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Newman NK, Macovsky MS, Rodrigues RR, Bruce AM, Pederson JW, Padiadpu J, Shan J, Williams J, Patil SS, Dzutsev AK, Shulzhenko N, Trinchieri G, Brown K, Morgun A. Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. Nat Protoc 2024; 19:1750-1778. [PMID: 38472495 DOI: 10.1038/s41596-024-00960-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/29/2023] [Indexed: 03/14/2024]
Abstract
We present Transkingdom Network Analysis (TkNA), a unique causal-inference analytical framework that offers a holistic view of biological systems by integrating data from multiple cohorts and diverse omics types. TkNA helps to decipher key players and mechanisms governing host-microbiota (or any multi-omic data) interactions in specific conditions or diseases. TkNA reconstructs a network that represents a statistical model capturing the complex relationships between different omics in the biological system. It identifies robust and reproducible patterns of fold change direction and correlation sign across several cohorts to select differential features and their per-group correlations. The framework then uses causality-sensitive metrics, statistical thresholds and topological criteria to determine the final edges forming the transkingdom network. With the subsequent network's topological features, TkNA identifies nodes controlling a given subnetwork or governing communication between kingdoms and/or subnetworks. The computational time for the millions of correlations necessary for network reconstruction in TkNA typically takes only a few minutes, varying with the study design. Unlike most other multi-omics approaches that find only associations, TkNA focuses on establishing causality while accounting for the complex structure of multi-omic data. It achieves this without requiring huge sample sizes. Moreover, the TkNA protocol is user friendly, requiring minimal installation and basic familiarity with Unix. Researchers can access the TkNA software at https://github.com/CAnBioNet/TkNA/ .
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Affiliation(s)
- Nolan K Newman
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | | | - Richard R Rodrigues
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Microbiome and Genetics Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Amanda M Bruce
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jacob W Pederson
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Jyothi Padiadpu
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jigui Shan
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua Williams
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sankalp S Patil
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Amiran K Dzutsev
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Natalia Shulzhenko
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Giorgio Trinchieri
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Kevin Brown
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.
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2
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Li X, Xiang F, Liu T, Chen Z, Zhang M, Li J, Kang X, Wu R. Leveraging existing 16S rRNA gene surveys to decipher microbial signatures and dysbiosis in cervical carcinogenesis. Sci Rep 2024; 14:11532. [PMID: 38773342 PMCID: PMC11109339 DOI: 10.1038/s41598-024-62531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
The presence of dysbiotic cervicovaginal microbiota has been observed to be linked to the persistent development of cervical carcinogenesis mediated by the human papillomavirus (HPV). Nevertheless, the characteristics of the cervical microbiome in individuals diagnosed with cervical cancer (CC) are still not well understood. Comprehensive analysis was conducted by re-analyzing the cervical 16S rRNA sequencing datasets of a total of 507 samples from six previously published studies. We observed significant alpha and beta diversity differences in between CC, cervical intraepithelial neoplasia (CIN) and normal controls (NC), but not between HPV and NC in the combined dataset. Meta-analysis revealed that opportunistic pernicious microbes Streptococcus, Fusobacterium, Pseudomonas and Anaerococcus were enriched in CC, while Lactobacillus was depleted compared to NC. Members of Gardnerella, Sneathia, Pseudomonas, and Fannyhessea have significantly increased relative abundance compared to other bacteria in the CIN group. Five newly identified bacterial genera were found to differentiate CC from NC, with an area under the curve (AUC) of 0.8947. Moreover, co-occurrence network analysis showed that the most commonly encountered Lactobacillus was strongly negatively correlated with Prevotella. Overall, our study identified a set of potential biomarkers for CC from samples across different geographic regions. Our meta-analysis provided significant insights into the characteristics of dysbiotic cervicovaginal microbiota undergoing CC, which may lead to the development of noninvasive CC diagnostic tools and therapeutic interventions.
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Affiliation(s)
- Xiaoxiao Li
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 164 Lanxi Road, Shanghai, 200062, China
| | - Fenfen Xiang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 164 Lanxi Road, Shanghai, 200062, China
| | - Tong Liu
- Department of Molecular Science, Uppsala Biocenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Zixi Chen
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 164 Lanxi Road, Shanghai, 200062, China
| | - Mengzhe Zhang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 164 Lanxi Road, Shanghai, 200062, China
| | - Jinpeng Li
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 164 Lanxi Road, Shanghai, 200062, China
| | - Xiangdong Kang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 164 Lanxi Road, Shanghai, 200062, China.
| | - Rong Wu
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 164 Lanxi Road, Shanghai, 200062, China.
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Hurst R, Brewer DS, Gihawi A, Wain J, Cooper CS. Cancer invasion and anaerobic bacteria: new insights into mechanisms. J Med Microbiol 2024; 73:001817. [PMID: 38535967 PMCID: PMC10995961 DOI: 10.1099/jmm.0.001817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/27/2024] [Indexed: 04/07/2024] Open
Abstract
There is growing evidence that altered microbiota abundance of a range of specific anaerobic bacteria are associated with cancer, including Peptoniphilus spp., Porphyromonas spp., Fusobacterium spp., Fenollaria spp., Prevotella spp., Sneathia spp., Veillonella spp. and Anaerococcus spp. linked to multiple cancer types. In this review we explore these pathogenic associations. The mechanisms by which bacteria are known or predicted to interact with human cells are reviewed and we present an overview of the interlinked mechanisms and hypotheses of how multiple intracellular anaerobic bacterial pathogens may act together to cause host cell and tissue microenvironment changes associated with carcinogenesis and cancer cell invasion. These include combined effects on changes in cell signalling, DNA damage, cellular metabolism and immune evasion. Strategies for early detection and eradication of anaerobic cancer-associated bacterial pathogens that may prevent cancer progression are proposed.
