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Shastry RP, Ghate SD, Hameed A, Prasad Rao RS, Bhandary YP, Shetty R. Emergence of rare and low abundant anaerobic gut Firmicutes is associated with a significant downfall of Klebsiella in human colon cancer. Microb Pathog 2024; 193:106726. [PMID: 38848931 DOI: 10.1016/j.micpath.2024.106726] [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: 01/10/2024] [Revised: 05/25/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Gut bacterial dysbiosis has been linked to several gastrointestinal diseases, including deadly colorectal cancer (CRC), a leading cause of mortality in cancer patients. However, perturbation in gut bacteriome during colon cancer (CC, devoid of colorectal malignancy) remains poorly explored. Here, 16S rRNA gene amplicon sequencing was carried out for fecal DNA samples targeted to hypervariable V3-V4 region by employing MiSeq platform to explore the gut bacterial community shift in CC patients. While alpha diversity indices predicted high species richness and diversity, beta diversity showed marked gut bacterial compositional dissimilarity in CC versus healthy controls (HC, n = 10 each). We observed a significant (p < 0.05, Wilcoxon Rank-Sum test) emergence of low-abundant anaerobic taxa, including Parvimonas and Peptostreptococcus, in addition to Subdoligranulum, Coprococcus, Holdemanella, Solobacterium, Bilophila, Blautia, Dorea, Moryella and several unidentified taxa, mainly affiliated to Firmicutes, in CC patients. In addition, we also traced the emergence of putative probiotic taxon Slackia, belonging to Actinomycetota, in CC patients. The emergence of anaerobic Firmicutes in CC is accompanied by a significant (p < 0.05) decline in the Klebsiella, as determined through linear discriminant analysis effect size (LEfSe) and heat tree analyses. Shifts in core microbiome and variation in network correlation were also witnessed. Taken together, this study highlighted a significant and consistent emergence of rare anaerobic Firmicutes suggesting possible anaerobiosis driving gut microbial community shift, which could be exploited in designing diagnostic and therapeutic tools targeted to CC.
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Affiliation(s)
- Rajesh P Shastry
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangaluru, 575018, India.
| | - Sudeep D Ghate
- Center for Bioinformatics, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - R Shyama Prasad Rao
- Center for Bioinformatics, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Yashodhar P Bhandary
- Division of Cell Biology and Molecular Genetics, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Rohan Shetty
- Department of Surgical Oncology, Yenepoya Medical College Hospital, Deralakatte, Mangaluru, 575018, India
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Acheampong DA, Jenjaroenpun P, Wongsurawat T, Krulilung A, Pomyen Y, Kandel S, Kunadirek P, Chuaypen N, Kusonmano K, Nookaew I. CAIM: Coverage-based Analysis for Identification of Microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591018. [PMID: 38746391 PMCID: PMC11091946 DOI: 10.1101/2024.04.25.591018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.
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Affiliation(s)
- Daniel A. Acheampong
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Division of Medical Bioinformatics, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Division of Medical Bioinformatics, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Alongkorn Krulilung
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yotsawat Pomyen
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Sangam Kandel
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Pattapon Kunadirek
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, 10150, Thailand
- Systems Biology and Bioinformatics Research Laboratory, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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3
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Xiang K, Li CX, Chen R, Zhao CH. Genetically predicted gut microbiome and risk of oral cancer. Cancer Causes Control 2024; 35:429-435. [PMID: 37815646 DOI: 10.1007/s10552-023-01800-0] [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: 06/01/2023] [Accepted: 09/08/2023] [Indexed: 10/11/2023]
Abstract
PURPOSE Mounting evidence suggests a possible link between gut microbiome and oral cancer, pointing to some potential modifiable targets for disease prevention. In the present study, Mendelian randomization (MR) was used to explore whether there was a causal link between gut microbiome and oral cancer. METHODS The single nucleotide polymorphisms (SNPs) significantly associated with gut microbiome were served as instrumental variables. MR analyses were performed using genetic approaches such as inverse variance weighting (IVW), MR Egger and weighted median, with IVW as the primary approach, supplemented by MR Egger and weighted median. Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) and MR-Egger regression were used to detect the presence of horizontal pleiotropy and identify outlier SNPs. RESULTS Causal effect estimates indicated that genetically predicted abundance of Prevotellaceae was associated with higher risk of oral cancer (odds ratio (OR) 1.80, 95% confidence interval (CI) 1.16-2.81, p = 0.009). There was no evidence of notable heterogeneity and horizontal pleiotropy. CONCLUSION Genetically derived estimates suggest that Prevotellaceae may be associated with the risk of oral cancer. Such robust evidence should be given priority in future studies and explore the underlying mechanisms.
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Affiliation(s)
- Kun Xiang
- Key Laboratory of Oral Diseases Research of Anhui Province, College & Hospital of Stomatology, Anhui Medical University, Hefei, 230032, Anhui, People's Republic of China
| | - Cheng-Xi Li
- Key Laboratory of Oral Diseases Research of Anhui Province, College & Hospital of Stomatology, Anhui Medical University, Hefei, 230032, Anhui, People's Republic of China
| | - Ran Chen
- Key Laboratory of Oral Diseases Research of Anhui Province, College & Hospital of Stomatology, Anhui Medical University, Hefei, 230032, Anhui, People's Republic of China.
| | - Chun-Hui Zhao
- Key Laboratory of Oral Diseases Research of Anhui Province, College & Hospital of Stomatology, Anhui Medical University, Hefei, 230032, Anhui, People's Republic of China.
