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Rodríguez-Santiago Y, Garay-Canales CA, Nava-Castro KE, Morales-Montor J. Sexual dimorphism in colorectal cancer: molecular mechanisms and treatment strategies. Biol Sex Differ 2024; 15:48. [PMID: 38867310 PMCID: PMC11170921 DOI: 10.1186/s13293-024-00623-1] [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: 01/26/2024] [Accepted: 05/26/2024] [Indexed: 06/14/2024] Open
Abstract
INTRODUCTION Sexual dimorphism significantly influences cancer incidence and prognosis. Notably, females exhibit a lower risk and favorable prognosis for non-reproductive cancers compared to males, a pattern observable beyond the scope of risk behaviors such as alcohol consumption and smoking. Colorectal cancer, ranking third in global prevalence and second in mortality, disproportionately affects men. Sex steroid hormones, particularly estrogens and androgens, play crucial roles in cancer progression, considering epidemiological in vivo and in vitro, in general estrogens imparting a protective effect in females and androgens correlating with an increasing risk of colorectal cancer development. MAIN BODY The hormonal impact on immune response is mediated by receptor interactions, resulting in heightened inflammation, modulation of NF-kB, and fostering an environment conducive to cancer progression and metastasis. These molecules also influence the enteric nervous system, that is a pivotal in neuromodulator release and intestinal neuron stimulation, also contributes to cancer development, as evidenced by nerve infiltration into tumors. Microbiota diversity further intersects with immune, hormonal, and neural mechanisms, influencing colorectal cancer dynamics. A comprehensive understanding of hormonal influences on colorectal cancer progression, coupled with the complex interplay between immune responses, microbiota diversity and neurotransmitter imbalances, underpins the development of more targeted and effective therapies. CONCLUSIONS Estrogens mitigate colorectal cancer risk by modulating anti-tumor immune responses, enhancing microbial diversity, and curbing the pro-tumor actions of the sympathetic and enteric nervous systems. Conversely, androgens escalate tumor growth by dampening anti-tumor immune activity, reducing microbial diversity, and facilitating the release of tumor-promoting factors by the nervous system. These findings hold significant potential for the strategic purposing of drugs to fine-tune the extensive impacts of sex hormones within the tumor microenvironment, promising advancements in colorectal cancer therapies.
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Affiliation(s)
- Yair Rodríguez-Santiago
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, 04510, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, 1er piso, Circuito de Posgrados, Ciudad Universitaria, Ciudad de México, 04510, México
| | - Claudia Angelica Garay-Canales
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, 04510, México
| | - Karen Elizabeth Nava-Castro
- Grupo de Biología y Química Atmosféricas, Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, 04510, México
| | - Jorge Morales-Montor
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, 04510, México.
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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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Niu C, Zhang J, Okolo P. Greasing the Wheels of Pharmacotherapy for Colorectal Cancer: the Role of Natural Polyphenols. Curr Nutr Rep 2023; 12:662-678. [PMID: 38041707 DOI: 10.1007/s13668-023-00512-w] [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] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE OF REVIEW The main purpose of this review, mainly based on preclinical studies, is to summarize the pharmacological and biochemical evidence regarding natural polyphenols against colorectal cancer and highlight areas that require future research. RECENT FINDINGS Typically, colorectal cancer is a potentially preventable and curable cancer arising from benign precancerous polyps found in the colon's inner lining. Colorectal cancer is the third most common cancer, with a lifetime risk of approximately 4 to 5%. Genetic background and environmental factors play major roles in the pathogenesis of colorectal cancer. Theoretically, a multistep process of colorectal carcinogenesis provides enough time for anti-tumor pharmacotherapy of colorectal cancer. Chronic colonic inflammation, oxidative stress, and gut microbiota imbalance have been found to increase the risk for colorectal cancer development by creating genotoxic stress within the intestinal environment to generate genetic mutations and epigenetic modifications. Currently, numerous natural polyphenols have shown anti-tumor properties against colorectal cancer in preclinical research, especially in colorectal cancer cell lines. In this review, the current literature regarding the etiology and epidemiology of colorectal cancer is briefly outlined. We highlight the findings of natural polyphenols in colorectal cancer from in vitro and in vivo studies. The scarcity of human trials data undermines the clinical use of natural polyphenols as anti-colorectal cancer agents, which should be undertaken in the future.
