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Chang CC, Liu TC, Lu CJ, Chiu HC, Lin WN. Explainable machine learning model for identifying key gut microbes and metabolites biomarkers associated with myasthenia gravis. Comput Struct Biotechnol J 2024; 23:1572-1583. [PMID: 38650589 PMCID: PMC11035017 DOI: 10.1016/j.csbj.2024.04.025] [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: 11/19/2023] [Revised: 03/14/2024] [Accepted: 04/07/2024] [Indexed: 04/25/2024] Open
Abstract
Diagnostic markers for myasthenia gravis (MG) are limited; thus, innovative approaches are required for supportive diagnosis and personalized care. Gut microbes are associated with MG pathogenesis; however, few studies have adopted machine learning (ML) to identify the associations among MG, gut microbiota, and metabolites. In this study, we developed an explainable ML model to predict biomarkers for MG diagnosis. We enrolled 19 MG patients and 10 non-MG individuals. Stool samples were collected and microbiome assessment was performed using 16S rRNA sequencing. Untargeted metabolic profiling was conducted to identify fecal amplicon significant variants (ASVs) and metabolites. We developed an explainable ML model in which the top ASVs and metabolites are combined to identify the best predictive performance. This model uses the SHapley Additive exPlanations method to generate both global and personalized explanations. Fecal microbe-metabolite composition differed significantly between groups. The key bacterial families were Lachnospiraceae and Ruminococcaceae, and the top three features were Lachnospiraceae, inosine, and methylhistidine. An ML model trained with the top 1 % ASVs and top 15 % metabolites combined outperformed all other models. Personalized explanations revealed different patterns of microbe-metabolite contributions in patients with MG. The integration of the microbiota-metabolite features and the development of an explainable ML framework can accurately identify MG and provide personalized explanations, revealing the associations between gut microbiota, metabolites, and MG. An online calculator employing this algorithm was developed that provides a streamlined interface for MG diagnosis screening and conducting personalized evaluations.
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Affiliation(s)
- Che-Cheng Chang
- PhD Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Neurology, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Tzu-Chi Liu
- Graduate Institute of Business Administration, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chi-Jie Lu
- Graduate Institute of Business Administration, Fu Jen Catholic University, New Taipei City, Taiwan
- Artificial Intelligence Development Center, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Information Management, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Hou-Chang Chiu
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Neurology, Taipei Medical University, Shuang-Ho Hospital, New Taipei City, Taiwan
| | - Wei-Ning Lin
- PhD Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan
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Yu J, Li L, Tao X, Chen Y, Dong D. Metabolic interactions of host-gut microbiota: New possibilities for the precise diagnosis and therapeutic discovery of gastrointestinal cancer in the future-A review. Crit Rev Oncol Hematol 2024; 203:104480. [PMID: 39154670 DOI: 10.1016/j.critrevonc.2024.104480] [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: 06/19/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024] Open
Abstract
Gastrointestinal (GI) cancer continues to pose a significant global health challenge. Recent advances in our understanding of the complex relationship between the host and gut microbiota have shed light on the critical role of metabolic interactions in the pathogenesis and progression of GI cancer. In this study, we examined how microbiota interact with the host to influence signalling pathways that impact the formation of GI tumours. Additionally, we investigated the potential therapeutic approach of manipulating GI microbiota for use in clinical settings. Revealing the complex molecular exchanges between the host and gut microbiota facilitates a deeper understanding of the underlying mechanisms that drive cancer development. Metabolic interactions hold promise for the identification of microbial signatures or metabolic pathways associated with specific stages of cancer. Hence, this study provides potential strategies for the diagnosis, treatment and management of GI cancers to improve patient outcomes.
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Affiliation(s)
- Jianing Yu
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; College of Pharmacy, Dalian Medical University, China
| | - Lu Li
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Xufeng Tao
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China.
| | - Yanwei Chen
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China.
| | - Deshi Dong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China.
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Kuriki N, Asahi Y, Okamoto M, Noiri Y, Ebisu S, Machi H, Suzuki M, Hayashi M. Synergistic effects of arginine and fluoride on human dental biofilm control. J Dent 2024; 149:105307. [PMID: 39178800 PMCID: PMC11391429 DOI: 10.1016/j.jdent.2024.105307] [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: 07/11/2024] [Revised: 08/07/2024] [Accepted: 08/10/2024] [Indexed: 08/26/2024] Open
Abstract
OBJECTIVES The aim of this study was to quantitatively and comprehensively investigate the combined effects of arginine and fluoride on the suppression of pathogenicity using an in situ biofilm model and next-generation sequencing (NGS). METHODS Using the in situ model, dental biofilms were formed and the viable bacterial counts and arginine activity in the arginine- and fluoride-containing dentifrice and control groups were measured. We also compared their effects on the bacterial microbiota and predictive functional factors in the control, arginine (arg), and arginine + fluoride (argF) groups using NGS analysis. RESULTS Compared to the control treatment, the use of 8 % arginine and 1450 ppm fluoride toothpaste resulted in significantly high oral NH4+ concentrations without affecting the number of viable bacteria (P < 0.05). NGS analysis revealed that the oral microbiota of the control, arg, and argF groups were significantly different. Heat map analysis of the predicted functional factors revealed that the arg group had different properties from the other groups and activated specific substrate metabolic pathways; contrastingly, argF treatment inhibited the activity of these pathways and prevented an increase in the abundance of bacterial genera that utilize substrates such as sucrose, suggesting the synergistic effect of arginine and fluoride. CONCLUSIONS This study indicates that the combination of arginine and fluoride has a synergistic effect on the bacterial microbiota and pathogenicity of dental biofilms compared with arginine alone. CLINICAL SIGNIFICANCE Our findings suggest that the combination of arginine and fluoride could be used as an effective prebiotic and may inhibit the growth of bacteria associated with dental diseases.
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Affiliation(s)
- Nanako Kuriki
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry, Osaka, Japan; Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA.
| | - Yoko Asahi
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Motoki Okamoto
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Yuichiro Noiri
- Division of Cariology, Operative Dentistry and Endodontics, Department of Oral Health Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shigeyuki Ebisu
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Hiroyuki Machi
- Osaka University Dental Technology Institute, Osaka, Japan
| | - Maiko Suzuki
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Mikako Hayashi
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry, Osaka, Japan
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Ren YM, Zhuang ZY, Xie YH, Yang PJ, Xia TX, Xie YL, Liu ZH, Kang ZR, Leng XX, Lu SY, Zhang L, Chen JX, Xu J, Zhao EH, Wang Z, Wang M, Cui Y, Tan J, Liu Q, Jiang WH, Xiong H, Hong J, Chen YX, Chen HY, Fang JY. BCAA-producing Clostridium symbiosum promotes colorectal tumorigenesis through the modulation of host cholesterol metabolism. Cell Host Microbe 2024; 32:1519-1535.e7. [PMID: 39106870 DOI: 10.1016/j.chom.2024.07.012] [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: 06/02/2023] [Revised: 01/21/2024] [Accepted: 07/11/2024] [Indexed: 08/09/2024]
Abstract
Identification of potential bacterial players in colorectal tumorigenesis has been a focus of intense research. Herein, we find that Clostridium symbiosum (C. symbiosum) is selectively enriched in tumor tissues of patients with colorectal cancer (CRC) and associated with higher colorectal adenoma recurrence after endoscopic polypectomy. The tumorigenic effect of C. symbiosum is observed in multiple murine models. Single-cell transcriptome profiling along with functional assays demonstrates that C. symbiosum promotes the proliferation of colonic stem cells and enhances cancer stemness. Mechanistically, C. symbiosum intensifies cellular cholesterol synthesis by producing branched-chain amino acids (BCAAs), which sequentially activates Sonic hedgehog signaling. Low dietary BCAA intake or blockade of cholesterol synthesis by statins could partially abrogate the C. symbiosum-induced cell proliferation in vivo and in vitro. Collectively, we reveal C. symbiosum as a bacterial driver of colorectal tumorigenesis, thus identifying a potential target in CRC prediction, prevention, and treatment.
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Affiliation(s)
- Yi-Meng Ren
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zi-Yan Zhuang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yuan-Hong Xie
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Peng-Jie Yang
- Chinese Academy of Sciences Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tian-Xue Xia
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yi-Le Xie
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zhu-Hui Liu
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zi-Ran Kang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Xiao-Xu Leng
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Shi-Yuan Lu
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Lu Zhang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Jin-Xian Chen
- Division of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jia Xu
- Division of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - En-Hao Zhao
- Division of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zheng Wang
- Division of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ming Wang
- Division of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yun Cui
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Juan Tan
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei-Hong Jiang
- Chinese Academy of Sciences Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hua Xiong
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
| | - Hao-Yan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
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5
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Ding R, Lu J, Huang X, Deng M, Wei H, Jiang G, Zhu H, Yuan H. The effect of immunotherapy PD-1 blockade on acute bone cancer pain: Insights from transcriptomic and microbiomic profiling. Int Immunopharmacol 2024; 142:113100. [PMID: 39244901 DOI: 10.1016/j.intimp.2024.113100] [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: 05/20/2024] [Revised: 08/08/2024] [Accepted: 09/03/2024] [Indexed: 09/10/2024]
Abstract
INTRODUCTION The skeletal system ranks as the third most common site for cancer metastasis, often leading to pain with nociceptive and neuropathic features. Programmed cell death protein 1 (PD-1)-targeting therapeutic antibodies offer effective cancer treatment but can cause treatment-related acute pain. Understanding the mechanisms of this pain and identifying potential interventions is still a challenge. METHODS A murine model of bone cancer pain was established using Lewis lung carcinoma (LLC) cells, followed by intravenous administration of nivolumab, a human anti-PD-1 monoclonal antibody. Pain thresholds were measured, and micro-CT images of the skeletal system were obtained. High-throughput sequencing of the spinal cord/colon transcriptome during the acute phase of bone cancer pain and gut microbiota analysis at the end of the treatment were performed. Immunofluorescence staining and western blot experiments assessed spinal cord microglia activation and acute pain-associated molecules. RESULTS PD-1 inhibition with nivolumab protected against bone degradation initiated by LLC cell administration but consistently induced acute pain during nivolumab treatment. Spinal cord and colon transcriptomics revealed an immunopathological pattern during tumor progression and the acute pain phase, with notable changes in interleukin and S100 gene families. Gut microbiota analysis post-immunotherapy showed a decline in beneficial bacteria associated with short-chain fatty acid (SCFA) production. Activation of spinal cord microglia and enhanced glycolytic metabolism were confirmed as key factors in inducing acute pain following immunotherapy. CONCLUSIONS This study reveals that nivolumab induces acute pain by activating microglia and enhancing glycolytic metabolism in the treatment of bone cancer and uncovers connections between transcriptomic changes, gut microbiota, and acute pain following immune checkpoint blockade (ICB) treatment. It offers novel insights into the relationship between immune checkpoint blockade therapies and pain management.
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Affiliation(s)
- Ruifeng Ding
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Jinfang Lu
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xingshuai Huang
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Mengqiu Deng
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Huawei Wei
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Guowei Jiang
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Hongwei Zhu
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Hongbin Yuan
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China.
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Zhou T, Wu J, Khan A, Hu T, Wang Y, Salama ES, Su S, Han H, Jin W, Li X. A probiotic Limosilactobacillus fermentum GR-3 mitigates colitis-associated tumorigenesis in mice via modulating gut microbiome. NPJ Sci Food 2024; 8:61. [PMID: 39242568 PMCID: PMC11379937 DOI: 10.1038/s41538-024-00307-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 08/29/2024] [Indexed: 09/09/2024] Open
Abstract
Bacterial therapy for colorectal cancer (CRC) represents a burgeoning frontier. The probiotic Limosilactobacillus fermentum GR-3, derived from traditional food "Jiangshui", exhibited superior antioxidant capacity by producing indole derivatives ICA and IPA. In an AOM/DSS-induced CRC mouse model, GR-3 treatment alleviated weight loss, colon shortening, rectal bleeding and intestinal barrier disruption by reducing oxidative stress and inflammation. GR-3 colonization in distant colon induced apoptosis and reduced tumor incidence by 51.2%, outperforming the control strain and vitamin C. The beneficial effect of GR-3 on CRC was associated with gut microbiome modulation, increasing SCFA producer Lachnospiraceae NK4A136 group and suppressing pro-inflammatory strain Bacteroides. Metagenomic and metabolic analyses revealed that GR-3 intervention upregulated antioxidant genes (xseA, ALDH) and butyrate synthesis gene (bcd), while increasing beneficial metabolites (SCFAs, ICA, IPA, VB12 and VD3) and reducing harmful secondary bile acids. Overall, GR-3 emerges as a promising candidate in CRC therapy, offering effective gut microbiome remediation.