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Sulit AK, Daigneault M, Allen-Vercoe E, Silander OK, Hock B, McKenzie J, Pearson J, Frizelle FA, Schmeier S, Purcell R. Bacterial lipopolysaccharide modulates immune response in the colorectal tumor microenvironment. NPJ Biofilms Microbiomes 2023; 9:59. [PMID: 37612266 PMCID: PMC10447454 DOI: 10.1038/s41522-023-00429-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Immune responses can have opposing effects in colorectal cancer (CRC), the balance of which may determine whether a cancer regresses, progresses, or potentially metastasizes. These effects are evident in CRC consensus molecular subtypes (CMS) where both CMS1 and CMS4 contain immune infiltrates yet have opposing prognoses. The microbiome has previously been associated with CRC and immune response in CRC but has largely been ignored in the CRC subtype discussion. We used CMS subtyping on surgical resections from patients and aimed to determine the contributions of the microbiome to the pleiotropic effects evident in immune-infiltrated subtypes. We integrated host gene-expression and meta-transcriptomic data to determine the link between immune characteristics and microbiome contributions in these subtypes and identified lipopolysaccharide (LPS) binding as a potential functional mechanism. We identified candidate bacteria with LPS properties that could affect immune response, and tested the effects of their LPS on cytokine production of peripheral blood mononuclear cells (PBMCs). We focused on Fusobacterium periodonticum and Bacteroides fragilis in CMS1, and Porphyromonas asaccharolytica in CMS4. Treatment of PBMCs with LPS isolated from these bacteria showed that F. periodonticum stimulates cytokine production in PBMCs while both B. fragilis and P. asaccharolytica had an inhibitory effect. Furthermore, LPS from the latter two species can inhibit the immunogenic properties of F. periodonticum LPS when co-incubated with PBMCs. We propose that different microbes in the CRC tumor microenvironment can alter the local immune activity, with important implications for prognosis and treatment response.
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Affiliation(s)
- A K Sulit
- School of Natural Sciences, Massey University, Auckland, New Zealand.
- Department of Surgery and Critical Care, University of Otago, Christchurch, New Zealand.
| | - M Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | - E Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | - O K Silander
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - B Hock
- Haematology Research Group, University of Otago, Christchurch, New Zealand
| | - J McKenzie
- Haematology Research Group, University of Otago, Christchurch, New Zealand
| | - J Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - F A Frizelle
- Department of Surgery and Critical Care, University of Otago, Christchurch, New Zealand
| | - S Schmeier
- School of Natural Sciences, Massey University, Auckland, New Zealand
- Evotec SE, Hamburg, Germany
| | - R Purcell
- Department of Surgery and Critical Care, University of Otago, Christchurch, New Zealand
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5
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Aiyoshi T, Kakihara T, Watanabe E, Tanaka N, Ogata Y, Masuoka H, Kurokawa R, Fujishiro J, Masumoto K, Suda W. A comprehensive microbial analysis of pediatric patients with acute appendicitis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:695-704. [PMID: 37029071 DOI: 10.1016/j.jmii.2023.03.006] [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: 06/23/2022] [Revised: 02/06/2023] [Accepted: 03/12/2023] [Indexed: 04/09/2023]
Abstract
BACKGROUND Pathogenesis of pediatric acute appendicitis (AA) is yet to be elucidated. Therefore, we performed a comprehensive microbial analysis of saliva, feces, and appendiceal lumen of AA patients using 16S ribosomal RNA (rRNA) gene amplicon sequencing to elucidate the pathogenesis of pediatric AA. METHODS This study included 33 AA patients and 17 healthy controls (HCs) aged <15 y. Among the AA patients, 18 had simple appendicitis, and 15 had complicated appendicitis. Salivary and fecal samples were obtained from both groups. The contents of the appendiceal lumen were collected from the AA group. All samples were analyzed using 16S rRNA gene amplicon sequencing. RESULTS The relative abundance of Fusobacterium was significantly higher in the saliva of AA patients as compared to that in HCs (P = 0.011). Bacteroides, Escherichia, Fusobacterium, Coprobacillus, and Flavonifractor were significantly increased in the feces of AA patients, as compared to that in HCs (P = 0.020, 0.010, 0.029, 0.031, and 0.002, respectively). In the appendiceal lumen, Bacteroides, Parvimonas, Fusobacterium, and Alloprevotella were the top bacterial genera with an average relative abundance >5% (16.0%, 9.1%, 7.9%, and 6.0%, respectively). CONCLUSIONS The relative abundance of Fusobacterium was high in the appendiceal lumen of pediatric AA patients. Moreover, the relative abundance of Fusobacterium was significantly higher in the saliva and feces of pediatric AA patients than in those of healthy children. These results suggest that ectopic colonization of oral Fusobacterium in the appendix might play an important role in the pathogenesis of pediatric AA.
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Affiliation(s)
- Tsubasa Aiyoshi
- Department of Pediatric Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomo Kakihara
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eiichiro Watanabe
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan; Division of Surgery, Department of Surgical Specialties, National Center for Child Health and Development, Tokyo, Japan
| | - Nao Tanaka
- Department of Pediatric Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yusuke Ogata
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroaki Masuoka
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Rina Kurokawa
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Fujishiro
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kouji Masumoto
- Department of Pediatric Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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6
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Romero-Garmendia I, Garcia-Etxebarria K. From Omic Layers to Personalized Medicine in Colorectal Cancer: The Road Ahead. Genes (Basel) 2023; 14:1430. [PMID: 37510334 PMCID: PMC10379575 DOI: 10.3390/genes14071430] [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: 05/25/2023] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Colorectal cancer is a major health concern since it is a highly diagnosed cancer and the second cause of death among cancers. Thus, the most suitable biomarkers for its diagnosis, prognosis, and treatment have been studied to improve and personalize the prevention and clinical management of colorectal cancer. The emergence of omic techniques has provided a great opportunity to better study CRC and make personalized medicine feasible. In this review, we will try to summarize how the analysis of the omic layers can be useful for personalized medicine and the existing difficulties. We will discuss how single and multiple omic layer analyses have been used to improve the prediction of the risk of CRC and its outcomes and how to overcome the challenges in the use of omic layers in personalized medicine.