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Affiliation(s)
- Chengu Niu
- Internal Medicine Residency Program, Rochester General Hospital, Rochester, NY, 14621, USA.
| | - Jing Zhang
- Rainier Springs Behavioral Health Hospital, Vancouver, 98686, USA
| | - Patrick Okolo
- Division of Gastroenterology, Rochester General Hospital, Rochester, NY, 14621, USA
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Bucci V, Ward DV, Bhattarai S, Rojas-Correa M, Purkayastha A, Holler D, Qu MD, Mitchell WG, Yang J, Fountain S, Zeamer A, Forconi CS, Fujimori G, Odwar B, Cawley C, Moormann AM, Wessolossky M, Maldonado-Contreras A. The intestinal microbiota predicts COVID-19 severity and fatality regardless of hospital feeding method. mSystems 2023; 8:e0031023. [PMID: 37548476 PMCID: PMC10469851 DOI: 10.1128/msystems.00310-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
SARS-CoV-2-positive patients exhibit gut and oral microbiome dysbiosis, which is associated with various aspects of COVID-19 disease (1-4). Here, we aim to identify gut and oral microbiome markers that predict COVID-19 severity in hospitalized patients, specifically severely ill patients compared to moderately ill ones. Moreover, we investigate whether hospital feeding (solid versus enteral), an important cofounder, influences the microbial composition of hospitalized COVID-19 patients. We used random forest classification machine learning models with interpretable secondary analyses. The gut, but not the oral microbiota, was a robust predictor of both COVID-19-related fatality and severity of hospitalized patients, with a higher predictive value than most clinical variables. In addition, perturbations of the gut microbiota due to enteral feeding did not associate with species that were predictive of COVID-19 severity. IMPORTANCE SARS-CoV-2 infection leads to wide-ranging, systemic symptoms with sometimes unpredictable morbidity and mortality. It is increasingly clear that the human microbiome plays an important role in how individuals respond to viral infections. Our study adds to important literature about the associations of gut microbiota and severe COVID-19 illness during the early phase of the pandemic before the availability of vaccines. Increased understanding of the interplay between microbiota and SARS-CoV-2 may lead to innovations in diagnostics, therapies, and clinical predictions.
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Affiliation(s)
- Vanni Bucci
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Doyle V. Ward
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Shakti Bhattarai
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Mayra Rojas-Correa
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ayan Purkayastha
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Devon Holler
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ming Da Qu
- Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - William G. Mitchell
- Department of Internal Medicine/Pediatrics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Jason Yang
- Department of Medicine - Internal Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Samuel Fountain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Abigail Zeamer
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Catherine S. Forconi
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Gavin Fujimori
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Boaz Odwar
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Caitlin Cawley
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ann M. Moormann
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Mireya Wessolossky
- Department of Medicine - Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ana Maldonado-Contreras
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program of Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Center for Microbiome Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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Giannopoulou N, Constantinou C. Recent Developments in Diagnostic and Prognostic Biomarkers for Colorectal Cancer: A Narrative Review. Oncology 2023; 101:675-684. [PMID: 37364542 DOI: 10.1159/000531474] [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: 01/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Colorectal cancer was reported as the second most common cause of cancer death worldwide, in the year 2020. This disease is an important public health problem considering its high incidence and mortality rates. SUMMARY The molecular events that lead to colorectal cancer include genetic and epigenetic abnormalities. Some of the most important molecular mechanisms involved include the APC/β-catenin pathway, the microsatellite pathway, and the CpG island hypermethylation. Evidence in the literature supports a role for the microbiota in the development of colon carcinogenesis, and specific microbes may contribute to or prevent carcinogenesis. Progress in prevention, screening, and management has improved the overall prognosis of the disease when diagnosed at an early stage; yet metastatic disease continues to have a poor long-term prognosis due to late-stage diagnosis and treatment failure. Biomarkers are a key tool for early detection and prognosis and aim to reduce morbidity and mortality associated with colorectal cancer. The main focus of this narrative review is to provide an update on the recent development of diagnostic and prognostic biomarkers in stool, blood, and tumor tissue samples. KEY MESSAGES The review focuses on recent investigations in microRNAs, cadherins, Piwi-interacting RNAs, circulating cell-free DNA, and microbiome biomarkers which can be applied for the diagnosis and prognosis of colorectal cancer.