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Affiliation(s)
- Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
| | - Jingyuan Wu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, 730000, China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Tianxiang Hu
- Georgia Cancer Center, Augusta University, 1410 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Yiqing Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, 730000, China
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China
| | - Shaochen Su
- Healthy Examination & Management Center, First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Huawen Han
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China.
| | - Weilin Jin
- Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China.
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
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Ravikrishnan A, Wijaya I, Png E, Chng KR, Ho EXP, Ng AHQ, Mohamed Naim AN, Gounot JS, Guan SP, Hanqing JL, Guan L, Li C, Koh JY, de Sessions PF, Koh WP, Feng L, Ng TP, Larbi A, Maier AB, Kennedy BK, Nagarajan N. Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes. Nat Commun 2024; 15:7751. [PMID: 39237540 PMCID: PMC11377447 DOI: 10.1038/s41467-024-52097-9] [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: 11/26/2023] [Accepted: 08/23/2024] [Indexed: 09/07/2024] Open
Abstract
While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun-metagenomic sequencing for high-resolution taxonomic and functional characterization of their gut microbiomes (n = 234). Joint species-level analysis with other Asian cohorts identified distinct age-associated shifts characterized by reduction in microbial richness, and specific Alistipes and Bacteroides species enrichment (e.g., Alistipes shahii and Bacteroides xylanisolvens). Functional analysis confirmed these changes correspond to metabolic potential expansion in aging towards alternate pathways synthesizing and utilizing amino-acid precursors, vis-à-vis dominant microbial guilds producing butyrate in gut from pyruvate (e.g., Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species (e.g., Parabacteroides goldsteinii) and pathobionts (e.g., Klebsiella pneumoniae), highlighting the microbiome's role as biomarkers and potential targets for promoting healthy aging.
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Affiliation(s)
- Aarthi Ravikrishnan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Indrik Wijaya
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Eileen Png
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Kern Rei Chng
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Eliza Xin Pei Ho
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Amanda Hui Qi Ng
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Ahmad Nazri Mohamed Naim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Jean-Sebastien Gounot
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Shou Ping Guan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Jasinda Lee Hanqing
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Lihuan Guan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Chenhao Li
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Jia Yu Koh
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Paola Florez de Sessions
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Woon-Puay Koh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Brenner Centre for Molecular Medicine, Singapore, 117609, Republic of Singapore
| | - Lei Feng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Tze Pin Ng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Anis Larbi
- Singapore Immunology Network (SigN), Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore, 138648, Republic of Singapore
| | - Andrea B Maier
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, The Netherlands
| | - Brian K Kennedy
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
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Hilmi M, Khati I, Turpin A, Andremont A, Burdet C, Grall N, Vidal J, Bousquet PJ, Rousseau B, Bihan-Benjamin CL. Association between the antibiotics use and recurrence in patients with resected colorectal cancer: EVADER-1, a nation-wide pharmaco-epidemiologic study. Dig Liver Dis 2024:S1590-8658(24)00892-2. [PMID: 39232868 DOI: 10.1016/j.dld.2024.07.030] [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: 02/29/2024] [Revised: 07/18/2024] [Accepted: 07/29/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND The impact of antibiotics (ATBs) on the risk of colorectal cancer (CRC) recurrence after curative resection remains unknown. METHODS Using the French nation-wide database of cancer patients, all newly diagnosed non-metastatic CRC patients resected between 01/2012 and 12/2014 were included. The perioperative ATB intake (from 6 months before surgery until 1 year after) was classified according to the class, the period of use (pre- vs post-resection), the disease stage (localized and locally advanced), and the primary tumor location (colon and rectum/junction). The primary endpoint was the 3-year disease-free survival (DFS). The impact of ATB was assessed using time-dependent multivariate Cox models. RESULTS A total of 35,496 CRC patients were included. Seventy-nine percent of patients had at least one ATB intake. Outpatient ATB intake after surgery was associated with unfavorable 3-year DFS. The ATBs associated with decreased 3-year DFS were cephalosporins, streptogramins, quinolones, penicillin A with beta-lactamase inhibitors, and antifungals with differential effects according to the primary tumor location and disease stage. CONCLUSION These findings suggest that ATBs modulate the risk of recurrence after early CRC resection with a differential impact of the ATB classes depending on disease stage and tumor site.
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Affiliation(s)
- Marc Hilmi
- Department of Medical Oncology, Institut Curie, Versailles Saint-Quentin University, Saint-Cloud, France; GERCOR, Paris, France
| | - Ines Khati
- Department of Health Data and Assessment, Health Survey, Data-science and Assessment Division, French National Cancer Institute (INCa), Boulogne Billancourt, France
| | - Anthony Turpin
- GERCOR, Paris, France; Department of Medical Oncology, Lille University Hospital, Lille, France
| | | | - Charles Burdet
- Department of Epidemiology, Biostatistics and Clinical Research, Bichat Hospital, AP-HP, Paris, France
| | - Nathalie Grall
- Microbiology Laboratory, Bichat-Claude Bernard University Hospital, AP-HP, Paris, France
| | - Joana Vidal
- Department of Medicine, Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medical Oncology, Hospital del Mar, IMIM, CIBERONC, Barcelona, Spain
| | - Philippe-Jean Bousquet
- Department of Health Data and Assessment, Health Survey, Data-science and Assessment Division, French National Cancer Institute (INCa), Boulogne Billancourt, France
| | - Benoît Rousseau
- GERCOR, Paris, France; Department of Medicine, Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, USA.
| | - Christine Le Bihan-Benjamin
- Department of Health Data and Assessment, Health Survey, Data-science and Assessment Division, French National Cancer Institute (INCa), Boulogne Billancourt, France
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9
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Li Y, Han S. Metabolomic Applications in Gut Microbiota-Host Interactions in Human Diseases. Gastroenterol Clin North Am 2024; 53:383-397. [PMID: 39068001 DOI: 10.1016/j.gtc.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The human gut microbiota, consisting of trillions of microorganisms, encodes diverse metabolic pathways that impact numerous aspects of host physiology. One key way in which gut bacteria interact with the host is through the production of small metabolites. Several of these microbiota-dependent metabolites, such as short-chain fatty acids, have been shown to modulate host diseases. In this review, we examine how disease-associated metabolic signatures are identified using metabolomic platforms, and where metabolomics is applied in gut microbiota-disease interactions. We further explore how integration of metagenomic and metabolomic data in human studies can facilitate biomarkers discoveries in precision medicine.
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Affiliation(s)
- Yuxin Li
- Biochemistry Graduate Program, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shuo Han
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.
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10
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Cao C, Yue S, Lu A, Liang C. Host-Gut Microbiota Metabolic Interactions and Their Role in Precision Diagnosis and Treatment of Gastrointestinal Cancers. Pharmacol Res 2024; 207:107321. [PMID: 39038631 DOI: 10.1016/j.phrs.2024.107321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 06/30/2024] [Accepted: 07/17/2024] [Indexed: 07/24/2024]
Abstract
The critical role of the gut microbiome in gastrointestinal cancers is becoming increasingly clear. Imbalances in the gut microbial community, referred to as dysbiosis, are linked to increased risks for various forms of gastrointestinal cancers. Pathogens like Fusobacterium and Helicobacter pylori relate to the onset of esophageal and gastric cancers, respectively, while microbes such as Porphyromonas gingivalis and Clostridium species have been associated with a higher risk of pancreatic cancer. In colorectal cancer, bacteria such as Fusobacterium nucleatum are known to stimulate the growth of tumor cells and trigger cancer-promoting pathways. On the other hand, beneficial microbes like Bifidobacteria offer a protective effect, potentially inhibiting the development of gastrointestinal cancers. The potential for therapeutic interventions that manipulate the gut microbiome is substantial, including strategies to engineer anti-tumor metabolites and employ microbiota-based treatments. Despite the progress in understanding the influence of the microbiome on gastrointestinal cancers, significant challenges remain in identifying and understanding the precise contributions of specific microbial species and their metabolic products. This knowledge is essential for leveraging the role of the gut microbiome in the development of precise diagnostics and targeted therapies for gastrointestinal cancers.
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Affiliation(s)
- Chunhao Cao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, 999077, Hong Kong Special Administrative Region of China
| | - Siran Yue
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, 999077, Hong Kong Special Administrative Region of China
| | - Aiping Lu
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, 999077, Hong Kong Special Administrative Region of China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China; Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.
| | - Chao Liang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, 999077, Hong Kong Special Administrative Region of China; State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 100850, China.
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11
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Liu J, Wang WJ, Xu GF, Wang YX, Lin Y, Zheng X, Yao SH, Zheng KH. Does Microbiome Contribute to Longevity? Compositional and Functional Differences in Gut Microbiota in Chinese Long-Living (>90 Years) and Elderly (65-74 Years) Adults. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:461-469. [PMID: 39149810 DOI: 10.1089/omi.2024.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The study of longevity and its determinants has been revitalized with the rise of microbiome scholarship. The gut microbiota have been established to play essential protective, metabolic, and physiological roles in human health and disease. The gut dysbiosis has been identified as an important factor contributing to the development of multiple diseases. Accordingly, it is reasonable to hypothesize that the gut microbiota of long-living individuals have healthy antiaging-associated gut microbes, which, by extension, might provide specific molecular targets for antiaging treatments and interventions. In the present study, we compared the gut microbiota of Chinese individuals in two different age groups, long-living adults (aged over 90 years) and elderly adults (aged 65-74 years) who were free of major diseases. We found significantly lower relative abundances of bacteria in the genera Sutterella and Megamonas in the long-living individuals. Furthermore, we established that while biological processes such as autophagy (GO:0006914) and telomere maintenance through semiconservative replication (GO:0032201) were enhanced in the long-living group, response to lipopolysaccharide (GO:0032496), nicotinamide adenine dinucleotide oxidation (GO:0006116), and S-adenosyl methionine metabolism (GO:0046500) were weakened. Moreover, the two groups were found to differ with respect to amino acid metabolism. We suggest that these compositional and functional differences in the gut microbiota may potentially be associated with mechanisms that contribute to determining longevity or aging.
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Affiliation(s)
- Jie Liu
- Medical School, Quzhou College of Technology, Quzhou, China
| | | | - Ge-Fang Xu
- People's Hospital of Kaihua, Quzhou, China
| | | | - Ying Lin
- People's Hospital of Kaihua, Quzhou, China
| | - Xin Zheng
- Medical School, Quzhou College of Technology, Quzhou, China
| | - Shui-Hong Yao
- Medical School, Quzhou College of Technology, Quzhou, China
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12
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Kundu P, Beura S, Mondal S, Das AK, Ghosh A. Machine learning for the advancement of genome-scale metabolic modeling. Biotechnol Adv 2024; 74:108400. [PMID: 38944218 DOI: 10.1016/j.biotechadv.2024.108400] [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: 10/25/2023] [Revised: 05/13/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the interrelations between genotype, phenotype, and external environment. The recent advancement of high-throughput experimental approaches and multi-omics strategies has generated a plethora of new and precise information from wide-ranging biological domains. On the other hand, the continuously growing field of machine learning (ML) and its specialized branch of deep learning (DL) provide essential computational architectures for decoding complex and heterogeneous biological data. In recent years, both multi-omics and ML have assisted in the escalation of CBM. Condition-specific omics data, such as transcriptomics and proteomics, helped contextualize the model prediction while analyzing a particular phenotypic signature. At the same time, the advanced ML tools have eased the model reconstruction and analysis to increase the accuracy and prediction power. However, the development of these multi-disciplinary methodological frameworks mainly occurs independently, which limits the concatenation of biological knowledge from different domains. Hence, we have reviewed the potential of integrating multi-disciplinary tools and strategies from various fields, such as synthetic biology, CBM, omics, and ML, to explore the biochemical phenomenon beyond the conventional biological dogma. How the integrative knowledge of these intersected domains has improved bioengineering and biomedical applications has also been highlighted. We categorically explained the conventional genome-scale metabolic model (GEM) reconstruction tools and their improvement strategies through ML paradigms. Further, the crucial role of ML and DL in omics data restructuring for GEM development has also been briefly discussed. Finally, the case-study-based assessment of the state-of-the-art method for improving biomedical and metabolic engineering strategies has been elaborated. Therefore, this review demonstrates how integrating experimental and in silico strategies can help map the ever-expanding knowledge of biological systems driven by condition-specific cellular information. This multiview approach will elevate the application of ML-based CBM in the biomedical and bioengineering fields for the betterment of society and the environment.
