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Bommana S, Hu YJ, Kama M, Wang R, Kodimerla R, Jijakli K, Read TD, Dean D. Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji. mBio 2024; 15:e0306323. [PMID: 38117091 PMCID: PMC10790706 DOI: 10.1128/mbio.03063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Chlamydia trachomatis (Ct) is the most common sexually transmitted bacterium globally. Endocervical and vaginal microbiome interactions are rarely examined within the context of Ct or among vulnerable populations. We evaluated 258 vaginal and 92 paired endocervical samples from Fijian women using metagenomic shotgun sequencing. Over 37% of the microbiomes could not be classified into sub-community state types (subCSTs). We, therefore, developed subCSTs IV-D0, IV-D1, IV-D2, and IV-E-dominated primarily by Gardnerella vaginalis-to improve classification. Among paired microbiomes, the endocervix had a significantly higher alpha diversity and, independently, higher diversity for high-risk human papilloma virus (HPV) genotypes compared to low-risk and no HPV. Ct-infected endocervical networks had smaller clusters without interactions with potentially beneficial Lactobacillus spp. Overall, these data suggest that G. vaginalis may generate polymicrobial biofilms that predispose to and/or promote Ct and possibly HPV persistence and pathogenicity. Our findings expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding Pacific Islanders.
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Affiliation(s)
- Sankhya Bommana
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Ruohong Wang
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Reshma Kodimerla
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Kenan Jijakli
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Timothy D. Read
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deborah Dean
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Department of Bioengineering, Joint Graduate Program, University of California San Francisco and University of California Berkeley, San Francisco, California, USA
- Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, California, USA
- University of California San Francisco, Benioff Center for Microbiome Medicine, San Francisco, California, USA
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2
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Blaustein RA, Shen Z, Kashaf SS, Lee-Lin S, Conlan S, Bosticardo M, Delmonte OM, Holmes CJ, Taylor ME, Banania G, Nagao K, Dimitrova D, Kanakry JA, Su H, Holland SM, Bergerson JRE, Freeman AF, Notarangelo LD, Kong HH, Segre JA. Expanded microbiome niches of RAG-deficient patients. Cell Rep Med 2023; 4:101205. [PMID: 37757827 PMCID: PMC10591041 DOI: 10.1016/j.xcrm.2023.101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.
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Affiliation(s)
- Ryan A Blaustein
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - ShihQueen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Cassandra J Holmes
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Monica E Taylor
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Glenna Banania
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Keisuke Nagao
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Dimana Dimitrova
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jennifer A Kanakry
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Helen Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
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3
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Niiya A, Hamaguchi Y, Mishima H, Miura S, Komatsu N, Nagata K, Hasegawa Y, Miura K, Yoshiura KI. Four conserved amino acids on human papillomavirus E6 predict clinical high-risk types. J Med Virol 2023; 95:e29049. [PMID: 37621086 DOI: 10.1002/jmv.29049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Human papillomavirus (HPV) types included in the genus alpha papillomavirus (alpha-HPVs) are subdivided into high- and low-risk HPVs associated with tumorigenicity. According to conventional risk classification, over 30 alpha-HPVs remain unclassified and HPV groups phylogenetically classified using the L1 gene do not exactly correspond to the conventional risk classification groups. Here, we propose a novel cervical lesion progression risk classification strategy. Using four E6 risk distinguishable amino acids (E6-RDAAs), we successfully expanded the conventional classification to encompass alpha-HPVs and resolve discrepancies. We validated our classification system using alpha-HPV-targeted sequence data of 325 cervical swab specimens from participants in Japan. Clinical outcomes significantly correlated with the E6-RDAA classification. Four of five HPV types in the data set that were not conventionally classified (HPV30, 34, 67, and 69) were high-risk according to our classification criteria. This report sheds light on the carcinogenicity of rare genital HPV types using a novel risk classification strategy.