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Affiliation(s)
- Nefeli Giannopoulou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus
| | - Constantina Constantinou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus
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Gherman A, Balacescu L, Popa C, Cainap C, Vlad C, Cainap SS, Balacescu O. Baseline Expression of Exosomal miR-92a-3p and miR-221-3p Could Predict the Response to First-Line Chemotherapy and Survival in Metastatic Colorectal Cancer. Int J Mol Sci 2023; 24:10622. [PMID: 37445798 DOI: 10.3390/ijms241310622] [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: 05/03/2023] [Revised: 06/10/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
The status of predictive biomarkers in metastatic colorectal cancer is currently underdeveloped. Our study aimed to investigate the predictive value of six circulating exosomal miRNAs derived from plasma (miR-92a-3p, miR-143-3p, miR-146a-5p, miR-221-3p, miR-484, and miR-486-5p) for chemosensitivity, resistance patterns, and survival. Thirty-one metastatic colorectal cancer patients were selected before receiving first-line irinotecan- or oxaliplatin-based chemotherapy. Blood samples were harvested at baseline and 4-6 months after the initiation of chemotherapy. The levels of exosomal expression for each miRNA were analyzed by qPCR. Our results for patients receiving first-line FOLFOX showed significantly higher baseline levels of miR-92a-3p (p = 0.007 **), miR-146a-5p (p = 0.036 *), miR-221-3p (p = 0.047 *), and miR-484 (p = 0.009 **) in non-responders (NR) vs. responders (R). Of these, miR-92a-3p (AUC = 0.735), miR-221-3p (AUC = 0.774), and miR-484 (AUC = 0.725) demonstrated a predictive ability to discriminate responses from non-responses, regardless of the therapy used. Moreover, Cox regression analysis indicated that higher expression levels of miR-92a-3p (p = 0.008 **), miR-143-3p (p = 0.009 **), miR-221-3p (p = 0.016 *), and miR-486-5p (p = 0.019 *) at baseline were associated with worse overall survival, while patients expressing higher baseline miR-92a-3p (p = 0.003 **) and miR-486-5p (p = 0.003 **) had lower rates of progression-free survival. No predictive values for candidate microRNAs were found for the post-chemotherapy period. In line with these findings, we conclude that the increased baseline exosomal expression of miR-92a-3p and miR-221-3p seems to predict a lack of response to chemotherapy and lower OS. However, further prospective studies on more patients are needed before drawing practice-changing conclusions.
