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Wyatt M, Choudhury A, Von Dohlen G, Heileson JL, Forsse JS, Rajakaruna S, Zec M, Tfaily MM, Greathouse L. Randomized control trial of moderate dose vitamin D alters microbiota stability and metabolite networks in healthy adults. Microbiol Spectr 2024:e0008324. [PMID: 39189761 DOI: 10.1128/spectrum.00083-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 07/10/2024] [Indexed: 08/28/2024] Open
Abstract
Evidence indicates that both vitamin D and the gut microbiome are involved in the process of colon carcinogenesis. However, it is unclear what effects supplemental vitamin D3 has on the gut microbiome and its metabolites in healthy adults. We conducted a double-blind, randomized, placebo-controlled trial to identify the acute and long-term microbiota structural and metabolite changes that occur in response to a moderate dose (4,000 IU) of vitamin D3 for 12 weeks in healthy adults. Our results demonstrated a significant increase in serum 25-hydroxy-vitamin D (25(OH)D) in the treatment group compared to placebo (P < 0.0001). Vitamin D3 significantly increased compositional similarity (P < 0.0001) in the treatment group, and enriched members of the Bifidobacteriaceae family. We also identified a significant inverse relationship between the percent change in serum 25(OH)D and microbial stability in the treatment group (R = -0.52, P < 0.019). Furthermore, vitamin D3 supplementation resulted in notable metabolic shifts, in addition to resulting in a drastic rewiring of key gut microbial-metabolic associations. In conclusion, we show that a moderate dose of vitamin D3 among healthy adults has unique acute and persistent effects on the fecal microbiota, and suggest novel mechanisms by which vitamin D may affect the host-microbiota relationship. IMPORTANCE Preventative measures to reduce the rise in early-onset colorectal cancer are of critical need. Both vitamin D, dietary and serum levels, and the gut microbiome are implicated in the etiology of colorectal cancer. By understanding the intimate relationship between vitamin D, the gut microbiome, and its metabolites, we may be able to identify key mechanisms that can be targeted for intervention, including inflammation and metabolic dysfunction. Furthermore, the similarity of vitamin D to cholesterol, which is metabolized by the gut microbiome, gives precedence to its ability to produce metabolites that can be further studied and leveraged for controlling colorectal cancer incidence and mortality.
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Affiliation(s)
- Madhur Wyatt
- Human Health Performance and Recreation, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
| | - Ankan Choudhury
- Human Science and Design, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
| | - Gabriella Von Dohlen
- Human Science and Design, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
| | - Jeffery L Heileson
- Human Health Performance and Recreation, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
- Nutrition Services Division, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Jeffrey S Forsse
- Human Health Performance and Recreation, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
- Department of Biology, Baylor University, Waco, Texas, USA
| | - Sumudu Rajakaruna
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, The University of Arizona, Tucson, Arizona, USA
| | - Manja Zec
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, The University of Arizona, Tucson, Arizona, USA
| | - Leigh Greathouse
- Human Science and Design, Robbins College of Health and Human Sciences, Baylor University, Waco, Texas, USA
- Department of Biology, Baylor University, Waco, Texas, USA
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2
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Wu YJ, Xiong JF, Zhan CN, Xu H. Gut microbiota alterations in colorectal adenoma-carcinoma sequence based on 16S rRNA gene sequencing: A systematic review and meta-analysis. Microb Pathog 2024; 195:106889. [PMID: 39197689 DOI: 10.1016/j.micpath.2024.106889] [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: 04/29/2024] [Revised: 08/12/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
BACKGROUND Most sporadic colorectal cancers (CRC) develop through the adenoma-carcinoma sequence. While dysbiosis of the intestinal flora contributes to CRC's pathogenesis, precise microbial taxa closely associated with the colorectal adenoma-carcinoma sequence remain elusive. This meta-analysis aimed to summarize the features of intestinal flora in patients with AD and CRC. METHODS PubMed, Embase, Cochrane Library, and Web of Science were searched for case-control studies comparing the relative abundance of gut microbiota in the feces of patients with AD, CRC, and healthy controls (HC) from inception to January 2024. The weighted mean difference (WMD) with a 95 % confidence interval (CI) was used to display the results. The Newcastle-Ottawa Scale (NOS) was used to assess the quality of the entailed literature. Publication bias was evaluated with the Egger's and Begg's tests. RESULTS Eleven studies were included, involving 477 CRC patients, 628 AD patients, and 864 healthy controls. Compared with HC, the patients with AD had a significantly lower Chao 1 index (WMD = -30.17, 95 % CI [-41.10, -19.23], P < 0.001) and Shannon index (WMD = -0.11 95 % CI [-0.18, -0.04], P = 0.002). Compared with AD, the CRC patients had a significantly higher Chao1 index (WMD = 22.09, 95 % CI [7.59, 36.00], P = 0.003) and Shannon index (WMD = 0.08, 95 % CI [0.00, 0.15], P = 0.037). Enterobacteriaceae (WMD = 0.03 95 % CI [0.00,0.05], P = 0.047; WMD = 0.02 95 % CI [0.00,0.04], P = 0.027) significantly increased in the order of Control-AD-CRC, while that of Blautia (WMD = -0.00 95 % CI [-0.01, -0.00], P = 0.001; WMD = -0.00 95 % CI [-0.00, -0.00], P = 0.002) was reduced. Compared with HC, the relative abundance of Proteobacteria (WMD = 0.05 95 % CI [0.03,0.07], P < 0.001), Fusobacteria (WMD = 0.02 95 % CI [0.00,0.03], P = 0.042), Streptococcaceae (WMD = 0.03 95 % CI [0.01,0.05], P = 0.017), Prevotellaceae (WMD = 0.02 95 % CI [0.00,0.04], P = 0.040), and Escherichia-Shigella (WMD = 0.06 95 % CI [0.01, 0.11], P = 0.021) was enriched in the CRC group. The relative abundance of Alistipes (WMD = 0.00 95 % CI [0.00,0.01], P = 0.032) and Streptococcus (WMD = 0.00 95 % CI [0.00,0.00], P = 0.001) was increased in the AD vs HC. The relative abundance of Firmicutes (WMD = -0.07 95 % CI [-0.12, -0.03], P = 0.003), Bifidobacteria (WMD = -0.03 95 % CI [-0.05, -0.01], P = 0.016), and Klebsiella (WMD = -0.01 95 % CI [-0.01, -0.00], P = 0.001) was decreased in the CRC vs HC. Compared with AD, the relative abundance of Firmicutes (WMD = -0.04 95 % CI [-0.07, -0.02], P = 0.002), Peptostreptococcaceae (WMD = -0.03 95 % CI [-0.05, -0.00], P = 0.021), Lachnospiraceae (WMD = -0.04 95 % CI [-0.08,-0.00], P = 0.037), Ruminococcaceae (WMD = -0.06 95 % CI [-0.09,-0.03], P < 0.001), Faecalibacterium (WMD = -0.01 95 % CI [-0.02, -0.01], P = 0.001), and Lachnoclostridium (WMD = -0.02 95 % CI [-0.03, -0.00], P = 0.040) was decreased in the CRC group, while Proteobacteria (WMD = 0.04 95 % CI [0.02,0.05], P < 0.001) was increased. CONCLUSIONS The dysbiosis characterized by reduced levels of short-chain fatty acid (SCFA)-producing bacteria, decreased anti-inflammatory bacteria, increased pro-inflammatory bacteria, and an elevation of bacteria with cytotoxic effects damaging to DNA may represent the specific microbial signature of colorectal adenoma/carcinoma. Further research is required to elucidate the mechanisms by which gut dysbiosis leads to the progression from AD to CRC and to explore the potential of specific microbiota markers in clinical treatment and non-invasive screening.
