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Szóstak N, Handschuh L, Samelak-Czajka A, Tomela K, Pietrzak B, Schmidt M, Galus Ł, Mackiewicz J, Mackiewicz A, Kozlowski P, Philips A. Gut Mycobiota Dysbiosis Is Associated with Melanoma and Response to Anti-PD-1 Therapy. Cancer Immunol Res 2024; 12:427-439. [PMID: 38315788 PMCID: PMC10985481 DOI: 10.1158/2326-6066.cir-23-0592] [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: 07/21/2023] [Revised: 11/15/2023] [Accepted: 01/31/2024] [Indexed: 02/07/2024]
Abstract
Recent research indicates that gut microbiota may be vital in the advancement of melanoma. In this study, we found that melanoma patients exhibited a distinct gut mycobiota structure compared with healthy participants. Candida albicans, Candida dubliniensis, and Neurospora crassa were more abundant in samples from patients with melanoma, whereas Saccharomyces cerevisiae and Debaryomyces hansenii were less abundant. During anti-PD-1 treatment, the relative amount of Malassezia restricta and C. albicans increased. A higher level of Saccharomyces paradoxus was associated with a positive response to anti-PD-1 treatment, whereas a higher level of Tetrapisispora blattae was associated with a lack of clinical benefits. High levels of M. restricta and C. albicans, elevated serum lactate dehydrogenase, and being overweight were linked to increased risk of melanoma progression and poorer response to anti-PD-1 treatment. Thus, this study has revealed melanoma-associated mycobiome dysbiosis, characterized by altered fungal composition and fungi species associated with a higher risk of melanoma progression, identifying a role for the gut mycobiome in melanoma progression.
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Affiliation(s)
- Natalia Szóstak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Tomela
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Chair of Medical Biotechnology, Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Bernadeta Pietrzak
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Marcin Schmidt
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Łukasz Galus
- Department of Medical and Experimental Oncology, Institute of Oncology, Poznan University of Medical Sciences, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Institute of Oncology, Poznan University of Medical Sciences, Poland
| | - Andrzej Mackiewicz
- Chair of Medical Biotechnology, Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Garvey M. Intestinal Dysbiosis: Microbial Imbalance Impacts on Colorectal Cancer Initiation, Progression and Disease Mitigation. Biomedicines 2024; 12:740. [PMID: 38672096 PMCID: PMC11048178 DOI: 10.3390/biomedicines12040740] [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: 03/08/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
The human gastrointestinal tract houses a diverse range of microbial species that play an integral part in many biological functions. Several preclinical studies using germ-free mice models have demonstrated that the gut microbiome profoundly influences carcinogenesis and progression. Colorectal cancer appears to be associated with microbial dysbiosis involving certain bacterial species, including F. nucleatum, pks+ E. coli, and B. fragilis, with virome commensals also disrupted in patients. A dysbiosis toward these pro-carcinogenic species increases significantly in CRC patients, with reduced numbers of the preventative species Clostridium butyicum, Roseburia, and Bifidobacterium evident. There is also a correlation between Clostridium infection and CRC. F. nucleatum, in particular, is strongly associated with CRC where it is associated with therapeutic resistance and poor outcomes in patients. The carcinogenic mode of action of pathogenic bacteria in CRC is a result of genotoxicity, epigenetic alterations, ROS generation, and pro-inflammatory activity. The aim of this review is to discuss the microbial species and their impact on colorectal cancer in terms of disease initiation, progression, and metastasis. The potential of anticancer peptides as anticancer agents or adjuvants is also discussed, as novel treatment options are required to combat the high levels of resistance to current pharmaceutical options.
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Affiliation(s)
- Mary Garvey
- Department of Life Science, Atlantic Technological University, F91 YW50 Sligo, Ireland;
- Centre for Precision Engineering, Materials and Manufacturing Research (PEM), Atlantic Technological University, F91 YW50 Sligo, Ireland
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Roy S, Ray D, Laha I, Choudhury L. Human Mycobiota and Its Role in Cancer Progression, Diagnostics and Therapeutics: A Link Lesser-Known. Cancer Invest 2024; 42:44-62. [PMID: 38186047 DOI: 10.1080/07357907.2024.2301733] [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: 03/16/2023] [Accepted: 01/01/2024] [Indexed: 01/09/2024]
Abstract
Although not as well studied as the bacterial component of the human microbiota, the commensal fungi or mycobiota play important roles in maintaining our health by augmenting our immune system. This mycobiota is also associated with various fatal diseases like opportunistic mycoses, and even cancer, with different cancers having respective type-specific mycobiota. The different fungal species which comprise these different intratumoral mycobiota play important roles in cancer progression. The aim of this review paper is to decipher the association between mycobiota and cancer, and shed light on new avenues in cancer diagnosis, and the development of new anti-cancer therapeutics.