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Affiliation(s)
- Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), 48940 Leioa, Spain
| | - Koldo Garcia-Etxebarria
- Biodonostia, Gastrointestinal Genetics Group, 20014 San Sebastián, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain
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Negrut RL, Cote A, Maghiar AM. Exploring the Potential of Oral Microbiome Biomarkers for Colorectal Cancer Diagnosis and Prognosis: A Systematic Review. Microorganisms 2023; 11:1586. [PMID: 37375087 DOI: 10.3390/microorganisms11061586] [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: 05/23/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
There is growing evidence indicating that the oral microbiota, specifically certain periodontopathogens such as Fusobacterium nucleatum, may play a role in the development of colorectal cancer and that it could potentially be used as a biomarker for diagnosing colorectal cancer (CRC). The question beneath this systematic review is whether the development or progression of colorectal cancer can be attributed to the presence of certain oral bacteria, which could be used for discovering non-invasive biomarkers for CRC. This review aims to give an overview of the actual status of published studies regarding the oral pathogens related to colorectal cancer and assess the effectiveness of the oral microbiome derived biomarkers. A systematic literature search was performed using four databases, Web of Science, Scopus, PubMed, and Science Direct, on the 3rd and 4th of March 2023. The studies that did not have matching inclusion/exclusion criteria were winnowed out. A total of fourteen studies were included. The risk of bias was performed by using QUADAS-2. After assessing the studies, the general conclusion is that oral microbiota-based biomarkers can become a promising non-invasive tool for detecting CRC, but further research is needed in order to determine the mechanisms of oral dysbiosis in colorectal carcinogenesis.
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Affiliation(s)
- Roxana Loriana Negrut
- Department Medicine, Doctoral School of Biomedical Sciences, Faculty of Medicine and Pharmacy, University of Oradea, 410087 Oradea, Romania
- County Clinical Emergency Hospital Bihor, 410087 Oradea, Romania
| | - Adrian Cote
- Department of Surgical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Adrian Marius Maghiar
- Department Medicine, Doctoral School of Biomedical Sciences, Faculty of Medicine and Pharmacy, University of Oradea, 410087 Oradea, Romania
- Department of Surgical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
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8
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Huang Z, Chang Y, Hao K, Tan Y, Ding L, Wang L, Wang Z, Pan Z, Gao H, Wu J, Zhu Y, Gao Q, Bi Y, Yang R. Immunomagnetic-bead enriched culturomics (IMBEC) for isolating pathobionts from feces of colorectal cancer patients. IMETA 2023; 2:e100. [PMID: 38868439 PMCID: PMC10989793 DOI: 10.1002/imt2.100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 06/14/2024]
Abstract
Culturomics employs various cultivating conditions to obtain different types of bacteria and new species. However, current culturomics lacks a highly efficient method for isolating specific pathobionts. Immunomagnetic bead technology, which uses magnetic beads conjugated with antibodies for capturing the antigen to realize enrichment of the targets, has been employed as an alternative method. In this study, we developed a novel method, immunomagnetic bead-enriched culturomics (IMBEC), in which magnetic bead-conjugated antibodies purified from the fecal samples of patients with colorectal cancer (CRC) were used to enrich and isolate potential pathobionts. A protocol for enriching potential pathobionts via immunomagnetic capture was developed by optimizing the concentrations of coupling reagents, NaCl, and detergent. The efficacy of pathobiont enrichment was compared between antibody-coated magnetic beads (antibody group) and nonconjugated blank magnetic beads (blank group). To determine the proinflammatory potential of isolates from both groups, we investigated their ability to induce cytokine production in THP-1 macrophages. This protocol was employed for isolating bacteria from 10 fecal samples of patients with CRC, which were simultaneously compared with those isolated from the blank group. A total of 209 bacterial species were isolated from both groups, including 173 from the antibody group, 160 from the blank group, and 124 from both groups. Bacteria isolated from the antibody group produced more proinflammatory cytokines than those isolated from the blank group. IMBEC is a promising method for relatively specific isolation of potential pathobionts for a particular disease of interest.
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Affiliation(s)
- Ziran Huang
- The Key and Characteristic Laboratory of Modern Pathogen Biology, School of Basic Medical SciencesGuizhou Medical UniversityGuiyangChina
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yuxiao Chang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Kun Hao
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
| | - Yafang Tan
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
| | - Lei Ding
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Likun Wang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhen Wang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhiyuan Pan
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Hong Gao
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Jiahong Wu
- The Key and Characteristic Laboratory of Modern Pathogen Biology, School of Basic Medical SciencesGuizhou Medical UniversityGuiyangChina
| | - Yubing Zhu
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Qi Gao
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
| | - Yujing Bi
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
| | - Ruifu Yang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (BZ0329)BeijingChina
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Microbiota Phenotype Promotes Anastomotic Leakage in a Model of Rats with Ischemic Colon Resection. Microorganisms 2023; 11:microorganisms11030680. [PMID: 36985253 PMCID: PMC10054737 DOI: 10.3390/microorganisms11030680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Anastomotic leakage (AL) is a major cause of morbidity and mortality after colorectal surgery, but the mechanism behind this complication is still not fully understood. Despite the advances in surgical techniques and perioperative care, the complication rates have remained steady. Recently, it has been suggested that colon microbiota may be involved in the development of complications after colorectal surgery. The aim of this study was to evaluate the association of gut microbiota in the development of colorectal AL and their possible virulence strategies to better understand the phenomenon. Using 16S rRNA sequencing of samples collected on the day of surgery and the sixth day following surgery, we analyzed the changes in tissue-associated microbiota at anastomotic sites created in a model of rats with ischemic colon resection. We discovered a trend for lower microbial diversity in the AL group compared to non-leak anastomosis (NLA). There were no differences in relative abundance in the different types of microbial respiration between these groups and the high abundance of the facultative anaerobic Gemella palaticanis is a marker species that stands out as a distinctive feature.
