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Simoneau CR, Chen PY, Xing GK, Hayashi JM, Chen IP, Khalid MM, Meyers NL, Taha TY, Leon KE, Suryawanshi RK, McCavitt-Malvido M, Ashuach T, Fontaine KA, Rodriguez L, Joehnk B, Walcott K, Vasudevan S, Fang X, Maishan M, Schultz S, Roose JP, Matthay MA, Sil A, Arjomandi M, Yosef N, Ott M. NF-κB inhibitor alpha controls SARS-CoV-2 infection in ACE2-overexpressing human airway organoids. Sci Rep 2024; 14:15351. [PMID: 38961189 PMCID: PMC11222426 DOI: 10.1038/s41598-024-66003-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that recapitulate the cell-intrinsic response to arising viral variants are needed. Here we describe an adult stem cell-derived human airway organoid model overexpressing the ACE2 receptor (ACE2-OE) that supports robust viral replication while maintaining 3D architecture and cellular diversity of the airway epithelium. ACE2-OE organoids were infected with SARS-CoV-2 variants and subjected to single-cell RNA-sequencing. Interferon-lambda was upregulated in cells with low-level infection while the NF-kB inhibitor alpha gene (encoding IkBa) was consistently upregulated in infected cells, and its expression positively correlated with infection levels. Confocal microscopy showed more IkBa expression in infected than bystander cells, but found concurrent nuclear translocation of NF-kB that IkBa usually prevents. Overexpressing a nondegradable IkBa mutant reduced NF-kB translocation and increased viral infection. These data demonstrate the functionality of ACE2-OE organoids in SARS-CoV-2 research and underscore that the strength of the NF-kB feedback loop in infected cells controls viral replication.
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Affiliation(s)
- Camille R Simoneau
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Galen K Xing
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Irene P Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Mir M Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Taha Y Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Kristoffer E Leon
- Gladstone Institute of Virology, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Tal Ashuach
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Lauren Rodriguez
- ImmunoX CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Bastian Joehnk
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | | | - Xiaohui Fang
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mazharul Maishan
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shawn Schultz
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Michael A Matthay
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mehrdad Arjomandi
- Medical Service, San Francisco VA Healthcare System, San Francisco, CA, USA
- Division of Pulmonary and Critical Care, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Melanie Ott
- Gladstone Institute of Virology, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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2
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Xu QQ, Yu DD, Fan XD, Cui HR, Dai QQ, Zhong XY, Zhang XY, Zhao C, You LZ, Shang HC. Chinese Medicine for Treatment of COVID-19: A Review of Potential Pharmacological Components and Mechanisms. Chin J Integr Med 2024:10.1007/s11655-024-3909-z. [PMID: 38958885 DOI: 10.1007/s11655-024-3909-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 07/04/2024]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute infectious respiratory disease that has been prevalent since December 2019. Chinese medicine (CM) has demonstrated its unique advantages in the fight against COVID-19 in the areas of disease prevention, improvement of clinical symptoms, and control of disease progression. This review summarized the relevant material components of CM in the treatment of COVID-19 by searching the relevant literature and reports on CM in the treatment of COVID-19 and combining with the physiological and pathological characteristics of the novel coronavirus. On the basis of sorting out experimental methods in vivo and in vitro, the mechanism of herb action was further clarified in terms of inhibiting virus invasion and replication and improving related complications. The aim of the article is to explore the strengths and characteristics of CM in the treatment of COVID-19, and to provide a basis for the research and scientific, standardized treatment of COVID-19 with CM.
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Affiliation(s)
- Qian-Qian Xu
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Dong-Dong Yu
- The Geriatrics Center, First Affiliated Hospital, Anhui University of Chinese Medicine, Hefei, 230031, China
| | - Xiao-Dan Fan
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - He-Rong Cui
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Qian-Qian Dai
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Xiao-Ying Zhong
- School of Medical Information Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 51006, China
| | - Xin-Yi Zhang
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Chen Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang-Zhen You
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China.