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Affiliation(s)
- Souvik Roy
- Post-Graduate & Research Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, India
| | - Dhrisaj Ray
- 5th Year Integrated M. Sc. (5 year integrated) students, Post-Graduate & Research Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, India
| | - Ishani Laha
- 5th Year Integrated M. Sc. (5 year integrated) students, Post-Graduate & Research Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, India
| | - Lopamudra Choudhury
- State-Aided College Teacher, Department of Microbiology, Sarsuna College (Affiliated to Calcutta University), Kolkata, India
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Thavamani A, Sankararaman S, Al-Shakhshir H, Retuerto M, Velayuthan S, Sferra TJ, Ghannoum M. Impact of Erythromycin as a Prokinetic on the Gut Microbiome in Children with Feeding Intolerance-A Pilot Study. Antibiotics (Basel) 2023; 12:1606. [PMID: 37998808 PMCID: PMC10668753 DOI: 10.3390/antibiotics12111606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Studies have demonstrated that the gut microbiome changes upon exposure to systemic antibiotics. There is a paucity of literature regarding impact on the gut microbiome by long-term usage of erythromycin ethyl succinate (EES) when utilized as a prokinetic. METHODS Stool samples from pediatric patients with feeding intolerance who received EES (N = 8) as a prokinetic were analyzed for both bacteriome and mycobiome. Age-matched children with similar clinical characteristics but without EES therapy were included as controls (N = 20). RESULTS In both groups, Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant bacterial phyla. Ascomycota was the most abundant fungal phyla, followed by Basidiomycota. There were no significant differences in richness between the groups for both bacterial and fungal microbiome. Alpha diversity (at genus and species levels) and beta diversity (at the genus level) were not significantly different between the groups for both bacterial and fungal microbiome. At the species level, there was a significant difference between the groups for fungal microbiota, with a p-value of 0.029. We also noted that many fungal microorganisms had significantly higher p-values in the EES group than controls at both genera and species levels. CONCLUSIONS In this observational case-control study, the prokinetic use of EES was associated with changes in beta diversity between the groups for mycobiome at the species level. Many fungal microorganisms were significantly higher in the EES group when compared to the controls. Confirmation of these results in larger trials will provide further evidence regarding the impact of EES on gut microbiota when utilized as a prokinetic agent.
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Affiliation(s)
- Aravind Thavamani
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, UH Rainbow Babies and Children’s Hospital, Cleveland, OH 44106, USA; (A.T.); (S.V.); (T.J.S.)
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Senthilkumar Sankararaman
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, UH Rainbow Babies and Children’s Hospital, Cleveland, OH 44106, USA; (A.T.); (S.V.); (T.J.S.)
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Hilmi Al-Shakhshir
- Department of Radiology and Imaging Sciences, Emory School of Medicine, Atlanta, GA 30307, USA;
- Department of Radiology and Imaging Sciences Atlanta VA Medical Center, Decatur, GA 30033, USA
| | - Mauricio Retuerto
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (M.R.); (M.G.)
| | - Sujithra Velayuthan
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, UH Rainbow Babies and Children’s Hospital, Cleveland, OH 44106, USA; (A.T.); (S.V.); (T.J.S.)
- Division of Pediatric Neurogastroenterology and Motility, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Thomas J. Sferra
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, UH Rainbow Babies and Children’s Hospital, Cleveland, OH 44106, USA; (A.T.); (S.V.); (T.J.S.)
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mahmoud Ghannoum
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (M.R.); (M.G.)
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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Abstract
The microbiome may impact cancer development, progression and treatment responsiveness, but its fungal components remain insufficiently studied in this context. In this review, we highlight accumulating evidence suggesting a possible involvement of commensal and pathogenic fungi in modulation of cancer-related processes. We discuss the mechanisms by which fungi can influence tumour biology, locally by activity exerted within the tumour microenvironment, or remotely through secretion of bioactive metabolites, modulation of host immunity and communications with neighbouring bacterial commensals. We examine prospects of utilising fungi-related molecular signatures in cancer diagnosis, patient stratification and assessment of treatment responsiveness, while highlighting challenges and limitations faced in performing such research. In all, we demonstrate that fungi likely constitute important members of mucosal and tumour-residing microbiomes. Exploration of fungal inter-kingdom interactions with the bacterial microbiome and the host and decoding of their causal impacts on tumour biology may enable their harnessing into cancer diagnosis and treatment.