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Affiliation(s)
- Akari Niiya
- Department of Obstetrics and Gynecology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yo Hamaguchi
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Leading Medical Research Core Unit, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shoko Miura
- Department of Obstetrics and Gynecology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Nahoko Komatsu
- Department of Obstetrics and Gynecology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Koh Nagata
- Department of Obstetrics and Gynecology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuri Hasegawa
- Department of Obstetrics and Gynecology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kiyonori Miura
- Department of Obstetrics and Gynecology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Leading Medical Research Core Unit, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Leading Medical Research Core Unit, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Zeng PYF, Cecchini MJ, Barrett JW, Shammas-Toma M, De Cecco L, Serafini MS, Cavalieri S, Licitra L, Hoebers F, Brakenhoff RH, Leemans CR, Scheckenbach K, Poli T, Wang X, Liu X, Laxague F, Prisman E, Poh C, Bose P, Dort JC, Shaikh MH, Ryan SEB, Dawson A, Khan MI, Howlett CJ, Stecho W, Plantinga P, Daniela da Silva S, Hier M, Khan H, MacNeil D, Mendez A, Yoo J, Fung K, Lang P, Winquist E, Palma DA, Ziai H, Amelio AL, Li SSC, Boutros PC, Mymryk JS, Nichols AC. Immune-based classification of HPV-associated oropharyngeal cancer with implications for biomarker-driven treatment de-intensification. EBioMedicine 2022; 86:104373. [PMID: 36442320 PMCID: PMC9706534 DOI: 10.1016/j.ebiom.2022.104373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND There is significant interest in treatment de-escalation for human papillomavirus-associated (HPV+) oropharyngeal squamous cell carcinoma (OPSCC) patients given the generally favourable prognosis. However, 15-30% of patients recur after primary treatment, reflecting a need for improved risk-stratification tools. We sought to develop a molecular test to risk stratify HPV+ OPSCC patients. METHODS We created an immune score (UWO3) associated with survival outcomes in six independent cohorts comprising 906 patients, including blinded retrospective and prospective external validations. Two aggressive radiation de-escalation cohorts were used to assess the ability of UWO3 to identify patients who recur. Multivariate Cox models were used to assess the associations between the UWO3 immune class and outcomes. FINDINGS A three-gene immune score classified patients into three immune classes (immune rich, mixed, or immune desert) and was strongly associated with disease-free survival in six datasets, including large retrospective and prospective datasets. Pooled analysis demonstrated that the immune rich group had superior disease-free survival compared to the immune desert (HR = 9.0, 95% CI: 3.2-25.5, P = 3.6 × 10-5) and mixed (HR = 6.4, 95% CI: 2.2-18.7, P = 0.006) groups after adjusting for age, sex, smoking status, and AJCC8 clinical stage. Finally, UWO3 was able to identify patients from two small treatment de-escalation cohorts who remain disease-free after aggressive de-escalation to 30 Gy radiation. INTERPRETATION With additional prospective validation, the UWO3 score could enable biomarker-driven clinical decision-making for patients with HPV+ OPSCC based on robust outcome prediction across six independent cohorts. Prospective de-escalation and intensification clinical trials are currently being planned. FUNDING CIHR, European Union, and the NIH.
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Affiliation(s)
- Peter Y F Zeng
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Matthew J Cecchini
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - John W Barrett
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Matthew Shammas-Toma
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Loris De Cecco
- Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumouri, Milan, Italy
| | - Mara S Serafini
- Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumouri, Milan, Italy
| | - Stefano Cavalieri
- Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumouri, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Lisa Licitra
- Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumouri, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Frank Hoebers
- Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, Maastricht, the Netherlands
| | - Ruud H Brakenhoff
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, Cancer Center Amsterdam, the Netherlands
| | - C René Leemans
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, Cancer Center Amsterdam, the Netherlands
| | - Kathrin Scheckenbach
- Department of Otolaryngology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tito Poli
- Unit of Maxillofacial Surgery, Department of Medicine and Surgery, University of Parma-University Hospital of Parma, Parma, Italy
| | - Xiaowei Wang
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, Chicago, IL, USA
| | - Xinyi Liu
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, Chicago, IL, USA
| | - Francisco Laxague
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Eitan Prisman
- Division of Otolaryngology- Head and Neck Surgery, Department of Surgery, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Catherine Poh
- Division of Otolaryngology- Head and Neck Surgery, Department of Surgery, Vancouver General Hospital, Vancouver, British Columbia, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pinaki Bose
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Calgary, Calgary, Alberta, Canada
| | - Joseph C Dort
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Calgary, Calgary, Alberta, Canada
| | - Mushfiq H Shaikh
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Sarah E B Ryan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Alice Dawson
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Mohammed I Khan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - William Stecho
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Paul Plantinga
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | | | - Michael Hier
- Department of Otolaryngology Head and Neck Surgery, McGill University, Montreal, Quebec, Canada
| | - Halema Khan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Danielle MacNeil
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Adrian Mendez
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - John Yoo
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Kevin Fung
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Pencilla Lang
- Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Eric Winquist
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - David A Palma
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Hedyeh Ziai
- Department of Otolaryngology - Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Antonio L Amelio
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shawn S-C Li
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA, USA
| | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada; Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Anthony C Nichols
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada.