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10
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Xiang X, Wang X, Shang Y, Ding Y. Microfluidic intestine-on-a-chip: Current progress and further perspectives of probiotic-foodborne pathogen interactions. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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11
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Zhang H, Zhang H, Jiang Q. Progress in research of gut microbiota in colorectal cancer. Shijie Huaren Xiaohua Zazhi 2023; 31:138-142. [DOI: 10.11569/wcjd.v31.i4.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The human gut microbiota is a large and complex microbial community that is linked to human health and disease. Intestinal homeostasis is dependent on the tight interplay between the host and gut microbiota. Moreover, the gut microbiota plays an important role in digestion and metabolism. In recent years, the gut microbiota is still the most studied topic, and numerous studies have shown that the gut microbiota is closely related to colorectal cancer. In this paper, we will review the relationship between the gut microbiota and colorectal cancer pathogenesis, prevention, and treatment, with an aim to provide some new ideas for the research of colorectal cancer.
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Affiliation(s)
- Hao Zhang
- Department of Laboratory Medicine, Chengbei District, Hangzhou First People's Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Hong Zhang
- Department of Laboratory Medicine, Chengbei District, Hangzhou First People's Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Qin Jiang
- Department of Laboratory Medicine, Chengbei District, Hangzhou First People's Hospital, Hangzhou 310022, Zhejiang Province, China
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12
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Yuan H, Gui R, Wang Z, Fang F, Zhao H. Gut microbiota: A novel and potential target for radioimmunotherapy in colorectal cancer. Front Immunol 2023; 14:1128774. [PMID: 36798129 PMCID: PMC9927011 DOI: 10.3389/fimmu.2023.1128774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers, with a high mortality rate, and is a major burden on human health worldwide. Gut microbiota regulate human immunity and metabolism through producing numerous metabolites, which act as signaling molecules and substrates for metabolic reactions in various biological processes. The importance of host-gut microbiota interactions in immunometabolic mechanisms in CRC is increasingly recognized, and interest in modulating the microbiota to improve patient's response to therapy has been raising. However, the specific mechanisms by which gut microbiota interact with immunotherapy and radiotherapy remain incongruent. Here we review recent advances and discuss the feasibility of gut microbiota as a regulatory target to enhance the immunogenicity of CRC, improve the radiosensitivity of colorectal tumor cells and ameliorate complications such as radiotoxicity. Currently, great breakthroughs in the treatment of non-small cell lung cancer and others have been achieved by radioimmunotherapy, but radioimmunotherapy alone has not been effective in CRC patients. By summarizing the recent preclinical and clinical evidence and considering regulatory roles played by microflora in the gut, such as anti-tumor immunity, we discuss the potential of targeting gut microbiota to enhance the efficacy of radioimmunotherapy in CRC and expect this review can provide references and fresh ideas for the clinical application of this novel strategy.
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Affiliation(s)
- Hanghang Yuan
- Department of Nuclear Medicine, The First Hospital of Jilin University, Changchun, China,National Health Commission (NHC) Key laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Ruirui Gui
- Department of Nuclear Medicine, The First Hospital of Jilin University, Changchun, China,National Health Commission (NHC) Key laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Zhicheng Wang
- National Health Commission (NHC) Key laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Fang Fang
- National Health Commission (NHC) Key laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China,*Correspondence: Fang Fang, ; Hongguang Zhao,
| | - Hongguang Zhao
- Department of Nuclear Medicine, The First Hospital of Jilin University, Changchun, China,*Correspondence: Fang Fang, ; Hongguang Zhao,
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13
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Tokuno H, Itoga T, Kasuga J, Okuma K, Hasuko K, Masuyama H, Benno Y. Method for estimating disease risk from microbiome data using structural equation modeling. Front Microbiol 2023; 14:1035002. [PMID: 36778866 PMCID: PMC9909428 DOI: 10.3389/fmicb.2023.1035002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/09/2023] [Indexed: 01/28/2023] Open
Abstract
The relationship between the human gut microbiota and disease is of increasing scientific interest. Previous investigations have focused on the differences in intestinal bacterial abundance between control and affected groups to identify disease biomarkers. However, different types of intestinal bacteria may have interacting effects and thus be considered biomarker complexes for disease. To investigate this, we aimed to identify a new kind of biomarker for atopic dermatitis using structural equation modeling (SEM). The biomarkers identified were latent variables, which are complex and derived from the abundance data for bacterial marker candidates. Groups of females and males classified as healthy participants [normal control (NC) (female: 321 participants, male: 99 participants)], and patients afflicted with atopic dermatitis only [AS (female: 45 participants, male: 13 participants)], with atopic dermatitis and other diseases [AM (female: 75 participants, male: 34 participants)], and with other diseases but without atopic dermatitis [OD (female: 1,669 participants, male: 866 participants)] were used in this investigation. The candidate bacterial markers were identified by comparing the intestinal microbial community compositions between the NC and AS groups. In females, two latent variables (lv) were identified; for lv1, the associated components (bacterial genera) were Alistipes, Butyricimonas, and Coprobacter, while for lv2, the associated components were Agathobacter, Fusicatenibacter, and Streptococcus. There was a significant difference in the lv2 scores between the groups with atopic dermatitis (AS, AM) and those without (NC, OD), and the genera identified for lv2 are associated with the suppression of inflammatory responses in the body. A logistic regression model to estimate the probability of atopic dermatitis morbidity with lv2 as an explanatory variable had an area under the curve (AUC) score of 0.66 when assessed using receiver operating characteristic (ROC) analysis, and this was higher than that using other logistic regression models. The results indicate that the latent variables, especially lv2, could represent the effects of atopic dermatitis on the intestinal microbiome in females. The latent variables in the SEM could thus be utilized as a new type of biomarker. The advantages identified for the SEM are as follows: (1) it enables the extraction of more sophisticated information when compared with models focused on individual bacteria and (2) it can improve the accuracy of the latent variables used as biomarkers, as the SEM can be expanded.