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Affiliation(s)
- Rachel Hurst
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich NR4 7UZ, UK
| | - Abraham Gihawi
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - John Wain
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Quadram Institute Biosciences, Colney Lane, Norwich, Norfolk, NR4 7UQ, UK
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
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4
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Wang M, Yu F, Li P. Intratumor microbiota in cancer pathogenesis and immunity: from mechanisms of action to therapeutic opportunities. Front Immunol 2023; 14:1269054. [PMID: 37868956 PMCID: PMC10587687 DOI: 10.3389/fimmu.2023.1269054] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023] Open
Abstract
Microbial species that dwell human bodies have profound effects on overall health and multiple pathological conditions. The tumor microenvironment (TME) is characterized by disordered vasculature, hypoxia, excessive nutrition and immunosuppression. Thus, it is a favorable niche for microbial survival and growth. Multiple lines of evidence support the existence of microorganisms within diverse types of cancers. Like gut microbiota, intratumoral microbes have been tightly associated with cancer pathogenesis. Intratumoral microbiota can affect cancer development through various mechanisms, including induction of host genetic mutation, remodeling of the immune landscape and regulation of cancer metabolism and oncogenic pathways. Tumor-associated microbes modulate the efficacy of anticancer therapies, suggesting their potential utility as novel targets for future intervention. In addition, a growing body of evidence has manifested the diagnostic, prognostic, and therapeutic potential of intratumoral microorganisms in cancer. Nevertheless, our knowledge of the diversity and biological function of intratumoral microbiota is still incomplete. A deeper appreciation of tumor microbiome will be crucial to delineate the key pathological mechanisms underlying cancer progression and hasten the development of personalized treatment approaches. Herein, we summarize the most recent progress of the research into the emerging roles of intratumoral microbiota in cancer and towards clarifying the sophisticated mechanisms involved. Moreover, we discuss the effect of intratumoral microbiota on cancer treatment response and highlight its potential clinical implications in cancer.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | | | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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5
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Newman NK, Zhang Y, Padiadpu J, Miranda CL, Magana AA, Wong CP, Hioki KA, Pederson JW, Li Z, Gurung M, Bruce AM, Brown K, Bobe G, Sharpton TJ, Shulzhenko N, Maier CS, Stevens JF, Gombart AF, Morgun A. Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome. MICROBIOME 2023; 11:208. [PMID: 37735685 PMCID: PMC10512512 DOI: 10.1186/s40168-023-01637-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/01/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND The gut microbiota contributes to macrophage-mediated inflammation in adipose tissue with consumption of an obesogenic diet, thus driving the development of metabolic syndrome. There is a need to identify and develop interventions that abrogate this condition. The hops-derived prenylated flavonoid xanthohumol (XN) and its semi-synthetic derivative tetrahydroxanthohumol (TXN) attenuate high-fat diet-induced obesity, hepatosteatosis, and metabolic syndrome in C57Bl/6J mice. This coincides with a decrease in pro-inflammatory gene expression in the gut and adipose tissue, together with alterations in the gut microbiota and bile acid composition. RESULTS In this study, we integrated and interrogated multi-omics data from different organs with fecal 16S rRNA sequences and systemic metabolic phenotypic data using a Transkingdom Network Analysis. By incorporating cell type information from single-cell RNA-seq data, we discovered TXN attenuates macrophage inflammatory processes in adipose tissue. TXN treatment also reduced levels of inflammation-inducing microbes, such as Oscillibacter valericigenes, that lead to adverse metabolic phenotypes. Furthermore, in vitro validation in macrophage cell lines and in vivo mouse supplementation showed addition of O. valericigenes supernatant induced the expression of metabolic macrophage signature genes that are downregulated by TXN in vivo. CONCLUSIONS Our findings establish an important mechanism by which TXN mitigates adverse phenotypic outcomes of diet-induced obesity and metabolic syndrome. TXN primarily reduces the abundance of pro-inflammatory gut microbes that can otherwise promote macrophage-associated inflammation in white adipose tissue. Video Abstract.