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Affiliation(s)
- Pritam Kundu
- School School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Satyajit Beura
- Department of Bioscience and Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - Suman Mondal
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Kumar Das
- Department of Bioscience and Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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13
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Cañellas-Socias A, Sancho E, Batlle E. Mechanisms of metastatic colorectal cancer. Nat Rev Gastroenterol Hepatol 2024; 21:609-625. [PMID: 38806657 DOI: 10.1038/s41575-024-00934-z] [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] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Despite extensive research and improvements in understanding colorectal cancer (CRC), its metastatic form continues to pose a substantial challenge, primarily owing to limited therapeutic options and a poor prognosis. This Review addresses the emerging focus on metastatic CRC (mCRC), which has historically been under-studied compared with primary CRC despite its lethality. We delve into two crucial aspects: the molecular and cellular determinants facilitating CRC metastasis and the principles guiding the evolution of metastatic disease. Initially, we examine the genetic alterations integral to CRC metastasis, connecting them to clinically marked characteristics of advanced CRC. Subsequently, we scrutinize the role of cellular heterogeneity and plasticity in metastatic spread and therapy resistance. Finally, we explore how the tumour microenvironment influences metastatic disease, emphasizing the effect of stromal gene programmes and the immune context. The ongoing research in these fields holds immense importance, as its future implications are projected to revolutionize the treatment of patients with mCRC, hopefully offering a promising outlook for their survival.
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Affiliation(s)
- Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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14
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Zhang L, Leng XX, Qi J, Wang N, Han JX, Tao ZH, Zhuang ZY, Ren Y, Xie YL, Jiang SS, Li JL, Chen H, Zhou CB, Cui Y, Chen X, Wang Z, Zhang ZZ, Hong J, Chen HY, Jiang W, Chen YX, Zhao X, Yu J, Fang JY. The adhesin RadD enhances Fusobacterium nucleatum tumour colonization and colorectal carcinogenesis. Nat Microbiol 2024; 9:2292-2307. [PMID: 39169124 DOI: 10.1038/s41564-024-01784-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 07/15/2024] [Indexed: 08/23/2024]
Abstract
Fusobacterium nucleatum can bind to host cells and potentiate intestinal tumorigenesis. Here we used a genome-wide screen to identify an adhesin, RadD, which facilitates the attachment of F. nucleatum to colorectal cancer (CRC) cells in vitro. RadD directly binds to CD147, a receptor overexpressed on CRC cell surfaces, which initiated a PI3K-AKT-NF-κB-MMP9 cascade, subsequently enhancing tumorigenesis in mice. Clinical specimen analysis showed that elevated radD gene levels in CRC tissues correlated positively with activated oncogenic signalling and poor patient outcomes. Finally, blockade of the interaction between RadD and CD147 in mice effectively impaired F. nucleatum attachment and attenuated F. nucleatum-induced oncogenic response. Together, our study provides insights into an oncogenic mechanism driven by F. nucleatum RadD and suggests that the RadD-CD147 interaction could be a potential therapeutic target for CRC.
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Affiliation(s)
- Lu Zhang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Xu Leng
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ni Wang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji-Xuan Han
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Hang Tao
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zi-Yan Zhuang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yimeng Ren
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Le Xie
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shan-Shan Jiang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Lu Li
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huimin Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng-Bei Zhou
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Cui
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zi-Zhen Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao-Yan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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15
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Zhang L, Li D, Zhang Y, Hu W, Lv H, Zhang X, Zhang H. Changes in the gut microbiota of esophageal carcinoma patients based on 16S rRNA gene sequencing: a systematic review and meta-analysis. Front Oncol 2024; 14:1366975. [PMID: 39267834 PMCID: PMC11390416 DOI: 10.3389/fonc.2024.1366975] [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: 01/08/2024] [Accepted: 07/16/2024] [Indexed: 09/15/2024] Open
Abstract
Background This study conducts a systematic review through meta-analysis, comparing the composition and diversity of the gut microbiome in patients with esophageal cancer and healthy individuals, and explores the relationship between risk factors and related factors of esophageal cancer. Methods According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), we comprehensively searched the databases of PubMed, Web of Science, Embase, Cochrane Library. In addition, we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis. We also implemented the Newcastle-Ottawa Scale (NOS), funnel plot analysis, Egger's test, and Begg's test to assess the risk of bias. Results In this study, a total of 328 studies were identified through the literature search. Among them, 117 duplicate studies were removed, and 202 studies were excluded based on inclusion and exclusion criteria. Finally, 9 studies were included in the analysis, involving a total of 216 patients with esophageal carcinoma and 352 healthy controls. Four studies provided Chao1 index for quantitative consolidation (ES = 637.41, 95% CI: 549.16 to 725.66, p = 0.000, I2 = 98.2%). Two studies [27, 29] reported ACE index (ES = 438.89, 95% CI: 362.42 to 515.35, p = 0.000, I2 = 97%). Seven studies [26,27,29,30,32] reported the Shannon index for quantitative consolidation (ES = 4.38, 95% CI: 3.95 to 4.81, p = 0.000, I2 = 99%). At the phylum level, the abundance of Bacteroidetes(ES = 37.8, 95% CI: 25.75 to 49.85, p = 0.000, I2 = 87.2%) and Proteobacteria(ES = 7.48, 95% CI: 5.02 to 8.85, p = 0.04, I2 = 2.4%) have statistical difference between ESCC and HC. There was no significant difference between ESCC and HC in the abundance of genera(p>0.05). Conclusions This observational meta-analysis revealed that changes in the GM were correlated with esophageal carcinoma, and variations in some advantageous GM might involve regional differences. Additionally, the study aims to facilitate early diagnosis of esophageal cancer and improve screening and diagnostic efficiency.
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Affiliation(s)
- Li Zhang
- Department of Pharmacology, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Delin Li
- Department of Medical Equipment, Jinan Mental Health Center, Jinan, China
| | - Yongsheng Zhang
- Department of Health Management, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Wenqi Hu
- Department of Health Management, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Haoyue Lv
- Department of Health Management, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Xiaodong Zhang
- Postgraduate Department, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, China
| | - Hongyu Zhang
- Department of Health Management, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
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16
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Dong X, Zhang K, Yi S, Wang L, Wang X, Li M, Liang S, Wang Y, Zeng Y. Multi-omics profiling combined with molecular docking reveals immune-inflammatory proteins as potential drug targets in colorectal cancer. Biochem Biophys Res Commun 2024; 739:150598. [PMID: 39213754 DOI: 10.1016/j.bbrc.2024.150598] [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: 06/19/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Colorectal cancer is globally ranked as the third most common malignant tumor. Its development involves a complex biological process driven by various genetic and epigenetic alterations. To elucidate the biological significance of the extensive omics data, we conducted comparative multi-omics studies on colorectal cancer patients at different clinical stages. Bioinformatics methods were applied to analyze multi-omics datasets and explore the molecular landscape. Drug prediction and molecular docking also were conducted to assess potential therapeutic interventions. In vitro experiments were used to validate the inhibitory effect on the migration and proliferation of cell lines. The results indicate up-regulated proteins involved in immune-inflammatory related pathways, while biomarkers related to muscular contraction and cell adhesion are significantly down-regulated. Drug prediction, coupled with in vitro experiments, suggests that AZ-628 may act as a potential drug to inhibit the proliferation and migration of CRC cell lines HCT-116 and HT-29 by regulating the aforementioned key biological pathways or proteins. Complementing these findings, metabolomics analysis unveiled a down-regulation of key carbon metabolism pathways, alongside an up-regulation in amino acid metabolism, particularly proline metabolism. This metabolic shift may reflect an adaptive response in cancer cells, favoring specific amino acids to support their growth. Together, these integrated results provide valuable insights into the intricate landscape of tumor development, highlighting the crossroads of immune regulation, cellular structure, and metabolic reprogramming in the tumorigenic process and providing valuable insights into cancer pathology.
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Affiliation(s)
- Xiaoping Dong
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - Kun Zhang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Siwei Yi
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - Lingxiang Wang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China; The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Xingyao Wang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - Mengtuo Li
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - Songping Liang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China
| | - YongJun Wang
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
| | - Yong Zeng
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China; Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha, 410081, China; The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
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17
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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.
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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;
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18
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Huang P, Ji F, Cheung AHK, Fu K, Zhou Q, Ding X, Chen D, Lin Y, Wang L, Jiao Y, Chu ESH, Kang W, To KF, Yu J, Wong CC. Peptostreptococcus stomatis promotes colonic tumorigenesis and receptor tyrosine kinase inhibitor resistance by activating ERBB2-MAPK. Cell Host Microbe 2024; 32:1365-1379.e10. [PMID: 39059397 DOI: 10.1016/j.chom.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/23/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024]
Abstract
Peptostreptococcus stomatis (P. stomatis) is enriched in colorectal cancer (CRC), but its causality and translational implications in CRC are unknown. Here, we show that P. stomatis accelerates colonic tumorigenesis in ApcMin/+ and azoxymethane/dextran sodium sulfate (AOM-DSS) models by inducing cell proliferation, suppressing apoptosis, and impairing gut barrier function. P. stomatis adheres to CRC cells through its surface protein fructose-1,6-bisphosphate aldolase (FBA) that binds to the integrin α6/β4 receptor on CRC cells, leading to the activation of ERBB2 and the downstream MEK-ERK-p90 cascade. Blockade of the FBA-integrin α6/β4 abolishes ERBB2-mitogen-activated protein kinase (MAPK) activation and the protumorigenic effect of P. stomatis. P. stomatis-driven ERBB2 activation bypasses receptor tyrosine kinase (RTK) blockade by EGFR inhibitors (cetuximab, erlotinib), leading to drug resistance in xenograft and spontaneous CRC models of KRAS-wild-type CRC. P. stomatis also abrogates BRAF inhibitor (vemurafenib) efficacy in BRAFV600E-mutant CRC xenografts. Thus, we identify P. stomatis as an oncogenic bacterium and a contributory factor for non-responsiveness to RTK inhibitors in CRC.
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Affiliation(s)
- Pingmei Huang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fenfen Ji
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, 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
| | - Kaili Fu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qiming Zhou
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao Ding
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Danyu Chen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yufeng Lin
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Luyao Wang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ying Jiao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eagle S H Chu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, 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
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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19
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Tanwar H, Gnanasekaran JM, Allison D, Chuang LS, He X, Aimetti M, Baima G, Costalonga M, Cross RK, Sears C, Mehandru S, Cho J, Colombel JF, Raufman JP, Thumbigere-Math V. Unravelling the Oral-Gut Axis: Interconnection Between Periodontitis and Inflammatory Bowel Disease, Current Challenges, and Future Perspective. J Crohns Colitis 2024; 18:1319-1341. [PMID: 38417137 PMCID: PMC11324343 DOI: 10.1093/ecco-jcc/jjae028] [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: 08/21/2023] [Revised: 12/04/2023] [Accepted: 02/27/2024] [Indexed: 03/01/2024]
Abstract
As the opposite ends of the orodigestive tract, the oral cavity and the intestine share anatomical, microbial, and immunological ties that have bidirectional health implications. A growing body of evidence suggests an interconnection between oral pathologies and inflammatory bowel disease [IBD], implying a shift from the traditional concept of independent diseases to a complex, reciprocal cycle. This review outlines the evidence supporting an 'oral-gut' axis, marked by a higher prevalence of periodontitis and other oral conditions in IBD patients and vice versa. We present an in-depth examination of the interconnection between oral pathologies and IBD, highlighting the shared microbiological and immunological pathways, and proposing a 'multi-hit' hypothesis in the pathogenesis of periodontitis-mediated intestinal inflammation. Furthermore, the review underscores the critical need for a collaborative approach between dentists and gastroenterologists to provide holistic oral-systemic healthcare.
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Affiliation(s)
- Himanshi Tanwar
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | | | - Devon Allison
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Ling-shiang Chuang
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Baima
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Massimo Costalonga
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Raymond K Cross
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cynthia Sears
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Saurabh Mehandru
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Pierre Raufman
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Vivek Thumbigere-Math
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
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20
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Sun Y, Zhang X, Hang D, Lau HCH, Du J, Liu C, Xie M, Pan Y, Wang L, Liang C, Zhou X, Chen D, Rong J, Zhao Z, Cheung AHK, Wu Y, Gou H, Wong CC, Du L, Deng J, Hu Z, Shen H, Miao Y, Yu J. Integrative plasma and fecal metabolomics identify functional metabolites in adenoma-colorectal cancer progression and as early diagnostic biomarkers. Cancer Cell 2024; 42:1386-1400.e8. [PMID: 39137727 DOI: 10.1016/j.ccell.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 02/09/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024]
Abstract
Changes in plasma and fecal metabolomes in colorectal cancer (CRC) progression (normal-adenoma-CRC) remain unclear. Here, plasma and fecal samples were collected from four independent cohorts of 1,251 individuals (422 CRC, 399 colorectal adenoma [CRA], and 430 normal controls [NC]). By metabolomic profiling, signature plasma and fecal metabolites with consistent shift across NC, CRA, and CRC are identified, including CRC-enriched oleic acid and CRC-depleted allocholic acid. Oleic acid exhibits pro-tumorigenic effects in CRC cells, patient-derived organoids, and two murine CRC models, whereas allocholic acid has opposing effects. By integrative analysis, we found that oleic acid or allocholic acid directly binds to α-enolase or farnesoid X receptor-1 in CRC cells, respectively, to modulate cancer-associated pathways. Clinically, we establish a panel of 17 plasma metabolites that accurately diagnoses CRC in a discovery and three validation cohorts (AUC = 0.848-0.987). Overall, we characterize metabolite signatures, mechanistic significance, and diagnostic potential of plasma and fecal metabolomes in CRC.
