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Pourkarim MR. Navigating Evolving Challenges in Blood Safety. Viruses 2024; 16:123. [PMID: 38257823 PMCID: PMC10821029 DOI: 10.3390/v16010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Blood safety remains a paramount public health concern, and health authorities maintain a high level of vigilance to prevent transfusion-transmitted infections (TTIs) [...].
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Affiliation(s)
- Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion, Tehran 14665-1157, Iran
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2
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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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3
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Mageiros L, Megremis S, Papadopoulos NG. The virome in allergy and asthma: A nascent, ineffable player. J Allergy Clin Immunol 2023; 152:1347-1351. [PMID: 37778473 DOI: 10.1016/j.jaci.2023.09.022] [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: 06/08/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Allergic diseases can be affected by virus-host interactions and are increasingly linked with the tissue-specific microbiome. High-throughput metagenomic sequencing has offered the opportunity to study the presence of viruses as an ecologic system, namely, the virome. Even though virome studies are technically challenging conceptually and analytically, they are already producing novel data expanding our understanding of the pathophysiologic mechanisms related to chronic inflammation and allergy. The importance of interspecies and intraspecies interactions is becoming apparent, as they can significantly, directly or indirectly, affect the host's response and antigenic state. Here, we emphasize the challenges and potential insights related to study of the virome in the context of allergy and asthma. We review the limited number of studies that have investigated the virome in these conditions, underlining the need for prospective, repeated sampling designs to unravel the virome's impact on disease development and its interplay with microbiota and immunity. The potential therapeutic use of bacteriophages, which are highly complex components of the virome, is discussed. There is clearly a need for further in-depth investigation of the virome as a system in allergic diseases.
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Affiliation(s)
- Leonardos Mageiros
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece; University of Manchester, Manchester, United Kingdom.
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Wang H, Xu S, Li S, Su B, Sherrill-Mix S, Liang G. Virome in immunodeficiency: what we know currently. Chin Med J (Engl) 2023; 136:2647-2657. [PMID: 37914672 PMCID: PMC10684123 DOI: 10.1097/cm9.0000000000002899] [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: 07/30/2023] [Indexed: 11/03/2023] Open
Abstract
ABSTRACT Over the past few years, the human virome and its complex interactions with microbial communities and the immune system have gained recognition as a crucial factor in human health. Individuals with compromised immune function encounter distinctive challenges due to their heightened vulnerability to a diverse range of infectious diseases. This review aims to comprehensively explore and analyze the growing evidence regarding the role of the virome in immunocompromised disease status. By surveying the latest literature, we present a detailed overview of virome alterations observed in various immunodeficiency conditions. We then delve into the influence and mechanisms of these virome changes on the pathogenesis of specific diseases in immunocompromised individuals. Furthermore, this review explores the clinical relevance of virome studies in the context of immunodeficiency, highlighting the potential diagnostic and therapeutic gains from a better understanding of virome contributions to disease manifestations.
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Affiliation(s)
- Hu Wang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Siqi Xu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Scott Sherrill-Mix
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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Cao L, Ma Y, Wan Z, Li B, Tian W, Zhang C, Li Y. Longitudinal anellome dynamics in the upper respiratory tract of children with acute respiratory tract infections. Virus Evol 2023; 9:vead045. [PMID: 37674817 PMCID: PMC10478798 DOI: 10.1093/ve/vead045] [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: 04/27/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 09/08/2023] Open
Abstract
Anelloviruses (AVs) are ubiquitous in humans and are the most abundant components of the commensal virome. Previous studies on the diversity, transmission, and persistence of AVs mainly focused on the blood or transplanted tissues from adults; however, the profile of the anellome in the respiratory tract in children are barely known. We investigated the anellome profile and their dynamics in the upper respiratory tract from a cohort of children with acute respiratory tract infections (ARTIs). Different to that in adult, betatorquevirus is the most abundant genus, followed by alphatorquevirus. We found that the relative abundance of betatorquevirus was higher in earlier time points, and in contrast, the abundance of alphatorquevirus was higher in later time points; these results might suggest that betatorquevirus decreased with age and alphatorquevirus increased with age in childhood. No difference regarding the diversity and abundance of anellome was found between single and multiple ARTIs, consistent with the idea that AV is not associated with certain disease. Most AVs are transient, and a small proportion (8 per cent) of them were found to be possibly persistent, with persistence time ranging from 1 month to as long as 56 months. Furthermore, the individual respiratory anellome appeared to be unique and dynamic, and the replacement of existing AVs with new ones are common over different time points. These findings demonstrate that betatorquevirus may be the early colonizer in children, and the individual respiratory anellome is unique, which are featured by both chronic infections and AV community replacement.