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Affiliation(s)
- Alexandra Gherman
- 11th Department of Medical Oncology, University of Medicine and Pharmacy "Iuliu Hatieganu", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
- Department of Medical Oncology, The Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
| | - Loredana Balacescu
- 11th Department of Medical Oncology, University of Medicine and Pharmacy "Iuliu Hatieganu", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
| | - Calin Popa
- "Prof. Dr. Octavian Fodor" Regional Institute of Gastroenterology and Hepatology Cluj-Napoca, 19-21 Croitorilor Street, 400162 Cluj-Napoca, Romania
- Department of Surgery, Surgery Unit No 3, University of Medicine and Pharmacy "Iuliu Hațieganu" Cluj-Napoca, 19-21 Croitorilor Street, 400162 Cluj-Napoca, Romania
| | - Calin Cainap
- 11th Department of Medical Oncology, University of Medicine and Pharmacy "Iuliu Hatieganu", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
- Department of Medical Oncology, The Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
| | - Catalin Vlad
- Department of Surgery, The Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
- Department of Oncology, "Iuliu Hatieganu" University of Medicine and Pharmacy, 8 Victor Babes Street, 400012 Cluj-Napoca, Romania
| | - Simona S Cainap
- Department of Mother and Child, Pediatric Cardiology, University of Medicine and Pharmacy "Iuliu Hatieganu", 19-21 Croitorilor Street, 400162 Cluj-Napoca, Romania
- Department of Paediatric Cardiology, Pediatric Clinic No 2, Emergency County Hospital for Children, 68 Motilor Street, 400370 Cluj-Napoca, Romania
| | - Ovidiu Balacescu
- 11th Department of Medical Oncology, University of Medicine and Pharmacy "Iuliu Hatieganu", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
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Hu W, Di Q, Liang T, Zhou N, Chen H, Zeng Z, Luo Y, Shaker M. Effects of in vitro simulated digestion and fecal fermentation of polysaccharides from straw mushroom (Volvariella volvacea) on its physicochemical properties and human gut microbiota. Int J Biol Macromol 2023; 239:124188. [PMID: 36996950 DOI: 10.1016/j.ijbiomac.2023.124188] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/06/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
Herein, the fermentation and digestion behavior of Volvariella volvacea polysaccharide (VVP) were examined through the in vitro simulation experiment. The results revealed that succeeding the simulated salivary gastrointestinal digestion, the molecular weight of VVP was reduced by only 8.9 %. In addition, the reducing sugar, uronic acid, monosaccharide composition and Fourier transform infrared spectroscopy characteristics of VVP did not change significantly, which indicate that saliva-gastrointestinal could not digest VVP. However, 48 h of fecal fermentation of VVP dramatically reduced its molecular weight by 40.4 %. Furthermore, the molar ratios of the monosaccharide composition altered considerably due to the degradation of VVP by microorganisms and the metabolysis into different short-chain fatty acids (SCFAs). Meanwhile, the VVP also raised the proportion of Bacteroidetes to Firmicutes and promoted the proliferation of some beneficial bacteria including Bacteroides and Phascolarctobacterium, whereas it inhibited the growth of unfavorable bacteria such as Escherichia-shigella. Therefore, VVP has the potential to have a positive influence on health and hinder diseases by improving the intestinal microbial environment. These findings provide a theoretical foundation to further develop Volvariella volvacea as a healthy functional food.
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Affiliation(s)
- Wei Hu
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Qing Di
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Tao Liang
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Na Zhou
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Hongxia Chen
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Zhihong Zeng
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China.
| | - Yang Luo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Majid Shaker
- Chongqing 2D Materials Institute, Chongqing 400714, China; Lehrstuhl für Physikalische Chemie II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstr. 3, Erlangen 91058, Germany
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Analyses of regulatory network and discovery of potential biomarkers for Korean rockfish (Sebastes schlegelii) in responses to starvation stress through transcriptome and metabolome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101061. [PMID: 36796184 DOI: 10.1016/j.cbd.2023.101061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
Whether in aquaculture or in nature, starvation stress limits the growth of fish. The purpose of the study was to clarify the detailed molecular mechanisms underlying starvation stress in Korean rockfish (Sebastes schlegelii) through liver transcriptome and metabolome analysis. Transcriptome results showed that liver genes associated with cell cycle and fatty acid synthesis were down-regulated, whereas those related to fatty acid decomposition were up-regulated in the experimental group (EG; starved for 72 days) compared to the control group (CG; feeding). Metabolomic results showed that there were significant differences in the levels of metabolites related to nucleotide metabolism and energy metabolism, such as purine metabolism, histidine metabolism and oxidative phosphorylation. Five fatty acids (C22:6n-3; C22:5n-3; C20:5n-3; C20:4n-3; C18:3n-6) were selected as possible biomarkers of starvation stress from the differential metabolites of metabolome. Subsequently, correlation between these differential genes of lipid metabolism and cell cycle and differential metabolites were analyzed, and observed that these five fatty acids were significantly correlated with the differential genes. These results provide new clues for understanding the role of fatty acid metabolism and cell cycle in fish under starvation stress. It also provides a reference for promoting the biomarker identification of starvation stress and stress tolerance breeding research.