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Affiliation(s)
- Aurelia Saftien
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jens Puschhof
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eran Elinav
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
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Christinaki AC, Theelen B, Zania A, Coutinho SDA, Cabañes JF, Boekhout T, Kouvelis VN. Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia. Sci Rep 2023; 13:6308. [PMID: 37072481 PMCID: PMC10113387 DOI: 10.1038/s41598-023-33486-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
Mitogenomes are essential due to their contribution to cell respiration. Recently they have also been implicated in fungal pathogenicity mechanisms. Members of the basidiomycetous yeast genus Malassezia are an important fungal component of the human skin microbiome, linked to various skin diseases, bloodstream infections, and they are increasingly implicated in gut diseases and certain cancers. In this study, the comparative analysis of Malassezia mitogenomes contributed to phylogenetic tree construction for all species. The mitogenomes presented significant size and gene order diversity which correlates to their phylogeny. Most importantly, they showed the inclusion of large inverted repeats (LIRs) and G-quadruplex (G4) DNA elements, rendering Malassezia mitogenomes a valuable test case for elucidating the evolutionary mechanisms responsible for this genome diversity. Both LIRs and G4s coexist and convergently evolved to provide genome stability through recombination. This mechanism is common in chloroplasts but, hitherto, rarely found in mitogenomes.
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Affiliation(s)
- Anastasia C Christinaki
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Alkmini Zania
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | | | - Javier F Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Vassili N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Athens, Greece.
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Moeckel C, Bakhl K, Georgakopoulos-Soares I, Zaravinos A. The Efficacy of Tumor Mutation Burden as a Biomarker of Response to Immune Checkpoint Inhibitors. Int J Mol Sci 2023; 24:ijms24076710. [PMID: 37047684 PMCID: PMC10095310 DOI: 10.3390/ijms24076710] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/21/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Cancer is one of the leading causes of death in the world; therefore, extensive research has been dedicated to exploring potential therapeutics, including immune checkpoint inhibitors (ICIs). Initially, programmed-death ligand-1 was the biomarker utilized to predict the efficacy of ICIs. However, its heterogeneous expression in the tumor microenvironment, which is critical to cancer progression, promoted the exploration of the tumor mutation burden (TMB). Research in various cancers, such as melanoma and lung cancer, has shown an association between high TMB and response to ICIs, increasing its predictive value. However, the TMB has failed to predict ICI response in numerous other cancers. Therefore, future research is needed to analyze the variations between cancer types and establish TMB cutoffs in order to create a more standardized methodology for using the TMB clinically. In this review, we aim to explore current research on the efficacy of the TMB as a biomarker, discuss current approaches to overcoming immunoresistance to ICIs, and highlight new trends in the field such as liquid biopsies, next generation sequencing, chimeric antigen receptor T-cell therapy, and personalized tumor vaccines.
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Affiliation(s)
- Camille Moeckel
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Katrina Bakhl
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ilias Georgakopoulos-Soares
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Apostolos Zaravinos
- Department of Life Sciences, European University Cyprus, Diogenis Str., 6, Nicosia 2404, Cyprus
- Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
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8
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Gowen R, Gamal A, Di Martino L, McCormick TS, Ghannoum MA. Modulating the Microbiome for Crohn's Disease Treatment. Gastroenterology 2023; 164:828-840. [PMID: 36702360 PMCID: PMC10152883 DOI: 10.1053/j.gastro.2023.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/12/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023]
Abstract
The central role of the gut microbiota in the regulation of health and disease has been convincingly demonstrated. Polymicrobial interkingdom interactions between bacterial (the bacteriome) and fungal (the mycobiome) communities of the gut have become a prominent focus for development of potential therapeutic approaches. In addition to polymicrobial interactions, the complex gut ecosystem also mediates interactions between the host and the microbiota. These interactions are complex and bidirectional; microbiota composition can be influenced by host immune response, disease-specific therapeutics, antimicrobial drugs, and overall ecosystems. However, the gut microbiota also influences host immune response to a drug or therapy by potentially transforming the drug's structure and altering bioavailability, activity, or toxicity. This is especially true in cases where the gut microbiota has produced a biofilm. The negative ramifications of biofilm formation include alteration of gut permeability, enhanced antimicrobial resistance, and alteration of host immune response effectiveness. Natural modulation of the gut microbiota, using probiotic and prebiotic approaches, may also be used to affect the host microbiome, a type of "natural" modulation of the host microbiota composition. In this review, we discuss potential bidirectional interactions between microbes and host, and we describe the changes in gut microbiota induced by probiotic and prebiotic approaches as well as their potential clinical consequences, including biofilm formation. We outline a systematic approach to designing probiotics capable of altering the host microbiota in disease states, using Crohn's disease as a model chronic disease. Understanding how the effective changes in the microbiome may enhance treatment efficacy may unlock the possibility of modulating the gut microbiome to improve treatment using a natural approach.