| | - Hong-Cai Shang
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
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Wang Q, Guo F, Zhang Q, Hu T, Jin Y, Yang Y, Ma Y. Organoids in gastrointestinal diseases: from bench to clinic. MedComm (Beijing) 2024; 5:e574. [PMID: 38948115 PMCID: PMC11214594 DOI: 10.1002/mco2.574] [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: 11/28/2023] [Revised: 04/15/2024] [Accepted: 04/26/2024] [Indexed: 07/02/2024] Open
Abstract
The etiology of gastrointestinal (GI) diseases is intricate and multifactorial, encompassing complex interactions between genetic predisposition and gut microbiota. The cell fate change, immune function regulation, and microenvironment composition in diseased tissues are governed by microorganisms and mutated genes either independently or through synergistic interactions. A comprehensive understanding of GI disease etiology is imperative for developing precise prevention and treatment strategies. However, the existing models used for studying the microenvironment in GI diseases-whether cancer cell lines or mouse models-exhibit significant limitations, which leads to the prosperity of organoids models. This review first describes the development history of organoids models, followed by a detailed demonstration of organoids application from bench to clinic. As for bench utilization, we present a layer-by-layer elucidation of organoid simulation on host-microbial interactions, as well as the application in molecular mechanism analysis. As for clinical adhibition, we provide a generalized interpretation of organoid application in GI disease simulation from inflammatory disorders to malignancy diseases, as well as in GI disease treatment including drug screening, immunotherapy, and microbial-targeting and screening treatment. This review draws a comprehensive and systematical depiction of organoids models, providing a novel insight into the utilization of organoids models from bench to clinic.
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Affiliation(s)
- Qinying Wang
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Fanying Guo
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qinyuan Zhang
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - TingTing Hu
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - YuTao Jin
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yongzhi Yang
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yanlei Ma
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
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Shafqat A, Masters MC, Tripathi U, Tchkonia T, Kirkland JL, Hashmi SK. Long COVID as a Disease of Accelerated Biological Aging: An Opportunity to Translate Geroscience Interventions. Ageing Res Rev 2024:102400. [PMID: 38945306 DOI: 10.1016/j.arr.2024.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
It has been four years since long COVID-the protracted consequences that survivors of COVID-19 face-was first described. Yet, this entity continues to devastate the quality of life of an increasing number of COVID-19 survivors without any approved therapy. Furthermore, there remains a paucity of clinical trials addressing the biological root causes of this disease. Notably, the symptoms of long COVID-including but not limited to exercise intolerance, cognitive impairment, orthostasis, and functional decline-are typically seen with advancing age. Leveraging this similarity, we posit that Geroscience-which aims to target the biological drivers of aging to prevent age-associated conditions as a group-could offer promising therapeutic avenues for long COVID. Bearing this in mind, this review presents a framework for studying long COVID as a state of effectively accelerated biological aging. Thus, we comprehensively review here the role of biological hallmarks of aging in long COVID, identifying research gaps and proposing directions for future preclinical and clinical studies.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Mary Clare Masters
- Division of Infectious Diseases, Northwestern University, Chicago, IL, USA
| | - Utkarsh Tripathi
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Tamara Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA; Department of Internal Medicine, Mayo Clinic, Rochester,, MN, USA
| | - Shahrukh K Hashmi
- Department of Internal Medicine, Mayo Clinic, Rochester,, MN, USA; Research and Innovation Center, Department of Health, Abu Dhabi, UAE; College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
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5
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Yan J, Monlong J, Cougoule C, Lacroix-Lamandé S, Wiedemann A. Mapping the scientific output of organoids for animal and human modeling infectious diseases: a bibliometric assessment. Vet Res 2024; 55:81. [PMID: 38926765 PMCID: PMC11210181 DOI: 10.1186/s13567-024-01333-7] [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: 12/01/2023] [Accepted: 04/11/2024] [Indexed: 06/28/2024] Open
Abstract
The escalation of antibiotic resistance, pandemics, and nosocomial infections underscores the importance of research in both animal and human infectious diseases. Recent advancements in three-dimensional tissue cultures, or "organoids", have revolutionized the development of in vitro models for infectious diseases. Our study conducts a bibliometric analysis on the use of organoids in modeling infectious diseases, offering an in-depth overview of this field's current landscape. We examined scientific contributions from 2009 onward that focused on organoids in host‒pathogen interactions using the Web of Science Core Collection and OpenAlex database. Our analysis included temporal trends, reference aging, author, and institutional productivity, collaborative networks, citation metrics, keyword cluster dynamics, and disruptiveness of organoid models. VOSviewer, CiteSpace, and Python facilitated this analytical assessment. The findings reveal significant growth and advancements in organoid-based infectious disease research. Analysis of keywords and impactful publications identified three distinct developmental phases in this area that were significantly influenced by outbreaks of Zika and SARS-CoV-2 viruses. The research also highlights the synergistic efforts between academia and publishers in tackling global pandemic challenges. Through mostly consolidating research efforts, organoids are proving to be a promising tool in infectious disease research for both human and animal infectious disease. Their integration into the field necessitates methodological refinements for better physiological emulation and the establishment of extensive organoid biobanks. These improvements are crucial for fully harnessing the potential of organoids in understanding infectious diseases and advancing the development of targeted treatments and vaccines.