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9
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El-Sokkary MMA. Molecular characterization of gut microbial structure and diversity associated with colorectal cancer patients in Egypt. Pan Afr Med J 2022; 43:119. [PMID: 36721476 PMCID: PMC9860093 DOI: 10.11604/pamj.2022.43.119.30037] [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: 05/31/2021] [Accepted: 07/13/2022] [Indexed: 11/05/2022] Open
Abstract
Introduction a large number of microbes colonizing the gut are highly diverse and complex in their structure, as this complex structure of gut microbiota acts as an indicator of a diseased state. Recently, there is a need for improved biomarkers for colorectal cancer (CRC) and advanced adenoma. Among the CRC associated organisms, bacteria are the most common causes of serious disease and deaths. To understand the dynamic interaction among bacteria colonizing the gut, different approaches have been implicated. Methods in this study, faecal microbial markers were evaluated for detecting CRC. As most of these organisms are anaerobic, different molecular tools are of great values for rapid detection of these bacteria. Samples from Tumor Hospital were screened for the presence of different pathogens by both usual polymerase chain reaction (PCR) and a real-time assay. Results in a total of 34 samples, by PCR method, bifidobacterium, fusobacterium and Escherichia coli (E. coli) were mainly identified in almost all samples. However, a clear variation in bacterial composition could be observed in Porphyromonas gingivalis, Prevotella intermedia and Peptostreptococcus magnus, where positive results could be detected only in diseased samples. In addition, E. faecium and E. saphenum were mainly identified in diseased samples. In contrast, providencia could be detected mainly in control samples. In realtime assay, the relative abundance was higher for fusobacterium and bifidobacterium markers in CRC patients compared to control samples. However, such increased in abundance has never been observed in both fusobacterium and bifidobacterium in the same sample. Conclusion these results demonstrated increased abundance of fusobacterium or bifidobacterium can be considered as a sign for impairment or a diseased condition and the possibility of use of the faecal microbiotain CRC patients as a marker for detecting the disease.
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Affiliation(s)
- Mohamed Mohamed Adel El-Sokkary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt,Corresponding author: Mohamed Mohamed Adel El-Sokkary, Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.
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10
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Jin M, Wu J, Shi L, Zhou B, Shang F, Chang X, Dong X, Deng S, Liu L, Cai K, Nie X, Zhang T, Fan J, Liu H. Gut microbiota distinct between colorectal cancers with deficient and proficient mismatch repair: A study of 230 CRC patients. Front Microbiol 2022; 13. [DOI: 10.3389/fmicb.2022.993285] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023] Open
Abstract
Colorectal cancers (CRCs) with deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) exhibit heterogeneous tumor characteristics, distinct responses to immunotherapy, and different survival outcomes. However, it is unclear whether gut microbiota is distinct between CRCs with different MMR status. In this study, we used immunohistochemistry for four major MMR proteins to determine the MMR status in 230 CRC patients. The gut microbiota was profiled in cancerous and adjacent normal tissues by using bacterial 16S rRNA sequencing. The differences in microbiota diversity, composition and related metabolic pathways between patients with dMMR and pMMR CRCs were explored. Linear discriminant analysis effect size (LEfSe) analysis was further applied to validate the significant taxonomic differences at the genus level. In our study cohort, dMMR status was identified in 29 of 230 (12.61%) tumors. The richness (alpha-diversity) of gut microbiome in dMMR tumor tissue was higher compared with pMMR tumor tissues. The microbial community composition (beta-diversity) between the two groups was significantly different. The dMMR group was enriched considerably for some microbiota, including Fusobacteria, Firmicutes, Verrucomicrobia, and Actinobacteria at the phylum level and Fusobacterium, Akkermansia, Bifidobacterium, Faecalibacterium, Streptococcus, and Prevotella bacteria at the genus level. However, the pMMR group was dominated by Proteobacteria at the phylum level and Serratia, Cupriavidus and Sphingobium at the genus level. Moreover, a wide variety of microbiota associated functional pathways were observed with different MMR status. KEGG pathway analysis indicated a higher abundance of the biosynthesis and metabolic pathways of glycan and nucleotide, cell growth and death pathways, genetic replication and repair pathways in dMMR samples compared with the pMMR group. These findings demonstrate that CRC patients with different MMR status have distinct gut bacterial community richness, compositions and related metabolic pathways, suggesting basis that may explain the effectiveness of immunotherapy in dMMR tumors.