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Affiliation(s)
- Hidetaka Tokuno
- Symbiosis Solutions Inc., Tokyo, Japan,*Correspondence: Hidetaka Tokuno,
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14
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Wang L, Yu KC, Hou YQ, Guo M, Yao F, Chen ZX. Gut microbiome in tumorigenesis and therapy of colorectal cancer. J Cell Physiol 2023; 238:94-108. [PMID: 36409765 DOI: 10.1002/jcp.30917] [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: 08/02/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/22/2022]
Abstract
Colorectal cancer (CRC) is the malignant tumor with the highest incidence in the digestive system, and the gut microbiome plays a crucial role in CRC tumorigenesis and therapy. The gastrointestinal tract is the organ harboring most of the microbiota in humans. Changes in the gut microbiome in CRC patients suggest possible host-microbe interactions, thereby hinting the potential tumorigenesis, which provides new perspective for preventing, diagnosing, or treating CRC. In this review, we discuss the effects of gut microbiome dysbiosis on CRC, and reveal the mechanisms by which gut microbiome dysbiosis leads to CRC. Gut microbiome modulation with the aim to reverse the established gut microbial dysbiosis is a novel strategy for the prevention and treatment of CRC. In addition, this review summarizes that probiotic antagonize CRC tumorigenesis by protecting intestinal barrier function, inhibiting cancer cell proliferation, resisting oxidative stress, and enhancing host immunity. Finally, we highlight clinical applications of the gut microbiome, such as gut microbiome analysis-based biomarker screening and prediction, and microbe modulation-based CRC prevention, treatment enhancement, and treatment side effect reduction. This review provides the reference for the clinical application of gut microbiome in the prevention and treatment of CRC.
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Affiliation(s)
- Ling Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, People's Republic of China
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, People's Republic of China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, People's Republic of China
| | - Ke-Chun Yu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yun-Qing Hou
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Min Guo
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Fan Yao
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhen-Xia Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, People's Republic of China
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, People's Republic of China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, People's Republic of China
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15
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Gradisteanu Pircalabioru G, Chifiriuc MC, Picu A, Petcu LM, Trandafir M, Savu O. Snapshot into the Type-2-Diabetes-Associated Microbiome of a Romanian Cohort. Int J Mol Sci 2022; 23:ijms232315023. [PMID: 36499348 PMCID: PMC9741184 DOI: 10.3390/ijms232315023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/19/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
The prevalence of type 2 diabetes mellitus (T2D) is alarmingly increasing worldwide, urgently calling for a better understanding of the underlying mechanisms in order to step up prevention and improve therapeutic approaches. It is becoming evident that the gut microbiota seem to have an endless capacity to impact T2D. In this study, we profile the gut microbiome patterns in T2D patients from Romania, by using quantitative Real-Time PCR and next generation sequencing. We enrolled a total of 150 individuals (105 T2D patients, 50 of them without metformin treatment and 45 healthy volunteers). The levels of potentially beneficial butyrate-producing bacteria were significantly reduced, while potentially pathogenic microorganisms such as Enterobacteriaceae and Fusobacterium were enriched in T2D patients. We evaluated the correlation between clinical parameters and gut microbiota and identified the genera Bacteroides, Alistipes, Dialister, Bilophila and Sutterella as possible detrimental factors in T2D. Our findings suggest that the gut microbiota may be a potential target in novel approaches to halt the development of T2D-associated complications.
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Affiliation(s)
- Gratiela Gradisteanu Pircalabioru
- Research Institute of University of Bucharest (ICUB), 050095 Bucharest, Romania;
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Correspondence:
| | - Mariana-Carmen Chifiriuc
- Research Institute of University of Bucharest (ICUB), 050095 Bucharest, Romania;
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Romanian Academy, 010071 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
| | - Ariana Picu
- “N.C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 020042 Bucharest, Romania; (A.P.); (L.M.P.); (O.S.)
| | - Laura Madalina Petcu
- “N.C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 020042 Bucharest, Romania; (A.P.); (L.M.P.); (O.S.)
| | - Maria Trandafir
- Department of Doctoral School, “Carol Davila” University of Medicine and Pharmacy, 5th District, 050474 Bucharest, Romania;
| | - Octavian Savu
- “N.C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 020042 Bucharest, Romania; (A.P.); (L.M.P.); (O.S.)
- Department of Doctoral School, “Carol Davila” University of Medicine and Pharmacy, 5th District, 050474 Bucharest, Romania;
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16
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Li S, He M, Lei Y, Liu Y, Li X, Xiang X, Wu Q, Wang Q. Oral Microbiota and Tumor-A New Perspective of Tumor Pathogenesis. Microorganisms 2022; 10:2206. [PMID: 36363799 PMCID: PMC9692822 DOI: 10.3390/microorganisms10112206] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 09/11/2023] Open
Abstract
Microorganisms have long been known to play key roles in the initiation and development of tumors. The oral microbiota and tumorigenesis have been linked in epidemiological research relating to molecular pathology. Notably, some bacteria can impact distal tumors by their gastrointestinal or blood-borne transmission under pathological circumstances. Certain bacteria drive tumorigenesis and progression through direct or indirect immune system actions. This review systemically discusses the recent advances in the field of oral microecology and tumor, including the oncogenic role of oral microbial abnormalities and various potential carcinogenesis mechanisms (excessive inflammatory response, host immunosuppression, anti-apoptotic activity, and carcinogen secretion) to introduce future directions for effective tumor prevention.