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Affiliation(s)
- N K Newman
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Y Zhang
- School of Biological and Population Health Sciences, Nutrition Program, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- Present address: Oregon Health & Science University, Portland, OR, USA
| | - J Padiadpu
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - C L Miranda
- Department of Pharmaceutical Sciences, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - A A Magana
- Department of Chemistry, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - C P Wong
- School of Biological and Population Health Sciences, Nutrition Program, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - K A Hioki
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
- Present address: UMASS, Amherst, MA, USA
| | - J W Pederson
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Z Li
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - M Gurung
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Present address: Children Nutrition Center, USDA, Little Rock, AR, USA
| | - A M Bruce
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - K Brown
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
- Chemical, Biological & Environmental Engineering, Oregon State University, Corvallis, OR, USA
| | - G Bobe
- Department of Animal Sciences, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - T J Sharpton
- Department of Microbiology, Department of Statistics, Oregon State University, Corvallis, OR, USA
| | - N Shulzhenko
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA.
| | - C S Maier
- Department of Chemistry, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - J F Stevens
- Department of Pharmaceutical Sciences, Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - A F Gombart
- Department of Biochemistry and Biophysics, Linus Pauling Institute, Corvallis, OR, USA.
| | - A Morgun
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
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Dorobisz K, Dorobisz T, Zatoński T. The Microbiome's Influence on Head and Neck Cancers. Curr Oncol Rep 2023; 25:163-171. [PMID: 36696075 PMCID: PMC9947050 DOI: 10.1007/s11912-022-01352-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 01/26/2023]
Abstract
PURPOSE OF REVIEW Head and neck tumors (HNC) rank sixth among cancers worldwide. Due to their late diagnosis and poor prognosis, they are a clinical challenge. However, recent years have seen a dynamic development of science on the microbiome. The aim of the study is to discuss the role of the microbiome in HNC, the impact of the microbiome on oncogenesis, the course of the disease, as well as on treatment, and its toxicity. RECENT FINDINGS The microbiome's influence on oncogenesis, the course of the disease, and the effectiveness of oncological treatment have been confirmed in cancers of the colon, pancreas, lungs, and prostate. There is no solid literature on HNC. Many studies indicate disruption of the oral microbiome and periodontal disease as potential cancer risk factors. Disruption of the microbiome increases radiotherapy's toxicity, intensifying radiation reactions. The microbiome plays an important role in cancer. It is a new target in research into new therapies. It may also be a prognostic marker of cancer development. Changes in the composition of the microbiome modulate the effectiveness of oncological treatment. More research is needed on the microbiome and its effects on HNC.
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Affiliation(s)
- Karolina Dorobisz
- Department of Otolaryngology, Head and Neck Surgery, Wrocław Medical University, Borowska 213, 50-556, Wrocław, Poland.
| | - Tadeusz Dorobisz
- Department of Vascular and General Surgery, Wrocław Medical University, Borowska 213, 50-556, Wrocław, Poland.
| | - Tomasz Zatoński
- Department of Otolaryngology, Head and Neck Surgery, Wrocław Medical University, Borowska 213, 50-556, Wrocław, Poland.
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Vikramdeo KS, Anand S, Pierce JY, Singh AP, Singh S, Dasgupta S. Distribution of microbiota in cervical preneoplasia of racially disparate populations. BMC Cancer 2022; 22:1074. [PMID: 36258167 PMCID: PMC9578267 DOI: 10.1186/s12885-022-10112-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUNDS Microbiome dysbiosis is an important contributing factor in tumor development and thus may be a risk predictor for human malignancies. In the United States, women with Hispanic/Latina (HIS) and African American (AA) background have a higher incidence of cervical cancer and poorer outcomes than Caucasian American (CA) women. METHODS Here, we assessed the distribution pattern of microbiota in cervical intraepithelial neoplasia (CIN) lesions obtained from HIS (n = 12), AA (n = 12), and CA (n = 12) women, who were screened for CC risk assessment. We employed a 16S rRNA gene sequencing approach adapted from the NIH-Human Microbiome Project to identify the microbial niche in all CIN lesions (n = 36). RESULTS We detected an appreciably decreased abundance of beneficial Lactobacillus in the CIN lesions of the AA and HIS women compared to the CA women. Differential abundance of potentially pathogenic Prevotella, Delftia, Gardnerella, and Fastidiosipila was also evident among the various racial groups. An increased abundance of Micrococcus was also evident in AA and HIS women compared to the CA women. The detection level of Rhizobium was higher among the AA ad CA women compared to the HIS women. In addition to the top 10 microbes, a unique niche of 27 microbes was identified exclusively in women with a histopathological diagnosis of CIN. Among these microbes, a group of 8 microbiota; Rubellimicrobium, Podobacter, Brevibacterium, Paracoccus, Atopobium, Brevundimonous, Comamonous, and Novospingobium was detected only in the CIN lesions obtained from AA and CA women. CONCLUSIONS Microbial dysbiosis in the cervical epithelium represented by an increased ratio of potentially pathogenic to beneficial microbes may be associated with increased CC risk disparities. Developing a race-specific reliable panel of microbial markers could be beneficial for CC risk assessment, disease prevention, and/or therapeutic guidance.
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Affiliation(s)
- Kunwar Somesh Vikramdeo
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pathology, College of Medicine, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
| | - Shashi Anand
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pathology, College of Medicine, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
| | | | - Ajay Pratap Singh
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pathology, College of Medicine, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Seema Singh
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pathology, College of Medicine, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Santanu Dasgupta
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.
- Department of Pathology, College of Medicine, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA.
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA.