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Sattar RSA, Verma R, Nimisha, Kumar A, Dar GM, Apurva, Sharma AK, Kumari I, Ahmad E, Ali A, Mahajan B, Saluja SS. Diagnostic and prognostic biomarkers in colorectal cancer and the potential role of exosomes in drug delivery. Cell Signal 2022; 99:110413. [PMID: 35907519 DOI: 10.1016/j.cellsig.2022.110413] [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: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/03/2022]
Abstract
Colorectal cancer (CRC) is third most common cancer with second most common cause of death worldwide. One fourth to one fifth of the CRC cases are detected at advance stage. Early detection of colorectal cancer might help in decreasing mortality and morbidity worldwide. CRC being a heterogeneous disease, new non-invasive approaches are needed to complement and improve the screening and management of CRC. Reliable and early detectable biomarkers would improve diagnosis, prognosis, therapeutic responses, and will enable the prediction of drug response and recurrence risk. Over the past decades molecular research has demonstrated the potentials of CTCs, ctDNAs, circulating mRNA, ncRNAs, and exosomes as tumor biomarkers. Non-invasive screening approaches using fecal samples for identification of altered gut microbes in CRC is also gaining attention. Exosomes can be potential candidates that can be employed in the drug delivery system. Further, the integration of in vitro, in vivo and in silico models that involve CRC biomarkers will help to understand the interactions occurring at the cellular level. This review summarizes recent update on CRC biomarkers and their application along with the nanoparticles followed by the application of organoid culture in CRC.
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Affiliation(s)
- Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Renu Verma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ghulam Mehdi Dar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Indu Kumari
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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12
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Unlocking the Potential of the Human Microbiome for Identifying Disease Diagnostic Biomarkers. Diagnostics (Basel) 2022; 12:diagnostics12071742. [PMID: 35885645 PMCID: PMC9315466 DOI: 10.3390/diagnostics12071742] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023] Open
Abstract
The human microbiome encodes more than three million genes, outnumbering human genes by more than 100 times, while microbial cells in the human microbiota outnumber human cells by 10 times. Thus, the human microbiota and related microbiome constitute a vast source for identifying disease biomarkers and therapeutic drug targets. Herein, we review the evidence backing the exploitation of the human microbiome for identifying diagnostic biomarkers for human disease. We describe the importance of the human microbiome in health and disease and detail the use of the human microbiome and microbiota metabolites as potential diagnostic biomarkers for multiple diseases, including cancer, as well as inflammatory, neurological, and metabolic diseases. Thus, the human microbiota has enormous potential to pave the road for a new era in biomarker research for diagnostic and therapeutic purposes. The scientific community needs to collaborate to overcome current challenges in microbiome research concerning the lack of standardization of research methods and the lack of understanding of causal relationships between microbiota and human disease.