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Affiliation(s)
- Simin Li
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Mingxin He
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Yumeng Lei
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Yang Liu
- Wuhan Asia General Hospital Affiliated to Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xinquan Li
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xiaochen Xiang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Qingming Wu
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Qiang Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
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17
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Hou X, Zheng Z, Wei J, Zhao L. Effects of gut microbiota on immune responses and immunotherapy in colorectal cancer. Front Immunol 2022; 13:1030745. [PMID: 36426359 PMCID: PMC9681148 DOI: 10.3389/fimmu.2022.1030745] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/24/2022] [Indexed: 08/13/2023] Open
Abstract
Accumulating evidence suggests that gut microbial dysbiosis is implicated in colorectal cancer (CRC) initiation and progression through interaction with host immune system. Given the intimate relationship between the gut microbiota and the antitumor immune responses, the microbiota has proven to be effective targets in modulating immunotherapy responses of preclinical CRC models. However, the proposed putative mechanisms of how these bacteria affect immune responses and immunotherapy efficacy remains obscure. In this review, we summarize recent findings of clinical gut microbial dysbiosis in CRC patients, the reciprocal interactions between gut microbiota and the innate and/or the adaptive immune system, as well as the effect of gut microbiota on immunotherapy response in CRC. Increased understanding of the gut microbiota-immune system interactions will benefit the rational application of microbiota to the clinical promising biomarker or therapeutic strategy as a cancer immunotherapy adjuvant.
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Affiliation(s)
| | | | | | - Ling Zhao
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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18
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Ghosh J, Schultz BM, Chan J, Wultsch C, Singh R, Shureiqi I, Chow S, Doymaz A, Varriano S, Driscoll M, Muse J, Kleiman FE, Krampis K, Issa JPJ, Sapienza C. Epigenome-Wide Study Identifies Epigenetic Outliers in Normal Mucosa of Patients with Colorectal Cancer. Cancer Prev Res (Phila) 2022; 15:755-766. [PMID: 36219239 PMCID: PMC9623234 DOI: 10.1158/1940-6207.capr-22-0258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 01/31/2023]
Abstract
Nongenetic predisposition to colorectal cancer continues to be difficult to measure precisely, hampering efforts in targeted prevention and screening. Epigenetic changes in the normal mucosa of patients with colorectal cancer can serve as a tool in predicting colorectal cancer outcomes. We identified epigenetic changes affecting the normal mucosa of patients with colorectal cancer. DNA methylation profiling on normal colon mucosa from 77 patients with colorectal cancer and 68 controls identified a distinct subgroup of normally-appearing mucosa with markedly disrupted DNA methylation at a large number of CpGs, termed as "Outlier Methylation Phenotype" (OMP) and are present in 15 of 77 patients with cancer versus 0 of 68 controls (P < 0.001). Similar findings were also seen in publicly available datasets. Comparison of normal colon mucosa transcription profiles of patients with OMP cancer with those of patients with non-OMP cancer indicates genes whose promoters are hypermethylated in the OMP patients are also transcriptionally downregulated, and that many of the genes most affected are involved in interactions between epithelial cells, the mucus layer, and the microbiome. Analysis of 16S rRNA profiles suggests that normal colon mucosa of OMPs are enriched in bacterial genera associated with colorectal cancer risk, advanced tumor stage, chronic intestinal inflammation, malignant transformation, nosocomial infections, and KRAS mutations. In conclusion, our study identifies an epigenetically distinct OMP group in the normal mucosa of patients with colorectal cancer that is characterized by a disrupted methylome, altered gene expression, and microbial dysbiosis. Prospective studies are needed to determine whether OMP could serve as a biomarker for an elevated epigenetic risk for colorectal cancer development. PREVENTION RELEVANCE Our study identifies an epigenetically distinct OMP group in the normal mucosa of patients with colorectal cancer that is characterized by a disrupted methylome, altered gene expression, and microbial dysbiosis. Identification of OMPs in healthy controls and patients with colorectal cancer will lead to prevention and better prognosis, respectively.
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Affiliation(s)
- Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Bryant M. Schultz
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Joe Chan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Claudia Wultsch
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, New York.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Rajveer Singh
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, New York
| | - Imad Shureiqi
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Stephanie Chow
- Nutrition Department, School of Urban Public Health at Hunter College, New York, New York
| | - Ahmet Doymaz
- Department of Chemistry, Hunter College, City University of New York, New York, New York
| | - Sophia Varriano
- The Graduate Center, City University of New York, New York, New York
| | | | - Jennifer Muse
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Frida E. Kleiman
- Department of Chemistry, Hunter College, City University of New York, New York, New York
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, New York.,Department of Biological Sciences, Hunter College, City University of New York, New York, New York.,Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | | | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania.,Corresponding Author: Carmen Sapienza, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, 3307 N. Broad Street, Room 300, Philadelphia, PA 19140. Phone: 215-707-7373; E-mail:
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19
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Romero-Garmendia I, Garcia-Etxebarria K. Host Genetics and Microbiota Interactions in Colorectal Cancer: Shared or Independent Risk? Microorganisms 2022; 10:2129. [PMID: 36363721 PMCID: PMC9697093 DOI: 10.3390/microorganisms10112129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 07/30/2023] Open
Abstract
The role of microbiota in colorectal cancer has been studied since alterations in its composition were observed. In addition, there are more and more pieces of evidence that microbiota could be implicated in colorectal cancer progression. Thus, the components of the microbiota could be biomarkers for the diagnosis and prognosis of colorectal cancer. In addition, it is important to address how the microbiota interacts with the host and how the host shapes the microbiota, in order to understand the biological pathways and mechanisms involved in their relationship and the consequences of their interactions in colorectal cancer. Thereby, it could be possible to find feasible measures and treatments to prevent or better diagnose colorectal cancer. In this review, we will try to summarize the role of the microbiota in colorectal cancer and its interactions with the host and the host genetics, coming to some conclusions that could be useful to find the gaps in our knowledge and propose future steps in this field.