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Ali A, Ara A, Kashyap MK. Gut microbiota: Role and Association with Tumorigenesis in Different Malignancies. Mol Biol Rep 2022; 49:8087-8107. [PMID: 35543828 DOI: 10.1007/s11033-022-07357-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 02/07/2023]
Abstract
The microbiota has been associated with different cancer and may vary from patient to patient. A specific microbial strain can alter the progression of cancer and therapeutic outcome in response to anti-cancer therapy. The variations in microbiota contributed due to the individual microbiome of the microorganism are responsible for diverse clinical outcomes. The expansion of microbiota subpopulation during dysbiosis can lead to toxin production, inducing inflammation and cancer. The microbiota can be a dual-edged sword because it can be tumor-suppressive or oncogenic in the case of the gut. The transition of cancer cells from early to late-stage also impacts the composition of the microbiota, and this alteration could change the behavior of cancer. Multi-omics platforms derived data from an individual's multi-dimensional data (DNA, mRNA, microRNA, protein, metabolite, microbiota, and microbiome), i.e., individualome, to exploit it for personalized tailored treatment for different cancers in a precise manner. A number of studies suggest the importance of microbiota and its add-in suitability to existing treatment options for different malignancies. Furthermore, in vitro, and in vivo studies and cancer clinical trials suggest that probiotics have driven modulation of gut microbiota and other sites discourage the aggressive behavior and progression of different cancers.
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Affiliation(s)
- Altamas Ali
- Department of Biosciences, Jamia Millia Islamia (A central University), Jamia Nagar, 110025, New Delhi, India
| | - Anam Ara
- Department of Biosciences, Jamia Millia Islamia (A central University), Jamia Nagar, 110025, New Delhi, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute/Amity Medical School, Amity University Haryana, Amity Education Valley, Panchgaon (Manesar), Gurugram, HR, 122413, India.
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Hakimjavadi H, George SH, Taub M, Dodds LV, Sanchez-Covarrubias AP, Huang M, Pearson JM, Slomovitz BM, Kobetz EN, Gharaibeh R, Sowamber R, Pinto A, Chamala S, Schlumbrecht MP. The vaginal microbiome is associated with endometrial cancer grade and histology. CANCER RESEARCH COMMUNICATIONS 2022; 2:447-455. [PMID: 35928983 PMCID: PMC9345414 DOI: 10.1158/2767-9764.crc-22-0075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/31/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
The human microbiome has been strongly correlated with disease pathology and outcomes, yet remains relatively underexplored in patients with malignant endometrial disease. In this study, vaginal microbiome samples were prospectively collected at the time of hysterectomy from 61 racially and ethnically diverse patients from three disease conditions: 1) benign gynecologic disease (controls, n=11), 2) low-grade endometrial carcinoma (n=30), and 3) high-grade endometrial carcinoma (n=20). Extracted DNA underwent shotgun metagenomics sequencing, and microbial α and β diversities were calculated. Hierarchical clustering was used to describe community state types (CST), which were then compared by microbial diversity and grade. Differential abundance was calculated, and machine learning utilized to assess the predictive value of bacterial abundance to distinguish grade and histology. Both α- and β-diversity were associated with patient tumor grade. Four vaginal CST were identified that associated with grade of disease. Different histologies also demonstrated variation in CST within tumor grades. Using supervised clustering algorithms, critical microbiome markers at the species level were used to build models that predicted benign vs carcinoma, high-grade carcinoma versus benign, and high-grade versus low-grade carcinoma with high accuracy. These results confirm that the vaginal microbiome segregates not just benign disease from endometrial cancer, but is predictive of histology and grade. Further characterization of these findings in large, prospective studies is needed to elucidate their potential clinical applications.
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Affiliation(s)
- Hesamedin Hakimjavadi
- Department of Pathology, Children's Hospital of Los Angeles, Los Angeles, California
| | - Sophia H. George
- Sylvester Comprehensive Cancer Center, Miami, Florida
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, Florida
| | - Michael Taub
- Sylvester Comprehensive Cancer Center, Miami, Florida
| | - Leah V. Dodds
- Sylvester Comprehensive Cancer Center, Miami, Florida
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, Florida
| | - Alex P. Sanchez-Covarrubias
- Sylvester Comprehensive Cancer Center, Miami, Florida
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, Florida
| | - Marilyn Huang
- Sylvester Comprehensive Cancer Center, Miami, Florida
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, Florida
| | - J. Matt Pearson
- Sylvester Comprehensive Cancer Center, Miami, Florida
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, Florida
| | - Brian M. Slomovitz
- Department of Obstetrics and Gynecology, Mount Sinai Medical Center, Miami, Florida
| | - Erin N. Kobetz
- Sylvester Comprehensive Cancer Center, Miami, Florida
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Raad Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida
| | | | - Andre Pinto
- Sylvester Comprehensive Cancer Center, Miami, Florida
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida
| | - Srikar Chamala
- Department of Pathology, Children's Hospital of Los Angeles, Los Angeles, California
| | - Matthew P. Schlumbrecht
- Sylvester Comprehensive Cancer Center, Miami, Florida
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, Florida
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10
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Tamanai-Shacoori Z, Le Gall-David S, Moussouni F, Sweidan A, Polard E, Bousarghin L, Jolivet-Gougeon A. SARS-CoV-2 and Prevotella spp.: friend or foe? A systematic literature review. J Med Microbiol 2022; 71. [PMID: 35511246 DOI: 10.1099/jmm.0.001520] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During this global pandemic of the COVID-19 disease, a lot of information has arisen in the media and online without scientific validation, and among these is the possibility that this disease could be aggravated by a secondary bacterial infection such as Prevotella, as well as the interest or not in using azithromycin, a potentially active antimicrobial agent. The aim of this study was to carry out a systematic literature review, to prove or disprove these allegations by scientific arguments. The search included Medline, PubMed, and Pubtator Central databases for English-language articles published 1999-2021. After removing duplicates, a total of final eligible studies (n=149) were selected. There were more articles showing an increase of Prevotella abundance in the presence of viral infection like that related to Human Immunodeficiency Virus (HIV), Papillomavirus (HPV), Herpesviridae and respiratory virus, highlighting differences according to methodologies and patient groups. The arguments for or against the use of azithromycin are stated in light of the results of the literature, showing the role of intercurrent factors, such as age, drug consumption, the presence of cancer or periodontal diseases. However, clinical trials are lacking to prove the direct link between the presence of Prevotella spp. and a worsening of COVID-19, mainly those using azithromycin alone in this indication.
