-Chao Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Hong Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Bing-Er Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Ying-Ying Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Ying-Chao Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Tian-Tian Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Xin Cheng
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Hong-Ri Ruan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Jian-Tao Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China
| | - Hong-Bin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, China.
| |
Collapse
|
49
|
Pernigoni N, Guo C, Gallagher L, Yuan W, Colucci M, Troiani M, Liu L, Maraccani L, Guccini I, Migliorini D, de Bono J, Alimonti A. The potential role of the microbiota in prostate cancer pathogenesis and treatment. Nat Rev Urol 2023; 20:706-718. [PMID: 37491512 DOI: 10.1038/s41585-023-00795-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
The human body hosts a complex and dynamic population of trillions of microorganisms - the microbiota - which influences the body in homeostasis and disease, including cancer. Several epidemiological studies have associated specific urinary and gut microbial species with increased risk of prostate cancer; however, causal mechanistic data remain elusive. Studies have associated bacterial generation of genotoxins with the occurrence of TMPRSS2-ERG gene fusions, a common, early oncogenic event during prostate carcinogenesis. A subsequent study demonstrated the role of the gut microbiota in prostate cancer endocrine resistance, which occurs, at least partially, through the generation of androgenic steroids fuelling oncogenic signalling via the androgen receptor. These studies present mechanistic evidence of how the host microbiota might be implicated in prostate carcinogenesis and tumour progression. Importantly, these findings also reveal potential avenues for the detection and treatment of prostate cancer through the profiling and modulation of the host microbiota. The latter could involve approaches such as the use of faecal microbiota transplantation, prebiotics, probiotics, postbiotics or antibiotics, which can be used independently or combined with existing treatments to reverse therapeutic resistance and improve clinical outcomes in patients with prostate cancer.
Collapse
Affiliation(s)
- Nicolò Pernigoni
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Christina Guo
- Institute of Cancer Research, London, UK
- Royal Marsden Hospital, London, UK
| | | | - Wei Yuan
- Institute of Cancer Research, London, UK
| | - Manuel Colucci
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Martina Troiani
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Lei Liu
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Luisa Maraccani
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine, Padova, Italy
| | - Ilaria Guccini
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Denis Migliorini
- Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Léman, Lausanne and Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Johann de Bono
- Institute of Cancer Research, London, UK
- Royal Marsden Hospital, London, UK
| | - Andrea Alimonti
- Institute of Oncology Research, Bellinzona, Switzerland.
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
- Veneto Institute of Molecular Medicine, Padova, Italy.
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland.
- Department of Medicine, University of Padova, Padova, Italy.
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
50
|
Wei K, Gong F, Wu J, Tang W, Liao F, Han Z, Pei Z, Lei H, Wang L, Shao M, Liu Z, Cheng L. Orally Administered Silicon Hydrogen Nanomaterials as Target Therapy to Treat Intestinal Diseases. ACS NANO 2023; 17:21539-21552. [PMID: 37843009 DOI: 10.1021/acsnano.3c06551] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The occurrence and development of inflammatory bowel diseases (IBDs) are inextricably linked to the excessive production of reactive oxygen species (ROS). Thus, there is an urgent need to develop innovative tactics to combat IBDs and scavenge excess ROS from affected areas. Herein, silicon hydrogen nanoparticles (SiH NPs) with ROS-scavenging ability were prepared by etching Si nanowires (NWs) with hydrogen fluoride (HF) to alleviate the symptoms associated with IBD by orally targeting the inflamed colonic sites. The strong reductive Si-H bonds showed excellent stability in the gastric and intestinal fluids, which exhibited efficient ROS-scavenging effects to protect cells from high oxidative stress-induced death. After oral delivery, the negatively charged SiH NPs were specifically adsorbed to the positively charged inflammatory epithelial tissues of the colon for an extended period via electrostatic interactions to prolong the colonic residence time. SiH NPs exhibited significant preventive and therapeutic effects in dextran sodium sulfate-induced prophylactic and therapeutic mouse models by inhibiting colonic shortening, reducing the secretion of pro-inflammatory cytokines, regulating macrophage polarization, and protecting the colonic barrier. As determined using 16S rDNA high-throughput sequencing, the oral administration of SiH NPs treatment led to changes in the abundance of the intestinal microbiome, which improved the bacterial diversity and restored the relative abundance of beneficial bacteria after the inflamed colon. Overall, our findings highlight the broad application of SiH-based anti-inflammatory drugs in the treatment of IBD and other inflammatory diseases.
Collapse
Affiliation(s)
- Kailu Wei
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Fei Gong
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Jie Wu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Wei Tang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Fan Liao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Zhihui Han
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Zifan Pei
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Huali Lei
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Li Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Mingwang Shao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
- Macao Institute of Materials Science and Engineering, Macau University of Science and Technology, Taipa 999078, Macau SAR, China
| | - Liang Cheng
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
- Macao Institute of Materials Science and Engineering, Macau University of Science and Technology, Taipa 999078, Macau SAR, China
| |
Collapse
|