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Teixeira M, Silva F, Ferreira RM, Pereira T, Figueiredo C, Oliveira HP. A review of machine learning methods for cancer characterization from microbiome data. NPJ Precis Oncol 2024; 8:123. [PMID: 38816569 PMCID: PMC11139966 DOI: 10.1038/s41698-024-00617-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Recent studies have shown that the microbiome can impact cancer development, progression, and response to therapies suggesting microbiome-based approaches for cancer characterization. As cancer-related signatures are complex and implicate many taxa, their discovery often requires Machine Learning approaches. This review discusses Machine Learning methods for cancer characterization from microbiome data. It focuses on the implications of choices undertaken during sample collection, feature selection and pre-processing. It also discusses ML model selection, guiding how to choose an ML model, and model validation. Finally, it enumerates current limitations and how these may be surpassed. Proposed methods, often based on Random Forests, show promising results, however insufficient for widespread clinical usage. Studies often report conflicting results mainly due to ML models with poor generalizability. We expect that evaluating models with expanded, hold-out datasets, removing technical artifacts, exploring representations of the microbiome other than taxonomical profiles, leveraging advances in deep learning, and developing ML models better adapted to the characteristics of microbiome data will improve the performance and generalizability of models and enable their usage in the clinic.
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Affiliation(s)
- Marco Teixeira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal.
- Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Francisco Silva
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
| | - Rui M Ferreira
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Tania Pereira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Ceu Figueiredo
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Hélder P Oliveira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
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Chen H, Ma Y, Xu J, Wang W, Lu H, Quan C, Yang F, Lu Y, Wu H, Qiu M. Circulating microbiome DNA as biomarkers for early diagnosis and recurrence of lung cancer. Cell Rep Med 2024; 5:101499. [PMID: 38582085 PMCID: PMC11031421 DOI: 10.1016/j.xcrm.2024.101499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/19/2023] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
Lung cancer mortality is exacerbated by late-stage diagnosis. Emerging evidence indicates the potential clinical significance of distinct microbial signatures as diagnostic and prognostic biomarkers across various cancers. However, circulating microbiome DNA (cmDNA) profiles are underexplored in lung cancer (LC). Here, whole-genome sequencing is performed on plasma of LC patients and healthy controls (HCs). Differentially enriched microbial species are identified between LC and HC. A diagnostic model is developed, which has a high sensitivity of 87.7% and achieves an AUC of 93.2% in the independent validation dataset. Crucially, this model demonstrates the capability to detect early-stage LC, achieving a sensitivity of 86.5% for stage I and 87.1% for tumors <1 cm. In addition, we construct a cmDNA model for recurrence, which precisely predicts LC recurrence after surgery. Overall, this study highlights the significant alterations of cmDNA profiles in LC, indicating its potential as biomarkers for early diagnosis and recurrence.
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Affiliation(s)
- Haiming Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Yi Ma
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Juqing Xu
- Department of Hematology and Oncology, Geriatric Hospital of Nanjing Medical University, Nanjing 210009, China
| | - Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Hao Lu
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China
| | - Cheng Quan
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Yiming Lu
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China.
| | - Hao Wu
- Department of Thoracic Surgery, Shenzhen Second People's Hospital, Shenzhen 518035, China.
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China.
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3
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Ma Y, Chen H, Li H, Zheng M, Zuo X, Wang W, Wang S, Lu Y, Wang J, Li Y, Wang J, Qiu M. Intratumor microbiome-derived butyrate promotes lung cancer metastasis. Cell Rep Med 2024; 5:101488. [PMID: 38565146 PMCID: PMC11031379 DOI: 10.1016/j.xcrm.2024.101488] [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: 05/18/2022] [Revised: 12/01/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Most recurrences of lung cancer (LC) occur within 3 years after surgery, but the underlying mechanism remains unclear. Here, we collect LC tissues with shorter (<3 years, recurrence group) and longer (>3 years, non-recurrence group) recurrence-free survival. By using 16S sequencing, we find that intratumor microbiome diversity is lower in the recurrence group and butyrate-producing bacteria are enriched in the recurrence group. The intratumor microbiome signature and circulating microbiome DNA can accurately predict LC recurrence. We prove that intratumor injection of butyrate-producing bacteria Roseburia can promote subcutaneous tumor growth. Mechanistically, bacteria-derived butyrate promotes LC metastasis by increasing expression of H19 in tumor cells through inhibiting HDAC2 and increasing H3K27 acetylation at the H19 promoter and inducing M2 macrophage polarization. Depletion of macrophages partially abolishes the metastasis-promoting effect of butyrate. Our results provide evidence for the cross-talk between the intratumor microbiome and LC metastasis and suggest the potential prognostic and therapeutic value of the intratumor microbiome.