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Affiliation(s)
- Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), 48940 Leioa, Spain
| | - Koldo Garcia-Etxebarria
- Gastrointestinal Genetics Group, Biodonostia, 20014 San Sebastián, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain
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20
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Koustas E, Trifylli EM, Sarantis P, Papadopoulos N, Aloizos G, Tsagarakis A, Damaskos C, Garmpis N, Garmpi A, Papavassiliou AG, Karamouzis MV. Implication of gut microbiome in immunotherapy for colorectal cancer. World J Gastrointest Oncol 2022; 14:1665-1674. [PMID: 36187397 PMCID: PMC9516653 DOI: 10.4251/wjgo.v14.i9.1665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/09/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) constitutes the third most frequently reported malignancy in the male population and the second most common in women in the last two decades. Colon carcinogenesis is a complex, multifactorial event, resulting from genetic and epigenetic aberrations, the impact of environmental factors, as well as the disturbance of the gut microbial ecosystem. The relationship between the intestinal microbiome and carcinogenesis was relatively undervalued in the last decade. However, its remarkable effect on metabolic and immune functions on the host has been in the spotlight as of recent years. There is a strong relationship between gut microbiome dysbiosis, bowel pathogenicity and responsiveness to anti-cancer treatment; including immunotherapy. Modifications of bacteriome consistency are closely associated with the immunologic response to immunotherapeutic agents. This condition that implies the necessity of gut microbiome manipulation. Thus, creatingan optimal response for CRC patients to immunotherapeutic agents. In this paper, we will review the current literature observing how gut microbiota influence the response of immunotherapy on CRC patients.
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Affiliation(s)
- Evangelos Koustas
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Eleni-Myrto Trifylli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Panagiotis Sarantis
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Nikolaos Papadopoulos
- 1st Department of Internal Medicine, 417 Army Share Fund Hospital of Athens, Athens 11521, Attica, Greece
| | - Georgios Aloizos
- 1st Department of Internal Medicine, 417 Army Share Fund Hospital of Athens, Athens 11521, Attica, Greece
| | | | - Christos Damaskos
- N.S. Christeas Laboratory of Experimental Surgery and Surgical Research, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Nikolaos Garmpis
- Second Department of Propedeutic Surgery, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Anna Garmpi
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Michalis V Karamouzis
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
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21
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Microbiome Profile of Dogs with Stage IV Multicentric Lymphoma: A Pilot Study. Vet Sci 2022; 9:vetsci9080409. [PMID: 36006324 PMCID: PMC9414525 DOI: 10.3390/vetsci9080409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/21/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Lymphoma is a common type of hematopoietic cancer encountered in small animal practices. Canine multicentric lymphoma represents 80% of lymphoma cases and is characterized by a spread of the disease in multiple lymph nodes and organs as well. A causal role of the gut microbiota in disease spread has been shown in different diseases. In this study, the gut microbiome of dogs diagnosed with stage IV multicentric lymphoma has been analyzed and compared with that of healthy dogs to evaluate potential changes linked to lymphoma and disease spread. Abstract Changes in the gut microbiome can be associated with diseases and affect the overall health of an individual. In the current study, the gut microbiome profile of dogs diagnosed with advanced stages of multicentric lymphoma was compared with that of healthy dogs and analyzed. For this purpose, dogs from veterinary hospitals diagnosed with lymphoma were selected and were further narrowed down to cases of stage IV multicentric lymphoma. Fecal samples from the selected sick and healthy dogs were collected and analyzed using MiSeq sequencing. The gut microbiota in the two groups of dogs was statistically analyzed and compared. The results revealed significant differences in the microbial populations present in sick and healthy dogs. Phylum Actinobacteria and two species (Corynebacterium amycolatum and Streptococcus lutetiensis) were found in high proportions in sick dogs and may be considered as potential biomarkers for canine stage IV multicentric lymphoma. Further investigations need to be conducted to understand the mechanisms they might be involved in.
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22
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Zhao L, Zhang X, Zhou Y, Fu K, Lau HCH, Chun TWY, Cheung AHK, Coker OO, Wei H, Wu WKK, Wong SH, Sung JJY, To KF, Yu J. Parvimonas micra promotes colorectal tumorigenesis and is associated with prognosis of colorectal cancer patients. Oncogene 2022; 41:4200-4210. [PMID: 35882981 PMCID: PMC9439953 DOI: 10.1038/s41388-022-02395-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Large-scale fecal shotgun metagenomic sequencing revealed the high abundance of Parvimonas micra in colorectal cancer (CRC) patients. We investigated the role and clinical significance of P. micra in colorectal tumorigenesis. The abundance of P. micra was examined in 309 fecal samples and 165 colon biopsy tissues of CRC patients and healthy subjects. P. micra was significantly enriched in fecal samples from 128 CRC patients compared to 181 healthy subjects (P < 0.0001); and in colon tissue biopsies from 52 CRC patients compared to 61 healthy subjects (P < 0.0001). Multivariate analysis showed that P. micra is an independent risk factor of poor survival in CRC patients (Hazard Ratio: 1.93). P. micra strain was isolated from feces of a CRC patient. Apcmin/+ mice gavaged with P. micra showed significantly higher tumor burden and tumor load (both P < 0.01). Consistently, gavage of P. micra significantly promoted colonocyte proliferation in conventional mice, which was further confirmed by germ-free mice. P. micra colonization up-regulated genes involved in cell proliferation, stemness, angiogenesis and invasiveness/metastasis; and enhanced Th17 cells infiltration and expression of Th17 cells-secreted cytokines (Il-17, Il-22, and Il-23) in the colon of Apcmin/+, conventional and germ-free mice. P. micra-conditioned medium significantly promoted the differentiation of CD4+ T cells to Th17 cells (IL-17+CD4+ phenotype) and enhanced the oncogenic Wnt signaling pathway. In conclusion, P. micra promoted colorectal tumorigenesis in mice by inducing colonocyte proliferation and altering Th17 immune response. P. micra may act as a prognostic biomarker for poor survival of CRC patients.