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Affiliation(s)
- Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Disease, Yunan Geiatric Medical Center, Kunming, Yunnan, China
| | - Xiang Zhang
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Dong Hang
- Department of Epidemiology, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Harry Cheuk-Hay Lau
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jie Du
- Biotree Metabolomics Technology Research Center, Shanghai, China
| | - Chuanfa Liu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mingxu Xie
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yasi Pan
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Le Wang
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Cong Liang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xingyu Zhou
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Danyu Chen
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jiamei Rong
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Disease, Yunan Geiatric Medical Center, Kunming, Yunnan, China
| | - Zengren Zhao
- Department of Gastrointestinal Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Alvin Ho-Kwan Cheung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuet Wu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hongyan Gou
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chi Chun Wong
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lingbin Du
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Junliang Deng
- Biotree Metabolomics Technology Research Center, Shanghai, China
| | - Zhibin Hu
- Department of Epidemiology, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongbing Shen
- Department of Epidemiology, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Disease, Yunan Geiatric Medical Center, Kunming, Yunnan, China.
| | - Jun Yu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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21
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Kubosawa Y, Sujino T, Miyamoto K, Kayashima A, Minezaki D, Morioka K, Iwata K, Miyazaki K, Masunaga T, Mizutani M, Akimoto T, Takatori Y, Matsuura N, Nakayama A, Takabayashi K, Nakamoto N, Honda A, Kato M, Yahagi N, Kanai T. Distinctive duodenal microbiomes and bile acid profiles in duodenal tumor patients revealed by prospective observational study. Sci Rep 2024; 14:18705. [PMID: 39134638 PMCID: PMC11319767 DOI: 10.1038/s41598-024-69820-7] [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: 11/18/2023] [Accepted: 08/08/2024] [Indexed: 08/15/2024] Open
Abstract
The incidence of duodenal tumors (DTs) is increasing. However, the mechanisms underlying its development remain unclear. Environmental factors, including the microbiome and bile acids (BAs), are believed to influence tumor development. Therefore, we conducted a single-center, prospective, observational study to investigate the potential differences between patients with DTs and healthy controls (HCs) based on these factors. In addition, the BAs in the duodenal fluid were measured using liquid chromatography-tandem mass spectrometry. We recruited 41 patients and performed 16S rRNA-seq. There was no difference in the observed ASVs or PCoA plot of Bray-Curtis dissimilarity between the DTs and HCs. The lithocholic acid concentration was significantly lower in the DT group than in the control group. The ratio of CDCA to LCA was significantly higher in patients with DTs. No significant differences in microbiota were observed between DTs and HCs. In patients with DTs, the lithocholic acid concentration in duodenal was significantly lower than in HCs.
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Affiliation(s)
- Yoko Kubosawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
- Keio Global Research Institute, Keio Univerisy, Mita, Tokyo, 108-0073, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Central Research Institute, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Torocho, Kita-ku, Saitama-shi, Saitama, 331-0804, Japan
| | - Atsuto Kayashima
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Daisuke Minezaki
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kohei Morioka
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kentaro Iwata
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kurato Miyazaki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Teppei Masunaga
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Mari Mizutani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Teppei Akimoto
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yusaku Takatori
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Noriko Matsuura
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Atsushi Nakayama
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kaoru Takabayashi
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Akira Honda
- Division of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, 3-20-1 chuo, Ami-machi, Inashiki-gun, Ibaraki, 300-0395, Japan
| | - Motohiko Kato
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Naohisa Yahagi
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
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22
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Wang S, Jiang Y, Che L, Wang RH, Li SC. Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. Nucleic Acids Res 2024; 52:e61. [PMID: 38884260 DOI: 10.1093/nar/gkae515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/23/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.
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Affiliation(s)
- Shuai Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Yiqi Jiang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Lijia Che
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Ruo Han Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Shuai Cheng Li
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
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23
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Su ACY, Ding X, Lau HCH, Kang X, Li Q, Wang X, Liu Y, Jiang L, Lu Y, Liu W, Ding Y, Cheung AHK, To KF, Yu J. Lactococcus lactis HkyuLL 10 suppresses colorectal tumourigenesis and restores gut microbiota through its generated alpha-mannosidase. Gut 2024; 73:1478-1488. [PMID: 38599786 PMCID: PMC11347254 DOI: 10.1136/gutjnl-2023-330835] [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: 08/03/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
OBJECTIVE Probiotic Lactococcus lactis is known to confer health benefits to humans. Here, we aimed to investigate the role of L. lactis in colorectal cancer (CRC). DESIGN L. lactis abundance was evaluated in patients with CRC (n=489) and healthy individuals (n=536). L. lactis was isolated from healthy human stools with verification by whole genome sequencing. The effect of L. lactis on CRC tumourigenesis was assessed in transgenic Apc Min/+ mice and carcinogen-induced CRC mice. Faecal microbiota was profiled by metagenomic sequencing. Candidate proteins were characterised by nano liquid chromatography-mass spectrometry. Biological function of L. lactis conditioned medium (HkyuLL 10-CM) and functional protein was studied in human CRC cells, patient-derived organoids and xenograft mice. RESULTS Faecal L. lactis was depleted in patients with CRC. A new L. lactis strain was isolated from human stools and nomenclated as HkyuLL 10. HkyuLL 10 supplementation suppressed CRC tumourigenesis in Apc Min/+ mice, and this tumour-suppressing effect was confirmed in mice with carcinogen-induced CRC. Microbiota profiling revealed probiotic enrichment including Lactobacillus johnsonii in HkyuLL 10-treated mice. HkyuLL 10-CM significantly abrogated the growth of human CRC cells and patient-derived organoids. Such protective effect was attributed to HkyuLL 10-secreted proteins, and we identified that α-mannosidase was the functional protein. The antitumourigenic effect of α-mannosidase was demonstrated in human CRC cells and organoids, and its supplementation significantly reduced tumour growth in xenograft mice. CONCLUSION HkyuLL 10 suppresses CRC tumourigenesis in mice through restoring gut microbiota and secreting functional protein α-mannosidase. HkyuLL 10 administration may serve as a prophylactic measure against CRC.
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Affiliation(s)
- Anthony Chin Yang Su
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao Ding
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Harry Cheuk Hay Lau
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Xing Kang
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Qing Li
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Xueliang Wang
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Yali Liu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Lanping Jiang
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Yinghong Lu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Weixin Liu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Yanqiang Ding
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Alvin Ho-Kwan Cheung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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24
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Mai X, Yang S, Chen Q, Chen K. Gut microbial composition is altered in sarcopenia: A systematic review and meta-analysis of clinical studies. PLoS One 2024; 19:e0308360. [PMID: 39106230 DOI: 10.1371/journal.pone.0308360] [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: 04/26/2024] [Accepted: 07/23/2024] [Indexed: 08/09/2024] Open
Abstract
Increasing evidence has shown that gut microbiota (GM) was involved in the pathophysiology of musculoskeletal disorders through multiple pathways such as protein anabolism, chronic inflammation and immunity, and imbalanced metabolism. We performed a systematic review and meta-analysis of human studies to evaluate GM diversity differences between individuals with and without sarcopenia, and explore bacteria with potential to become biomarkers. PubMed, Embase and Cochrane library were systematically searched from inception to February 16, 2024. Studies were included if they (1) sampled adults with sarcopenia, and (2) performed GM analysis and reported α-diversity, β-diversity or relative abundance. The methodological quality of included studies and the certainty of evidence were assessed through the Joanna Briggs Institute critical appraisal checklist for analytical cross-sectional studies and the Grades of Recommendation, Assessment, Development and Evaluation (GRADE) Working Group system, respectively. Weighted standardized mean differences (SMDs) and corresponding 95% confidence intervals (CIs) were estimated for α-diversity indices using a fixed-effects and a random-effects model. Beta diversity and the relative abundance of GM were summarized qualitatively. A total of 19 studies involving 6,565 participants were included in this study. Compared with controls, significantly moderate decrease in microbial richness in participants with sarcopenia were found (Chao1: SMD = -0.44; 95%CI, -0.64 to -0.23, I2 = 57.23%, 13 studies; observed species: SMD = -0.68; 95%CI, -1.00 to -0.37, I2 = 66.07%, 5 studies; ACE index: SMD = -0.30; 95%CI, -0.56 to -0.04, I2 = 8.12%, 4 studies), with very low certainty of evidence. Differences in β-diversity were consistently observed in 84.6% of studies and 97.3% of participants. The detailed analysis of the gut microbial differential abundance identified a loss of Prevotellaceae, Prevotella, and Megamonas in sarcopenia compared with non-sarcopenia. In conclusion, sarcopenia was found to be associated with reduced richness of GM, and supplementing intestinal bacteria described above may contribute to preventing and treating this muscle disease. The research protocol was registered and approved in PROSPERO (CRD42023412849).
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Affiliation(s)
- Xiaohong Mai
- Department of Geriatric Psychiatry, Shaoxing Seventh People's Hospital, Shaoxing, China
| | - Shuyi Yang
- Department of Microbial Detection, Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Qifeng Chen
- Department of Non-Communicable Diseases Control and Prevention, Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Kangkang Chen
- Department of Non-Communicable Diseases Control and Prevention, Shaoxing Center for Disease Control and Prevention, Shaoxing, China
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25
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Mizutani S, Tamaki A, Shiba S, Salim F, Yamada M, Takamaru H, Nakajima T, Yoshida N, Ikuta S, Yachida T, Shibata T, Soga T, Saito Y, Fukuda S, Ishikawa H, Yamada T, Yachida S. Dynamics of the gut microbiome in FAP patients undergoing intensive endoscopic reduction of polyp burden. Gut 2024:gutjnl-2024-332381. [PMID: 39089862 DOI: 10.1136/gutjnl-2024-332381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024]
Affiliation(s)
- Sayaka Mizutani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Ayako Tamaki
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Satoshi Shiba
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Felix Salim
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Masayoshi Yamada
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Hiroyuki Takamaru
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Takeshi Nakajima
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Naohisa Yoshida
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto, Japan
| | - Shoko Ikuta
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Tatsuo Yachida
- Department of Gastroenterology & Neurology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yutaka Saito
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Hideki Ishikawa
- Department of Molecular-Targeting Prevention, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Shinichi Yachida
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
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26
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Vitale S, Calapà F, Colonna F, Luongo F, Biffoni M, De Maria R, Fiori ME. Advancements in 3D In Vitro Models for Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405084. [PMID: 38962943 PMCID: PMC11348154 DOI: 10.1002/advs.202405084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Indexed: 07/05/2024]
Abstract
The process of drug discovery and pre-clinical testing is currently inefficient, expensive, and time-consuming. Most importantly, the success rate is unsatisfactory, as only a small percentage of tested drugs are made available to oncological patients. This is largely due to the lack of reliable models that accurately predict drug efficacy and safety. Even animal models often fail to replicate human-specific pathologies and human body's complexity. These factors, along with ethical concerns regarding animal use, urge the development of suitable human-relevant, translational in vitro models.