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Gu W, Bhangale A, Heft Neal ME, Smith JD, Brummel C, McHugh JB, Spector ME, Mills RE, Brenner JC. Analysis of Human Papilloma Virus Content and Integration in Mucoepidermoid Carcinoma. Viruses 2022; 14. [PMID: 36366450 DOI: 10.3390/v14112353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 02/01/2023] Open
Abstract
Mucoepidermoid Carcinomas (MEC) represent the most common malignancies of salivary glands. Approximately 50% of all MEC cases are known to harbor CRTC1/3-MAML2 gene fusions, but the additional molecular drivers remain largely uncharacterized. Here, we sought to resolve controversy around the role of human papillomavirus (HPV) as a potential driver of mucoepidermoid carcinoma. Bioinformatics analysis was performed on 48 MEC transcriptomes. Subsequent targeted capture DNA sequencing was used to annotate HPV content and integration status in the host genome. HPV of any type was only identified in 1/48 (2%) of the MEC transcriptomes analyzed. Importantly, the one HPV16+ tumor expressed high levels of p16, had high expression of HPV16 oncogenes E6 and E7, and displayed a complex integration pattern that included breakpoints into 13 host genes including PIK3AP1, HIPI, OLFM4,SIRT1, ARAP2, TMEM161B-AS1, and EPS15L1 as well as 9 non-genic regions. In this cohort, HPV is a rare driver of MEC but may have a substantial etiologic role in cases that harbor the virus. Genetic mechanisms of host genome integration are similar to those observed in other head and neck cancers.
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Voigt AY, Emiola A, Johnson JS, Fleming ES, Nguyen H, Zhou W, Tsai KY, Fink C, Oh J. Skin Microbiome Variation with Cancer Progression in Human Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2022; 142:2773-2782.e16. [PMID: 35390349 PMCID: PMC9509417 DOI: 10.1016/j.jid.2022.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/13/2022]
Abstract
The skin microbiome plays a critical role in skin homeostasis and disorders. UVR is the major cause of nonmelanoma skin cancer, but other risk factors, including immune suppression, chronic inflammation, and antibiotic usage, suggest the microbiome as an additional, unexplored risk factor and potential disease biomarker. The overarching goal was to study the skin microbiome in squamous cell carcinoma (SCC) and premalignant actinic keratosis compared with that in healthy skin to identify skin cancer‒associated changes in the skin microbiome. We performed a high-resolution analysis of shotgun metagenomes of actinic keratosis and SCC in healthy skin, revealing the microbial community shifts specific to actinic keratosis and SCC. Most prominently, the relative abundance of pathobiont Staphylococcus aureus was increased at the expense of commensal Cutibacterium acnes in SCC compared with that in healthy skin, and enrichment of functional pathways in SCC reflected this shift. Notably, C. acnes associated with lesional versus healthy skin differed at the strain level, suggesting the specific functional changes associated with its depletion in SCC. Our study revealed a transitional microbial dysbiosis from healthy skin to actinic keratosis to SCC, supporting further investigation of the skin microbiome for use as a biomarker and providing hypotheses for studies investigating how these microbes might influence skin cancer progression.
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Affiliation(s)
- Anita Y Voigt
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Akintunde Emiola
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Kenneth Y Tsai
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA; Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Christine Fink
- Department of Dermatology, Venereology, and Allergology, University Medical Center, Ruprecht-Karl University of Heidelberg, Heidelberg, Germany
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
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7
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Chen C, Hao L, Zhang Z, Tian L, Zhang X, Zhu J, Jie Z, Tong X, Xiao L, Zhang T, Jin X, Xu X, Yang H, Wang J, Kristiansen K, Jia H. Cervicovaginal microbiome dynamics after taking oral probiotics. J Genet Genomics 2021; 48:716-726. [PMID: 34391676 DOI: 10.1016/j.jgg.2021.03.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022]
Abstract
The vaginal microbiota is less complex than the gut microbiota, and the colonization of Lactobacillus in the female vagina is considered to be critical for reproductive health. Oral probiotics have been suggested as promising means to modulate vaginal homeostasis in the general population. In this study, 60 Chinese women were followed for over a year before, during, and after treatment with the probiotics Lactobacillus rhamnosus GR-1 and Lactobacillusreuteri RC-14. Shotgun metagenomic data of 1334 samples from multiple body sites did not support a colonization route of the probiotics from the oral cavity to the intestinal tract and then to the vagina. Our analyses enable the classification of the cervicovaginal microbiome into a stable state and a state of dysbiosis. The microbiome in the stable group steadily maintained a relatively high abundance of Lactobacilli over 1 year, which was not affected by probiotic intake, whereas in the dysbiosis group, the microbiota was more diverse and changed markedly over time. Data from a subset of the dysbiosis group suggests this subgroup possibly benefited from supplementation with the probiotics, indicating that probiotics supplementation can be prescribed for women in a subclinical microbiome setting of dysbiosis, providing opportunities for targeted and personalized microbiome reconstitution.
