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Teixeira M, Silva F, Ferreira RM, Pereira T, Figueiredo C, Oliveira HP. A review of machine learning methods for cancer characterization from microbiome data. NPJ Precis Oncol 2024; 8:123. [PMID: 38816569 PMCID: PMC11139966 DOI: 10.1038/s41698-024-00617-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Recent studies have shown that the microbiome can impact cancer development, progression, and response to therapies suggesting microbiome-based approaches for cancer characterization. As cancer-related signatures are complex and implicate many taxa, their discovery often requires Machine Learning approaches. This review discusses Machine Learning methods for cancer characterization from microbiome data. It focuses on the implications of choices undertaken during sample collection, feature selection and pre-processing. It also discusses ML model selection, guiding how to choose an ML model, and model validation. Finally, it enumerates current limitations and how these may be surpassed. Proposed methods, often based on Random Forests, show promising results, however insufficient for widespread clinical usage. Studies often report conflicting results mainly due to ML models with poor generalizability. We expect that evaluating models with expanded, hold-out datasets, removing technical artifacts, exploring representations of the microbiome other than taxonomical profiles, leveraging advances in deep learning, and developing ML models better adapted to the characteristics of microbiome data will improve the performance and generalizability of models and enable their usage in the clinic.
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Affiliation(s)
- Marco Teixeira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal.
- Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Francisco Silva
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
| | - Rui M Ferreira
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Tania Pereira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Ceu Figueiredo
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Hélder P Oliveira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
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2
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Raoul P, De Gaetano V, Sciaraffia G, Ormea G, Cintoni M, Pozzo C, Strippoli A, Gasbarrini A, Mele MC, Rinninella E. Gastric Cancer, Immunotherapy, and Nutrition: The Role of Microbiota. Pathogens 2024; 13:357. [PMID: 38787209 PMCID: PMC11124250 DOI: 10.3390/pathogens13050357] [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: 03/15/2024] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Immune checkpoint inhibitors (ICI) have revolutionized the treatment of gastric cancer (GC), which still represents the third leading cause of cancer-related death in Western countries. However, ICI treatment outcomes vary between individuals and need to be optimized. Recent studies have shown that gut microbiota could represent a key influencer of immunotherapy responses. At the same time, the nutritional status and diet of GC patients are also predictive of immunotherapy treatment response and survival outcomes. The objective of this narrative review is to gather recent findings about the complex relationships between the oral, gastric, and gut bacterial communities, dietary factors/nutritional parameters, and immunotherapy responses. Perigastric/gut microbiota compositions/functions and their metabolites could be predictive of response to immunotherapy in GC patients and even overall survival. At the same time, the strong influence of diet on the composition of the microbiota could have consequences on immunotherapy responses through the impact of muscle mass in GC patients during immunotherapy. Future studies are needed to define more precisely the dietary factors, such as adequate daily intake of prebiotics, that could counteract the dysbiosis of the GC microbiota and the impaired nutritional status, improving the clinical outcomes of GC patients during immunotherapy.
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Affiliation(s)
- Pauline Raoul
- Clinical Nutrition Unit, Department of Medical and Abdominal Surgery and Endocrine-Metabolic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy (M.C.); (M.C.M.)
| | - Valeria De Gaetano
- School of Specialization in Internal Medicine, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.D.G.); (G.S.)
| | - Gianmario Sciaraffia
- School of Specialization in Internal Medicine, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.D.G.); (G.S.)
| | - Ginevra Ormea
- Degree Course in Pharmacy, Catholic University of the Sacred Heart, 00168 Rome, Italy;
| | - Marco Cintoni
- Clinical Nutrition Unit, Department of Medical and Abdominal Surgery and Endocrine-Metabolic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy (M.C.); (M.C.M.)