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Affiliation(s)
- Sara Vitale
- Department of Oncology and Molecular Medicine (OMM)Istituto Superiore di SanitàViale Regina Elena 299Rome00161Italy
| | - Federica Calapà
- Dipartimento di Medicina e Chirurgia traslazionaleUniversità Cattolica del Sacro CuoreLargo F. Vito 1RomeItaly
| | - Francesca Colonna
- Department of Oncology and Molecular Medicine (OMM)Istituto Superiore di SanitàViale Regina Elena 299Rome00161Italy
| | - Francesca Luongo
- Dipartimento di Medicina e Chirurgia traslazionaleUniversità Cattolica del Sacro CuoreLargo F. Vito 1RomeItaly
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine (OMM)Istituto Superiore di SanitàViale Regina Elena 299Rome00161Italy
| | - Ruggero De Maria
- Dipartimento di Medicina e Chirurgia traslazionaleUniversità Cattolica del Sacro CuoreLargo F. Vito 1RomeItaly
- Fondazione Policlinico Universitario “A. Gemelli” – IRCCSLargo F. Vito 1RomeItaly
| | - Micol E. Fiori
- Department of Oncology and Molecular Medicine (OMM)Istituto Superiore di SanitàViale Regina Elena 299Rome00161Italy
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27
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Ji G, Zhao J, Si X, Song W. Targeting bacterial metabolites in tumor for cancer therapy: An alternative approach for targeting tumor-associated bacteria. Adv Drug Deliv Rev 2024; 211:115345. [PMID: 38834140 DOI: 10.1016/j.addr.2024.115345] [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: 02/03/2024] [Revised: 05/11/2024] [Accepted: 05/29/2024] [Indexed: 06/06/2024]
Abstract
Emerging evidence reveal that tumor-associated bacteria (TAB) can facilitate the initiation and progression of multiple types of cancer. Recent work has emphasized the significant role of intestinal microbiota, particularly bacteria, plays in affecting responses to chemo- and immuno-therapies. Hence, it seems feasible to improve cancer treatment outcomes by targeting intestinal bacteria. While considering variable richness of the intestinal microbiota and diverse components among individuals, direct manipulating the gut microbiota is complicated in clinic. Tumor initiation and progression requires the gut microbiota-derived metabolites to contact and reprogram neoplastic cells. Hence, directly targeting tumor-associated bacteria metabolites may have the potential to provide alternative and innovative strategies to bypass the gut microbiota for cancer therapy. As such, there are great opportunities to explore holistic approaches that incorporates TAB-derived metabolites and related metabolic signals modulation for cancer therapy. In this review, we will focus on key opportunistic areas by targeting TAB-derived metabolites and related metabolic signals, but not bacteria itself, for cancer treatment, and elucidate future challenges that need to be addressed in this emerging field.
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Affiliation(s)
- Guofeng Ji
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jingjing Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, China
| | - Xinghui Si
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Jilin Biomedical Polymers Engineering Laboratory, Changchun 130022, China
| | - Wantong Song
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Jilin Biomedical Polymers Engineering Laboratory, Changchun 130022, China.
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28
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Hu X, Wu W, Zhi S, Xu W, Zhang Y, Li L, Tao Y, Duan G, Liao C, Wang L, Li L, Li Z, Li W. The first diagnosis of Severe Fever with Thrombocytopenia Syndrome caused by tick-borne Severe Fever with Thrombocytopenia Syndrome virus in Chongqing, China: A case report and literature review. Diagn Microbiol Infect Dis 2024; 109:116350. [PMID: 38761614 DOI: 10.1016/j.diagmicrobio.2024.116350] [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: 12/14/2023] [Revised: 04/17/2024] [Accepted: 05/09/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Severe Fever with Thrombocytopenia Syndrome (SFTS) is a tick-borne disease caused by the SFTS virus (SFTSV) which has the potential to become a pandemic and is currently a major public health concern. CASE PRESENTATION We present the case of a 74-year-old female from an urban area of Chongqing, with leukocytopenia, thrombocytopenia, organ function, inflammatory, blood coagulation, and immune abnormalities. SFTSV infection was confirmed through molecular detection and metagenomic next-generation sequencing (mNGS) analysis, indicating a diagnosis of SFTS due to the patient's history of tick bites. The patient received symptomatic and supportive therapy, including antibiotics, antiviral treatment, and antifungal therapy, and finally discharged from the hospital on day 18. CONCLUSIONS This study highlights the need for increased awareness, early diagnosis, and prompt treatment for tick-borne SFTS. It also provides a comprehensive understanding of the disease's characteristics, pathogenesis, detection methods, and available treatments.
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Affiliation(s)
- Xiefei Hu
- Medicine School of Chongqing University, Chongqing, China; Department of Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing 404100, China
| | - Wenyan Wu
- Department of Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing 404100, China
| | - Shenshen Zhi
- Department of Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing 404100, China
| | - Wenjuan Xu
- Department of Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing 404100, China
| | - Yuanyuan Zhang
- Department of Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing 404100, China
| | - Lijuan Li
- Department of Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing 404100, China
| | - Yang Tao
- Intensive Care Unit, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Gang Duan
- Chongqing Municipal Center for Disease Control and Prevention, Microbiological Testing Institute, Chongqing 400042, China
| | - Chunyan Liao
- Chongqing Municipal Center for Disease Control and Prevention, Microbiological Testing Institute, Chongqing 400042, China
| | - Ling Wang
- Chongqing Municipal Center for Disease Control and Prevention, Microbiological Testing Institute, Chongqing 400042, China
| | - Lingyi Li
- Department of Medical, Hangzhou Matridx Biotechnology Co., Ltd., No.2073 Jinchang road, Yuhang District, Hangzhou, Zhejiang, China
| | - Zhifeng Li
- Chongqing Municipal Center for Disease Control and Prevention, Microbiological Testing Institute, Chongqing 400042, China
| | - Wei Li
- Department of Clinical Laboratory, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing 404100, China.
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29
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Jin W, Guo C. Genetic manipulations of nonmodel gut microbes. IMETA 2024; 3:e216. [PMID: 39135697 PMCID: PMC11316930 DOI: 10.1002/imt2.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 08/15/2024]
Abstract
Hundreds of microbiota gene expressions are significantly different between healthy and diseased humans. The "bottleneck" preventing a mechanistic dissection of how they affect host biology/disease is that many genes are encoded by nonmodel gut commensals and not genetically manipulatable. Approaches to efficiently identify their gene transfer methodologies and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. This paper will introduce a step-by-step protocol to identify gene transfer conditions and build the gene manipulation tools for nonmodel gut microbes, focusing on Gram-negative Bacteroidia and Gram-positive Clostridia organisms. This protocol enables us to identify gene transfer methods and develop gene manipulation tools without prior knowledge of their genome sequences, by targeting bacterial 16s ribosomal RNAs or expanding their compatible replication origins combined with clustered regularly interspaced short palindromic repeats machinery. Such an efficient and generalizable approach will facilitate functional studies that causally connect gut microbiota genes to host diseases.
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Affiliation(s)
- Wen‐Bing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Friedman Center for Nutrition and Inflammation, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
| | - Chun‐Jun Guo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Friedman Center for Nutrition and Inflammation, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Joan and Sanford I. Weill Department of Medicine, Gastroenterology and Hepatology Division, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Department of Microbiology and Immunology, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell MedicineCornell UniversityNew YorkNew YorkUSA
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30
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Gao P, Duan Z, Xu G, Gong Q, Wang J, Luo K, Chen J. Harnessing and Mimicking Bacterial Features to Combat Cancer: From Living Entities to Artificial Mimicking Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2405075. [PMID: 39136067 DOI: 10.1002/adma.202405075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/23/2024] [Indexed: 08/29/2024]
Abstract
Bacterial-derived micro-/nanomedicine has garnered considerable attention in anticancer therapy, owing to the unique natural features of bacteria, including specific targeting ability, immunogenic benefits, physicochemical modifiability, and biotechnological editability. Besides, bacterial components have also been explored as promising drug delivery vehicles. Harnessing these bacterial features, cutting-edge physicochemical and biotechnologies have been applied to attenuated tumor-targeting bacteria with unique properties or functions for potent and effective cancer treatment, including strategies of gene-editing and genetic circuits. Further, the advent of bacteria-inspired micro-/nanorobots and mimicking artificial systems has furnished fresh perspectives for formulating strategies for developing highly efficient drug delivery systems. Focusing on the unique natural features and advantages of bacteria, this review delves into advances in bacteria-derived drug delivery systems for anticancer treatment in recent years, which has experienced a process from living entities to artificial mimicking systems. Meanwhile, a summary of relative clinical trials is provided and primary challenges impeding their clinical application are discussed. Furthermore, future directions are suggested for bacteria-derived systems to combat cancer.
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Affiliation(s)
- Peng Gao
- Department of General Surgery, Breast Disease Center, Department of Radiology, Huaxi MR Research Center (HMRRC), Liver Transplant Center, Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, NHC, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhenyu Duan
- Department of General Surgery, Breast Disease Center, Department of Radiology, Huaxi MR Research Center (HMRRC), Liver Transplant Center, Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, NHC, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, 610041, China
| | - Gang Xu
- Department of General Surgery, Breast Disease Center, Department of Radiology, Huaxi MR Research Center (HMRRC), Liver Transplant Center, Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, NHC, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiyong Gong
- Department of General Surgery, Breast Disease Center, Department of Radiology, Huaxi MR Research Center (HMRRC), Liver Transplant Center, Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, NHC, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, 610041, China
- Department of Radiology, West China Xiamen Hospital of Sichuan University, Xiamen, Fujian, 361000, China
| | - Jing Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Kui Luo
- Department of General Surgery, Breast Disease Center, Department of Radiology, Huaxi MR Research Center (HMRRC), Liver Transplant Center, Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, NHC, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province and Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, 610041, China
| | - Jie Chen
- Department of General Surgery, Breast Disease Center, Department of Radiology, Huaxi MR Research Center (HMRRC), Liver Transplant Center, Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, NHC, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
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31
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Peng X, Fan H, Liu J, Jiang X, Liu C, Yang Y, Zhai S. Embryo injected with Ochratoxin A induced jejunum injury in ducklings by activating the TLR4 signaling pathway: Involvement of intestinal microbiota. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 281:116666. [PMID: 38945100 DOI: 10.1016/j.ecoenv.2024.116666] [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: 04/08/2024] [Revised: 06/20/2024] [Accepted: 06/28/2024] [Indexed: 07/02/2024]
Abstract
Ochratoxin A (OTA) is a common mycotoxin that causes intestinal injury in humans and various animal species. OTA may lead to intestinal injury in offspring due to the maternal effect. The aim of this study was to investigate the mechanism of embryo injected with OTA induced jejunum injury in ducklings. The results showed that OTA disrupted the jejunum tight junctions in hatching ducklings, and promoted the secretion of inflammatory cytokines. And this inflammatory response was caused by the activation of the TLR4 signaling pathway. Moreover, embryo injected with OTA could cause damage to the intestinal barrier in 21-day-old ducks, characterized by shortened villi, crypt hyperplasia, disrupted intestinal tight junctions, increased level of LPS in the jejunum, activation of the TLR4 signaling pathway, and increased levels of pro-inflammatory cytokines. Meanwhile, OTA induced oxidative stress in the jejunum. And dysbiosis of gut microbiota was mainly characterized by an increased the relative abundance of Bacteroides, Megamonas, Fournierella, and decreased the relative abundance of Alistipes and Weissella. Interestingly, embryo injected with OTA did not induce these changes in the jejunum of antibiotics-treated 21-day-old ducks. In conclusion, embryo injected with OTA induced jejunum injury in ducklings by activating the TLR4 signaling pathway, which involvement of intestinal microbiota.
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Affiliation(s)
- Xin Peng
- College of Animal Science and Technology, Yangtze University, Jingzhou 434023, China
| | - Hailu Fan
- College of Animal Science and Technology, Yangtze University, Jingzhou 434023, China
| | - Jinhui Liu
- College of Animal Science and Technology, Yangtze University, Jingzhou 434023, China
| | - Xiayu Jiang
- College of Animal Science and Technology, Yangtze University, Jingzhou 434023, China
| | - Cheng Liu
- College of Animal Science and Technology, Yangtze University, Jingzhou 434023, China
| | - Ye Yang
- College of Animal Science and Technology, Yangtze University, Jingzhou 434023, China
| | - Shuangshuang Zhai
- College of Animal Science and Technology, Yangtze University, Jingzhou 434023, China.
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Ota G, Inoue R, Saito A, Kono Y, Kitayama J, Sata N, Horie H. Reduced Abundance of Phocaeicola in Mucosa-associated Microbiota Is Associated with Distal Colorectal Cancer Metastases Possibly through an Altered Local Immune Environment. J Anus Rectum Colon 2024; 8:235-245. [PMID: 39086872 PMCID: PMC11286368 DOI: 10.23922/jarc.2024-014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/17/2024] [Indexed: 08/02/2024] Open
Abstract
Objectives The aim of this study was to identify the microbiota whose decrease in tumor area was associated with the metastatic process of distal colorectal cancer (CRC). Methods Twenty-eight consecutive patients with distal CRC undergoing surgical resection in our hospital were enrolled. Microbiota in 28 specimens from surgically resected colorectal cancers were analyzed using 16S ribosomal ribonucleic acid gene amplicon sequencing and the relative abundance (RA) of microbiota was evaluated. The densities of tumor-infiltrating lymphocytes (TIL) and tumor associated macrophages (TAM) in the colorectal cancers were immunohistochemically evaluated. Results Phocaeicola was the most abundant microbiota in normal mucosa. The RA of Phocaeicola in tumor tissues tended to be lower than that in normal mucosa although the difference was not significant (p=0.0732). The RA of Phocaeicola at tumor sites did not correlate either with depth of tumor invasion (pT-stage) or tumor size, however they were significantly reduced in patients with nodal metastases (p<0.05) and those with distant metastases (p<0.001). The RA of Phocaeicola at tumor sites showed positive correlation with the densities of CD3(+) or CD8(+) TIL. Since P. vulgatus was the most dominant species (47%) of the Phocaeicola, the RA of P. vulgatus and CRC metastasis and its association with TIL and TAM were also investigated. P. vulgatus showed a similar trend to genus Phocaeicola but was not statistically significant. Conclusions A relative reduction of Phocaeicola attenuates the local anti-tumor immune response in distal CRC, which may facilitate metastatic spread.