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Affiliation(s)
- Jin Yan
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, China.
- Research Center of Digestive Disease, Central South University, Changsha, China.
- IRSD - Digestive Health Research Institute, University of Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France.
| | - Jean Monlong
- IRSD - Digestive Health Research Institute, University of Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Céline Cougoule
- Institut de Pharmacologie Et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Agnès Wiedemann
- IRSD - Digestive Health Research Institute, University of Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France.
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Sulaksono HLS, Annisa A, Ruslami R, Mufeeduzzaman M, Panatarani C, Hermawan W, Ekawardhani S, Joni IM. Recent Advances in Graphene Oxide-Based on Organoid Culture as Disease Model and Cell Behavior - A Systematic Literature Review. Int J Nanomedicine 2024; 19:6201-6228. [PMID: 38911499 PMCID: PMC11193994 DOI: 10.2147/ijn.s455940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/02/2024] [Indexed: 06/25/2024] Open
Abstract
Due to their ability to replicate the in vivo microenvironment through cell interaction and induce cells to stimulate cell function, three-dimensional cell culture models can overcome the limitations of two-dimensional models. Organoids are 3D models that demonstrate the ability to replicate the natural structure of an organ. In most organoid tissue cultures, matrigel made of a mouse tumor extracellular matrix protein mixture is an essential ingredient. However, its tumor-derived origin, batch-to-batch variation, high cost, and safety concerns have limited the usefulness of organoid drug development and regenerative medicine. Its clinical application has also been hindered by the fact that organoid generation is dependent on the use of poorly defined matrices. Therefore, matrix optimization is a crucial step in developing organoid culture that introduces alternatives as different materials. Recently, a variety of substitute materials has reportedly replaced matrigel. The purpose of this study is to review the significance of the latest advances in materials for cell culture applications and how they enhance build network systems by generating proper cell behavior. Excellence in cell behavior is evaluated from their cell characteristics, cell proliferation, cell differentiation, and even gene expression. As a result, graphene oxide as a matrix optimization demonstrated high potency in developing organoid models. Graphene oxide can promote good cell behavior and is well known for having good biocompatibility. Hence, advances in matrix optimization of graphene oxide provide opportunities for the future development of advanced organoid models.
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Affiliation(s)
| | - Annisa Annisa
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Rovina Ruslami
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Mufeeduzzaman Mufeeduzzaman
- Functional Nano Powder University Center of Excellence (FiNder U-CoE), Universitas Padjadjaran, Bandung, Indonesia
| | - Camellia Panatarani
- Functional Nano Powder University Center of Excellence (FiNder U-CoE), Universitas Padjadjaran, Bandung, Indonesia
- Department of Physics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Wawan Hermawan
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
- Functional Nano Powder University Center of Excellence (FiNder U-CoE), Universitas Padjadjaran, Bandung, Indonesia
| | - Savira Ekawardhani
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
- Functional Nano Powder University Center of Excellence (FiNder U-CoE), Universitas Padjadjaran, Bandung, Indonesia
| | - I Made Joni
- Functional Nano Powder University Center of Excellence (FiNder U-CoE), Universitas Padjadjaran, Bandung, Indonesia
- Department of Physics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
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van Dijk LLA, Rijsbergen LC, Rubio BT, Schmitz KS, Gommers L, Comvalius AD, Havelaar A, van Amerongen G, Schepp R, Lamers MM, GeurtsvanKessel CH, Haagmans BL, van Binnendijk R, de Swart RL, de Vries RD. Virus neutralization assays for human respiratory syncytial virus using airway organoids. Cell Mol Life Sci 2024; 81:267. [PMID: 38884678 DOI: 10.1007/s00018-024-05307-y] [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: 03/15/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
Neutralizing antibodies are considered a correlate of protection against severe human respiratory syncytial virus (HRSV) disease. Currently, HRSV neutralization assays are performed on immortalized cell lines like Vero or A549 cells. It is known that assays on these cell lines exclusively detect neutralizing antibodies (nAbs) directed to the fusion (F) protein. For the detection of nAbs directed to the glycoprotein (G), ciliated epithelial cells expressing the cellular receptor CX3CR1 are required, but generation of primary cell cultures is expensive and labor-intensive. Here, we developed a high-throughput neutralization assay based on the interaction between clinically relevant HRSV grown on primary cells with ciliated epithelial cells, and validated this assay using a panel of infant sera. To develop the high-throughput neutralization assay, we established a culture of differentiated apical-out airway organoids (Ap-O AO). CX3CR1 expression was confirmed, and both F- and G-specific monoclonal antibodies neutralized HRSV in the Ap-O AO. In a side-by-side neutralization assay on Vero cells and Ap-O AO, neutralizing antibody levels in sera from 125 infants correlated well, although titers on Ap-O AO were consistently lower. We speculate that these lower titers might be an actual reflection of the neutralizing antibody capacity in vivo. The organoid-based neutralization assay described here holds promise for further characterization of correlates of protection against HRSV disease.