- Research and Training Center in Human Nutrition, Catholic University of the Sacred Heart, 00168 Rome, Italy;
| | - Carmelo Pozzo
- Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (C.P.); (A.S.)
| | - Antonia Strippoli
- Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (C.P.); (A.S.)
| | - Antonio Gasbarrini
- Research and Training Center in Human Nutrition, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- Digestive Disease Center (CEMAD), Department of Medical and Abdominal Surgery and Endocrine-Metabolic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Maria Cristina Mele
- Clinical Nutrition Unit, Department of Medical and Abdominal Surgery and Endocrine-Metabolic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy (M.C.); (M.C.M.)
- Research and Training Center in Human Nutrition, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Emanuele Rinninella
- Clinical Nutrition Unit, Department of Medical and Abdominal Surgery and Endocrine-Metabolic Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy (M.C.); (M.C.M.)
- Research and Training Center in Human Nutrition, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy
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3
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Nie S, Wang A, Chen X, Gong Y, Yuan Y. Microbial-Related Metabolites May Be Involved in Eight Major Biological Processes and Represent Potential Diagnostic Markers in Gastric Cancer. Cancers (Basel) 2023; 15:5271. [PMID: 37958446 PMCID: PMC10649575 DOI: 10.3390/cancers15215271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Metabolites associated with microbes regulate human immunity, inhibit bacterial colonization, and promote pathogenicity. Integrating microbe and metabolome research in GC provides a direction for understanding the microbe-associated pathophysiological process of metabolic changes and disease occurrence. The present study included 30 GC patients with 30 cancerous tissues and paired non-cancerous tissues (NCs) as controls. LC-MS/MS metabolomics and 16S rRNA sequencing were performed to obtain the metabolic and microbial characteristics. Integrated analysis of the microbes and metabolomes was conducted to explore the coexistence relationship between the microbial and metabolic characteristics of GC and to identify microbial-related metabolite diagnostic markers. The metabolic analysis showed that the overall metabolite distribution differed between the GC tissues and the NC tissues: 25 metabolites were enriched in the NC tissues and 42 metabolites were enriched in the GC tissues. The α and β microbial diversities were higher in the GC tissues than in the NC tissues, with 11 differential phyla and 52 differential genera. In the correlation and coexistence integrated analysis, 66 differential metabolites were correlated and coexisted, with specific differential microbes. The microbes in the GC tissue likely regulated eight metabolic pathways. In the efficacy evaluation of the microbial-related differential metabolites in the diagnosis of GC, 12 differential metabolites (area under the curve [AUC] >0.9) exerted relatively high diagnostic efficiency, and the combined diagnostic efficacy of 5 to 6 microbial-related differential metabolites was higher than the diagnostic efficacy of a single feature. Therefore, microbial diversity and metabolite distribution differed between the GC tissues and the NC tissues. Microbial-related metabolites may be involved in eight major metabolism-based biological processes in GC and represent potential diagnostic markers.
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Affiliation(s)
- Siru Nie
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Ang Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Xiaohui Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China; (S.N.); (A.W.); (X.C.)
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang 110001, China
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4
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Wang M, Yang G, Tian Y, Zhang Q, Liu Z, Xin Y. The role of the gut microbiota in gastric cancer: the immunoregulation and immunotherapy. Front Immunol 2023; 14:1183331. [PMID: 37457738 PMCID: PMC10348752 DOI: 10.3389/fimmu.2023.1183331] [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: 03/13/2023] [Accepted: 05/11/2023] [Indexed: 07/18/2023] Open
Abstract
Gastric cancer (GC) is one of the most common cancers, leading to the deaths of millions of people worldwide. Therefore, early detection and effective therapeutic strategies are of great value for decreasing the occurrence of advanced GC. The human microbiota is involved not only in the maintenance of physiological conditions, but also in human diseases such as obesity, diabetes, allergic and atopic diseases, and cancer. Currently, the composition of the bacteria in the host, their functions, and their influence on disease progression and treatment are being discussed. Previous studies on the gut microbiome have mostly focused on Helicobacter pylori (Hp) owing to its significant role in the development of GC. Nevertheless, the enrichment and diversity of other bacteria that can modulate the tumor microenvironment are involved in the progression of GC and the efficacy of immunotherapy. This review provides systematic insight into the components of the gut microbiota and their application in GC, including the specific bacteria of GC, their immunoregulatory effect, and their diagnostic value. Furthermore, we discuss the relationship between the metabolism of microbes and their potential applications, which may serve as a new approach for the diagnosis and treatment of GC.