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Affiliation(s)
- Yi Ma
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Shanghai 200433, China
| | - Haiming Chen
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Haoran Li
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Meiling Zheng
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100010, China; Department of Chinese Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Xianglin Zuo
- Department of Science & Technology, Biobank of Jiangsu Cancer Hospital, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China
| | - Wenxiang Wang
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Shaodong Wang
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
| | - Yiming Lu
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Li
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China.
| | - Jie Wang
- Department of Science & Technology, Biobank of Jiangsu Cancer Hospital, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China.
| | - Mantang Qiu
- Department of Thoracic Surgery, Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China.
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Liu W, Pi Z, Wang X, Shang C, Song C, Wang R, He Z, Zhang X, Wan Y, Mao W. Microbiome and lung cancer: carcinogenic mechanisms, early cancer diagnosis, and promising microbial therapies. Crit Rev Oncol Hematol 2024; 196:104322. [PMID: 38460928 DOI: 10.1016/j.critrevonc.2024.104322] [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: 09/26/2023] [Revised: 02/13/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
Microbiomes in the lung, gut, and oral cavity are correlated with lung cancer initiation and progression. While correlations have been preliminarily established in earlier studies, delving into microbe-mediated carcinogenic mechanisms will extend our understanding from correlation to causation. Building upon the causative relationships between microbiome and lung cancer, a novel concept of microbial biomarkers has emerged, mainly encompassing cancer-specific bacteria and circulating microbiome DNA. They might function as noninvasive liquid biopsy techniques for lung cancer early detection. Furthermore, potential microbial therapies have displayed initial efficacy in lung cancer treatment, providing multiple avenues for therapeutic intervention. Herein, we will discuss the molecular mechanisms and signaling pathways through which microbes influence lung cancer initiation and development. Additionally, we will summarize recent findings on microbial biomarkers as a member of tumor liquid biopsy techniques and provide an overview of the latest advances in various microbe-assisted/mediated therapeutic approaches for lung cancer.
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Affiliation(s)
- Weici Liu
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Zheshun Pi
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Xiaokun Wang
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Chenwei Shang
- The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Chenghu Song
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Ruixin Wang
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Zhao He
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Xu Zhang
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China.
| | - Yuan Wan
- The Pq Laboratory of Biome Dx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton 13850, USA.
| | - Wenjun Mao
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu 214023, China.
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Liu Y, Kim ES, Guo H. Hepatitis B virus-related hepatocellular carcinoma exhibits distinct intratumoral microbiota and immune microenvironment signatures. J Med Virol 2024; 96:e29485. [PMID: 38377167 PMCID: PMC10916714 DOI: 10.1002/jmv.29485] [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] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/22/2024]
Abstract
Emerging evidence supports a high prevalence of cancer type-specific microbiota residing within tumor tissues. The intratumoral microbiome in hepatocellular carcinoma (HCC), especially in viral (hepatitis B virus [HBV]/hepatitis C virus [HCV]) HCC, has not been well characterized for their existence, composition, distribution, and biological functions. We report herein a finding of specific microbial signature in viral HCC as compared to non-HBV/non-HCV (NBNC) HCC. However, the significantly diverse tumor microbiome was only observed in HBV-related HCC, and Cutibacterium was identified as the representative taxa biomarker. Biological function of the unique tumor microbiota in modulating tumor microenvironment (TME) was characterized by using formalin-fixed paraffin-embedded (FFPE) tissue-based multiplex immunofluorescence histochemistry (mIFH) allowing simultaneous in situ detection of the liver cancer cells surrounded with high/low density of microbiota, and the infiltrating immune cells. In HBV_HCC, the intratumoral microbiota are positively associated with increased tumor-infiltrating CD8+ T lymphocytes, but not the CD56+ NK cells. Two subtypes of myeloid-derived suppressor cells (MDSCs): monocytic MDSCs and polymorphonuclear MDSCs, were also found to be positively correlated with the intratumoral microbiota in HBV_HCC, indicating an inhibitory role of these microbial species in antitumor immunity and the contribution to the liver TME in combination of chronic viral hepatitis during HCC development.