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Affiliation(s)
- Yi-Jun Wu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jing-Fang Xiong
- Department of Geriatrics, Hangzhou Red Cross Hospital, Hangzhou, China
| | - Cheng-Nan Zhan
- Medical Service Community, Hangzhou Xiaoshan Hospital of TCM, Hangzhou, China
| | - Hong Xu
- Department of Gastroenterology and Hepatology, Hangzhou Red Cross Hospital, Hangzhou, China.
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Zhang S, Zhao Y, Lalsiamthara J, Peng Y, Qi L, Deng S, Wang Q. Current research progress on Prevotella intermedia and associated diseases. Crit Rev Microbiol 2024:1-18. [PMID: 39140115 DOI: 10.1080/1040841x.2024.2390594] [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: 12/23/2023] [Revised: 05/29/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
Prevotella intermedia is a Gram-negative anaerobic bacterium that is a common pathogen of periodontitis. Recent studies have revealed that P. intermedia is closely associated with a variety of diseases involving multiple systems. Under the action of its virulence factors such as cysteine protease and adhesins, P. intermedia has the ability to bind and invade various host cells including gingival fibroblasts. It can also copolymerize a variety of pathogenic bacteria, leading to interference with the host's immune inflammatory response and causing various diseases. In this article, we review the progress of research on P. intermedia virulence factors and bacterial pathogenesis, and the correlation between P. intermedia and various diseases.
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Affiliation(s)
- Shuyang Zhang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Yuheng Zhao
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Jonathan Lalsiamthara
- Molecular Microbiology & Immunology, School of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Yan Peng
- Key Laboratory of Green Cleaning Technology& Detergent of Zhejiang Province, Hangzhou, China
| | - Linlong Qi
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Shuli Deng
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Qingjing Wang
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
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Peng F, Hu M, Su Z, Hu L, Guo L, Yang K. Intratumoral Microbiota as a Target for Advanced Cancer Therapeutics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2405331. [PMID: 39054925 DOI: 10.1002/adma.202405331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/21/2024] [Indexed: 07/27/2024]
Abstract
In recent years, advancements in microbial sequencing technology have sparked an increasing interest in the bacteria residing within solid tumors and its distribution and functions in various tumors. Intratumoral bacteria critically modulate tumor oncogenesis and development through DNA damage induction, chronic inflammation, epigenetic alterations, and metabolic and immune regulation, while also influencing cancer treatment efficacy by affecting drug metabolism. In response to these discoveries, a variety of anti-cancer therapies targeting these microorganisms have emerged. These approaches encompass oncolytic therapy utilizing tumor-associated bacteria, the design of biomaterials based on intratumoral bacteria, the use of intratumoral bacterial components for drug delivery systems, and comprehensive strategies aimed at the eradication of tumor-promoting bacteria. Herein, this review article summarizes the distribution patterns of bacteria in different solid tumors, examines their impact on tumors, and evaluates current therapeutic strategies centered on tumor-associated bacteria. Furthermore, the challenges and prospects for developing drugs that target these bacterial communities are also explored, promising new directions for cancer treatment.
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Affiliation(s)
- Fei Peng
- Department of Pathology, the First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Mengyuan Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection & School for Radiological and Interdisciplinary Sciences (RAD-X), Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhiyue Su
- Department of Pathology, the First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Lin Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection & School for Radiological and Interdisciplinary Sciences (RAD-X), Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Lingchuan Guo
- Department of Pathology, the First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Kai Yang
- Department of Pathology, the First Affiliated Hospital of Soochow University, Suzhou, 215000, China
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection & School for Radiological and Interdisciplinary Sciences (RAD-X), Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, 215123, China
- Key Laboratory of Alkene-carbon Fibres-based Technology & Application for Detection of Major Infectious Diseases, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, 215123, China
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5
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Yalamarty R, Magesh S, John D, Chakladar J, Li WT, Brumund KT, Wang-Rodriguez J, Ongkeko WM. The intratumor microbiome varies by geographical location and anatomical site in head and neck squamous cell carcinoma. Curr Probl Cancer 2024; 50:101100. [PMID: 38820649 DOI: 10.1016/j.currproblcancer.2024.101100] [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: 11/02/2023] [Revised: 03/29/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024]
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is a highly heterogeneous cancer that is characterized by distinct phenotypes based on anatomical site and etiological agents. Recently, the intratumor microbiome has been implicated in cancer pathogenesis and progression. Although it is well established that the gut microbiome varies with geographical location and is highly influenced by factors such as diet, environment, and genetics, the intratumor microbiome is not very well characterized. In this review, we aim to characterize the HNSCC intratumor microbiome by geographical location and anatomical site. We conducted a review of primary literature from PubMed and assessed studies based on relevancy and recency. To the best of our knowledge, we are the first to comprehensively examine the tumor microenvironment of HNSCC with respect to these two primary factors on a large scale. Our results suggest that there are unique bacterial and fungal biomarkers for HNSCC for each of the following geographical locations: North America, Asia, Europe, Australia, and Africa. We also identified a panel of microbial biomarkers that are unique to two primary HNSCC anatomic sites, as well as microbial biomarkers associated with various etiological agents of HNSCC. Future study of these microbes may improve HNSCC diagnostic and therapeutic modalities by accounting for differences based on geographic regions and anatomical sites.
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Affiliation(s)
- Rishabh Yalamarty
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Shruti Magesh
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Daniel John
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jaideep Chakladar
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Wei Tse Li
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; University of California San Francisco School of Medicine, San Francisco, CA 94143, USA
| | - Kevin T Brumund
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Division of Head and Neck Surgery, Department of Surgery, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jessica Wang-Rodriguez
- Pathology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; Department of Pathology, UC San Diego School of Medicine, San Diego, CA 92093, USA
| | - Weg M Ongkeko
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA.
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6
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Zhang W, Yin Y, Jiang Y, Yang Y, Wang W, Wang X, Ge Y, Liu B, Yao L. Relationship between vaginal and oral microbiome in patients of human papillomavirus (HPV) infection and cervical cancer. J Transl Med 2024; 22:396. [PMID: 38685022 PMCID: PMC11059664 DOI: 10.1186/s12967-024-05124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND The aim of this study was to assess the microbial variations and biomarkers in the vaginal and oral environments of patients with human papillomavirus (HPV) and cervical cancer (CC) and to develop novel prediction models. MATERIALS AND METHODS This study included 164 samples collected from both the vaginal tract and oral subgingival plaque of 82 women. The participants were divided into four distinct groups based on their vaginal and oral samples: the control group (Z/KZ, n = 22), abortion group (AB/KAB, n = 17), HPV-infected group (HP/KHP, n = 21), and cervical cancer group (CC/KCC, n = 22). Microbiota analysis was conducted using full-length 16S rDNA gene sequencing with the PacBio platform. RESULTS The vaginal bacterial community in the Z and AB groups exhibited a relatively simple structure predominantly dominated by Lactobacillus. However, CC group shows high abundances of anaerobic bacteria and alpha diversity. Biomarkers such as Bacteroides, Mycoplasma, Bacillus, Dialister, Porphyromonas, Anaerococcus, and Prevotella were identified as indicators of CC. Correlations were established between elevated blood C-reactive protein (CRP) levels and local/systemic inflammation, pregnancy, childbirth, and abortion, which contribute to unevenness in the vaginal microenvironment. The altered microbial diversity in the CC group was confirmed by amino acid metabolism. Oral microbial diversity exhibited an inverse pattern to that of the vaginal microbiome, indicating a unique relationship. The microbial diversity of the KCC group was significantly lower than that of the KZ group, indicating a link between oral health and cancer development. Several microbes, including Fusobacterium, Campylobacter, Capnocytophaga, Veillonella, Streptococcus, Lachnoanaerobaculum, Propionibacterium, Prevotella, Lactobacillus, and Neisseria, were identified as CC biomarkers. Moreover, periodontal pathogens were associated with blood CRP levels and oral hygiene conditions. Elevated oral microbial amino acid metabolism in the CC group was closely linked to the presence of pathogens. Positive correlations indicated a synergistic relationship between vaginal and oral bacteria. CONCLUSION HPV infection and CC impact both the vaginal and oral microenvironments, affecting systemic metabolism and the synergy between bacteria. This suggests that the use of oral flora markers is a potential screening tool for the diagnosis of CC.