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Affiliation(s)
- Zohreh Tamanai-Shacoori
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Sandrine Le Gall-David
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Fouzia Moussouni
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Alaa Sweidan
- Laboratory of Microbiology, Department of Life and Earth Sciences, Faculty of Sciences, Lebanese University, Hadath Campus, Beirut, Lebanon
| | - Elisabeth Polard
- Teaching Hospital Rennes, Service de Pharmacovigilance, F-35033 Rennes, France
| | - Latifa Bousarghin
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Anne Jolivet-Gougeon
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
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11
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Kato I, Zhang J, Sun J. Bacterial-Viral Interactions in Human Orodigestive and Female Genital Tract Cancers: A Summary of Epidemiologic and Laboratory Evidence. Cancers (Basel) 2022; 14:425. [PMID: 35053587 PMCID: PMC8773491 DOI: 10.3390/cancers14020425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Infectious agents, including viruses, bacteria, fungi, and parasites, have been linked to pathogenesis of human cancers, whereas viruses and bacteria account for more than 99% of infection associated cancers. The human microbiome consists of not only bacteria, but also viruses and fungi. The microbiome co-residing in specific anatomic niches may modulate oncologic potentials of infectious agents in carcinogenesis. In this review, we focused on interactions between viruses and bacteria for cancers arising from the orodigestive tract and the female genital tract. We examined the interactions of these two different biological entities in the context of human carcinogenesis in the following three fashions: (1) direct interactions, (2) indirect interactions, and (3) no interaction between the two groups, but both acting on the same host carcinogenic pathways, yielding synergistic or additive effects in human cancers, e.g., head and neck cancer, liver cancer, colon cancer, gastric cancer, and cervical cancer. We discuss the progress in the current literature and summarize the mechanisms of host-viral-bacterial interactions in various human cancers. Our goal was to evaluate existing evidence and identify gaps in the knowledge for future directions in infection and cancer.
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Affiliation(s)
- Ikuko Kato
- Department of Oncology and Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jilei Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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12
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Regulation of Lysosomal Associated Membrane Protein 3 (LAMP3) in Lung Epithelial Cells by Coronaviruses (SARS-CoV-1/2) and Type I Interferon Signaling. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2022. [DOI: 10.1515/cmb-2022-0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Abstract
Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) infection is a major risk factor for mortality and morbidity in critical care hospitals around the world. Lung epithelial type II cells play a major role in the recognition and clearance of respiratory viruses as well as repair of lung injury in response to environmental toxicants. Gene expression profiling studies revealed that mouse lung epithelial type II cells express several cell-specific markers including surfactant proteins and Lysosomal associated membrane protein 3 (LAMP3) located in lysosomes, endosomes and lamellar bodies. These intracellular organelles are involved in vesicular transport and facilitate viral entry and release of the viral genome into the host cell cytoplasm. In this study, regulation of LAMP3 expression in human lung epithelial cells by several respiratory viruses and type I interferon signaling was investigated. Respiratory viruses including SARS-CoV-1 and SARS-CoV-2 significantly induced LAMP3 expression in lung epithelial cells within 24 hours after infection that required the presence of ACE2 viral entry receptors. Time course experiments revealed that the induced expression of LAMP3 was correlated with the induced expression of Interferon–beta (IFNB1) and STAT1 at mRNA levels. LAMP3 was also induced by direct IFN-beta treatment in multiple lung epithelial cell lines or by infection with influenza virus lacking the non-structural protein1(NS1) in NHBE bronchial epithelial cells. LAMP3 expression was also induced by several respiratory viruses in human lung epithelial cells including RSV and HPIV3. Location in lysosomes and endosomes aswell as induction by respiratory viruses and type I Interferon suggests that LAMP3 may have an important role in inter-organellar regulation of innate immunity and a potential target for therapeutic modulation in health and disease. Furthermore, bioinformatics revealed that a subset of lung type II genes were differentially regulated in the lungs of COVID-19 patients.