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Affiliation(s)
- Laura L A van Dijk
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Laurine C Rijsbergen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Bruno Tello Rubio
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Katharina S Schmitz
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Lennert Gommers
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Anouskha D Comvalius
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Alexander Havelaar
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Geert van Amerongen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Rutger Schepp
- Center of Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Corine H GeurtsvanKessel
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Rob van Binnendijk
- Center of Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rik L de Swart
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Rory D de Vries
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands.
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8
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Salwig S, Drefs J, Lücke J. Zero-shot denoising of microscopy images recorded at high-resolution limits. PLoS Comput Biol 2024; 20:e1012192. [PMID: 38857280 DOI: 10.1371/journal.pcbi.1012192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
Conventional and electron microscopy visualize structures in the micrometer to nanometer range, and such visualizations contribute decisively to our understanding of biological processes. Due to different factors in recording processes, microscopy images are subject to noise. Especially at their respective resolution limits, a high degree of noise can negatively effect both image interpretation by experts and further automated processing. However, the deteriorating effects of strong noise can be alleviated to a large extend by image enhancement algorithms. Because of the inherent high noise, a requirement for such algorithms is their applicability directly to noisy images or, in the extreme case, to just a single noisy image without a priori noise level information (referred to as blind zero-shot setting). This work investigates blind zero-shot algorithms for microscopy image denoising. The strategies for denoising applied by the investigated approaches include: filtering methods, recent feed-forward neural networks which were amended to be trainable on noisy images, and recent probabilistic generative models. As datasets we consider transmission electron microscopy images including images of SARS-CoV-2 viruses and fluorescence microscopy images. A natural goal of denoising algorithms is to simultaneously reduce noise while preserving the original image features, e.g., the sharpness of structures. However, in practice, a tradeoff between both aspects often has to be found. Our performance evaluations, therefore, focus not only on noise removal but set noise removal in relation to a metric which is instructive about sharpness. For all considered approaches, we numerically investigate their performance, report their denoising/sharpness tradeoff on different images, and discuss future developments. We observe that, depending on the data, the different algorithms can provide significant advantages or disadvantages in terms of their noise removal vs. sharpness preservation capabilities, which may be very relevant for different virological applications, e.g., virological analysis or image segmentation.