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Affiliation(s)
- Chen Chen
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, Universitetsparken 13, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Lilan Hao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zhe Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Liu Tian
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Jie Zhu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zhuye Jie
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, Universitetsparken 13, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Xin Tong
- BGI-Shenzhen, Shenzhen 518083, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China; BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Tao Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, Universitetsparken 13, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, Universitetsparken 13, University of Copenhagen, DK-2100 Copenhagen, Denmark; BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China.
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8
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Ganly I, Pei Z, Hao Y, Ma Y, Rosenthal M, Wu Z, Migliacci J, Huang B, Katabi N, Tseng W, Brown S, Tang YW, Yang L. Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing. Sci Rep 2021; 11:3867. [PMID: 33594114 PMCID: PMC7886861 DOI: 10.1038/s41598-021-83197-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
The aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which were then matched with a control patient by age, gender, race, smoking status and alcohol status. DNA was extracted from oral wash samples from all patients and whole genome shotgun sequencing performed. The raw sequence data was cleaned, reads aligned with the human genome (GRCH38), nonhuman reads identified and then HPV genotypes identified using HPViewer. In the 50 patients with OC-SCC, the most common subsite was tongue in 26 (52%). All patients were treated with primary resection and neck dissection. All but 2 tumors were negative on p16 immunohistochemistry. There were no statistically significant differences between the cases and controls in terms of gender, age, race/ethnicity, alcohol drinking, and cigarette smoking. There was no statistically significant difference between the cancer samples and control samples in the nonhuman DNA reads (medians 4,228,072 vs. 5,719,715, P value = 0.324). HPV was detected in 5 cases (10%) of OC-SCC (genotypes 10, 16, 98) but only 1 tumor sample (genotype 16) yielded a high number of reads to suggest a role in the etiology of OC-SCC. HPV was detected in 4 control patients (genotypes 16, 22, 76, 200) but all had only 1–2 HPV reads per human genome. Genotypes of HPV are rarely found in patients with oral cancer.
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Affiliation(s)
- Ian Ganly
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA.
| | - Zhiheng Pei
- Department of Pathology, New York University School of Medicine, New York, 10016, USA.,Department of Medicine, New York University School of Medicine, New York, 10016, USA.,Department of Veterans Affairs, New York Harbor Healthcare System, New York, USA
| | - Yuhan Hao
- Department of Pathology, New York University School of Medicine, New York, 10016, USA.,Applied Bioinformatics Laboratories, New York University School of Medicine, New York, 10016, USA.,Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10016, USA
| | - Yingfei Ma
- Department of Medicine, New York University School of Medicine, New York, 10016, USA.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000, China
| | - Matthew Rosenthal
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Zhenglin Wu
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Jocelyn Migliacci
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Bin Huang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Nora Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Wenzhi Tseng
- Department of Pathology, New York University School of Medicine, New York, 10016, USA
| | - Stuart Brown
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, 10016, USA
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Medical Affairs, Cepheid, Danaher Diagnostic Platform, Shanghai, China
| | - Liying Yang
- Department of Pathology, New York University School of Medicine, New York, 10016, USA. .,Department of Medicine, New York University School of Medicine, New York, 10016, USA.