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Affiliation(s)
- Meiqi Wang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Ge Yang
- College of Basic Medical Sciences and Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Yuan Tian
- College of Basic Medical Sciences and Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Qihe Zhang
- College of Basic Medical Sciences and Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Zhuo Liu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Ying Xin
- College of Basic Medical Sciences and Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
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5
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Xi J, Li Y, Zhang H, Bai Z. Dynamic variations of the gastric microbiota: Key therapeutic points in the reversal of Correa's cascade. Int J Cancer 2023; 152:1069-1084. [PMID: 36029278 DOI: 10.1002/ijc.34264] [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: 03/31/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 01/21/2023]
Abstract
Correa's cascade is a dynamic process in the development of intestinal-type gastric cancer (GC), and its pathological features, gastric microbiota and interactions between microorganisms and their hosts vary at different developmental stages. The characteristics of cells, tissues and gastric microbiota before or after key therapeutic points are critical for monitoring malignant transformation and early tumour reversal. This review summarises the pathological features of gastric mucosa, characteristics of gastric microbiota, specific microbial markers, microbe-microbe interactions and microbe-host interactions at different stages in Correa's cascade. The markers related to each Correa's cascade point were analysed in detail. We attempted to identify key therapeutic points for early cancer reversal and provide a novel approach to reduce the incidence of GC and improve precise treatment.
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Affiliation(s)
- Jiahui Xi
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,Key Laboratory of Biotherapy and Regenerative Medicine, Gansu Province, Lanzhou, China
| | - Yonghong Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumour, Gansu Provincial Hospital, Lanzhou, China
| | - Hui Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,General Surgery Department, The First Hospital of Lanzhou University, Lanzhou, China
| | - Zhongtian Bai
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,Key Laboratory of Biotherapy and Regenerative Medicine, Gansu Province, Lanzhou, China.,General Surgery Department, The First Hospital of Lanzhou University, Lanzhou, China
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6
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Fakharian F, Asgari B, Nabavi-Rad A, Sadeghi A, Soleimani N, Yadegar A, Zali MR. The interplay between Helicobacter pylori and the gut microbiota: An emerging driver influencing the immune system homeostasis and gastric carcinogenesis. Front Cell Infect Microbiol 2022; 12:953718. [PMID: 36046747 PMCID: PMC9423097 DOI: 10.3389/fcimb.2022.953718] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/25/2022] [Indexed: 01/06/2023] Open
Abstract
The human gut microbiota are critical for preserving the health status because they are required for digestion and nutrient acquisition, the development of the immune system, and energy metabolism. The gut microbial composition is greatly influenced by the colonization of the recalcitrant pathogen Helicobacter pylori (H. pylori) and the conventional antibiotic regimens that follow. H. pylori is considered to be the main microorganism in gastric carcinogenesis, and it appears to be required for the early stages of the process. However, a non-H. pylori microbiota profile is also suggested, primarily in the later stages of tumorigenesis. On the other hand, specific groups of gut microbes may produce beneficial byproducts such as short-chain fatty acids (acetate, butyrate, and propionate) that can modulate inflammation and tumorigenesis pathways. In this review, we aim to present how H. pylori influences the population of the gut microbiota to modify the host immunity and trigger the development of gastric carcinogenesis. We will also highlight the effect of the gut microbiota on immunotherapeutic approaches such as immune checkpoint blockade in cancer treatment to present a perspective for further development of innovative therapeutic paradigms to prevent the progression of H. pylori-induced stomach cancer.