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Affiliation(s)
- Sebastian Salwig
- Machine Learning Lab, Department of Medical Physics and Acoustics, School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Jakob Drefs
- Machine Learning Lab, Department of Medical Physics and Acoustics, School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Jörg Lücke
- Machine Learning Lab, Department of Medical Physics and Acoustics, School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
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9
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Alonso-Menchén D, Sánchez-Carrillo C, Alcalá L, Soriano-Martín A, Cercenado E, Burillo A, Serrano-Lobo J, Pérez-Latorre L, Muñoz P, Bouza E. Bloodstream infections: trends and evolution of incidence and etiology in a 12-year period (2010-2021). Infect Dis (Lond) 2024; 56:441-450. [PMID: 38407125 DOI: 10.1080/23744235.2024.2320333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
INTRODUCTION The epidemiological evolution of bloodstream infections (BSIs) in the last decade is not clearly defined. Our aim was to analyze the changes in the workload in our institution and to describe the evolution of the incidence and etiology of BSIs in a 12-year period, including the COVID-19 pandemic. METHODS All blood cultures received in the laboratory of a tertiary general hospital between 2010 and 2021 were analyzed. Bloodstream infection episodes refer to each episode of bacteremia or fungemia in each patient. Incidence rates per 1000 admissions and per 100,000 population were calculated. RESULTS No significant changes in the incidence of BSI episodes/1000 admissions were observed (mean, 31.1), while estimated population-based incidences showed declining trends (mean, 182.8/100,000 inhabitants). There was a slight increase in BSI episodes per 1000 admissions caused by Gram-negatives (mean, 16.6/1000 admissions) and E. coli was the most frequent pathogen (mean, 8.5/1000 admissions). There was no significant rise in episodes caused by ESBL- and carbapenemase-producing E. coli or K. pneumoniae, with a decline in those caused by methicillin-resistant S. aureus. A spike in BSI episodes, fungal BSIs and catheter-related infections was detected in 2020, during the COVID-19 outbreak. CONCLUSIONS No clear increase in the incidence of BSI episodes was detected in our center over this period. Gram-negatives are the most frequent etiology, with no clear rise in antimicrobial resistance phenotypes. The COVID-19 pandemic accounted for a small increase in BSI episodes in 2020, probably related to the increase of catheter-related infections.
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Affiliation(s)
- David Alonso-Menchén
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CIBERES CB06/06/0058), Madrid, Spain
| | - Luis Alcalá
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CIBERES CB06/06/0058), Madrid, Spain
| | - Ana Soriano-Martín
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Emilia Cercenado
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CIBERES CB06/06/0058), Madrid, Spain
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Almudena Burillo
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Julia Serrano-Lobo
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Leire Pérez-Latorre
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Infecciosas-CIBERINFEC, Madrid, Spain
| | - Patricia Muñoz
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CIBERES CB06/06/0058), Madrid, Spain
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Emilio Bouza
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CIBERES CB06/06/0058), Madrid, Spain
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
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10
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Pasha ABT, Kotlarz N, Holcomb D, Reckling S, Kays J, Bailey E, Guidry V, Christensen A, Berkowitz S, Engel LS, de Los Reyes F, Harris A. Monitoring SARS-CoV-2 RNA in wastewater from a shared septic system and sub-sewershed sites to expand COVID-19 disease surveillance. JOURNAL OF WATER AND HEALTH 2024; 22:978-992. [PMID: 38935450 DOI: 10.2166/wh.2024.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/21/2024] [Indexed: 06/29/2024]
Abstract
Wastewater-based epidemiology has expanded as a tool for collecting COVID-19 surveillance data, but there is limited information on the feasibility of this form of surveillance within decentralized wastewater systems (e.g., septic systems). This study assessed SARS-CoV-2 RNA concentrations in wastewater samples from a septic system servicing a mobile home park (66 households) and from two pumping stations serving a similarly sized (71 households) and a larger (1,000 households) neighborhood within a nearby sewershed over 35 weeks in 2020. Also, raw wastewater from a hospital in the same sewershed was sampled. The mobile home park samples had the highest detection frequency (39/39 days) and mean concentration of SARS-CoV-2 RNA (2.7 × 107 gene copies/person/day for the N1) among the four sampling sites. N1 gene and N2 gene copies were highly correlated across mobile home park samples (Pearson's r = 0.93, p < 0.0001). In the larger neighborhood, new COVID-19 cases were reported every week during the sampling period; however, we detected SARS-CoV-2 RNA in 12% of the corresponding wastewater samples. The results of this study suggest that sampling from decentralized wastewater infrastructure can be used for continuous monitoring of SARS-CoV-2 infections.
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Affiliation(s)
- A B Tanvir Pasha
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | - Nadine Kotlarz
- Center for Human Health and the Environment, NC State, Raleigh, NC, USA
| | - David Holcomb
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Stacie Reckling
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Judith Kays
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | | | - Virginia Guidry
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Ariel Christensen
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Steven Berkowitz
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Lawrence S Engel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Francis de Los Reyes
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | - Angela Harris
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA E-mail:
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11
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Shen Q, Zhou YH, Zhou YQ. A prospects tool in virus research: Analyzing the applications of organoids in virus studies. Acta Trop 2024; 254:107182. [PMID: 38479469 DOI: 10.1016/j.actatropica.2024.107182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/28/2024]
Abstract
Organoids have emerged as a powerful tool for understanding the biology of the respiratory, digestive, nervous as well as urinary system, investigating infections, and developing new therapies. This article reviews recent progress in the development of organoid and advancements in virus research. The potential applications of these models in studying virul infections, pathogenesis, and antiviral drug discovery are discussed.