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Affiliation(s)
- Yuanjie Liu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine
- Cancer Microbiome Facility, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine
| | - Elena S. Kim
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine
| | - Haitao Guo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine
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Kim G, Park C, Yoon YK, Park D, Lee JE, Lee D, Sun P, Park S, Yun C, Kang DH, Chung C. Prediction of lung cancer using novel biomarkers based on microbiome profiling of bronchoalveolar lavage fluid. Sci Rep 2024; 14:1691. [PMID: 38242941 PMCID: PMC10799071 DOI: 10.1038/s41598-024-52296-w] [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: 05/11/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Abstract
There is an unmet need for biomarkers for the diagnosis of lung cancer and decision criteria for lung biopsy. We comparatively investigated the lung microbiomes of patients with lung cancer and benign lung diseases. Patients who underwent bronchoscopy at Chungnam National University Hospital between June 2021 and June 2022 were enrolled. Bronchoalveolar lavage fluid (BALF) was collected from 24 patients each with lung cancer and benign lung diseases. The samples were analyzed using 16S rRNA-based metagenomic sequencing. We found that alpha diversity and the beta diversity distribution (P = 0.001) differed significantly between patients with benign lung diseases and those with lung cancer. Firmicutes was the most abundant phylum in patients with lung cancer (33.39% ± 17.439), whereas Bacteroidota was the most abundant phylum in patients with benign lung disease (31.132% ± 22.505), respectively. In differential abundance analysis, the most differentially abundant microbiota taxon was unclassified_SAR202_clade, belonging to the phylum Chloroflexi. The established prediction model distinguished patients with benign lung disease from those with lung cancer with a high accuracy (micro area under the curve [AUC] = 0.98 and macro AUC = 0.99). The BALF microbiome may be a novel biomarker for the detection of lung cancer.
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Affiliation(s)
- Gihyeon Kim
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Changho Park
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | | | - Dongil Park
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Jeong Eun Lee
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Dahye Lee
- Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Pureum Sun
- Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Shinyoung Park
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Changhee Yun
- Genome and Company, Pangyo-ro 255, Bundang-gu, Seongnam, Korea
| | - Da Hyun Kang
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon, Korea.
| | - Chaeuk Chung
- Department of Internal Medicine, College of Medicine, Chungnam National University, Daejeon, Korea.
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Souza VGP, Forder A, Pewarchuk ME, Telkar N, de Araujo RP, Stewart GL, Vieira J, Reis PP, Lam WL. The Complex Role of the Microbiome in Non-Small Cell Lung Cancer Development and Progression. Cells 2023; 12:2801. [PMID: 38132121 PMCID: PMC10741843 DOI: 10.3390/cells12242801] [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: 11/01/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
In recent years, there has been a growing interest in the relationship between microorganisms in the surrounding environment and cancer cells. While the tumor microenvironment predominantly comprises cancer cells, stromal cells, and immune cells, emerging research highlights the significant contributions of microbial cells to tumor development and progression. Although the impact of the gut microbiome on treatment response in lung cancer is well established, recent investigations indicate complex roles of lung microbiota in lung cancer. This article focuses on recent findings on the human lung microbiome and its impacts in cancer development and progression. We delve into the characteristics of the lung microbiome and its influence on lung cancer development. Additionally, we explore the characteristics of the intratumoral microbiome, the metabolic interactions between lung tumor cells, and how microorganism-produced metabolites can contribute to cancer progression. Furthermore, we provide a comprehensive review of the current literature on the lung microbiome and its implications for the metastatic potential of tumor cells. Additionally, this review discusses the potential for therapeutic modulation of the microbiome to establish lung cancer prevention strategies and optimize lung cancer treatment.