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Affiliation(s)
- Gaku Ota
- Department of Surgery, Jichi Medical University, Shimotsuke, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Hirakata, Japan
| | - Akira Saito
- Department of Surgery, Jichi Medical University, Shimotsuke, Japan
| | - Yoshihiko Kono
- Department of Surgery, Jichi Medical University, Shimotsuke, Japan
| | - Joji Kitayama
- Department of Surgery, Jichi Medical University, Shimotsuke, Japan
- Clinical Research Center, Division of Translational Research, Jichi Medical University, Shimotsuke, Japan
| | - Naohiro Sata
- Department of Surgery, Jichi Medical University, Shimotsuke, Japan
| | - Hisanaga Horie
- Department of Surgery, Jichi Medical University, Shimotsuke, Japan
- Department of Operating Room Management, Jichi Medical University Hospital, Shimotsuke, Japan
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Bars-Cortina D, Ramon E, Rius-Sansalvador B, Guinó E, Garcia-Serrano A, Mach N, Khannous-Lleiffe O, Saus E, Gabaldón T, Ibáñez-Sanz G, Rodríguez-Alonso L, Mata A, García-Rodríguez A, Obón-Santacana M, Moreno V. Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota. BMC Genomics 2024; 25:730. [PMID: 39075388 PMCID: PMC11285316 DOI: 10.1186/s12864-024-10621-7] [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: 04/08/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models. RESULTS As expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra. CONCLUSIONS Shotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.
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Affiliation(s)
- David Bars-Cortina
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, 08908, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain
| | - Elies Ramon
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, 08908, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain
| | - Blanca Rius-Sansalvador
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, 08908, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Doctoral Programme in Biomedicine, University of Barcelona (UB), Barcelona, 08907, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, 08908, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, 28029, Spain
| | - Ainhoa Garcia-Serrano
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, 14186, Sweden
| | - Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Olfat Khannous-Lleiffe
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, 08028, Spain
| | - Gemma Ibáñez-Sanz
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, 08908, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Gastroenterology Department, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, 08907, Spain
| | - Lorena Rodríguez-Alonso
- Gastroenterology Department, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, 08907, Spain
| | - Alfredo Mata
- Digestive System Service, Moisés Broggi Hospital, Sant Joan Despí, 08970, Spain
| | - Ana García-Rodríguez
- Endoscopy Unit, Digestive System Service, Viladecans Hospital-IDIBELL, Viladecans, 08840, Spain
| | - Mireia Obón-Santacana
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, 08908, Spain.
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, 28029, Spain.
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, 08908, Spain.
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, 28029, Spain.
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
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Xiang Y, Zhang C, Wang J, Cheng Y, Wang K, Wang L, Tong Y, Yan D. Role of blood metabolites in mediating the effect of gut microbiome on the mutated-RAS/BRAF metastatic colorectal cancer-specific survival. Int J Colorectal Dis 2024; 39:116. [PMID: 39046546 PMCID: PMC11269474 DOI: 10.1007/s00384-024-04686-9] [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] [Accepted: 07/09/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Recent studies have linked alterations in the gut microbiome and metabolic disruptions to the invasive behavior and metastasis of colorectal cancer (CRC), thus affecting patient prognosis. However, the specific relationship among gut microbiome, metabolite profiles, and mutated-RAS/BRAF metastatic colorectal cancer (M-mCRC) remains unclear. Furthermore, the potential mechanisms and prognostic implications of metabolic changes induced by gut microbiome alterations in patients with M-mCRC still need to be better understood. METHODS We conducted Mendelian randomization (MR) to evaluate the causal relationship of genetically predicted 196 gut microbiome features and 1400 plasma metabolites/metabolite ratios on M-mCRC-specific survival. Additionally, we identified significant gut microbiome-metabolites/metabolite ratio associations based on M-mCRC. Metabolite information was annotated, and functional annotation and pathway enrichment analyses were performed on shared proteins corresponding to significant metabolite ratios, aiming to reveal potential mechanisms by which gut microbiome influences M-mCRC prognosis via modulation of human metabolism. RESULTS We identified 11 gut microbiome features and 49 known metabolites/metabolite ratios correlated with M-mCRC-specific survival. Furthermore, we identified 17 gut microbiome-metabolite/metabolite ratio associations specific to M-mCRC, involving eight lipid metabolites and three bilirubin degradation products. The shared proteins corresponding to significant metabolite ratios were predominantly localized within the integral component of the membrane and exhibited enzymatic activities such as glucuronosyltransferase and UDP-glucuronosyltransferase, crucial in processes such as glucuronidation, bile secretion, and lipid metabolism. Moreover, these proteins were significantly enriched in pathways related to ascorbate and aldarate metabolism, pentose and glucuronate interconversions, steroid hormone biosynthesis, and bile secretion. CONCLUSION Our study offers novel insights into the potential mechanisms underlying the impact of the gut microbiome on the prognosis of M-mCRC. These findings serve as a meaningful reference for exploring potential therapeutic targets and strategies in the future.
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Affiliation(s)
- Yaoxian Xiang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Chan Zhang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Jing Wang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Yurong Cheng
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Kangjie Wang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Li Wang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Yingying Tong
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Dong Yan
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China.
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Kulecka M, Czarnowski P, Bałabas A, Turkot M, Kruczkowska-Tarantowicz K, Żeber-Lubecka N, Dąbrowska M, Paszkiewicz-Kozik E, Walewski J, Ługowska I, Koseła-Paterczyk H, Rutkowski P, Kluska A, Piątkowska M, Jagiełło-Gruszfeld A, Tenderenda M, Gawiński C, Wyrwicz L, Borucka M, Krzakowski M, Zając L, Kamiński M, Mikula M, Ostrowski J. Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients. Int J Mol Sci 2024; 25:8026. [PMID: 39125593 PMCID: PMC11311272 DOI: 10.3390/ijms25158026] [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: 06/24/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.
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Affiliation(s)
- Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Paweł Czarnowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Aneta Bałabas
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Maryla Turkot
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Kamila Kruczkowska-Tarantowicz
- Department of Internal Medicine and Hematology, Military Institute of Medicine—National Research Institute, 04-141 Warsaw, Poland
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Ewa Paszkiewicz-Kozik
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Iwona Ługowska
- Early Phase Clinical Trials Unit, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Hanna Koseła-Paterczyk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Agnieszka Jagiełło-Gruszfeld
- Department of Breast Cancer & Reconstructive Surgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Tenderenda
- Department of Oncological Surgery and Neuroendocrine Tumors, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Cieszymierz Gawiński
- Department of Oncology and Radiotherapy, Maria Sklodowska-Curie National Cancer Research Institute, 02-781 Warsaw, Poland
| | - Lucjan Wyrwicz
- Department of Oncology and Radiotherapy, Maria Sklodowska-Curie National Cancer Research Institute, 02-781 Warsaw, Poland
| | - Magdalena Borucka
- Department of Lung and Chest Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Maciej Krzakowski
- Department of Lung and Chest Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Leszek Zając
- Department of Gastrointestinal Surgical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Kamiński
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
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Intarajak T, Udomchaiprasertkul W, Khoiri AN, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Cheevadhanarak S. Distinct gut microbiomes in Thai patients with colorectal polyps. World J Gastroenterol 2024; 30:3336-3355. [PMID: 39086748 PMCID: PMC11287419 DOI: 10.3748/wjg.v30.i27.3336] [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: 02/21/2024] [Revised: 04/30/2024] [Accepted: 05/31/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence [e.g., tubular adenoma (TA)] often progress to malignancy and are closely associated with changes in the composition of the gut microbiome. There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway, such as hyperplastic polyps (HP). Exploration of microbiome alterations associated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis. AIM To investigate gut microbiome signatures, microbial associations, and microbial functions in HP and TA patients. METHODS Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps [control group (CT), n = 40], patients with HP (n = 52), and patients with TA (n = 60). Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA. Analytical techniques in this study included differential abundance analysis, co-occurrence network analysis, and differential pathway analysis. RESULTS Colorectal cancer (CRC)-associated bacteria, including Streptococcus gallolyticus (S. gallolyticus), Bacteroides fragilis, and Clostridium symbiosum, were identified as characteristic microbial species in TA patients. Mediterraneibacter gnavus, associated with dysbiosis and gastrointestinal diseases, was significantly differentially abundant in the HP and TA groups. Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively, whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis (e.g., mevalonate); S. gallolyticus was a major contributor. Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients, whereas TA patients exhibited co-occurrence of CRC-associated bacteria. Furthermore, the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients. CONCLUSION This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development, providing insights concerning the roles of microbial species, functional pathways, and microbial interactions in colorectal carcinogenesis.
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Affiliation(s)
- Thoranin Intarajak
- Bioinformatics Unit, Chulabhorn Royal Academy, Lak Si 10210, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | | | - Ahmad Nuruddin Khoiri
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Weerayuth Kittichotirat
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Chinae Thammarongtham
- National Center for Genetic Engineering and Biotechnology, King Mongkut's University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- Systems Biology and Bioinformatics Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bank Khun Thian 10150, Bangkok, Thailand
- Fungal Biotechnology Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bang Khun Thian 10150, Bangkok, Thailand
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Herlo LF, Salcudean A, Sirli R, Iurciuc S, Herlo A, Nelson-Twakor A, Alexandrescu L, Dumache R. Gut Microbiota Signatures in Colorectal Cancer as a Potential Diagnostic Biomarker in the Future: A Systematic Review. Int J Mol Sci 2024; 25:7937. [PMID: 39063179 PMCID: PMC11276678 DOI: 10.3390/ijms25147937] [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: 06/05/2024] [Revised: 07/06/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
The gut microbiota has acquired significant attention in recent years for its potential as a diagnostic biomarker for colorectal cancer (CRC). In this literature review, we looked at the studies exploring alterations in gut microbiota composition associated with CRC, the potential mechanisms linking gut dysbiosis to CRC development, and the diagnostic approaches utilizing gut microbiota analysis. Our research has led to the conclusion that individuals with CRC often display alterations in their gut microbiota composition compared to healthy individuals. These alterations can include changes in the diversity, abundance, and type of bacteria present in the gut. While the use of gut microbiota as a diagnostic biomarker for CRC holds promise, further research is needed to validate its effectiveness and standardize testing protocols. Additionally, considerations such as variability in the microbiota composition among individuals and potential factors must be addressed before microbiota-based tests can be widely implemented in clinical practice.
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Affiliation(s)
- Lucian-Flavius Herlo
- Doctoral School, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Andreea Salcudean
- Discipline of Sociobiology, Department of Ethics and Social Sciences, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540136 Targu Mures, Romania;
| | - Roxana Sirli
- Advanced Regional Research Center in Gastroenterology and Hepatology, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Stela Iurciuc
- Cardiology Department, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Alexandra Herlo
- Department XIII, Discipline of Infectious Diseases, Victor Babes University of Medicine and Pharmacy Timisoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Andreea Nelson-Twakor
- Department of Internal Medicine, County Clinical Emergency Hospital of Constanta, 900647 Constanta, Romania;
| | - Luana Alexandrescu
- Department of Gastroenterology, County Clinical Emergency Hospital of Constanta, 900647 Constanta, Romania;
| | - Raluca Dumache
- Department of Forensic Medicine, Bioethics, Medical ethics and Medical Law, Victor Babes University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania;
- Center for Ethics in Human Genetic Identifications, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
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Palanikumar I, Sinha H, Raman K. Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models. iScience 2024; 27:110358. [PMID: 39092173 PMCID: PMC11292516 DOI: 10.1016/j.isci.2024.110358] [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: 11/30/2023] [Revised: 04/10/2024] [Accepted: 06/20/2024] [Indexed: 08/04/2024] Open
Abstract
Utilization of 16S rRNA data in constraint-based modeling to characterize microbial communities confronts a major hurdle of lack of species-level resolution, impeding the construction of community models. We introduce "Panera," an innovative framework designed to model communities under this uncertainty and yet perform metabolic inferences using pan-genus metabolic models (PGMMs). We demonstrated PGMMs' utility for comprehending the metabolic capabilities of a genus and in characterizing community models using amplicon data. The unique, adaptable nature of PGMMs unlocks their potential in building hybrid communities, combining genome-scale metabolic models (GSMMs) and PGMMs. Notably, these models provide predictions comparable to the standard GSMM-based community models, while achieving a nearly 46% reduction in error compared to the genus model-based communities. In essence, "Panera" presents a potent and effective approach to aid in metabolic modeling by enabling robust predictions of community metabolic potential when dealing with amplicon data, and offers insights into genus-level metabolic landscapes.