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Affiliation(s)
- Wei Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- School/Hospital of Stomatology, Lanzhou University, Lanzhou, China
- Healthy Examination & Management Center of Lanzhou University Second Hospital, Lanzhou, China
| | - Yanfei Yin
- Healthy Examination & Management Center of Lanzhou University Second Hospital, Lanzhou, China
| | - Yisha Jiang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Yangyang Yang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Wentao Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Xiaoya Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Yan Ge
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Department of Gynecology, Lanzhou University First Hospital, Lanzhou, China
| | - Bin Liu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.
- School/Hospital of Stomatology, Lanzhou University, Lanzhou, China.
| | - Lihe Yao
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.
- Department of Neurology, Lanzhou University First Hospital, Lanzhou, China.
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7
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Giampazolias E, da Costa MP, Lam KC, Lim KHJ, Cardoso A, Piot C, Chakravarty P, Blasche S, Patel S, Biram A, Castro-Dopico T, Buck MD, Rodrigues RR, Poulsen GJ, Palma-Duran SA, Rogers NC, Koufaki MA, Minutti CM, Wang P, Vdovin A, Frederico B, Childs E, Lee S, Simpson B, Iseppon A, Omenetti S, Kelly G, Goldstone R, Nye E, Suárez-Bonnet A, Priestnall SL, MacRae JI, Zelenay S, Patil KR, Litchfield K, Lee JC, Jess T, Goldszmid RS, Sousa CRE. Vitamin D regulates microbiome-dependent cancer immunity. Science 2024; 384:428-437. [PMID: 38662827 PMCID: PMC7615937 DOI: 10.1126/science.adh7954] [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: 03/14/2023] [Accepted: 03/04/2024] [Indexed: 05/03/2024]
Abstract
A role for vitamin D in immune modulation and in cancer has been suggested. In this work, we report that mice with increased availability of vitamin D display greater immune-dependent resistance to transplantable cancers and augmented responses to checkpoint blockade immunotherapies. Similarly, in humans, vitamin D-induced genes correlate with improved responses to immune checkpoint inhibitor treatment as well as with immunity to cancer and increased overall survival. In mice, resistance is attributable to the activity of vitamin D on intestinal epithelial cells, which alters microbiome composition in favor of Bacteroides fragilis, which positively regulates cancer immunity. Our findings indicate a previously unappreciated connection between vitamin D, microbial commensal communities, and immune responses to cancer. Collectively, they highlight vitamin D levels as a potential determinant of cancer immunity and immunotherapy success.
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Affiliation(s)
- Evangelos Giampazolias
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Cancer Immunosurveillance Group, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | | | - Khiem C. Lam
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology (LICI), Center for Cancer Research (CCR), National Cancer Institute (NCI), 37 Convent Drive, Bethesda, MD 20892-0001, USA
| | - Kok Haw Jonathan Lim
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College, London, UK
| | - Ana Cardoso
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Cécile Piot
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Probir Chakravarty
- Bioinformatics and Biostatistics STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sonja Blasche
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Swara Patel
- Cancer Immunosurveillance Group, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Adi Biram
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tomas Castro-Dopico
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael D. Buck
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard R. Rodrigues
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Microbiome and Genetics Core, LICI, CCR, NCI, 37 Convent Drive, Bethesda, MD 20892-0001, USA
| | - Gry Juul Poulsen
- National Center of Excellence for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Faculty of Medicine, Aalborg University, Department of Gastroenterology and Hepatology, Aalborg University Hospital, A.C. Meyers Vænge 15, A DK-2450 Copenhagen, Denmark
| | | | - Neil C. Rogers
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Maria A. Koufaki
- Cancer Inflammation and Immunity Group, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Carlos M. Minutti
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Pengbo Wang
- Cancer Immunosurveillance Group, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Alexander Vdovin
- Cancer Immunosurveillance Group, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Bruno Frederico
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eleanor Childs
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sonia Lee
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ben Simpson
- Tumor ImmunoGenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, 72 Huntley St, London WC1E 6DD, UK
| | - Andrea Iseppon
- AhRimmunity Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sara Omenetti
- AhRimmunity Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Robert Goldstone
- Bioinformatics and Biostatistics STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emma Nye
- Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alejandro Suárez-Bonnet
- Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
| | - Simon L. Priestnall
- Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
| | - James I. MacRae
- Metabolomics STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Santiago Zelenay
- Cancer Inflammation and Immunity Group, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Kiran Raosaheb Patil
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Kevin Litchfield
- Tumor ImmunoGenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, 72 Huntley St, London WC1E 6DD, UK
| | - James C. Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Institute of Liver and Digestive Health, Division of Medicine, Royal Free Hospital, University College London, London, NW3 2QG, UK
| | - Tine Jess
- National Center of Excellence for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Faculty of Medicine, Aalborg University, Department of Gastroenterology and Hepatology, Aalborg University Hospital, A.C. Meyers Vænge 15, A DK-2450 Copenhagen, Denmark
| | - Romina S. Goldszmid
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology (LICI), Center for Cancer Research (CCR), National Cancer Institute (NCI), 37 Convent Drive, Bethesda, MD 20892-0001, USA
| | - Caetano Reis e Sousa
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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8
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Qin Y, Li Z, Liu T, Ma J, Liu H, Zhou Y, Wang S, Zhang L, Peng Q, Ye P, Duan N, Wang W, Wang X. Prevotella intermedia boosts OSCC progression through ISG15 upregulation: a new target for intervention. J Cancer Res Clin Oncol 2024; 150:206. [PMID: 38644421 PMCID: PMC11033248 DOI: 10.1007/s00432-024-05730-5] [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: 02/03/2024] [Accepted: 03/28/2024] [Indexed: 04/23/2024]
Abstract
PURPOSE Periodontitis-associated bacteria, such as Porphyromonas gingivalis and Fusobacterium nucleatum, are closely linked to the risk of oral squamous cell carcinoma (OSCC). Emerging studies have indicated that another common periodontal pathogen, Prevotella intermedia (P. intermedia), is enriched in OSCC and could affect the occurrence and progression of OSCC. Our aim is to determine the effects of P. intermedia on the progression of OSCC and the role of antibiotics in reversing these effects. METHODS In this study, a murine xenograft model of OSCC was established, and the mice were injected intratumorally with PBS (control group), P. intermedia (P.i group), or P. intermedia combined with an antibiotic cocktail administration (P.i + ABX group), respectively. The effects of P. intermedia and ABX administration on xenograft tumor growth, invasion, angiogenesis, and metastasis were investigated by tumor volume measurement and histopathological examination. Enzyme-linked immunosorbent assay (ELISA) was used to investigate the changes in serum cytokine levels. Immunohistochemistry (IHC) was adopted to analyze the alterations in the levels of inflammatory cytokines and infiltrated immune cells in OSCC tissues of xenograft tumors. Transcriptome sequencing and analysis were conducted to determine differential expression genes among various groups. RESULTS Compared with the control treatment, P. intermedia treatment significantly promoted tumor growth, invasion, angiogenesis, and metastasis, markedly affected the levels of inflammatory cytokines, and markedly altered M2 macrophages and regulatory T cells (Tregs) infiltration in the tumor microenvironment. However, ABX administration clearly abolished these effects of P. intermedia. Transcriptome and immunohistochemical analyses revealed that P. intermedia infection increased the expression of interferon-stimulated gene 15 (ISG15). Correlation analysis indicated that the expression level of ISG15 was positively correlated with the Ki67 expression level, microvessel density, serum concentrations and tissue expression levels of inflammatory cytokines, and quantities of infiltrated M2 macrophages and Tregs. However, it is negatively correlated with the quantities of infiltrated CD4+ and CD8+ T cells. CONCLUSION In conclusion, intratumoral P. intermedia infection aggravated OSCC progression, which may be achieved through upregulation of ISG15. This study sheds new light on the possible pathogenic mechanism of intratumoral P. intermedia in OSCC progression, which could be a prospective target for OSCC prevention and treatment.