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13
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Lam KC, Araya RE, Huang A, Chen Q, Di Modica M, Rodrigues RR, Lopès A, Johnson SB, Schwarz B, Bohrnsen E, Cogdill AP, Bosio CM, Wargo JA, Lee MP, Goldszmid RS. Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment. Cell 2021; 184:5338-5356.e21. [PMID: 34624222 PMCID: PMC8650838 DOI: 10.1016/j.cell.2021.09.019] [Citation(s) in RCA: 230] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 06/27/2021] [Accepted: 09/13/2021] [Indexed: 12/14/2022]
Abstract
The tumor microenvironment (TME) influences cancer progression and therapy response. Therefore, understanding what regulates the TME immune compartment is vital. Here we show that microbiota signals program mononuclear phagocytes in the TME toward immunostimulatory monocytes and dendritic cells (DCs). Single-cell RNA sequencing revealed that absence of microbiota skews the TME toward pro-tumorigenic macrophages. Mechanistically, we show that microbiota-derived stimulator of interferon genes (STING) agonists induce type I interferon (IFN-I) production by intratumoral monocytes to regulate macrophage polarization and natural killer (NK) cell-DC crosstalk. Microbiota modulation with a high-fiber diet triggered the intratumoral IFN-I-NK cell-DC axis and improved the efficacy of immune checkpoint blockade (ICB). We validated our findings in individuals with melanoma treated with ICB and showed that the predicted intratumoral IFN-I and immune compositional differences between responder and non-responder individuals can be transferred by fecal microbiota transplantation. Our study uncovers a mechanistic link between the microbiota and the innate TME that can be harnessed to improve cancer therapies.
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Affiliation(s)
- Khiem C Lam
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Romina E Araya
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - April Huang
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Leidos Biomedical Research, Bethesda, MD 20892, USA
| | - Quanyi Chen
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Kelly Government Solutions, Bethesda, MD 20892, USA
| | - Martina Di Modica
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Richard R Rodrigues
- Leidos Biomedical Research, Bethesda, MD 20892, USA; Microbiome and Genetics Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Amélie Lopès
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sarah B Johnson
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin Schwarz
- Immunity to Pulmonary Pathogens Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Eric Bohrnsen
- Immunity to Pulmonary Pathogens Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Alexandria P Cogdill
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Catharine M Bosio
- Immunity to Pulmonary Pathogens Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maxwell P Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Romina S Goldszmid
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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14
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Fichorova RN, DeLong AK, Cu-Uvin S, King CC, Jamieson DJ, Klein RS, Sobel JD, Vlahov D, Yamamoto HS, Mayer KH. Protozoan-Viral-Bacterial Co-Infections Alter Galectin Levels and Associated Immunity Mediators in the Female Genital Tract. Front Cell Infect Microbiol 2021; 11:649940. [PMID: 34422675 PMCID: PMC8375472 DOI: 10.3389/fcimb.2021.649940] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/29/2021] [Indexed: 01/05/2023] Open
Abstract
Co-infections with sexually transmittable pathogens are common and more likely in women with disturbed vaginal bacteriome. Among those pathogens, the protozoan parasite Trichomonas vaginalis (TV) is most common after accounting for the highly persistent DNA viruses human papillomavirus (HPV) and genital herpes. The parasitic infection often concurs with the dysbiotic syndrome diagnosed as bacterial vaginosis (BV) and both are associated with risks of superimposed viral infections. Yet, the mechanisms of microbial synergisms in evading host immunity remain elusive. We present clinical and experimental evidence for a new role of galectins, glycan-sensing family of proteins, in mixed infections. We assessed participants of the HIV Epidemiology Research Study (HERS) at each of their incident TV visits (223 case visits) matched to controls who remained TV-negative throughout the study. Matching criteria included age, race, BV (by Nugent score), HIV status, hysterectomy, and contraceptive use. Non-matched variables included BV status at 6 months before the matched visit, and variables examined at baseline, within 6 months of and/or at the matched visit e.g. HSV-2, HPV, and relevant laboratory and socio-demographic parameters. Conditional logistic regression models using generalized estimating equations calculated odds ratios (OR) for incident TV occurrence with each log10 unit higher cervicovaginal concentration of galectins and cytokines. Incident TV was associated with higher levels of galectin-1, galectin-9, IL-1β and chemokines (ORs 1.53 to 2.91, p <0.001). Galectin-9, IL-1β and chemokines were up and galectin-3 down in TV cases with BV or intermediate Nugent versus normal Nugent scores (p <0.001). Galectin-9, IL-1β and chemokines were up in TV-HIV and down in TV-HPV co-infections. In-vitro, TV synergized with its endosymbiont Trichomonasvirus (TVV) and BV bacteria to upregulate galectin-1, galectin-9, and inflammatory cytokines. The BV-bacterium Prevotella bivia alone and together with TV downregulated galectin-3 and synergistically upregulated galectin-1, galectin-9 and IL-1β, mirroring the clinical findings of mixed TV–BV infections. P. bivia also downregulated TVV+TV-induced anti-viral response e.g. IP-10 and RANTES, providing a mechanism for conducing viral persistence in TV-BV co-infections. Collectively, the experimental and clinical data suggest that galectin-mediated immunity may be dysregulated and exploited by viral–protozoan–bacterial synergisms exacerbating inflammatory complications from dysbiosis and sexually transmitted infections.