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13
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Anipindi M, Bitetto D. Diagnostic and Therapeutic Uses of the Microbiome in the Field of Oncology. Cureus 2022; 14:e24890. [PMID: 35698690 PMCID: PMC9184241 DOI: 10.7759/cureus.24890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2022] [Indexed: 11/21/2022] Open
Abstract
Cancer is a leading cause of death worldwide and it can affect almost every part of the human body. Effective screening and early diagnosis of cancers is extremely difficult due to the multifactorial etiology of the disease and delayed presentation of the patients. The available treatments are usually not specific to the affected organ system, leading to intolerable systemic side effects and early withdrawal from therapies. In vivo and in vitro studies have revealed an association of specific microbiome signatures with individual cancers. The cancer-related human microbiome has also been shown to affect the response of tissues to chemotherapy, immunotherapy, and radiation. This is an excellent opportunity for us to design specific screening markers using the microbiome to prevent cancers and diagnose them early. We can also develop precise treatments that can target cancer-affected specific organ systems and probably use a lesser dose of chemotherapy or radiation for the same effect. This prevents adverse effects and early cessation of treatments. However, we need further studies to exactly clarify and characterize these associations. In this review article, we focus on the association of the microbiome with individual cancers and highlight its future role in cancer screenings, diagnosis, prognosis, and treatments.
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14
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Zhou Z, Wang Y, Ji R, Zhang D, Ma C, Ma W, Ma Y, Jiang X, Du K, Zhang R, Chen P. Vanillin Derivatives Reverse Fusobacterium nucleatum-Induced Proliferation and Migration of Colorectal Cancer Through E-Cadherin/β-Catenin Pathway. Front Pharmacol 2022; 13:841918. [PMID: 35308221 PMCID: PMC8931468 DOI: 10.3389/fphar.2022.841918] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/21/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is a common clinical malignant tumor and closely related to intestinal microbiome disorders. Especially, Fusobacterium nucleatum (F. nucleatum) is one of the most prevalent pathogens in CRC. However, its change in CRC patients of Northwest China, an area with a high incidence of gastrointestinal tumors, is unclear, and therapeutic strategies targeting F. nucleatum remain unresolved. Here, fecal samples of healthy people and CRC patients were studied using 16S rRNA sequencing to explore microbial community alterations. Additionally, vanillin derivate (IPM711 and IPM712) intervention by coculture with CRC cells and potential mechanism were investigated. Results showed that intestinal microbial homeostasis was gradually dysregulated, and the abundance of Fusobacterium was higher in CRC patients. Moreover, IPM711 and IPM712 showed better anti-F. nucleatum activity than vanillin by increasing cell membrane permeability and destroying bacterial integrity. In addition, IPM711 and IPM712 could downregulate the expression of E-cadherin and β-catenin, thus, suppressing the migration of HCT116. Collectively, IPM711 and IPM712 have both anticolorectal cancer and anti-F. nucleatum activities, providing potential natural product drug candidates for microbe-targeted strategies for the treatment of CRC.
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Affiliation(s)
- Zhongkun Zhou
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Yiqing Wang
- The First Hospital of Lanzhou University, Lanzhou, China
| | - Rui Ji
- The First Hospital of Lanzhou University, Lanzhou, China
| | - Dekui Zhang
- The Second Hospital of Lanzhou University, Lanzhou, China
| | - Chi Ma
- The Second Hospital of Lanzhou University, Lanzhou, China
| | - Wantong Ma
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Yunhao Ma
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xinrong Jiang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Kangjia Du
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Rentao Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Peng Chen
- School of Pharmacy, Lanzhou University, Lanzhou, China
- *Correspondence: Peng Chen,
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15
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Sholl J, Sepich-Poore GD, Knight R, Pradeu T. Redrawing therapeutic boundaries: microbiota and cancer. Trends Cancer 2022; 8:87-97. [PMID: 34844910 PMCID: PMC8770609 DOI: 10.1016/j.trecan.2021.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023]
Abstract
The unexpected roles of the microbiota in cancer challenge explanations of carcinogenesis that focus on tumor-intrinsic properties. Most tumors contain bacteria and viruses, and the host's proximal and distal microbiota influence both cancer incidence and therapeutic responsiveness. Continuing the history of cancer-microbe research, these findings raise a key question: to what extent is the microbiota relevant for clinical oncology? We approach this by critically evaluating three issues: how the microbiota provides a predictive biomarker of cancer growth and therapeutic responsiveness, the microbiota's causal role(s) in cancer development, and how therapeutic manipulations of the microbiota improve patient outcomes in cancer. Clarifying the conceptual and empirical aspects of the cancer-associated microbiota can orient future research and guide its implementation in clinical oncology.