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Affiliation(s)
- Farzaneh Fakharian
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behnoush Asgari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Soleimani
- Department of Microbiology, Faculty of Biological Sciences and Technology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Abbas Yadegar, ;
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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7
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Nath AN, Retnakumar RJ, Francis A, Chhetri P, Thapa N, Chattopadhyay S. Peptic Ulcer and Gastric Cancer: Is It All in the Complex Host-Microbiome Interplay That Is Encoded in the Genomes of "Us" and "Them"? Front Microbiol 2022; 13:835313. [PMID: 35547123 PMCID: PMC9083406 DOI: 10.3389/fmicb.2022.835313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
It is increasingly being recognized that severe gastroduodenal diseases such as peptic ulcer and gastric cancer are not just the outcomes of Helicobacter pylori infection in the stomach. Rather, both diseases develop and progress due to the perfect storms created by a combination of multiple factors such as the expression of different H. pylori virulence proteins, consequent human immune responses, and dysbiosis in gastrointestinal microbiomes. In this mini review, we have discussed how the genomes of H. pylori and other gastrointestinal microbes as well as the genomes of different human populations encode complex and variable virulome–immunome interplay, which influences gastroduodenal health. The heterogeneities that are encrypted in the genomes of different human populations and in the genomes of their respective resident microbes partly explain the inconsistencies in clinical outcomes among the H. pylori-infected people.
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Affiliation(s)
- Angitha N Nath
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - R J Retnakumar
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.,Manipal Academy of Higher Education, Manipal, India
| | - Ashik Francis
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Prakash Chhetri
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Tadong, India
| | - Namrata Thapa
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Tadong, India
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Gomes MS, Pereira L. Special Issue: From Host-Pathogen Interaction to Host-Directed Therapies. Microorganisms 2021; 9:microorganisms9122606. [PMID: 34946207 PMCID: PMC8707891 DOI: 10.3390/microorganisms9122606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Maria Salomé Gomes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
- Correspondence: (M.S.G.); (L.P.)
| | - Luisa Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: (M.S.G.); (L.P.)
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9
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Di DS, Li C, Dai Y, Wei MH, Wang SS, Song WJ, Zhou HL, Cui Y, Zhang RY, Huang Q, Wang Q. Integrative Analysis of LGR5/6 Gene Variants, Gut Microbiota Composition and Osteoporosis Risk in Elderly Population. Front Microbiol 2021; 12:765008. [PMID: 34795657 PMCID: PMC8593465 DOI: 10.3389/fmicb.2021.765008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Objective: This study aimed to explore the relationships between the common variants of R-spondin/Wnt signaling genes, gut microbiota composition, and osteoporosis (OP) risk in elderly Chinese Han population. Design: Dual-energy X-ray absorptiometry was used to obtain the OP-associated measurements at multiple skeleton sites among all 1,168 participants. Genotyping data was obtained by using the next-generation sequencing in the discovery stage (n = 400, 228 OP patients) and SNPscan technology in the replication stage (n = 768, 356 OP patients). Bioinformatic analysis was performed to provide more evidence for the genotype-OP associations. The 16S ribosomal RNA gene high-throughput sequencing technology was adopted to explore OP-associated gut microbiota variations. Results: The genetic variants of rs10920362 in the LGR6 gene (P-FDR = 1.19 × 10–6) and rs11178860 in the LGR5 gene (P-FDR = 1.51 × 10–4) were found to associate with OP risk significantly. Several microbial taxa were associated with the BMDs and T-scores at multiple skeleton sites. The associations between rs10920362 and BMD-associated microbiota maintained significance after adjusting confounders. The rs10920362 CT/TT genotype associated with a decreased relative abundance of Actinobacteria (β = −1.32, P < 0.001), Bifidobacteriaceae (β = −1.70, P < 0.001), and Bifidobacterium (β = −1.70, P < 0.001) compared to the CC genotype. Conclusion: Our findings suggested that the variants loci of LGR6 may be associate with OP pathogenesis via gut microbiota modifications. The relationship between host genetics and gut microbiome provides new perspectives about OP prevention and treatment.