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Affiliation(s)
- Yao Qin
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Zhiyuan Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Ting Liu
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Jingjing Ma
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Hong Liu
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Yifan Zhou
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Shuai Wang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Lei Zhang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Qiao Peng
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Pei Ye
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Ning Duan
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Wenmei Wang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
| | - Xiang Wang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
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9
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Liang W, Zhou Z, Gao Q, Zhu Z, Zhu J, Lin J, Wen Y, Qian F, Wang L, Zhai Y, Lv J, Zhang H, Zhong F, Du H. Tumor-derived Prevotella intermedia aggravates gastric cancer by enhancing Perilipin 3 expression. Cancer Sci 2024; 115:1141-1153. [PMID: 38287724 PMCID: PMC11007001 DOI: 10.1111/cas.16080] [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: 11/04/2023] [Revised: 12/20/2023] [Accepted: 01/07/2024] [Indexed: 01/31/2024] Open
Abstract
The indigenous microbial milieu within tumorous tissues exerts a pivotal influence on the genesis and advancement of gastric cancer (GC). This investigation scrutinizes the functions and molecular mechanisms attributed to Prevotella intermedia in the malignant evolution of GC. Isolation of P. intermedia from paired GC tissues was undertaken. Quantification of P. intermedia abundance in 102 tissues was accomplished using quantitative real-time PCR (qRT-PCR). Assessment of the biological effects of P. intermedia on GC cells was observed using culture medium supernatant. Furthermore, the protein profile of GC cells treated with tumor-derived P. intermedia was examined through label-free protein analysis. The functionality of perilipin 3 (PLIN3) was subsequently confirmed using shRNA. Our investigation revealed that the relative abundance of P. intermedia in tumor tissues significantly surpassed that of corresponding healthy tissues. The abundance of P. intermedia exhibited correlations with tumor differentiation (p = 0.006), perineural invasion (p = 0.004), omentum majus invasion (p = 0.040), and the survival duration of GC patients (p = 0.042). The supernatant derived from tumor-associated P. intermedia bolstered the proliferation, clone formation, migration, and invasion of GC cells. After indirect co-cultivation with tumor-derived P. intermedia, dysregulation of 34 proteins, including PLIN3, was discerned in GC cells. Knockdown of PLIN3 mitigated the malignancy instigated by P. intermedia in GC cells. Our findings posit that P. intermedia from the tumor microenvironment plays a substantial role in the malignant progression of GC via the modulation of PLIN3 expression. Moreover, the relative abundance of P. intermedia might serve as a potential biomarker for the diagnosis and prognosis of GC.
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Affiliation(s)
- Wei Liang
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Zhengyang Zhou
- Department of General SurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Qizhao Gao
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Zhichen Zhu
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Jie Zhu
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Jiayao Lin
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Yicheng Wen
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Feinan Qian
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Liang Wang
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Yaxuan Zhai
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Jingnan Lv
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Haifang Zhang
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Fengyun Zhong
- Department of General SurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Hong Du
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
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10
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Zhou Y, Qin Y, Ma J, Li Z, Heng W, Zhang L, Liu H, Li R, Zhang M, Peng Q, Ye P, Duan N, Liu T, Wang W, Wang X. Heat-killed Prevotella intermedia promotes the progression of oral squamous cell carcinoma by inhibiting the expression of tumor suppressors and affecting the tumor microenvironment. Exp Hematol Oncol 2024; 13:33. [PMID: 38515216 PMCID: PMC10956211 DOI: 10.1186/s40164-024-00500-y] [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: 10/25/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Oral microbial dysbiosis contributes to the development of oral squamous cell carcinoma (OSCC). Our previous study showed that Prevotella intermedia (P. intermedia) were enriched in the oral mucosal surface, plaque, and saliva of patients with OSCC. Intratumoral microbiome could reshape the immune system and influence the development of various tumors. However, the invasion status of human OSCC tissues by P. intermedia and the pathway through which intratumoral P. intermedia potentiates tumor progression remain unexplored. METHODS P. intermedia in human OSCC or normal tissues was detected by FISH. A mouse OSCC cell line SCC7 was adopted to investigate the effects of heat-killed P. intermedia treatment on cell proliferation, invasion, and cytokine release by using CCK-8 assay, transwell invasion assay and ELISA. Moreover, we established a mouse transplanted tumor model by using SCC7 cells, injected heat-killed P. intermedia into tumor tissues, and investigated the effects of heat-killed P. intermedia on tumor growth, invasion, cytokine levels, immune cell infiltrations, and expression levels by using gross observation, H&E staining, ELISA, immunohistochemistry, mRNA sequencing, and transcriptomic analysis. RESULTS Our results indicated that P. intermedia were abundant in OSCC and surrounding muscle tissues. Heat-killed P. intermedia promoted SCC7 cell proliferation, invasion and proinflammatory cytokine secretions, accelerated transplanted tumor growth in mice, exacerbate muscle and perineural invasion of OSCC, elevated the serum levels of IL-17A, IL-6, TNF-α, IFN-γ, and PD-L1, induced Treg cells M2 type macrophages in mouse transplanted tumors. The data of transcriptomic analysis revealed that heat-killed P. intermedia increased the expression levels of inflammatory cytokines and chemokines while reduced the expression levels of some tumor suppressor genes in mouse transplanted tumors. Additionally, IL-17 signaling pathway was upregulated whereas GABAergic system was downregulated by heat-killed P. intermedia treatment. CONCLUSIONS Taken together, our results suggest that P. intermedia could inhibit the expression of tumor suppressors, alter the tumor microenvironment, and promote the progression of OSCC.