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Affiliation(s)
- Liuyang Zhao
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiang Zhang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yunfei Zhou
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kaili Fu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Harry Cheuk-Hay Lau
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tommy Wai-Yiu Chun
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Alvin Ho-Kwan Cheung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Olabisi Oluwabukola Coker
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hong Wei
- Center of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - William Ka-Kei Wu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sunny Hei Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Joseph Jao-Yiu Sung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, Shenzhen, The Chinese University of Hong Kong, Hong Kong SAR, China.
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23
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Chen S, Gui R, Zhou XH, Zhang JH, Jiang HY, Liu HT, Fu YF. Combined Microbiome and Metabolome Analysis Reveals a Novel Interplay Between Intestinal Flora and Serum Metabolites in Lung Cancer. Front Cell Infect Microbiol 2022; 12:885093. [PMID: 35586253 PMCID: PMC9108287 DOI: 10.3389/fcimb.2022.885093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
As the leading cause of cancer death, lung cancer seriously endangers human health and quality of life. Although many studies have reported the intestinal microbial composition of lung cancer, little is known about the interplay between intestinal microbiome and metabolites and how they affect the development of lung cancer. Herein, we combined 16S ribosomal RNA (rRNA) gene sequencing and liquid chromatography-mass spectrometry (LC-MS) technology to analyze intestinal microbiota composition and serum metabolism profile in a cohort of 30 lung cancer patients with different stages and 15 healthy individuals. Compared with healthy people, we found that the structure of intestinal microbiota in lung cancer patients had changed significantly (Adonis, p = 0.021). In order to determine how intestinal flora affects the occurrence and development of lung cancer, the Spearman rank correlation test was used to find the connection between differential microorganisms and differential metabolites. It was found that as thez disease progressed, L-valine decreased. Correspondingly, the abundance of Lachnospiraceae_UCG-006, the genus with the strongest association with L-valine, also decreased in lung cancer groups. Correlation analysis showed that the gut microbiome and serum metabolic profile had a strong synergy, and Lachnospiraceae_UCG-006 was closely related to L-valine. In summary, this study described the characteristics of intestinal flora and serum metabolic profiles of lung cancer patients with different stages. It revealed that lung cancer may be the result of the mutual regulation of L-valine and Lachnospiraceae_UCG-006 through the aminoacyl-tRNA biosynthesis pathway, and proposed that L-valine may be a potential marker for the diagnosis of lung cancer.
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Affiliation(s)
- Sai Chen
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Rong Gui
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiong-hui Zhou
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jun-hua Zhang
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hai-ye Jiang
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hai-ting Liu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yun-feng Fu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Yun-feng Fu,
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24
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Pratt M, Forbes JD, Knox NC, Van Domselaar G, Bernstein CN. Colorectal Cancer Screening in Inflammatory Bowel Diseases-Can Characterization of GI Microbiome Signatures Enhance Neoplasia Detection? Gastroenterology 2022; 162:1409-1423.e1. [PMID: 34998802 DOI: 10.1053/j.gastro.2021.12.287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/28/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
Current noninvasive methods for colorectal cancer (CRC) screening are not optimized for persons with inflammatory bowel diseases (IBDs), requiring patients to undergo frequent interval screening via colonoscopy. Although colonoscopy-based screening reduces CRC incidence in IBD patients, rates of interval CRC remain relatively high, highlighting the need for more targeted approaches. In recent years, the discovery of disease-specific microbiome signatures for both IBD and CRC has begun to emerge, suggesting that stool-based biomarker detection using metagenomics and other culture-independent technologies may be useful for personalized, early, noninvasive CRC screening in IBD patients. Here we discuss the utility of the stool microbiome as a noninvasive CRC screening tool. Comparing the performance of multiple microbiome-based CRC classifiers, including several multi-cohort meta-analyses, we find that noninvasive detection of colorectal adenomas and carcinomas from microbial biomarkers is an active area of study with promising early results.
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Affiliation(s)
- Molly Pratt
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jessica D Forbes
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Natalie C Knox
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Gary Van Domselaar
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Charles N Bernstein
- Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; University of Manitoba IBD Clinical and Research Centre, Winnipeg, Manitoba, Canada.
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25
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Leaky Gum: The Revisited Origin of Systemic Diseases. Cells 2022; 11:cells11071079. [PMID: 35406643 PMCID: PMC8997512 DOI: 10.3390/cells11071079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/10/2022] Open
Abstract
The oral cavity is the gateway for microorganisms into your body where they disseminate not only to the directly connected respiratory and digestive tracts but also to the many remote organs. Oral microbiota, travelling to the end of the intestine and circulating in our bodies through blood vessels, not only affect a gut microbiome profile but also lead to many systemic diseases. By gathering information accumulated from the era of focal infection theory to the age of revolution in microbiome research, we propose a pivotal role of “leaky gum”, as an analogy of “leaky gut”, to underscore the importance of the oral cavity in systemic health. The oral cavity has unique structures, the gingival sulcus (GS) and the junctional epithelium (JE) below the GS, which are rarely found anywhere else in our body. The JE is attached to the tooth enamel and cementum by hemidesmosome (HD), which is structurally weaker than desmosome and is, thus, vulnerable to microbial infiltration. In the GS, microbial biofilms can build up for life, unlike the biofilms on the skin and intestinal mucosa that fall off by the natural process. Thus, we emphasize that the GS and the JE are the weakest leaky point for microbes to invade the human body, making the leaky gum just as important as, or even more important than, the leaky gut.
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