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Affiliation(s)
- Indumathi Palanikumar
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
- Department of Data Science and AI, Wadhwani School of Data Science and AI, IIT Madras, Chennai 600 036, India
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Salim F, Mizutani S, Shiba S, Takamaru H, Yamada M, Nakajima T, Yachida T, Soga T, Saito Y, Fukuda S, Yachida S, Yamada T. Fusobacterium species are distinctly associated with patients with Lynch syndrome colorectal cancer. iScience 2024; 27:110181. [PMID: 38993678 PMCID: PMC11237946 DOI: 10.1016/j.isci.2024.110181] [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: 12/07/2023] [Revised: 03/11/2024] [Accepted: 06/01/2024] [Indexed: 07/13/2024] Open
Abstract
Accumulating evidence demonstrates clear correlation between the gut microbiota and sporadic colorectal cancer (CRC). Despite this, there is limited understanding of the association between the gut microbiota and CRC in Lynch Syndrome (LS), a hereditary type of CRC. Here, we analyzed fecal shotgun metagenomic and targeted metabolomic of 71 Japanese LS subjects. A previously published Japanese sporadic CRC cohort, which includes non-LS controls, was utilized as a non-LS cohort (n = 437). LS subjects exhibited reduced microbial diversity and low-Faecalibacterium enterotypes compared to non-LS. Patients with LS-CRC had higher levels of Fusobacterium nucleatum and fap2. Differential fecal metabolites and functional genes suggest heightened degradation of lysine and arginine in LS-CRC. A comparison between LS and non-LS subjects prior to adenoma formation revealed distinct fecal metabolites of LS subjects. These findings suggest that the gut microbiota plays a more responsive role in CRC tumorigenesis in patients with LS than those without LS.
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Affiliation(s)
- Felix Salim
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Sayaka Mizutani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Satoshi Shiba
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Hiroyuki Takamaru
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku 104-0045, Tokyo, Japan
| | - Masayoshi Yamada
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku 104-0045, Tokyo, Japan
| | - Takeshi Nakajima
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku 104-0045, Tokyo, Japan
| | - Tatsuo Yachida
- Department of Gastroenterology & Neurology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa 761-0793, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Yutaka Saito
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku 104-0045, Tokyo, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa 210-0821, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
- Metagen, Inc., Tsuruoka, Yamagata 997-0052, Japan
- Metagen Theurapeutics, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
- Metagen, Inc., Tsuruoka, Yamagata 997-0052, Japan
- Metagen Theurapeutics, Inc., Tsuruoka, Yamagata 997-0052, Japan
- digzyme, Inc., Minato-ku, Tokyo 105-0004, Japan
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Jing Z, Zheng W, Jianwen S, Hong S, Xiaojian Y, Qiang W, Yunfeng Y, Xinyue W, Shuwen H, Feimin Z. Gut microbes on the risk of advanced adenomas. BMC Microbiol 2024; 24:264. [PMID: 39026166 PMCID: PMC11256391 DOI: 10.1186/s12866-024-03416-z] [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: 04/07/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND More than 90% of colorectal cancer (CRC) arises from advanced adenomas (AA) and gut microbes are closely associated with the initiation and progression of both AA and CRC. OBJECTIVE To analyze the characteristic microbes in AA. METHODS Fecal samples were collected from 92 AA and 184 negative control (NC). Illumina HiSeq X sequencing platform was used for high-throughput sequencing of microbial populations. The sequencing results were annotated and compared with NCBI RefSeq database to find the microbial characteristics of AA. R-vegan package was used to analyze α diversity and β diversity. α diversity included box diagram, and β diversity included Principal Component Analysis (PCA), principal co-ordinates analysis (PCoA), and non-metric multidimensional scaling (NMDS). The AA risk prediction models were constructed based on six kinds of machine learning algorithms. In addition, unsupervised clustering methods were used to classify bacteria and viruses. Finally, the characteristics of bacteria and viruses in different subtypes were analyzed. RESULTS The abundance of Prevotella sp900557255, Alistipes putredinis, and Megamonas funiformis were higher in AA, while the abundance of Lilyvirus, Felixounavirus, and Drulisvirus were also higher in AA. The Catboost based model for predicting the risk of AA has the highest accuracy (bacteria test set: 87.27%; virus test set: 83.33%). In addition, 4 subtypes (B1V1, B1V2, B2V1, and B2V2) were distinguished based on the abundance of gut bacteria and enteroviruses (EVs). Escherichia coli D, Prevotella sp900557255, CAG-180 sp000432435, Phocaeicola plebeiuA, Teseptimavirus, Svunavirus, Felixounavirus, and Jiaodavirus are the characteristic bacteria and viruses of 4 subtypes. The results of Catboost model indicated that the accuracy of prediction improved after incorporating subtypes. The accuracy of discovery sets was 100%, 96.34%, 100%, and 98.46% in 4 subtypes, respectively. CONCLUSION Prevotella sp900557255 and Felixounavirus have high value in early warning of AA. As promising non-invasive biomarkers, gut microbes can become potential diagnostic targets for AA, and the accuracy of predicting AA can be improved by typing.
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Affiliation(s)
- Zhuang Jing
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China
| | - Wu Zheng
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China
| | - Song Jianwen
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China
| | - Shen Hong
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
| | - Yu Xiaojian
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China
| | - Wei Qiang
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China
| | - Yin Yunfeng
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China
| | - Wu Xinyue
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China
| | - Han Shuwen
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China.
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China.
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China.
- ICL, Junia, Université Catholique de Lille, Lille, France.
| | - Zhao Feimin
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China.
- Fifth School of Clinical Medicine of Zhejiang Chinese Medical University (Huzhou Central Hospital), Huzhou, Zhejiang Province, China.
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, Zhejiang Province, China.
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Wang X, Zhang Q, Xu R, Li X, Hong Z. Research progress on the correlation between intestinal flora and colorectal cancer. Front Oncol 2024; 14:1416806. [PMID: 39087025 PMCID: PMC11288818 DOI: 10.3389/fonc.2024.1416806] [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: 04/13/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most common gastrointestinal malignancies in the world. With the rapid pace of life and changes in diet structure, the incidence and mortality of CRC increase year by year posing a serious threat to human health. As the most complex and largest microecosystem in the human body, intestinal microecology is closely related to CRC. It is an important factor that affects and participates in the occurrence and development of CRC. Advances in next-generation sequencing technology and metagenomics have provided new insights into the ecology of gut microbes. It also helps to link intestinal flora with CRC, and the relationship between intestinal flora and CRC can be continuously understood from different levels. This paper summarizes the relationship between intestinal flora and CRC and its potential role in the diagnosis of CRC providing evidence for early screening and treatment of CRC.
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Affiliation(s)
- Xinyu Wang
- The Health Management Center, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qian Zhang
- Department of Public Health, Dalian Medical University, Dalian, Liaoning, China
| | - Rongxuan Xu
- Department of Public Health, Dalian Medical University, Dalian, Liaoning, China
| | - Xiaofeng Li
- Department of Public Health, Dalian Medical University, Dalian, Liaoning, China
| | - Zhijun Hong
- The Health Management Center, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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Tang T, Zhou Z, Chen M, Li N, Sun J, Chen Z, Xiao T, Wang X, Zhang L, Wang Y, Zhang H, Zheng X, Chen B, Ye F, Guan J. Plasma Metabolic Profiles-Based Prediction of Induction Chemotherapy Efficacy in Nasopharyngeal Carcinoma: Results of a Bidirectional Clinical Trial. Clin Cancer Res 2024; 30:2925-2936. [PMID: 38713248 PMCID: PMC11247322 DOI: 10.1158/1078-0432.ccr-23-3608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/23/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
PURPOSE The efficacy of induction chemotherapy (IC) as a primary treatment for advanced nasopharyngeal carcinoma (NPC) remains a topic of debate, with a lack of dependable biomarkers for predicting its efficacy. This study seeks to establish a predictive classifier using plasma metabolomics profiles. PATIENTS AND METHODS A total of 166 NPC patients enrolled in the clinical trial NCT05682703 who were undergoing IC were included in the study. Plasma lipoprotein profiles were obtained using 1H-nuclear magnetic resonance before and after IC treatment. An artificial intelligence-assisted radiomics method was developed to effectively evaluate its efficacy. Metabolic biomarkers were identified through a machine learning approach based on a discovery cohort and subsequently validated in a validation cohort that mimicked the most unfavorable real-world scenario. RESULTS Our research findings indicate that the effectiveness of IC varies among individual patients, with a correlation observed between efficacy and changes in metabolite profiles. Using machine learning techniques, it was determined that the extreme gradient boosting model exhibited notable efficacy, attaining an area under the curve (AUC) value of 0.792 (95% CI, 0.668-0.913). In the validation cohort, the model exhibited strong stability and generalizability, with an AUC of 0.786 (95% CI, 0.533-0.922). CONCLUSIONS In this study, we found that dysregulation of plasma lipoprotein may result in resistance to IC in NPC patients. The prediction model constructed based on the plasma metabolites' profile has good predictive capabilities and potential for real-world generalization. This discovery has implications for the development of treatment strategies and may offer insight into potential targets for enhancing the effectiveness of IC.
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Affiliation(s)
- Tingxi Tang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Zhenhua Zhou
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Min Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Department of Radiation Oncology, Peking University Shenzhen Hospital, Shenzhen, China.
| | - Nan Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Jianda Sun
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Department of Radiation Oncology, Meizhou People’s Hospital, Meizhou, China.
| | - Zekai Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Ting Xiao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Xiaoqing Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Longshan Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Yingqiao Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Hanbin Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Xiuting Zheng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Bei Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Feng Ye
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, China.
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Güven Gülhan Ü, Nikerel E, Çakır T, Erdoğan Sevilgen F, Durmuş S. Species-level identification of enterotype-specific microbial markers for colorectal cancer and adenoma. Mol Omics 2024; 20:397-416. [PMID: 38780313 DOI: 10.1039/d4mo00016a] [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: 05/25/2024]
Abstract
Enterotypes have been shown to be an important factor for population stratification based on gut microbiota composition, leading to a better understanding of human health and disease states. Classifications based on compositional patterns will have implications for personalized microbiota-based solutions. There have been limited enterotype based studies on colorectal adenoma and cancer. Here, an enterotype-based meta-analysis of fecal shotgun metagenomic studies was performed, including 1579 samples of healthy controls (CTR), colorectal adenoma (ADN) and colorectal cancer (CRC) in total. Gut microbiota of healthy people were clustered into three enterotypes (Ruminococcus-, Bacteroides- and Prevotella-dominated enterotypes). Reference-based enterotype assignments were performed for CRC and ADN samples, using the supervised machine learning algorithm, K-nearest neighbors. Differential abundance analyses and random forest classification were conducted on each enterotype between healthy controls and CRC-ADN groups, revealing novel enterotype-specific microbial markers for non-invasive CRC screening strategies. Furthermore, we identified microbial species unique to each enterotype that play a role in the production of secondary bile acids and short-chain fatty acids, unveiling the correlation between cancer-associated gut microbes and dietary patterns. The enterotype-based approach in this study is promising in elucidating the mechanisms of differential gut microbiome profiles, thereby improving the efficacy of personalized microbiota-based solutions.
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Affiliation(s)
- Ünzile Güven Gülhan
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, TR 34755, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| | - Fatih Erdoğan Sevilgen
- The Institute for Data Science & Artificial Intelligence, Boğaziçi University, Istanbul, TR 34342, Turkey
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| | - Saliha Durmuş
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
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Dong Y, Chen WH, Zhao XM. VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes. Genome Biol 2024; 25:177. [PMID: 38965579 PMCID: PMC11229495 DOI: 10.1186/s13059-024-03320-9] [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: 12/18/2023] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. VirRep combines a context-aware encoder and an evolution-aware encoder to improve sequence representation by incorporating k-mer patterns and sequence homologies. Benchmarking on both simulated and real datasets with varying viral proportions demonstrates that VirRep outperforms state-of-the-art methods. When applied to fecal metagenomes from a colorectal cancer cohort, VirRep identifies 39 high-quality viral species associated with the disease, many of which cannot be detected by existing methods.