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Affiliation(s)
- Rachael Gowen
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Ahmed Gamal
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Luca Di Martino
- University Hospitals Cleveland Medical Center, Cleveland, Ohio; Department of Medicine, Case Western Reserve University, Cleveland, Ohio; Case Digestive Health Research Institute, Case Western Reserve University, Cleveland Ohio
| | - Thomas S McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Mahmoud A Ghannoum
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio.
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9
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Beyond Bacteria: Fungi in the Tumor Microbiome. Cancers (Basel) 2023; 15:cancers15030572. [PMID: 36765530 PMCID: PMC9913087 DOI: 10.3390/cancers15030572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
The microbiota is widely recognized to influence diverse biological processes, including metabolism, neurological and cardiovascular functions, the inflammatory response and immunity [...].
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10
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Xu X, Ding F, Hu X, Yang F, Zhang T, Dong J, Xue Y, Liu T, Wang J, Jin Q. Upper respiratory tract mycobiome alterations in different kinds of pulmonary disease. Front Microbiol 2023; 14:1117779. [PMID: 37032908 PMCID: PMC10076636 DOI: 10.3389/fmicb.2023.1117779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The human respiratory tract is considered to be a polymicrobial niche, and an imbalance in the microorganism composition is normally associated with several respiratory diseases. In addition to the well-studied bacteriome, the existence of fungal species in the respiratory tract has drawn increasing attention and has been suggested to have a significant clinical impact. However, the understanding of the respiratory fungal microbiota (mycobiome) in pulmonary diseases is still insufficient. Methods In this study, we investigated the fungal community composition of oropharynx swab (OS) samples from patients with five kinds of pulmonary disease, including interstitial lung disease (ILD), bacterial pneumonia (BP), fungal pneumonia (FP), asthma (AS) and lung cancer (LC), and compared them with healthy controls (HCs), based on high-throughput sequencing of the amplified fungal internal transcribed spacer (ITS) region. Results The results showed significant differences in fungal composition and abundance between disease groups and HCs. Malassezia was the most significant genus, which was much more abundant in pulmonary diseases than in the control. In addition, many common taxa were shared among different disease groups, but differences in taxa abundance and specific species in distinct disease groups were also observed. Based on linear discriminant analysis effect size (LefSe), each group had its characteristic species. Furthermore, some species showed a significant correlation with the patient clinical characteristics. Discussion Our study deepened our understanding of the respiratory tract mycobiome in some diseases that are less studied and identified the commonalities and differences among different kinds of pulmonary disease. These results would provide the solid basis for further investigation of the association between the mycobiome and pathogenicity of pulmonary diseases.
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Affiliation(s)
- Xingye Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangping Ding
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xiangqi Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Xue
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Tao Liu,
| | - Jing Wang
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Jing Wang,
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Qi Jin,
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11
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Narunsky-Haziza L, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, Gavert N, Stajich JE, Amit G, González A, Wandro S, Perry G, Ariel R, Meltser A, Shaffer JP, Zhu Q, Balint-Lahat N, Barshack I, Dadiani M, Gal-Yam EN, Patel SP, Bashan A, Swafford AD, Pilpel Y, Knight R, Straussman R. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions. Cell 2022; 185:3789-3806.e17. [PMID: 36179670 PMCID: PMC9567272 DOI: 10.1016/j.cell.2022.09.005] [Citation(s) in RCA: 153] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/13/2022] [Accepted: 08/31/2022] [Indexed: 01/26/2023]
Abstract
Cancer-microbe associations have been explored for centuries, but cancer-associated fungi have rarely been examined. Here, we comprehensively characterize the cancer mycobiome within 17,401 patient tissue, blood, and plasma samples across 35 cancer types in four independent cohorts. We report fungal DNA and cells at low abundances across many major human cancers, with differences in community compositions that differ among cancer types, even when accounting for technical background. Fungal histological staining of tissue microarrays supported intratumoral presence and frequent spatial association with cancer cells and macrophages. Comparing intratumoral fungal communities with matched bacteriomes and immunomes revealed co-occurring bi-domain ecologies, often with permissive, rather than competitive, microenvironments and distinct immune responses. Clinically focused assessments suggested prognostic and diagnostic capacities of the tissue and plasma mycobiomes, even in stage I cancers, and synergistic predictive performance with bacteriomes.
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Affiliation(s)
- Lian Narunsky-Haziza
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Micronoma Inc., San Diego, CA, USA
| | - Ilana Livyatan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Cameron Martino
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Deborah Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Guy Amit
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel; Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Antonio González
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | | | - Gili Perry
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ruthie Ariel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Arnon Meltser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Justin P Shaffer
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Nora Balint-Lahat
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Iris Barshack
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Maya Dadiani
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Einav N Gal-Yam
- Breast Oncology Institute, Sheba Medical Center, Ramat Gan, Israel
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Amir Bashan
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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