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Affiliation(s)
- Dong-Sheng Di
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Can Li
- Department of Cancer Prevention and Control, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu Dai
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mu-Hong Wei
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan-Shan Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen-Jing Song
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao-Long Zhou
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Cui
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ru-Yi Zhang
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Huang
- Department of Rehabilitation Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Wang
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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10
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Zhou H, Yuan Y, Wang H, Xiang W, Li S, Zheng H, Wen Y, Ming Y, Chen L, Zhou J. Gut Microbiota: A Potential Target for Cancer Interventions. Cancer Manag Res 2021; 13:8281-8296. [PMID: 34764691 PMCID: PMC8572730 DOI: 10.2147/cmar.s328249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota plays a crucial role in many physiological processes in the human body. Dysbiosis can disrupt the intestinal barrier and alter metabolism and immune responses, leading to the development of diseases. Over the past few decades, evidence has accumulated linking changes in the composition of the gut microbiota to dozens of seemingly unrelated conditions, including cancer. Overall, the gut microbiota mainly affects the occurrence and development of cancer by damaging host DNA, forming and maintaining a pro-inflammatory environment, and affecting host immune responses. In addition, the gut microbiota can also affect the efficacy and toxicity of chemotherapy, radiotherapy, and immunotherapy. Scientists attempt to improve the efficacy and decrease the toxicity of these treatment modalities by fine-tuning the gut microbiota. The aim of this review is to assist researchers and clinicians in developing new strategies for the detection and treatment of tumors by providing the latest information on the intestinal microbiome and cancer, as well as exploring potential application prospects and mechanisms of action.
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Affiliation(s)
- Hu Zhou
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China
| | - Yuan Yuan
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China.,Department of Operation and Anaesthesia, Yibin First People's Hospital, Yibin, Sichuan, People's Republic of China
| | - Haorun Wang
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China
| | - Wei Xiang
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China
| | - Shenjie Li
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China
| | - Haowen Zheng
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China
| | - Yuqi Wen
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China
| | - Yang Ming
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China
| | - Ligang Chen
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China.,Academician (Expert) Workstation of Sichuan Province, Luzhou, Sichuan, People's Republic of China.,Neurological Diseases and Brain Function Laboratory, Luzhou, Sichuan, People's Republic of China
| | - Jie Zhou
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, People's Republic of China.,Academician (Expert) Workstation of Sichuan Province, Luzhou, Sichuan, People's Republic of China.,Neurological Diseases and Brain Function Laboratory, Luzhou, Sichuan, People's Republic of China
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11
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Li ZP, Liu JX, Lu LL, Wang LL, Xu L, Guo ZH, Dong QJ. Overgrowth of Lactobacillus in gastric cancer. World J Gastrointest Oncol 2021; 13:1099-1108. [PMID: 34616515 PMCID: PMC8465450 DOI: 10.4251/wjgo.v13.i9.1099] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/30/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Dysbiosis of the gastric microbiome is involved in the development of gastric cancer (GC). A number of studies have demonstrated an increase in the relative abundance of Lactobacillus in GC. In this review, we present data that support the overgrowth of Lactobacillus in GC from studies on molecular and bacterial culture of the gastric microbiome, discuss the heterogenic effects of Lactobacillus on the health of human stomach, and explore the potential roles of the overgrowth of Lactobacillus in gastric carcinogenesis. Further studies are required to examine the association between Lactobacillus and GC at strain and species levels, which would facilitate to elucidate its role in the carcinogenic process.