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Affiliation(s)
- Yifan Zhou
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Yao Qin
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Jingjing Ma
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Zhiyuan Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Weiwei Heng
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Lei Zhang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Hong Liu
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Ruowei Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Miaomiao Zhang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Qiao Peng
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Pei Ye
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Ning Duan
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Ting Liu
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
| | - Wenmei Wang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
| | - Xiang Wang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
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11
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Hsieh RH, Chien YJ, Lan WY, Lin YK, Lin YH, Chiang CF, Yang MT. Bacillus coagulans TCI711 Supplementation Improved Nonalcoholic Fatty Liver by Modulating Gut Microbiota: A Randomized, Placebo-Controlled, Clinical Trial. Curr Dev Nutr 2024; 8:102083. [PMID: 38510931 PMCID: PMC10951533 DOI: 10.1016/j.cdnut.2024.102083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 03/22/2024] Open
Abstract
Background Nonalcoholic fatty liver disease (NAFLD) has become one of the major problems of chronic liver disease worldwide. It not only causes damage to the liver but also engenders chronic hepatitis and cirrhosis. Recent studies have shown that regulating Bacillus coagulans can improve NAFLD. Objectives This trial explores whether B. coagulans TCI711 (BCT) could ameliorate NAFLD. Methods A total of 57 patients with NAFLD were recruited through FibroScan liver fibrosis scanner and divided into placebo (n = 28) and BCT-supplemented groups (n = 29). Specifically, 1 BCT probiotic capsule was supplemented daily for 8 wk. Furthermore, the blood, stool, and fatty liver content were then examined. Results Parameters evaluated for liver and kidney indicators showed no side effects after supplementing BCT. A significant reduction of 8.7% in the fatty liver was achieved by effectively suppressing the grade of fatty liver as revealed by controlled attenuation parameter. BCT also regulated gut microbiota profiles, with significant increases observed in Bifidobacterium, Eubacterium, Ruminococcaceae, and Sellimonas compared with the baseline. Conclusions BCT may improve NAFLD by regulating gut microbiota, and parameters evaluated for liver and kidney indicate no side effects.
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Affiliation(s)
- Rong-Hong Hsieh
- School of Nutrition and Health Sciences, Taipei Medical University, Taipei, Taiwan
| | - Yu-Ju Chien
- School of Nutrition and Health Sciences, Taipei Medical University, Taipei, Taiwan
| | - Wen-Yi Lan
- Center for General Education, Taipei Medical University, Taipei, Taiwan
| | - Yung-Kai Lin
- Institute of Food Safety and Risk Management, National Taiwan Ocean University, Keelung, Taiwan
- Department of Food Science, National Taiwan Ocean University, Keelung, Taiwan
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, Taiwan
| | | | - Chi-Fu Chiang
- Research & Design Center, TCI Co., Ltd., Taipei, Taiwan
| | - Ming-Ta Yang
- Center for General Education, Taipei Medical University, Taipei, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei, Taiwan
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12
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Liao Y, Wu YX, Tang M, Chen YW, Xie JR, Du Y, Wang TM, He YQ, Xue WQ, Zheng XH, Liu QY, Zheng MQ, Jia YJ, Tong XT, Zhou T, Li XZ, Yang DW, Diao H, Jia WH. Microbes translocation from oral cavity to nasopharyngeal carcinoma in patients. Nat Commun 2024; 15:1645. [PMID: 38388556 PMCID: PMC10883945 DOI: 10.1038/s41467-024-45518-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
The presence of oral microbes in extra-oral sites is linked to gastrointestinal cancers. However, their potential ectopically colonization in the nasopharynx and impact on local cancer development remains uncertain. Our study involving paired nasopharyngeal-oral microbial samples from nasopharyngeal carcinoma (NPC) patients and controls unveils an aberrant oral-to-nasopharyngeal microbial translocation associated with increased NPC risk (OR = 4.51, P = 0.012). Thirteen species are classified as oral-translocated and enriched in NPC patients. Among these, Fusobacterium nucleatum and Prevotella intermedia are validated through culturomics and clonal strain identification. Nasopharyngeal biopsy meta-transcriptomes confirm these microbes within tumors, influencing local microenvironment and cytokine response. These microbes correlate significantly with the Epstein-Barr virus (EBV) loads in the nasopharynx, exhibiting an increased dose-response relationship. Collectively, our study identifies oral microbes migrating to the nasopharynx, infiltrating tumors, impacting microenvironments and linking with EBV infection. These results enhance our understanding of abnormal microbial communication and their roles in carcinogenesis.
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Affiliation(s)
- Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Minzhong Tang
- Key Laboratory of Nasopharyngeal Carcinoma Molecular Epidemiology, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Yi-Wei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jin-Ru Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Du
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qiao-Yun Liu
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Mei-Qi Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi-Jing Jia
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xia-Ting Tong
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Hua Diao
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
- School of Public Health, Sun Yat-sen University, Guangzhou, China.
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13
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Xuan M, Gu X, Liu Y, Yang L, Li Y, Huang D, Li J, Xue C. Intratumoral microorganisms in tumors of the digestive system. Cell Commun Signal 2024; 22:69. [PMID: 38273292 PMCID: PMC10811838 DOI: 10.1186/s12964-023-01425-5] [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: 11/07/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024] Open
Abstract
Tumors of the digestive system pose a significant threat to human health and longevity. These tumors are associated with high morbidity and mortality rates, leading to a heavy economic burden on healthcare systems. Several intratumoral microorganisms are present in digestive system tumors, and their sources and abundance display significant heterogeneity depending on the specific tumor subtype. These microbes have a complex and precise function in the neoplasm. They can facilitate tumor growth through various mechanisms, such as inducing DNA damage, influencing the antitumor immune response, and promoting the degradation of chemotherapy drugs. Therefore, these microorganisms can be targeted to inhibit tumor progression for improving overall patient prognosis. This review focuses on the current research progress on microorganisms present in the digestive system tumors and how they influence the initiation, progression, and prognosis of tumors. Furthermore, the primary sources and constituents of tumor microbiome are delineated. Finally, we summarize the application potential of intratumoral microbes in the diagnosis, treatment, and prognosis prediction of digestive system tumors. Video Abstract.
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Affiliation(s)
- Mengjuan Xuan
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Yingru Liu
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, China
| | - Li Yang
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, China
| | - Yi Li
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, China
| | - Di Huang
- Department of Child Health Care, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Juan Li
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, China.
| | - Chen Xue
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, 450052, China.
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14
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Lee S, Lee I. Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data. Gut Microbes 2024; 16:2375679. [PMID: 38972064 PMCID: PMC11229738 DOI: 10.1080/19490976.2024.2375679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024] Open
Abstract
The gut microbiome, linked significantly to host diseases, offers potential for disease diagnosis through machine learning (ML) pipelines. These pipelines, crucial in modeling diseases using high-dimensional microbiome data, involve selecting profile modalities, data preprocessing techniques, and classification algorithms, each impacting the model accuracy and generalizability. Despite whole metagenome shotgun sequencing (WMS) gaining popularity for human gut microbiome profiling, a consensus on the optimal methods for ML pipelines in disease diagnosis using WMS data remains elusive. Addressing this gap, we comprehensively evaluated ML methods for diagnosing Crohn's disease and colorectal cancer, using 2,553 fecal WMS samples from 21 case-control studies. Our study uncovered crucial insights: gut-specific, species-level taxonomic features proved to be the most effective for profiling; batch correction was not consistently beneficial for model performance; compositional data transformations markedly improved the models; and while nonlinear ensemble classification algorithms typically offered superior performance, linear models with proper regularization were found to be more effective for diseases that are linearly separable based on microbiome data. An optimal ML pipeline, integrating the most effective methods, was validated for generalizability using holdout data. This research offers practical guidelines for constructing reliable disease diagnostic ML models with fecal WMS data.