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Affiliation(s)
- Raina N Fichorova
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States
| | - Allison K DeLong
- Center for Statistical Sciences, School of Public Health, Brown University, Providence, RI, United States
| | - Susan Cu-Uvin
- Department of Obstetrics and Gynecology, Brown University, The Miriam Hospital, Providence, RI, United States
| | - Caroline C King
- National Center for Chronic Disease Prevention and Health Promotion/Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Denise J Jamieson
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Robert S Klein
- Hudson Infectious Diseases Associates, Briarcliff Manor, NY, United States
| | - Jack D Sobel
- Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, United States
| | - David Vlahov
- Department of Community Health Systems, School of Nursing, University of California at San Francisco, San Francisco, CA, United States
| | - Hidemi S Yamamoto
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States
| | - Kenneth H Mayer
- The Fenway Institute, Fenway Health, Boston, MA, United States.,Department of Medicine, Beth Israel Deaconess Hospital, Harvard Medical School, Boston, MA, United States
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15
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Wu G, Zhao N, Zhang C, Lam YY, Zhao L. Guild-based analysis for understanding gut microbiome in human health and diseases. Genome Med 2021; 13:22. [PMID: 33563315 PMCID: PMC7874449 DOI: 10.1186/s13073-021-00840-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
To demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem's higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same "guild" if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of "guild" to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.
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Affiliation(s)
- Guojun Wu
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.,Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
| | - Naisi Zhao
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA.,Department of Public Health and Community Medicine, School of Medicine, Tufts University, Medford, MA, USA
| | - Chenhong Zhang
- Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA.,State Key Laboratory of Microbial Metabolism, Ministry of Education Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Y Lam
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.,Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
| | - Liping Zhao
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA. .,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA. .,Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA. .,State Key Laboratory of Microbial Metabolism, Ministry of Education Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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16
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Qingqing B, Jie Z, Songben Q, Juan C, Lei Z, Mu X. Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection. Microb Pathog 2020; 152:104617. [PMID: 33207260 DOI: 10.1016/j.micpath.2020.104617] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022]
Abstract
HPV persistent infection is a main event leading to the development of cervical intraepithelial neoplasia and cervical cancer. Earlier to distinguish HPV persistent and transient infection is meaningful but the methods are limited. This study used 16S rDNA sequencing to determine the cervicovaginal microbiota of HPV persistent infection, transient infection and health women. Sequences analysis was performed and according to subsequent statistical analysis, the structure of cervicovaginal microbiota of healthy and transient infection individuals is relatively single, Firmicutes occupy the main composition. However, that of the HPV persistent infection presented a complicated trend and the abundance of Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria was higher. The significance p-values of the average species abundance of Firmicutes, Proteobacteria and Bacteroides between HPV persistent and transient infection groups were 0.003, 0.018 and 0.005, respectively. The study also found 36 biomarkers of cervicovaginal microbiota dysbiosis for LDA score>4 among different groups. At genus level, Prevotella, Sphingomonas and Anaerococcus correlated with HPV persistent infection. At species level, Lactobacillus iners correlated with HPV transient infection. Besides, local immune microenvironment was changed with cervicovaginal microbiota dysbiosis. Interleukin-6 and TNF-α were significantly upregulated in cervical secretions from HPV persistent infection compared with those from transient infection and healthy women. Peripheral blood Regulatory T cells and myeloid-derived suppressor cells in patients with HPV persistent infection were also significantly increased. In conclusion, this study identified cervicovaginal microbiota dysbiosis closely related to HPV persistent infection, which provided a new idea and method for the prevention of cervical cancer.
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Affiliation(s)
- Bi Qingqing
- Department of Laboratory Medicine, Qingdao Central Hospital, Qingdao, China
| | - Zhu Jie
- Department of Laboratory Medicine, Qingdao Central Hospital, Qingdao, China
| | - Qu Songben
- Department of Laboratory Medicine, Qingdao Central Hospital, Qingdao, China
| | - Chen Juan
- Department of Laboratory Medicine, Qingdao Central Hospital, Qingdao, China
| | - Zhang Lei
- Department of Laboratory Medicine, Qingdao Central Hospital, Qingdao, China
| | - Xiaofeng Mu
- Department of Laboratory Medicine, Qingdao Central Hospital, Qingdao, China.
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17
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Nunes SC, Serpa J. Recycling the Interspecific Relations with Epithelial Cells: Bacteria and Cancer Metabolic Symbiosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1219:77-91. [PMID: 32130694 DOI: 10.1007/978-3-030-34025-4_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Several aspects of the human physiology are controlled by the microbiota that plays a key role in health and disease. In fact, microbial dysbiosis is associated with numerous diseases, including several types of cancer such as colon, gastric, esophageal, pancreatic, laryngeal, breast and gallbladder carcinomas.Metabolic symbiosis between non-malignant cells and the resident microbita is crucial for the host homeostasis. However, cancer cells are able to repurpose the pre-existing metabolic symbiosis, being able to recycle those relations and also create novel metabolic symbiosis, leading to profound alterations on the local microenvironment.In here we will explore some of these symbiotic metabolic interactions between bacteria and non-malignant cells in two different contexts: colon and uterine cervix. The way malignant cells are able to recycle these normal interactions and also create novel types of symbiotic metabolic relations will also be discussed.The knowledge of these complex interactions and recycling mechanisms is of extreme importance for cancer treatment, as new therapeutic targets could be developed.