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Affiliation(s)
- Jonathan Sholl
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000 Bordeaux, France.
| | | | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Thomas Pradeu
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000 Bordeaux, France.
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Abstract
The intestinal microbiota promote colorectal cancer, but their role in metastasis is poorly defined. In this issue of Cancer Cell, Bertocchi et al. report that intratumoral bacteria disrupt the gut vascular barrier, causing bacterial dissemination to the liver and the formation of a premetastatic niche, favoring recruitment of metastatic cells.
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Affiliation(s)
- Yoshitaka Murota
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA; Department of Infectious Diseases and Inflammation, University of Florida, Gainesville, FL, USA.
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17
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Velikova T, Krastev B, Lozenov S, Gencheva R, Peshevska-Sekulovska M, Nikolaev G, Peruhova M. Antibiotic-Related Changes in Microbiome: The Hidden Villain behind Colorectal Carcinoma Immunotherapy Failure. Int J Mol Sci 2021; 22:1754. [PMID: 33578709 PMCID: PMC7916407 DOI: 10.3390/ijms22041754] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 02/05/2023] Open
Abstract
The interplay between drugs and microbiota is critical for successful treatment. An accumulating amount of evidence has identified the significant impact of intestinal microbiota composition on cancer treatment response, particularly immunotherapy. The possible molecular pathways of the interaction between immune checkpoint inhibitors (ICIs) and the microbiome can be used to reverse immunotherapy tolerance in cancer by using various kinds of interventions on the intestinal bacteria. This paper aimed to review the data available on how the antibiotic-related changes in human microbiota during colorectal cancer (CRC) treatment can affect and determine ICI treatment outcomes. We also covered the data that support the potential intimate mechanisms of both local and systemic immune responses induced by changes in the intestinal microbiota. However, further better-powered studies are needed to thoroughly assess the clinical significance of antibiotic-induced alteration of the gut microbiota and its impact on CRC treatment by direct observations of patients receiving antibiotic treatment.
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Affiliation(s)
- Tsvetelina Velikova
- Department of Clinical Immunology, University Hospital Lozenetz, Sofia University St. Kliment Ohridski, Kozyak 1 Str., 1407 Sofia, Bulgaria
| | - Boris Krastev
- Clinic of Medical Oncology, MHAT Hospital for Women Health Nadezhda, 1330 Sofia, Bulgaria; (B.K.); (R.G.)
| | - Stefan Lozenov
- Laboratory for Control and Monitoring of the Antibiotic Resistance, National Centre for Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd, 1504 Sofia, Bulgaria;
| | - Radostina Gencheva
- Clinic of Medical Oncology, MHAT Hospital for Women Health Nadezhda, 1330 Sofia, Bulgaria; (B.K.); (R.G.)
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, Sofia University St. Kliment Ohridski, Kozyak 1 Str., 1407 Sofia, Bulgaria; (M.P.-S.); (M.P.)
| | - Georgi Nikolaev
- Faculty of Biology, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria;
| | - Milena Peruhova
- Department of Gastroenterology, University Hospital Lozenetz, Sofia University St. Kliment Ohridski, Kozyak 1 Str., 1407 Sofia, Bulgaria; (M.P.-S.); (M.P.)
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