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Affiliation(s)
- Qi Shen
- Institute of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 20036, China; Institute of Microbiology Laboratory, Shanghai Institute of Preventive Medicine, Shanghai 20036, China
| | - Yu-Han Zhou
- College of Public Health, Jilin University, Changchun 130021, China
| | - Yan-Qiu Zhou
- Institute of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 20036, China; Institute of Microbiology Laboratory, Shanghai Institute of Preventive Medicine, Shanghai 20036, China.
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12
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Liu N, Liu S, Xu X, Nong X, Chen H. Organoids as an in vitro model to study human tumors and bacteria. J Surg Oncol 2024; 129:1390-1400. [PMID: 38534036 DOI: 10.1002/jso.27626] [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: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
Organoids faithfully replicate the morphological structure, physiological functions, stable phenotype of the source tissue. Recent research indicates that bacteria can significantly influence the initiation, advancement, and treatment of tumors. This article provides a comprehensive review of the applications of organoid technology in tumor research, the relationship between bacteria and the genesis and development of tumors, and the exploration of the impact of bacteria on tumors and their applications in research.
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Affiliation(s)
- Naiyu Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shuxi Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaoyue Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - XianXian Nong
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hong Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
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13
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Raj ST, Bruce AW, Anbalagan M, Srinivasan H, Chinnappan S, Rajagopal M, Khanna K, Chandramoorthy HC, Mani RR. COVID-19 influenced gut dysbiosis, post-acute sequelae, immune regulation, and therapeutic regimens. Front Cell Infect Microbiol 2024; 14:1384939. [PMID: 38863829 PMCID: PMC11165100 DOI: 10.3389/fcimb.2024.1384939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) pandemic outbreak caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has garnered unprecedented global attention. It caused over 2.47 million deaths through various syndromes such as acute respiratory distress, hypercoagulability, and multiple organ failure. The viral invasion proceeds through the ACE2 receptor, expressed in multiple cell types, and in some patients caused serious damage to tissues, organs, immune cells, and the microbes that colonize the gastrointestinal tract (GIT). Some patients who survived the SARS-CoV-2 infection have developed months of persistent long-COVID-19 symptoms or post-acute sequelae of COVID-19 (PASC). Diagnosis of these patients has revealed multiple biological effects, none of which are mutually exclusive. However, the severity of COVID-19 also depends on numerous comorbidities such as obesity, age, diabetes, and hypertension and care must be taken with respect to other multiple morbidities, such as host immunity. Gut microbiota in relation to SARS-CoV-2 immunopathology is considered to evolve COVID-19 progression via mechanisms of biochemical metabolism, exacerbation of inflammation, intestinal mucosal secretion, cytokine storm, and immunity regulation. Therefore, modulation of gut microbiome equilibrium through food supplements and probiotics remains a hot topic of current research and debate. In this review, we discuss the biological complications of the physio-pathological effects of COVID-19 infection, GIT immune response, and therapeutic pharmacological strategies. We also summarize the therapeutic targets of probiotics, their limitations, and the efficacy of preclinical and clinical drugs to effectively inhibit the spread of SARS-CoV-2.
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Affiliation(s)
- Sterlin T. Raj
- Department of Molecular Biology, Ekka Diagnostics, Chennai, Tamil Nadu, India
| | - Alexander W. Bruce
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Muralidharan Anbalagan
- Department of Structural & Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Hemalatha Srinivasan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
| | - Sasikala Chinnappan
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
| | - Mogana Rajagopal
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
| | - Kushagra Khanna
- Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Harish C. Chandramoorthy
- Department of Microbiology and Clinical Parasitology, College of Medicine, King Khalid University, Abha, Saudi Arabia
- Center for Stem Cell Research, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Ravishankar Ram Mani
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
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14
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Özçam M, Lynch SV. The gut-airway microbiome axis in health and respiratory diseases. Nat Rev Microbiol 2024:10.1038/s41579-024-01048-8. [PMID: 38778224 DOI: 10.1038/s41579-024-01048-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Communication between the gut and remote organs, such as the brain or the cardiovascular system, has been well established and recent studies provide evidence for a potential bidirectional gut-airway axis. Observations from animal and human studies indicate that respiratory insults influence the activity of the gut microbiome and that microbial ligands and metabolic products generated by the gut microbiome shape respiratory immunity. Information exchange between these two large mucosal surface areas regulates microorganism-immune interactions, with significant implications for the clinical and treatment outcomes of a range of respiratory conditions, including asthma, chronic obstructive pulmonary disease and lung cancer. In this Review, we summarize the most recent data in this field, offering insights into mechanisms of gut-airway crosstalk across spatial and temporal gradients and their relevance for respiratory health.