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Affiliation(s)
- Le Cao
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, 99 North Gulou Road, Taizhou 225300, China
| | - Bing Li
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Weimin Tian
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
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Miao Q, Liang T, Pei N, Liu C, Pan J, Li N, Wang Q, Chen Y, Chen Y, Ma Y, Jin W, Zhang Y, Su Y, Yao Y, Huang Y, Zhou C, Bao R, Xu X, Chen W, Hu B, Li J. Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing. Respir Res 2022; 23:345. [PMCID: PMC9748891 DOI: 10.1186/s12931-022-02230-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/31/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
The application of clinical mNGS for diagnosing respiratory infections improves etiology diagnosis, however at the same time, it brings new challenges as an unbiased sequencing method informing all identified microbiomes in the specimen.
Methods
Strategy evaluation and metagenomic analysis were performed for the mNGS data generated between March 2017 and October 2019. Diagnostic strengths of four specimen types were assessed to pinpoint the more appropriate type for mNGS diagnosis of respiratory infections. Microbiome complexity was revealed between patient cohorts and infection types. A bioinformatic pipeline resembling diagnosis results was built based upon multiple bioinformatic parameters.
Results
The positive predictive values (PPVs) for mNGS diagnosing of non-mycobacterium, Nontuberculous Mycobacteria (NTM), and Aspergillus were obviously higher in bronchoalveolar lavage fluid (BALF) demonstrating the potency of BALF in mNGS diagnosis. Lung tissues and sputum were acceptable for diagnosis of the Mycobacterium tuberculosis (MTB) infections. Interestingly, significant taxonomy differences were identified in sufficient BALF specimens, and unique bacteriome and virome compositions were found in the BALF specimens of tumor patients. Our pipeline showed comparative diagnostic strength with the clinical microbiological diagnosis.
Conclusions
To achieve reliable mNGS diagnosis result, BALF specimens for suspicious common infections, and lung tissues and sputum for doubtful MTB infections are recommended to avoid the false results given by the complexed respiratory microbiomes. Our developed bioinformatic pipeline successful helps mNGS data interpretation and reduces manual corrections for etiology diagnosis.
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Costantini C, Nunzi E, Romani L. From the nose to the lungs: the intricate journey of airborne pathogens amidst commensal bacteria. Am J Physiol Cell Physiol 2022; 323:C1036-C1043. [PMID: 36036448 PMCID: PMC9529274 DOI: 10.1152/ajpcell.00287.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The recent COVID-19 pandemic has dramatically brought the pitfalls of airborne pathogens to the attention of the scientific community. Not only viruses but also bacteria and fungi may exploit air transmission to colonize and infect potential hosts and be the cause of significant morbidity and mortality in susceptible populations. The efforts to decipher the mechanisms of pathogenicity of airborne microbes have brought to light the delicate equilibrium that governs the homeostasis of mucosal membranes. The microorganisms already thriving in the permissive environment of the respiratory tract represent a critical component of this equilibrium and a potent barrier to infection by means of direct competition with airborne pathogens or indirectly via modulation of the immune response. Moving down the respiratory tract, physicochemical and biological constraints promote site-specific expansion of microbes that engage in cross talk with the local immune system to maintain homeostasis and promote protection. In this review, we critically assess the site-specific microbial communities that an airborne pathogen encounters in its hypothetical travel along the respiratory tract and discuss the changes in the composition and function of the microbiome in airborne diseases by taking fungal and SARS-CoV-2 infections as examples. Finally, we discuss how technological and bioinformatics advancements may turn microbiome analysis into a valuable tool in the hands of clinicians to predict the risk of disease onset, the clinical course, and the response to treatment of individual patients in the direction of personalized medicine implementation.
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Affiliation(s)
- Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Emilia Nunzi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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Widder S, Görzer I, Friedel B, Rahimi N, Schwarz S, Jaksch P, Knapp S, Puchhammer-Stöckl E. Correction: Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation. MICROBIOME 2022; 10:81. [PMID: 35644614 PMCID: PMC9150334 DOI: 10.1186/s40168-022-01285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Stefanie Widder
- Research Laboratory of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria.
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.
| | - Irene Görzer
- Center of Virology, Medical University Vienna, Vienna, Austria
| | - Benjamin Friedel
- Center of Virology, Medical University Vienna, Vienna, Austria
- Department for Internal Medicine, Diabetology, Endocrinology, Diakonissenkrankenhaus, ViDia Kliniken, Karlsruhe, Germany
| | - Nina Rahimi
- Research Laboratory of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stefan Schwarz
- Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Peter Jaksch
- Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Sylvia Knapp
- Research Laboratory of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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