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9
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Inkman MJ, Jayachandran K, Ellis TM, Ruiz F, McLellan MD, Miller CA, Wu Y, Ojesina AI, Schwarz JK, Zhang J. HPV-EM: an accurate HPV detection and genotyping EM algorithm. Sci Rep 2020; 10:14340. [PMID: 32868873 DOI: 10.1038/s41598-020-71300-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/07/2020] [Indexed: 11/09/2022] Open
Abstract
Accurate HPV genotyping is crucial in facilitating epidemiology studies, vaccine trials, and HPV-related cancer research. Contemporary HPV genotyping assays only detect < 25% of all known HPV genotypes and are not accurate for low-risk or mixed HPV genotypes. Current genomic HPV genotyping algorithms use a simple read-alignment and filtering strategy that has difficulty handling repeats and homology sequences. Therefore, we have developed an optimized expectation–maximization algorithm, designated HPV-EM, to address the ambiguities caused by repetitive sequencing reads. HPV-EM achieved 97–100% accuracy when benchmarked using cell line data and TCGA cervical cancer data. We also validated HPV-EM using DNA tiling data on an institutional cervical cancer cohort (96.5% accuracy). Using HPV-EM, we demonstrated HPV genotypic differences in recurrence and patient outcomes in cervical and head and neck cancers.
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10
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Hao Y, Ruiz R, Yang L, Neto AG, Amin MR, Kelly D, Achlatis S, Roof S, Bing R, Kannan K, Brown SM, Pei Z, Branski RC. Mitochondrial somatic mutations and the lack of viral genomic variation in recurrent respiratory papillomatosis. Sci Rep 2019; 9:16625. [PMID: 31719597 DOI: 10.1038/s41598-019-53148-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022] Open
Abstract
Recurrent Respiratory Papillomatosis (RRP) is a rare disease of the aerodigestive tract caused by the Human Papilloma Virus (HPV) that manifests as profoundly altered phonatory and upper respiratory anatomy. Current therapies are primarily symptomatic; enhanced insight regarding disease-specific biology of RRP is critical to improved therapeutics for this challenging population. Multiplex PCR was performed on oral rinses collected from twenty-three patients with adult-onset RRP every three months for one year. Twenty-two (95.6%) subjects had an initial HPV positive oral rinse. Of those subjects, 77.2% had an additional positive oral rinse over 12 months. A subset of rinses were then compared to tissue samples in the same patient employing HPViewer to determine HPV subtype concordance. Multiple HPV copies (60–787 per human cell) were detected in RRP tissue in each patient, but a single dominant HPV was found in individual samples. These data confirm persistent oral HPV infection in the majority of patients with RRP. In addition, three novel HPV6 isolates were found and identical HPV strains, at very low levels, were identified in oral rinses in two patients suggesting potential HPV subtype concordance. Finally, somatic heteroplasmic mtDNA mutations were observed in RRP tissue with 1.8 mutations per sample and two nonsynonymous variants. These data provide foundational insight into both the underlying pathophysiology of RRP, but also potential targets for intervention in this challenging patient cohort.
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11
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Tetz G, Brown SM, Hao Y, Tetz V. Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid-producing E. coli and Their Phages. Sci Rep 2019; 9:9685. [PMID: 31273267 PMCID: PMC6609616 DOI: 10.1038/s41598-019-46087-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022] Open
Abstract
The etiopathogenesis of type 1 diabetes (T1D), a common autoimmune disorder, is not completely understood. Recent studies suggested the gut microbiome plays a role in T1D. We have used public longitudinal microbiome data from T1D patients to analyze amyloid-producing bacterial composition and found a significant association between initially high amyloid-producing Escherichia coli abundance, subsequent E. coli depletion prior to seroconversion, and T1D development. In children who presented seroconversion or developed T1D, we observed an increase in the E. coli phage/E. coli ratio prior to E. coli depletion, suggesting that the decrease in E. coli was due to prophage activation. Evaluation of the role of phages in amyloid release from E. coli biofilms in vitro suggested an indirect role of the bacterial phages in the modulation of host immunity. This study for the first time suggests that amyloid-producing E. coli, their phages, and bacteria-derived amyloid might be involved in pro-diabetic pathway activation in children at risk for T1D.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, New York, NY, 10013, USA. .,Tetz Laboratories, New York, NY, 10027, USA.