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Affiliation(s)
- Sofia C Nunes
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School | Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Lisbon, Portugal
| | - Jacinta Serpa
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School | Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal.
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Lisbon, Portugal.
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18
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Picardo SL, Coburn B, Hansen AR. The microbiome and cancer for clinicians. Crit Rev Oncol Hematol 2019; 141:1-12. [PMID: 31202124 DOI: 10.1016/j.critrevonc.2019.06.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/23/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023] Open
Abstract
The human microbiome is an emerging target in cancer development and therapeutics. It may be directly oncogenic, through promotion of mucosal inflammation or systemic dysregulation, or may alter anti-cancer immunity/therapy. Microorganisms within, adjacent to and distant from tumors may affect cancer progression, and interactions and differences between these populations can influence the course of disease. Here we review the microbiome as it pertains to cancer for clinicians. The microbiota of cancers including colorectal, pancreas, breast and prostate are discussed. We examine "omics" technologies, microbiota associated with tumor tissue and tumor-site fluids such as feces and urine, as well as indirect effects of the gut microbiome. We describe roles of the microbiome in immunotherapy, and how it can be modulated to improve cancer therapeutics. While research is still at an early stage, there is potential to exploit the microbiome, as modulation may increase efficacy of treatments, reduce toxicities and prevent carcinogenesis.
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Affiliation(s)
- Sarah L Picardo
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, 700 University Avenue, Toronto, Ontario, M5G 0A1, Canada.
| | - Bryan Coburn
- Division of Infectious Diseases, University Health Network, Toronto, Canada.
| | - Aaron R Hansen
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, 700 University Avenue, Toronto, Ontario, M5G 0A1, Canada.
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19
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Santiago-Rodriguez TM, Hollister EB. Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut. Viruses 2019; 11:v11070656. [PMID: 31323792 PMCID: PMC6669467 DOI: 10.3390/v11070656] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023] Open
Abstract
The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.
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Affiliation(s)
| | - Emily B Hollister
- Diversigen Inc., 2450 Holcombe Blvd, Suite BCMA, 77021 Houston, TX, USA.
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20
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Norenhag J, Du J, Olovsson M, Verstraelen H, Engstrand L, Brusselaers N. The vaginal microbiota, human papillomavirus and cervical dysplasia: a systematic review and network meta-analysis. BJOG 2019; 127:171-180. [PMID: 31237400 DOI: 10.1111/1471-0528.15854] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2019] [Indexed: 01/18/2023]
Abstract
BACKGROUND Persistent infection with high-risk human papillomavirus can lead to cervical dysplasia and cancer. Recent studies have suggested associations between the composition of the vaginal microbiota, infection with human papillomavirus (HPV) and progression to cervical dysplasia and cancer. OBJECTIVE To assess how specific cervico-vaginal microbiota compositions are associated with HPV infection, cervical dysplasia and cancer, we conducted a systematic review and network meta-analysis (registered in PROSPERO: CRD42018112862). SEARCH STRATEGY PubMed, Web of science, Embase and Cochrane database. SELECTION CRITERIA All original studies describing at least two community state types of bacteria (CST), based on molecular techniques enabling identification of bacteria, and reporting the association with HPV infection, cervical dysplasia and/or cervical cancer. DATA COLLECTION AND ANALYSIS For the meta-analysis, a network map was constructed to provide an overview of the network relationships and to assess how many studies provided direct evidence for the different vaginal microbiota compositions and HPV, cervical dysplasia or cancer. Thereafter, the consistency of the model was assessed, and forest plots were constructed to pool and summarise the available evidence, presenting odds ratios and 95% confidence intervals. MAIN RESULTS Vaginal microbiota dominated by non-Lactobacilli species or Lactobacillus iners were associated with three to five times higher odds of any prevalent HPV and two to three times higher for high-risk HPV and dysplasia/cervical cancer compared with Lactobacillus crispatus. CONCLUSIONS These findings suggest an association between certain bacterial community types of the vaginal microbiota and HPV infection and HPV-related disease. This may be useful for guiding treatment options or serve as biomarkers for HPV-related disease. TWEETABLE ABSTRACT This network meta-analysis suggests an association between different vaginal bacterial community types and the risk of HPV.
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Affiliation(s)
- J Norenhag
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - J Du
- Department of Microbiology, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska Hospital, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - M Olovsson
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - H Verstraelen
- Department of Obstetrics & Gynaecology, Ghent University Hospital 0P4, Ghent University, Ghent, Belgium
| | - L Engstrand
- Department of Microbiology, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska Hospital, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - N Brusselaers
- Department of Microbiology, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska Hospital, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
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21
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Wang Q, Wang K, Wu W, Giannoulatou E, Ho JWK, Li L. Host and microbiome multi-omics integration: applications and methodologies. Biophys Rev 2019; 11:55-65. [PMID: 30627872 PMCID: PMC6381360 DOI: 10.1007/s12551-018-0491-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Our review summarises the application of integrating host omics with microbiome as well as the analytical methods and related tools applied in these studies. In addition, potential future directions are discussed.
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Affiliation(s)
- Qing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Kaicen Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Wenrui Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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