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Affiliation(s)
- Vanessa G. P. Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | | | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rachel Paes de Araujo
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
| | - Greg L. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Juliana Vieira
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Patricia P. Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Wan L. Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
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Kim BG, Kang N, Kim SY, Kim DH, Kim H, Kwon OJ, Huh HJ, Lee NY, Jhun BW. The lung microbiota in nontuberculous mycobacterial pulmonary disease. PLoS One 2023; 18:e0285143. [PMID: 37235629 DOI: 10.1371/journal.pone.0285143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The role of bacterial microbiota in the pathogenesis of nontuberculous mycobacterial pulmonary disease (NTM-PD) is unclear. We aimed to compare the bacterial microbiome of disease-invaded lesions and non-invaded lung tissue from NTM-PD patients. METHODS We analyzed lung tissues from 23 NTM-PD patients who underwent surgical lung resection. Lung tissues were collected in pairs from each patient, with one sample from a disease-involved site and the other from a non-involved site. Lung tissue microbiome libraries were constructed using 16S rRNA gene sequences (V3-V4 regions). RESULTS Sixteen (70%) patients had Mycobacterium avium complex (MAC)-PD, and the remaining seven (30%) had Mycobacterium abscessus-PD. Compared to non-involved sites, involved sites showed greater species richness (ACE, Chao1, and Jackknife analyses, all p = 0.001); greater diversity on the Shannon index (p = 0.007); and genus-level differences (Jensen-Shannon, PERMANOVA p = 0.001). Analysis of taxonomic biomarkers using linear discriminant analysis (LDA) effect sizes (LEfSe) demonstrated that several genera, including Limnohabitans, Rahnella, Lachnospira, Flavobacterium, Megamonas, Gaiella, Subdoligranulum, Rheinheimera, Dorea, Collinsella, and Phascolarctobacterium, had significantly greater abundance in involved sites (LDA >3.00, p <0.05, and q <0.05). In contrast, Acinetobacter had significantly greater abundance at non-involved sites (LDA = 4.27, p<0.001, and q = 0.002). Several genera were differentially distributed between lung tissues from MAC-PD (n = 16) and M. abscessus-PD (n = 7), and between nodular bronchiectatic form (n = 12) and fibrocavitary form (n = 11) patients. However, there was no genus with a significant q-value. CONCLUSIONS We identified differential microbial distributions between disease-invaded and normal lung tissues from NTM-PD patients, and microbial diversity was significantly higher in disease-invaded tissues. TRIAL REGISTRATION Clinical Trial registration number: NCT00970801.
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Affiliation(s)
- Bo-Guen Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Noeul Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Dae Hun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - O Jung Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Huang J, Huang J. Microbial Biomarkers for Lung Cancer: Current Understandings and Limitations. J Clin Med 2022; 11:jcm11247298. [PMID: 36555915 PMCID: PMC9782454 DOI: 10.3390/jcm11247298] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
As our "hidden organ", microbes widely co-exist at various sites on the human body. These microbes are collectively referred to as the microbiome. A considerable number of studies have already proven that the microbiome has significant impacts on human health and disease progression, including cancers. The recent discovery of cancer-specific microbiomes renders these cancer-associated microbes as potential biomarkers and therapeutic targets. While at low biomass levels, the lung microbiome still dramatically influences the initiation, progression and treatment of lung cancers. However, research on lung cancer-associated microbiomes is emerging, and most profiling studies are performed within three years. Unfortunately, there are substantial inconsistencies across these studies. Variations in microbial diversity were observed, and different microbial biomarkers for lung cancer have been proposed. In this review, we summarized the current findings of lung cancer microbiome studies and attempt to explain the potential reasons for the dissimilarities. Other than lung microbiomes, oral and airway microbiomes are highly related to lung microbiomes and are therefore included as well. In addition, several lung cancer-associated bacterial genera have been detected by different independent studies. These bacterial genera may not be perfect biomarkers, but they still serve as promising risk factors for lung cancers and show great prognostic value.