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Affiliation(s)
- Mustafa Özçam
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
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15
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Paužuolis M, Fatykhova D, Zühlke B, Schwecke T, Neyazi M, Samperio-Ventayol P, Aguilar C, Schlegel N, Dökel S, Ralser M, Hocke A, Krempl C, Bartfeld S. SARS-CoV-2 tropism to intestinal but not gastric epithelial cells is defined by limited ACE2 expression. Stem Cell Reports 2024; 19:629-638. [PMID: 38670110 PMCID: PMC11103887 DOI: 10.1016/j.stemcr.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection primarily affects the lung but can also cause gastrointestinal (GI) symptoms. In vitro experiments confirmed that SARS-CoV-2 robustly infects intestinal epithelium. However, data on infection of adult gastric epithelium are sparse and a side-by-side comparison of the infection in the major segments of the GI tract is lacking. We provide this direct comparison in organoid-derived monolayers and demonstrate that SARS-CoV-2 robustly infects intestinal epithelium, while gastric epithelium is resistant to infection. RNA sequencing and proteome analysis pointed to angiotensin-converting enzyme 2 (ACE2) as a critical factor, and, indeed, ectopic expression of ACE2 increased susceptibility of gastric organoid-derived monolayers to SARS-CoV-2. ACE2 expression pattern in GI biopsies of patients mirrors SARS-CoV-2 infection levels in monolayers. Thus, local ACE2 expression limits SARS-CoV-2 expression in the GI tract to the intestine, suggesting that the intestine, but not the stomach, is likely to be important in viral replication and possibly transmission.
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Affiliation(s)
- Mindaugas Paužuolis
- Research Centre for Infectious Diseases, Institute for Molecular Infection Biology, Julius Maximilians Universität Würzburg, Würzburg, Germany
| | - Diana Fatykhova
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Boris Zühlke
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Torsten Schwecke
- Core Facility for High-Throughput Mass Spectrometry, Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mastura Neyazi
- Research Centre for Infectious Diseases, Institute for Molecular Infection Biology, Julius Maximilians Universität Würzburg, Würzburg, Germany
| | - Pilar Samperio-Ventayol
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Carmen Aguilar
- Research Centre for Infectious Diseases, Institute for Molecular Infection Biology, Julius Maximilians Universität Würzburg, Würzburg, Germany
| | - Nicolas Schlegel
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Würzburg, Würzburg, Germany
| | - Simon Dökel
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Markus Ralser
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, UK; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andreas Hocke
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christine Krempl
- Institute for Virology and Immunobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Sina Bartfeld
- Research Centre for Infectious Diseases, Institute for Molecular Infection Biology, Julius Maximilians Universität Würzburg, Würzburg, Germany; Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
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16
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Cao B, Wang X, Yin W, Gao Z, Xia B. The human microbiota is a beneficial reservoir for SARS-CoV-2 mutations. mBio 2024; 15:e0318723. [PMID: 38530031 DOI: 10.1128/mbio.03187-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/14/2024] [Indexed: 03/27/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging. In particular, beneficial mutations in the spike (S) protein, which can either make a person more infectious or enable immunological escape, are providing a significant obstacle to the prevention and treatment of pandemics. However, how the virus acquires a high number of beneficial mutations in a short time remains a mystery. We demonstrate here that variations of concern may be mutated due in part to the influence of the human microbiome. We searched the National Center for Biotechnology Information database for homologous fragments (HFs) after finding a mutation and the six neighboring amino acids in a viral mutation fragment. Among the approximate 8,000 HFs obtained, 61 mutations in S and other outer membrane proteins were found in bacteria, accounting for 62% of all mutation sources, which is 12-fold higher than the natural variable proportion. A significant proportion of these bacterial species-roughly 70%-come from the human microbiota, are mainly found in the lung or gut, and share a composition pattern with COVID-19 patients. Importantly, SARS-CoV-2 RNA-dependent RNA polymerase replicates corresponding bacterial mRNAs harboring mutations, producing chimeric RNAs. SARS-CoV-2 may collectively pick up mutations from the human microbiota that change the original virus's binding sites or antigenic determinants. Our study clarifies the evolving mutational mechanisms of SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging, in particular advantageous mutations in the spike (S) protein, which either increase transmissibility or lead to immune escape and are posing a major challenge to pandemic prevention and treatment. However, how the virus acquires a high number of advantageous mutations in a short time remains a mystery. Here, we provide evidence that the human microbiota is a reservoir of advantageous mutations and aids mutational evolution and host adaptation of SARS-CoV-2. Our findings demonstrate a conceptual breakthrough on the mutational evolution mechanisms of SARS-CoV-2 for human adaptation. SARS-CoV-2 may grab advantageous mutations from the widely existing microorganisms in the host, which is undoubtedly an "efficient" manner. Our study might open a new perspective to understand the evolution of virus mutation, which has enormous implications for comprehending the trajectory of the COVID-19 pandemic.