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Affiliation(s)
- Sungho Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
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15
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Chen L, Zhao R, Kang Z, Cao Z, Liu N, Shen J, Wang C, Pan F, Zhou X, Liu Z, Yang Y, Chen Q. Delivery of short chain fatty acid butyrate to overcome Fusobacterium nucleatum-induced chemoresistance. J Control Release 2023; 363:43-56. [PMID: 37734673 DOI: 10.1016/j.jconrel.2023.09.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/10/2023] [Accepted: 09/17/2023] [Indexed: 09/23/2023]
Abstract
The gut microbiota is closely associated with the progression of colorectal cancer (CRC) in which Fusobacterium nucleatum (F. nucleatum) was found to induce cancer resistance to chemotherapeutics. To relieve F. nucleatum-induced drug resistance, herein, we found that short-chain fatty acid butyrate can inhibit the growth, enrichment and adhesion of F. nucleatum in colorectal cancer tissues by downregulating the expression of adhesion-associated outer membrane proteins, including RadD, FomA, and FadA, to reduce the colonization and invasion of F. nucleatum and relieve the chemoresistance induced by F. nucleatum. Leveraging the killing effect of butyrate on F. nucleatum, sodium butyrate (NaBu) was encapsulated in liposomes or prepared as NaBu tablets with Eudragit S100 coating and administered by intravenous injection or oral administration, respectively. Interestingly, both intravenous administration of NaBu liposomes and oral delivery of NaBu tablets could effectively inhibit the proliferation of F. nucleatum and significantly improve the therapeutic efficacy of oxaliplatin in mice with subcutaneous colorectal tumors, orthotopic colorectal tumors and even spontaneously formed colorectal tumors. Thus, our work provides a simple but effective formulation of NaBu to relieve F. nucleatum-induced chemoresistance, exhibiting ideal clinical application prospects.
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Affiliation(s)
- Linfu Chen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
| | - Rui Zhao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
| | - Zheyu Kang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
| | - Zhiqin Cao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
| | - Nanhui Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
| | - Jingjing Shen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
| | - Cheng Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
| | - Feng Pan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Xiao Zhou
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Qian Chen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, PR China.
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16
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Schorr L, Mathies M, Elinav E, Puschhof J. Intracellular bacteria in cancer-prospects and debates. NPJ Biofilms Microbiomes 2023; 9:76. [PMID: 37813921 PMCID: PMC10562400 DOI: 10.1038/s41522-023-00446-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
Recent evidence suggests that some human cancers may harbor low-biomass microbial ecosystems, spanning bacteria, viruses, and fungi. Bacteria, the most-studied kingdom in this context, are suggested by these studies to localize within cancer cells, immune cells and other tumor microenvironment cell types, where they are postulated to impact multiple cancer-related functions. Herein, we provide an overview of intratumoral bacteria, while focusing on intracellular bacteria, their suggested molecular activities, communication networks, host invasion and evasion strategies, and long-term colonization capacity. We highlight how the integration of sequencing-based and spatial techniques may enable the recognition of bacterial tumor niches. We discuss pitfalls, debates and challenges in decisively proving the existence and function of intratumoral microbes, while reaching a mechanistic elucidation of their impacts on tumor behavior and treatment responses. Together, a causative understanding of possible roles played by intracellular bacteria in cancer may enable their future utilization in diagnosis, patient stratification, and treatment.
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Affiliation(s)
- Lena Schorr
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Marius Mathies
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany
| | - Eran Elinav
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany.
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Jens Puschhof
- Microbiome and Cancer Division, German Cancer Research Center, Heidelberg, Germany.
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17
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Papoutsoglou G, Tarazona S, Lopes MB, Klammsteiner T, Ibrahimi E, Eckenberger J, Novielli P, Tonda A, Simeon A, Shigdel R, Béreux S, Vitali G, Tangaro S, Lahti L, Temko A, Claesson MJ, Berland M. Machine learning approaches in microbiome research: challenges and best practices. Front Microbiol 2023; 14:1261889. [PMID: 37808286 PMCID: PMC10556866 DOI: 10.3389/fmicb.2023.1261889] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Microbiome data predictive analysis within a machine learning (ML) workflow presents numerous domain-specific challenges involving preprocessing, feature selection, predictive modeling, performance estimation, model interpretation, and the extraction of biological information from the results. To assist decision-making, we offer a set of recommendations on algorithm selection, pipeline creation and evaluation, stemming from the COST Action ML4Microbiome. We compared the suggested approaches on a multi-cohort shotgun metagenomics dataset of colorectal cancer patients, focusing on their performance in disease diagnosis and biomarker discovery. It is demonstrated that the use of compositional transformations and filtering methods as part of data preprocessing does not always improve the predictive performance of a model. In contrast, the multivariate feature selection, such as the Statistically Equivalent Signatures algorithm, was effective in reducing the classification error. When validated on a separate test dataset, this algorithm in combination with random forest modeling, provided the most accurate performance estimates. Lastly, we showed how linear modeling by logistic regression coupled with visualization techniques such as Individual Conditional Expectation (ICE) plots can yield interpretable results and offer biological insights. These findings are significant for clinicians and non-experts alike in translational applications.
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Affiliation(s)
- Georgios Papoutsoglou
- Department of Computer Science, University of Crete, Heraklion, Greece
- JADBio Gnosis DA S.A., Science and Technology Park of Crete, Heraklion, Greece
| | - Sonia Tarazona
- Department of Applied Statistics and Operations Research and Quality, Polytechnic University of Valencia, Valencia, Spain
| | - Marta B. Lopes
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- Research and Development Unit for Mechanical and Industrial Engineering (UNIDEMI), Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, Portugal
| | - Thomas Klammsteiner
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Eliana Ibrahimi
- Department of Biology, University of Tirana, Tirana, Albania
| | - Julia Eckenberger
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Pierfrancesco Novielli
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- National Institute for Nuclear Physics, Bari Division, Bari, Italy
| | - Alberto Tonda
- UMR 518 MIA-PS, INRAE, Paris-Saclay University, Palaiseau, France
- Complex Systems Institute of Paris Ile-de-France (ISC-PIF) - UAR 3611 CNRS, Paris, France
| | - Andrea Simeon
- BioSense Institute, University of Novi Sad, Novi Sad, Serbia
| | - Rajesh Shigdel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Stéphane Béreux
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
- MaIAGE, INRAE, Paris-Saclay University, Jouy-en-Josas, France
| | - Giacomo Vitali
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
| | - Sabina Tangaro
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- National Institute for Nuclear Physics, Bari Division, Bari, Italy
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Andriy Temko
- Department of Electrical and Electronic Engineering, University College Cork, Cork, Ireland
| | - Marcus J. Claesson
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Magali Berland
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
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18
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Busi SB, Lei Z, Sumner LW, Amos-Landgraf JM. Integrated multi-omic analyses provide insight into colon adenoma susceptibility modulation by the gut microbiota. mSystems 2023; 8:e0015123. [PMID: 37458451 PMCID: PMC10469915 DOI: 10.1128/msystems.00151-23] [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: 02/10/2023] [Accepted: 06/06/2023] [Indexed: 09/01/2023] Open
Abstract
Colon cancer onset is strongly associated with the differences in microbial taxa in the gastrointestinal tract. Although recent studies highlight the role of individual taxa, the effect of a complex gut microbiome (GM) on the metabolome and host transcriptome is still unknown. We used a multi-omics approach to determine how differences in the GM affect the susceptibility to adenoma development in a rat model of human colon cancer. Ultra-high performance liquid chromatography mass spectrometry of feces collected prior to observable disease onset identified putative metabolite profiles that likely predict future disease severity. Transcriptome analyses performed after disease onset from normal colonic epithelium and tumor tissues show a correlation between GM and host gene expression. Integrated pathway analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis is enriched in rats with high tumors along with increased fatty acid metabolism and mucin biosynthesis. Targeted pyrosequencing of the Pirc allele indicates that the GM alters the mechanism of adenoma development and may drive an epigenetic pathway of tumor suppressor silencing. This study reveals how untargeted metabolomics identifies signatures of susceptibility and integrated analyses uncover pathways of differential mechanisms of loss of tumor suppressor gene function and for potential prevention and therapeutic intervention. IMPORTANCE The association between the gut microbiome and colon cancer is significant but difficult to test in model systems. This study highlights the association of differences in the pathogen-free gut microbiome to changes in the host transcriptome and metabolome that correlate with colon adenoma initiation and development in a rat genetic model of early colon cancer. The utilization of a multi-omics approach integrating metabolomics and transcriptomics reveals differences in pathways including bile acid biosynthesis and fatty acid metabolism. The study also shows that differences in gut microbiomes significantly alter the mechanism of adenoma formation, shifting from genetic changes to epigenetic changes that initiate the early loss of tumor suppressor function. These findings enhance our understanding of the gut microbiome's role in colon cancer susceptibility, offer insights into potential biomarkers and therapeutic targets, and may pave the way for future prevention and intervention strategies.