| | - Stuart M Brown
- New York University School of Medicine, Department of Cell Biology, New York, NY, 10016, USA
| | - Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, New York, 10012, USA.,New York Genome Center, New York, New York, 10013, USA
| | - Victor Tetz
- Human Microbiology Institute, New York, NY, 10013, USA
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12
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Sias C, Salichos L, Lapa D, Del Nonno F, Baiocchini A, Capobianchi MR, Garbuglia AR. Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples. Virol J 2019; 16:27. [PMID: 30832688 PMCID: PMC6398256 DOI: 10.1186/s12985-019-1132-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/15/2019] [Indexed: 02/05/2023] Open
Abstract
Background Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. Currently, there are no guidelines recommending HPV oral cavity screening as a mandatory test, and it remains unknown which HPV types should be included in HPV screening programs. Our goal was to assess HPV prevalence in oropharyngeal, anal, and cervical swabs using different sets of primers,which are able to amplify α, β, γ HPV types. Methods We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. All untyped strains were genetically characterized through PCR amplification and direct sequencing of partial L1 region, and the resulting sequences were classified through phylogenetic analysis. Results HPV prevalence was 20.9% in 124 oropharyngeal swab samples, including infections with multiple HPV types (5.6%). HPV prevalence in this anatomical site was significantly associated with serostatus: 63.3%in HIV positive and 36.3% in HIV negative patients (p < 0.05). Unclassified types were detected in 6 specimens. In our analysis, we did not observe any difference in HPV (α, β, γ) prevalence between men and women. Overall, β species were the most frequently detected 69.7%. When using anal swabs, for HIV positive patients, β genus prevalence was 1% and γ genus was 3.7% including 6 unclassified types. In cervical samples from 43 HIV positive women (18 HPV negative and 25 positive by MY09/11 PCR), only one sample was positivite for β1 species (2.4%) using FAP primers. Six of the untyped strains clustered with sequences from species 7, 9, 10, 8,12 of γ genus. Four sequences remained unclassified. Finally, β and γ HPV prevalence was significantly lower than their respective HPV prevalence as identified by the Luminex system in all anatomical sites that were analyzed in previous studies. Conclusion This study provides new information about viral isolates present in oropharyngeal site and it will contribute to improve the monitoring of HPV infection. Electronic supplementary material The online version of this article (10.1186/s12985-019-1132-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catia Sias
- Laboratory of Virology, "Lazzaro Spallanzani" National Institute for Infectious Diseases, IRCCS, Via Portuense, 292, 00149, Rome, Italy
| | - Leonidas Salichos
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Daniele Lapa
- Laboratory of Virology, "Lazzaro Spallanzani" National Institute for Infectious Diseases, IRCCS, Via Portuense, 292, 00149, Rome, Italy
| | - Franca Del Nonno
- Laboratory of Pathology, "Lazzaro Spallanzani" National Institute for Infectious Diseases, IRCCS, Rome, Italy
| | - Andrea Baiocchini
- Laboratory of Pathology, "Lazzaro Spallanzani" National Institute for Infectious Diseases, IRCCS, Rome, Italy
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, "Lazzaro Spallanzani" National Institute for Infectious Diseases, IRCCS, Via Portuense, 292, 00149, Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology, "Lazzaro Spallanzani" National Institute for Infectious Diseases, IRCCS, Via Portuense, 292, 00149, Rome, Italy.
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13
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Abstract
Recent studies suggest that alterations in the gut phagobiota may contribute to pathophysiological processes in mammals; however, the association of bacteriophage community structure with Parkinson's disease (PD) has not been yet characterized. Towards this end, we used a published dataset to analyse bacteriophage composition and determine the phage/bacteria ratio in faecal samples from drug-naive PD patients and healthy participants. Our analyses revealed significant alterations in the representation of certain bacteriophages in the phagobiota of PD patients. We identified shifts of the phage/bacteria ratio in lactic acid bacteria known to produce dopamine and regulate intestinal permeability, which are major factors implicated in PD pathogenesis. Furthermore, we observed the depletion of Lactococcus spp. in the PD group, which was most likely due to the increase of lytic c2-like and 936-like lactococcal phages frequently present in dairy products. Our findings add bacteriophages to the list of possible factors associated with the development of PD, suggesting that gut phagobiota composition may serve as a diagnostic tool as well as a target for therapeutic intervention, which should be confirmed in further studies. Our results open a discussion on the role of environmental phages and phagobiota composition in health and disease.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, New York, NY, 10027, USA.
| | - Stuart M Brown
- Tetz Laboratories, New York, NY, 10027, USA
- Applied Bioinformatics Laboratory, NYU School of Medicine, New York, NY, 10016, USA
| | - Yuhan Hao
- Tetz Laboratories, New York, NY, 10027, USA
- Applied Bioinformatics Laboratory, NYU School of Medicine, New York, NY, 10016, USA
| | - Victor Tetz
- Human Microbiology Institute, New York, NY, 10027, USA
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