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Affiliation(s)
- Zhi-Peng Li
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Ju-Xin Liu
- Clinical Laboratories, Qingdao Municipal Hospital, Qingdao 266071, Shandong Province, China
| | - Lin-Lin Lu
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Li-Li Wang
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Lin Xu
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Zong-Hao Guo
- Department of Clinical Medicine, Jining Medical University, Jining 272000, Shandong Province, China
| | - Quan-Jiang Dong
- Department of Gastroenterology and Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong Province, China
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12
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Pereira-Marques J, Ferreira RM, Machado JC, Figueiredo C. The influence of the gastric microbiota in gastric cancer development. Best Pract Res Clin Gastroenterol 2021; 50-51:101734. [PMID: 33975676 DOI: 10.1016/j.bpg.2021.101734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 01/31/2023]
Abstract
Colonization of the stomach by Helicobacter pylori is the trigger for a series of gastric mucosal changes that culminate in gastric cancer. Infection with this bacterium is considered the major risk factor for this malignancy. The introduction of high-throughput sequencing technologies coupled to advanced computational pipelines offered an improved understanding of the microbiome, and it is now currently accepted that, besides H. pylori, the stomach harbours a complex microbial community. While it is well established that H. pylori plays a central role in gastric carcinogenesis, the significance of the non-H. pylori microbiota is yet to be clarified. This review will address the state of the art on the relationship between the gastric microbiota and gastric cancer development, and identify areas where additional research is needed before translating microbiome research into preventive and therapeutic strategies to reduce gastric cancer burden.
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Affiliation(s)
- Joana Pereira-Marques
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal; Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.
| | - Rui M Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal; Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.
| | - Jose C Machado
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal; Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal; Department of Pathology, Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, 4200 - 319, Porto, Portugal.
| | - Ceu Figueiredo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal; Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal; Department of Pathology, Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, 4200 - 319, Porto, Portugal.
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13
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Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution. Microorganisms 2021; 9:microorganisms9020240. [PMID: 33503840 PMCID: PMC7912213 DOI: 10.3390/microorganisms9020240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/27/2022] Open
Abstract
The continuous characterization of genome-wide diversity in population and case–cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Especially interesting are the long-standing associations between humans and certain bacteria, such as the case of Helicobacter pylori, which could have been strong drivers of adaptation leading to coevolution. Some evidence on admixed gastric cancer cohorts have been suggested as supporting Homo-Helicobacter coevolution, but reliable experimental data that control both the bacterium and the host ancestries are lacking. Here, we conducted the first in vitro coinfection assays with dual human- and bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori. Our results showed that: (1) the host response to H. pylori infection was greatly shaped by the human ancestry, with variability on innate immune system and metabolism; (2) African human ancestry showed signs of coevolution with H. pylori while European ancestry appeared to be maladapted; and (3) mismatched ancestry did not seem to be an important differentiator of gene expression at the initial stages of infection as assayed here.
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14
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Pedro N, Pinto RJ, Cavadas B, Pereira L. Sub-Saharan African information potential to unveil adaptations to infectious disease. Hum Mol Genet 2021; 30:R138-R145. [PMID: 33461217 DOI: 10.1093/hmg/ddab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/10/2020] [Accepted: 01/05/2021] [Indexed: 12/09/2022] Open
Abstract
Sub-Saharan Africa is the most promising region of the world to conduct high-throughput studies to unveil adaptations to infectious diseases due to several reasons, namely, the longest evolving time-depth in the Homo sapiens phylogenetic tree (at least two-third older than any other worldwide region); the continuous burden of infectious diseases (still number one in health/life threat); and the coexistence of populations practising diverse subsistence modes (nomadic or seminomadic hunter-gatherers and agropastoralists, and sedentary agriculturalists, small urban and megacity groups). In this review, we will present the most up-to-date results that shed light on three main hypotheses related with this adaptation. One is the hypothesis of coevolution between host and pathogen, given enough time for the establishment of this highly dynamic relationship. The second hypothesis enunciates that the agricultural transition was responsible for the increase of the infectious disease burden, due to the huge expansion of the sedentary human population and the cohabitation with domesticates as main reservoirs of pathogens. The third hypothesis states that the boosting of our immune system against pathogens by past selection may have resulted in maladaptation of the developed hygienic societies, leading to an increase of allergic, inflammatory and autoimmune disorders. Further work will enlighten the biological mechanisms behind these main adaptations, which can be insightful for translation into diagnosis, prognosis and treatment interventions.
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Affiliation(s)
- Nicole Pedro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ricardo J Pinto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
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