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Affiliation(s)
| | - Juan Huang
- Correspondence: ; Tel.: +86-181-0818-9376
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Wu Z, Tang J, Zhuang R, Meng D, Zhang L, Gu C, Teng X, Zhu Z, Liu J, Pang J, Hu J, Lv X. The microbiome of lower respiratory tract and tumor tissue in lung cancer manifested as radiological ground-glass opacity. Front Bioeng Biotechnol 2022; 10:892613. [PMID: 36091439 PMCID: PMC9455596 DOI: 10.3389/fbioe.2022.892613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Recent studies have confirmed the existence of microbiota in the lungs. The relationship between lung ground-glass opacity (GGO) and microbiota in the lung microenvironment is not clear. In this study, we investigated the microbial composition and diversity in bronchoalveolar lavage fluid (BALF) of diseased lung segments and paired contralateral healthy lung segments from 11 GGO patients. Furthermore, lung GGO and paired normal tissues of 26 GGO patients were explored whether there are microbial characteristics related to GGO. Compared with the control group, the community richness of GGO tissue and BALF of GGO lung segment (α-diversity) and overall microbiome difference (β-diversity) had no significant difference. The microbiome composition of BALF of GGO segments is distinct from that of paired healthy lung segments [genus (Rothia), order (Lachnospiraceae), family (Lachnospiraceae), genus (Lachnospiraceae_NK4A136_group, Faecalibacterium), and species (Faecalibacterium prausnitzii, Bacteroides uniforms)]. GGO tissue and adjacent lung tissue had more significant differences at the levels of class, order, family, genus, and species level, and most of them are enriched in normal lung tissue. The area under the curve (AUC) using 10 genera-based biomarkers to predict GGO was 91.05% (95% CI: 81.93–100%). In conclusion, this study demonstrates there are significant differences in the lower respiratory tract and lung microbiome between GGO and the non-malignant control group through the BALF and lung tissues. Furthermore, some potential bacterial biomarkers showed good performance to predict GGO.
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Affiliation(s)
- Zhigang Wu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jie Tang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Runzhou Zhuang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Di Meng
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lichen Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Gu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Teng
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ziyue Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiacong Liu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jinghua Pang
- Department of Thoracic Surgery, Fenghua People’s Hospital, Ningbo, China
| | - Jian Hu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jian Hu, ; Xiayi Lv,
| | - Xiayi Lv
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jian Hu, ; Xiayi Lv,
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Klein M, Pragman AA, Wendt C. Biomarkers and the microbiome in the detection and treatment of early-stage non-small cell lung cancer. Semin Oncol 2022; 49:S0093-7754(22)00051-3. [PMID: 35914981 DOI: 10.1053/j.seminoncol.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/22/2022] [Accepted: 06/26/2022] [Indexed: 11/11/2022]
Abstract
Lung cancer is one of the most common and deadly cancers in the world. However, over the last several years, research into lung cancer screening and novel therapeutic approaches have provided promise that earlier detection combined with new treatment strategies may result in significantly improved outcomes. Biomarkers will most certainly play a major role in identifying those who may benefit from, and how to apply, these new treatment strategies. Here we discuss potential biomarkers, including the microbiome, in both detection and treatment strategies for early stage lung cancer.
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Affiliation(s)
- Mark Klein
- Hematology/Oncology Section, Primary Care Service Line, Minneapolis VA Health Care System, Minneapolis, Minnesota; Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota.
| | - Alexa A Pragman
- Infectious Disease Section, Primary Care Service Line, Minneapolis VA Health Care System, Minneapolis, Minnesota; Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Christine Wendt
- Pulmonary, Allergy, Critical Care and Sleep Medicine Section, Primary Care Service Line, Minneapolis VA Health Care System, Minneapolis, Minnesota; Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
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