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Affiliation(s)
- Susheel Bhanu Busi
- University of Missouri School of Medicine, Columbia, Missouri, USA
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Zhentian Lei
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- University of Missouri Metabolomics Center, Columbia, Missouri, USA
| | - Lloyd W. Sumner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- University of Missouri Metabolomics Center, Columbia, Missouri, USA
| | - James M. Amos-Landgraf
- University of Missouri School of Medicine, Columbia, Missouri, USA
- University of Missouri College of Veterinary Medicine, Columbia, Missouri, USA
- Rat Resource and Research Center, University of Missouri, Columbia, Missouri, USA
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19
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Zhang L, Feng Z, Li Y, Lv C, Li C, Hu Y, Fu M, Song L. Salivary and fecal microbiota: potential new biomarkers for early screening of colorectal polyps. Front Microbiol 2023; 14:1182346. [PMID: 37655344 PMCID: PMC10467446 DOI: 10.3389/fmicb.2023.1182346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Objective Gut microbiota plays an important role in colorectal cancer (CRC) pathogenesis through microbes and their metabolites, while oral pathogens are the major components of CRC-associated microbes. Multiple studies have identified gut and fecal microbiome-derived biomarkers for precursors lesions of CRC detection. However, few studies have used salivary samples to predict colorectal polyps. Therefore, in order to find new noninvasive colorectal polyp biomarkers, we searched into the differences in fecal and salivary microbiota between patients with colorectal polyps and healthy controls. Methods In this case-control study, we collected salivary and fecal samples from 33 patients with colorectal polyps (CP) and 22 healthy controls (HC) between May 2021 and November 2022. All samples were sequenced using full-length 16S rRNA sequencing and compared with the Nucleotide Sequence Database. The salivary and fecal microbiota signature of colorectal polyps was established by alpha and beta diversity, Linear discriminant analysis Effect Size (LEfSe) and random forest model analysis. In addition, the possibility of microbiota in identifying colorectal polyps was assessed by Receiver Operating Characteristic Curve (ROC). Results In comparison to the HC group, the CP group's microbial diversity increased in saliva and decreased in feces (p < 0.05), but there was no significantly difference in microbiota richness (p > 0.05). The principal coordinate analysis revealed significant differences in β-diversity of salivary and fecal microbiota between the CP and HC groups. Moreover, LEfSe analysis at the species level identified Porphyromonas gingivalis, Fusobacterium nucleatum, Leptotrichia wadei, Prevotella intermedia, and Megasphaera micronuciformis as the major contributors to the salivary microbiota, and Ruminococcus gnavus, Bacteroides ovatus, Parabacteroides distasonis, Citrobacter freundii, and Clostridium symbiosum to the fecal microbiota of patients with polyps. Salivary and fecal bacterial biomarkers showed Area Under ROC Curve of 0.8167 and 0.8051, respectively, which determined the potential of diagnostic markers in distinguishing patients with colorectal polyps from controls, and it increased to 0.8217 when salivary and fecal biomarkers were combined. Conclusion The composition and diversity of the salivary and fecal microbiota were significantly different in colorectal polyp patients compared to healthy controls, with an increased abundance of harmful bacteria and a decreased abundance of beneficial bacteria. A promising non-invasive tool for the detection of colorectal polyps can be provided by potential biomarkers based on the microbiota of the saliva and feces.
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Affiliation(s)
- Limin Zhang
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Ziying Feng
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yinghua Li
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Cuiting Lv
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Chunchun Li
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yue Hu
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Mingsheng Fu
- Department of Gastroenterology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Liang Song
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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20
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Huang X, Xie M, Lu X, Mei F, Song W, Liu Y, Chen L. The Roles of Periodontal Bacteria in Atherosclerosis. Int J Mol Sci 2023; 24:12861. [PMID: 37629042 PMCID: PMC10454115 DOI: 10.3390/ijms241612861] [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: 05/31/2023] [Revised: 08/05/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Atherosclerosis (AS) is an inflammatory vascular disease that constitutes a major underlying cause of cardiovascular diseases (CVD) and stroke. Infection is a contributing risk factor for AS. Epidemiological evidence has implicated individuals afflicted by periodontitis displaying an increased susceptibility to AS and CVD. This review concisely outlines several prevalent periodontal pathogens identified within atherosclerotic plaques, including Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Fusobacterium nucleatum. We review the existing epidemiological evidence elucidating the association between these pathogens and AS-related diseases, and the diverse mechanisms for which these pathogens may engage in AS, such as endothelial barrier disruption, immune system activation, facilitation of monocyte adhesion and aggregation, and promotion of foam cell formation, all of which contribute to the progression and destabilization of atherosclerotic plaques. Notably, the intricate interplay among bacteria underscores the complex impact of periodontitis on AS. In conclusion, advancing our understanding of the relationship between periodontal pathogens and AS will undoubtedly offer invaluable insights and potential therapeutic avenues for the prevention and management of AS.
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Affiliation(s)
- Xiaofei Huang
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (X.H.); (M.X.); (X.L.); (F.M.); (W.S.)
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
| | - Mengru Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (X.H.); (M.X.); (X.L.); (F.M.); (W.S.)
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
| | - Xiaofeng Lu
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (X.H.); (M.X.); (X.L.); (F.M.); (W.S.)
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
| | - Feng Mei
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (X.H.); (M.X.); (X.L.); (F.M.); (W.S.)
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
| | - Wencheng Song
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (X.H.); (M.X.); (X.L.); (F.M.); (W.S.)
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
| | - Yang Liu
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (X.H.); (M.X.); (X.L.); (F.M.); (W.S.)
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (X.H.); (M.X.); (X.L.); (F.M.); (W.S.)