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Affiliation(s)
- Yanqi Dong
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Xing-Ming Zhao
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
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Bai X, Duan Z, Deng J, Zhang Z, Fu R, Zhu C, Fan D. Ginsenoside Rh4 inhibits colorectal cancer via the modulation of gut microbiota-mediated bile acid metabolism. J Adv Res 2024:S2090-1232(24)00265-0. [PMID: 38969093 DOI: 10.1016/j.jare.2024.06.028] [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: 01/27/2024] [Revised: 05/15/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024] Open
Abstract
INTRODUCTION Dysbiosis of the gut microbiota is emerging as a pivotal factor in the pathogenesis of colorectal cancer (CRC). Ginsenoside Rh4 (Rh4) is an active compound isolated from ginseng with beneficial effects in modulating intestinal inflammation and gut microbiota dysbiosis, but how Rh4 regulates the gut microbiota to alleviate CRC remains underexplored. OBJECTIVES We investigated the impact of Rh4 on CRC and the mechanism of its action in inhibiting CRC via modulation of gut microbiota. METHODS We used the AOM/DSS model and employed transcriptomics, genomics and metabolomics techniques to explore the inhibitory impact of Rh4 on CRC. Furthermore, we employed experiments involving antibiotic treatment and fecal microbiota transplantation (FMT) to investigate the role of the gut microbiota. Finally, we elucidated the pivotal role of key functional bacteria and metabolites regulated by Rh4 in CRC. RESULTS Our research findings indicated that Rh4 repaired intestinal barrier damage caused by CRC, alleviated intestinal inflammation, and inhibited the development of CRC. Additionally, Rh4 inhibited CRC in a gut microbiota-dependent manner. Rh4 increased the diversity of gut microbiota, enriched the probiotic Akkermansia muciniphila (A. muciniphila), and alleviated gut microbiota dysbiosis caused by CRC. Subsequently, Rh4 regulated A. muciniphila-mediated bile acid metabolism. A. muciniphila promoted the production of UDCA by enhancing the activity of 7α-hydroxysteroid dehydrogenase (7α-HSDH). UDCA further activated FXR, modulated the TLR4-NF-κB signaling pathway, thus inhibiting the development of CRC. CONCLUSION Our results confirm that Rh4 inhibits CRC in a gut microbiota-dependent manner by modulating gut microbiota-mediated bile acid metabolism and promoting the production of UDCA, which further activates the FXR receptor and regulates the TLR4-NF-κB signaling pathway. Our results confirm that Rh4 has the potential to be used as a modulator of gut microbiota for preventing and treatment of CRC.
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Affiliation(s)
- Xue Bai
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an, 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, China
| | - Zhiguang Duan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an, 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, China
| | - Jianjun Deng
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an, 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, China
| | - Zhuo Zhang
- Plastic and Cosmetic Maxillofacial Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, China
| | - Rongzhan Fu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an, 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, China.
| | - Chenhui Zhu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an, 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, China.
| | - Daidi Fan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an, 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, China.
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Li Y, Qiao X, Feng Y, Zhou R, Zhang K, Pan Y, Yan T, Yan L, Yang S, Wei X, Li P, Xu C, Lv Z, Tian Z. Characterization of the gut microbiota and fecal metabolome in the osteosarcoma mouse model. Aging (Albany NY) 2024; 16:10841-10859. [PMID: 38967635 PMCID: PMC11272122 DOI: 10.18632/aging.205951] [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] [Accepted: 05/21/2024] [Indexed: 07/06/2024]
Abstract
Previous studies have reported the correlation between gut microbiota (GM), GM-derived metabolites, and various intestinal and extra-intestinal cancers. However, limited studies have investigated the correlation between GM, GM-derived metabolites, and osteosarcoma (OS). This study successfully established a female BALB/c nude mouse model of OS. Mice (n = 14) were divided into the following two groups (n = 7/group): OS group named OG, injected with Saos-2 OS cells; normal control group named NCG, injected with Matrigel. The GM composition and metabolites were characterized using 16S rDNA sequencing and untargeted metabolomics, respectively. Bioinformatics analysis revealed that amino acid metabolism was dysregulated in OS. The abundances of bone metabolism-related genera Alloprevotella, Rikenellaceae_RC9_gut_group, and Muribaculum were correlated with amino acid metabolism, especially histidine metabolism. These findings suggest the correlation between GM, GM-derived metabolites, and OS pathogenesis. Clinical significance: The currently used standard therapeutic strategies for OS, including surgery, chemotherapy, and radiation, are not efficacious. The findings of this study provided novel insights for developing therapeutic, diagnostic, and prognostic strategies for OS.
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Affiliation(s)
- Yuan Li
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Xiaochen Qiao
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Yi Feng
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Ruhao Zhou
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Kun Zhang
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Yongchun Pan
- Department of Orthopedics, Third People's Hospital of Datong City, Datong 037006, Shanxi, P.R. China
| | - Ting Yan
- Translational Medicine Center, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
| | - Lei Yan
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Sen Yang
- Department of Orthopedics, The Second People's Hospital of Changzhi, Changzhi 046000, Shanxi, P.R. China
| | - Xiaochun Wei
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Pengcui Li
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Chaojian Xu
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Zhi Lv
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Zhi Tian
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
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Tian K, Jing D, Lan J, Lv M, Wang T. Commensal microbiome and gastrointestinal mucosal immunity: Harmony and conflict with our closest neighbor. Immun Inflamm Dis 2024; 12:e1316. [PMID: 39023417 PMCID: PMC11256888 DOI: 10.1002/iid3.1316] [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: 01/31/2024] [Revised: 05/06/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND The gastrointestinal tract contains a wide range of microorganisms that have evolved alongside the immune system of the host. The intestinal mucosa maintains balance within the intestines by utilizing the mucosal immune system, which is controlled by the complex gut mucosal immune network. OBJECTIVE This review aims to comprehensively introduce current knowledge of the gut mucosal immune system, focusing on its interaction with commensal bacteria. RESULTS The gut mucosal immune network includes gut-associated lymphoid tissue, mucosal immune cells, cytokines, and chemokines. The connection between microbiota and the immune system occurs through the engagement of bacterial components with pattern recognition receptors found in the intestinal epithelium and antigen-presenting cells. This interaction leads to the activation of both innate and adaptive immune responses. The interaction between the microbial community and the host is vital for maintaining the balance and health of the host's mucosal system. CONCLUSION The gut mucosal immune network maintains a delicate equilibrium between active immunity, which defends against infections and damaging non-self antigens, and immunological tolerance, which allows for the presence of commensal microbiota and dietary antigens. This balance is crucial for the maintenance of intestinal health and homeostasis. Disturbance of gut homeostasis leads to enduring or severe gastrointestinal ailments, such as colorectal cancer and inflammatory bowel disease. Utilizing these factors can aid in the development of cutting-edge mucosal vaccines that have the ability to elicit strong protective immune responses at the primary sites of pathogen invasion.
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Affiliation(s)
- Kexin Tian
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical SchoolNanjing UniversityNanjingChina
- Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical SchoolNanjing UniversityNanjingChina
| | - Dehong Jing
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical SchoolNanjing UniversityNanjingChina
- Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical SchoolNanjing UniversityNanjingChina
| | - Junzhe Lan
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical SchoolNanjing UniversityNanjingChina
- Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical SchoolNanjing UniversityNanjingChina
| | - Mingming Lv
- Department of BreastWomen's Hospital of Nanjing Medical University, Nanjing Maternity, and Child Health Care HospitalNanjingChina
| | - Tingting Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical SchoolNanjing UniversityNanjingChina
- Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical SchoolNanjing UniversityNanjingChina
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Zhang P, Shi H, Guo R, Li L, Guo X, Yang H, Chang D, Cheng Y, Zhao G, Li S, Zhong Q, Zhang H, Zhao P, Fu C, Song Y, Yang L, Wang Y, Zhang Y, Jiang J, Wang T, Zhao J, Li Y, Wang B, Chen F, Zhao H, Wang Y, Wang J, Ma S. Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer. J Med Virol 2024; 96:e29809. [PMID: 39016466 DOI: 10.1002/jmv.29809] [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: 01/24/2024] [Revised: 06/15/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024]
Abstract
Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.
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Affiliation(s)
- Pan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Haitao Shi
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Lu Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Xiaoyan Guo
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Hui Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Danyan Chang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yan Cheng
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Gang Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Qingling Zhong
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Huan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ping Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Cui Fu
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yahua Song
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Longbao Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yan Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Jiong Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ting Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Juhui Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yong Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Biyuan Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Fenrong Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Hongli Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yonghua Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Jinhai Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Shiyang Ma
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
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49
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Wang Q, Guo F, Zhang Q, Hu T, Jin Y, Yang Y, Ma Y. Organoids in gastrointestinal diseases: from bench to clinic. MedComm (Beijing) 2024; 5:e574. [PMID: 38948115 PMCID: PMC11214594 DOI: 10.1002/mco2.574] [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: 11/28/2023] [Revised: 04/15/2024] [Accepted: 04/26/2024] [Indexed: 07/02/2024] Open
Abstract
The etiology of gastrointestinal (GI) diseases is intricate and multifactorial, encompassing complex interactions between genetic predisposition and gut microbiota. The cell fate change, immune function regulation, and microenvironment composition in diseased tissues are governed by microorganisms and mutated genes either independently or through synergistic interactions. A comprehensive understanding of GI disease etiology is imperative for developing precise prevention and treatment strategies. However, the existing models used for studying the microenvironment in GI diseases-whether cancer cell lines or mouse models-exhibit significant limitations, which leads to the prosperity of organoids models. This review first describes the development history of organoids models, followed by a detailed demonstration of organoids application from bench to clinic. As for bench utilization, we present a layer-by-layer elucidation of organoid simulation on host-microbial interactions, as well as the application in molecular mechanism analysis. As for clinical adhibition, we provide a generalized interpretation of organoid application in GI disease simulation from inflammatory disorders to malignancy diseases, as well as in GI disease treatment including drug screening, immunotherapy, and microbial-targeting and screening treatment. This review draws a comprehensive and systematical depiction of organoids models, providing a novel insight into the utilization of organoids models from bench to clinic.
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Affiliation(s)
- Qinying Wang
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Fanying Guo
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qinyuan Zhang
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - TingTing Hu
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - YuTao Jin
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yongzhi Yang
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yanlei Ma
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
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50
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Shi J, Shen H, Huang H, Zhan L, Chen W, Zhou Z, Lv Y, Xiong K, Jiang Z, Chen Q, Liu L. Gut microbiota characteristics of colorectal cancer patients in Hubei, China, and differences with cohorts from other Chinese regions. Front Microbiol 2024; 15:1395514. [PMID: 38962132 PMCID: PMC11220721 DOI: 10.3389/fmicb.2024.1395514] [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: 03/04/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
The research on the correlation or causality between gut microbiota and the occurrence, development, and treatment of colorectal cancer (CRC) is receiving increasing emphasis. At the same time, the incidence and mortality of colorectal cancer vary among individuals and regions, as does the gut microbiota. In order to gain a better understanding of the characteristics of the gut microbiota in CRC patients and the differences between different regions, we initially compared the gut microbiota of 25 CRC patients and 26 healthy controls in the central region of China (Hubei Province) using 16S rRNA high-throughput sequencing technology. The results showed that Corynebacterium, Enterococcus, Lactobacillus, and Escherichia-Shigella were significantly enriched in CRC patients. In addition, we also compared the potential differences in functional pathways between the CRC group and the healthy control group using PICRUSt's functional prediction analysis. We then analyzed and compared it with five cohort studies from various regions of China, including Central, East, and Northeast China. We found that geographical factors may affect the composition of intestinal microbiota in CRC patients. The composition of intestinal microbiota is crucial information that influences colorectal cancer screening, early detection, and the prediction of CRC treatment outcomes. This emphasizes the importance of conducting research on CRC-related gut microbiota in various regions of China.
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Affiliation(s)
- Jianguo Shi
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hexiao Shen
- School of Life Sciences and Health Engineering, Hubei University, Wuhan, China
| | - Hui Huang
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lifang Zhan
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Chen
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhuohui Zhou
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yongling Lv
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kai Xiong
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhiwei Jiang
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiyi Chen
- Department of Colorectal Disease, Intestinal Microenvironment Treatment Center, Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Lei Liu
- Department of Gastrointestinal Surgery, Intestinal Microenvironment Treatment Center, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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