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
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21
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Pani G. Fusobacterium & Co. at the Stem of Cancer: Microbe-Cancer Stem Cell Interactions in Colorectal Carcinogenesis. Cancers (Basel) 2023; 15:cancers15092583. [PMID: 37174049 PMCID: PMC10177588 DOI: 10.3390/cancers15092583] [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: 04/12/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Adult stem cells lie at the crossroads of tissue repair, inflammation, and malignancy. Intestinal microbiota and microbe-host interactions are pivotal to maintaining gut homeostasis and response to injury, and participate in colorectal carcinogenesis. Yet, limited knowledge is available on whether and how bacteria directly crosstalk with intestinal stem cells (ISC), particularly cancerous stem-like cells (CR-CSC), as engines for colorectal cancer initiation, maintenance, and metastatic dissemination. Among several bacterial species alleged to initiate or promote colorectal cancer (CRC), the pathobiont Fusobacterium Nucleatum has recently drawn significant attention for its epidemiologic association and mechanistic linkage with the disease. We will therefore focus on current evidence for an F. nucleatum-CRCSC axis in tumor development, highlighting the commonalities and differences between F. nucleatum-associated colorectal carcinogenesis and gastric cancer driven by Helicobacter Pylori. We will explore the diverse facets of the bacteria-CSC interaction, analyzing the signals and pathways whereby bacteria either confer "stemness" properties to tumor cells or primarily target stem-like elements within the heterogeneous tumor cell populations. We will also discuss the extent to which CR-CSC cells are competent for innate immune responses and participate in establishing a tumor-promoting microenvironment. Finally, by capitalizing on the expanding knowledge of how the microbiota and ISC crosstalk in intestinal homeostasis and response to injury, we will speculate on the possibility that CRC arises as an aberrant repair response promoted by pathogenic bacteria upon direct stimulation of intestinal stem cells.
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Affiliation(s)
- Giovambattista Pani
- Department of Translational Medicine and Surgery, Section of General Pathology, Faculty of Medicine, Università Cattolica del Sacro Cuore, Largo Francesco Vito, 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, L. go A. Gemelli 8, 00168 Rome, Italy
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22
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Microbial dynamics with CRC progression: a study of the mucosal microbiota at multiple sites in cancers, adenomatous polyps, and healthy controls. Eur J Clin Microbiol Infect Dis 2023; 42:305-322. [PMID: 36703031 PMCID: PMC9899194 DOI: 10.1007/s10096-023-04551-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023]
Abstract
Accumulating evidence has related the gut microbiota to colorectal cancer (CRC). Fusobacterium nucleatum has repeatedly been linked to colorectal tumorigenesis. The aim of this study was to investigate microbial composition in different sampling sites, in order to profile the microbial dynamics with CRC progression. Further, we characterized the tumor-associated F. nucleatum subspecies. Here, we conducted Illumina Miseq next-generation sequencing of the 16S rRNA V4 region in biopsy samples, to investigate microbiota alterations in cancer patients, patients with adenomatous polyp, and healthy controls in Norway. Further, Fusobacterium positive tumor biopsies were subjected to MinION nanopore sequencing of Fusobacterium-specific amplicons to characterize the Fusobacterium species and subspecies. We found enrichment of oral biofilm-associated bacteria, Fusobacterium, Gemella, Parvimonas, Granulicatella, Leptotrichia, Peptostreptococcus, Campylobacter, Selenomonas, Porphyromonas, and Prevotella in cancer patients compared to adenomatous polyp patients and control patients. Higher abundance of amplicon sequence variants (ASVs) classified as Phascolarctobacterium, Bacteroides vulgatus, Bacteroides plebeius, Bacteroides eggerthii, Tyzzerella, Desulfovibrio, Frisingicoccus, Eubacterium coprostanoligenes group, and Lachnospiraceae were identified in cancer and adenomatous polyp patients compared to healthy controls. F. nucleatum ssp. animalis was the dominating subspecies. F. nucleatum ssp. nucleatum, F. nucleatum ssp. vincentii, Fusobacterium pseudoperiodonticum, Fusobacterium necrophorum, and Fusobacterium gonidiaformans were identified in five samples. Several biofilm-associated bacteria were enriched at multiple sites in cancer patients. Another group of bacteria was enriched in both cancer and polyps, suggesting that they may have a role in polyp development and possibly early stages of CRC.
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23
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Rahman G, Morton JT, Martino C, Sepich-Poore GD, Allaband C, Guccione C, Chen Y, Hakim D, Estaki M, Knight R. BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526328. [PMID: 36778470 PMCID: PMC9915500 DOI: 10.1101/2023.01.30.526328] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Quantifying the differential abundance (DA) of specific taxa among experimental groups in microbiome studies is challenging due to data characteristics (e.g., compositionality, sparsity) and specific study designs (e.g., repeated measures, meta-analysis, cross-over). Here we present BIRDMAn (Bayesian Inferential Regression for Differential Microbiome Analysis), a flexible DA method that can account for microbiome data characteristics and diverse experimental designs. Simulations show that BIRDMAn models are robust to uneven sequencing depth and provide a >20-fold improvement in statistical power over existing methods. We then use BIRDMAn to identify antibiotic-mediated perturbations undetected by other DA methods due to subject-level heterogeneity. Finally, we demonstrate how BIRDMAn can construct state-of-the-art cancer-type classifiers using The Cancer Genome Atlas (TCGA) dataset, with substantial accuracy improvements over random forests and existing DA tools across multiple sequencing centers. Collectively, BIRDMAn extracts more informative biological signals while accounting for study-specific experimental conditions than existing approaches.
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Affiliation(s)
- Gibraan Rahman
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - James T Morton
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Celeste Allaband
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Yang Chen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Dermatology, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA
| | - Daniel Hakim
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Mehrbod Estaki
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Rob Knight
- 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, California, USA
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Therapeutic Target Identification and Inhibitor Screening against Riboflavin Synthase of Colorectal Cancer Associated Fusobacterium nucleatum. Cancers (Basel) 2022; 14:cancers14246260. [PMID: 36551744 PMCID: PMC9777469 DOI: 10.3390/cancers14246260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Colorectal cancer (CRC) ranks third among all cancers in terms of prevalence. There is growing evidence that gut microbiota has a role in the development of colorectal cancer. Fusobacterium nucleatum is overrepresented in the gastrointestinal tract and tumor microenvironment of patients with CRC. This suggests the role of F. nucleatum as a potential risk factor in the development of CRC. Hence, we aimed to explore whole genomes of F. nucleatum strains related to CRC to predict potential therapeutic markers through a pan-genome integrated subtractive genomics approach. In the current study, we identified 538 proteins as essential for F. nucleatum survival, 209 non-homologous to a human host, and 12 as drug targets. Eventually, riboflavin synthase (RiS) was selected as a therapeutic target for further processing. Three different inhibitor libraries of lead-like natural products, i.e., cyanobactins (n = 237), streptomycins (n = 607), and marine bacterial secondary metabolites (n = 1226) were screened against it. After the structure-based study, three compounds, i.e., CMNPD3609 (−7.63) > Malyngamide V (−7.03) > ZINC06804365 (−7.01) were prioritized as potential inhibitors of F. nucleatum. Additionally, the stability and flexibility of these compounds bound to RiS were determined via a molecular dynamics simulation of 50 ns. Results revealed the stability of these compounds within the binding pocket, after 5 ns. ADMET profiling showed compounds as drug-like, non-permeable to the blood brain barrier, non-toxic, and HIA permeable. Pan-genomics mediated drug target identification and the virtual screening of inhibitors is the preliminary step towards inhibition of this pathogenic oncobacterium and we suggest mouse model experiments to validate our findings.
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