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Affiliation(s)
- Birong Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong Guangya High School, Guangzhou, China
| | - Xiaoxi Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wanchao Yin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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17
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Hilberath J, Mast AS, Scherer S, Fuchs J, Schulte J, Sturm E, Warmann S, Slavetinsky C. Impact of COVID-19 on paediatric chronic intestinal failure: A tertiary care children's hospital experience. J Pediatr Gastroenterol Nutr 2024; 78:1171-1179. [PMID: 38477361 DOI: 10.1002/jpn3.12158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/11/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024]
Abstract
OBJECTIVES Paediatric patients with intestinal failure (IF) are at risk for both gastrointestinal (GI) and systemic complications, thus depending on a functioning network of multidisciplinary care. Data on the clinical impact of coronavirus disease 2019 (COVID-19) or the pandemic-related restrictions are limited. We aimed to analyse the clinical course of COVID-19 in children with IF, and to evaluate the perceived impact of the COVID-19 pandemic on IF patients and their caregivers by analysing quality of life (QoL), health-related QoL (HRQoL) and health care. METHODS Children with IF presenting at our intestinal rehabilitation centre were enrolled and interviewed about test-proven COVID-19 infection. A standardised questionnaire was offered to all caregivers of IF patients and to two control groups (children with inflammatory bowel disease and gastrointestinal healthy children). RESULTS Between December 2020 and November 2022, 25 out of 127 patients with IF contracted COVID-19. Forty-eight per cent had GI symptoms, 32% required additional intravenous fluids and 20% were hospitalized. Only 25% of vaccinated children showed signs of GI dysfunction, compared to 52% of unvaccinated children. Analysis of 93 questionnaires showed a negative impact on QoL and HRQoL (>66.7% and >27.8%, respectively). IF patients frequently experienced restrictions in health care, including appointments, services and supply of parenteral nutrition or medications. Caregiver burden increased significantly more often in caregivers of children with IF (p = 0.007). CONCLUSIONS Paediatric patients with IF contracting COVID-19 have an increased risk for GI dysfunction which may be alleviated by vaccination. Children and their caregivers were highly burdened by pandemic-related restrictions and reductions in health care provision.
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Affiliation(s)
- Johannes Hilberath
- Paediatric Gastroenterology and Hepatology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Anna-Sophia Mast
- Department of Haematology and Oncology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Simon Scherer
- Paediatric Surgery and Urology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Jörg Fuchs
- Paediatric Surgery and Urology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Johannes Schulte
- Department of Haematology and Oncology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Ekkehard Sturm
- Paediatric Gastroenterology and Hepatology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Steven Warmann
- Paediatric Surgery and Urology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Christoph Slavetinsky
- Paediatric Surgery and Urology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
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18
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Li AY, Li WX, Li J. Emerging trends in management of long COVID with a focus on pulmonary rehabilitation: A review. THE CLINICAL RESPIRATORY JOURNAL 2024; 18:e13777. [PMID: 38775379 PMCID: PMC11110486 DOI: 10.1111/crj.13777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/10/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
Long COVID, or post-acute sequelae of COVID-19 (PASC), represents a complex condition with persistent symptoms following SARS-Cov-2 infection. The symptoms include fatigue, dyspnoea, cognitive impairment, decreased quality of life in variable levels of severity. Potential mechanisms behind long COVID include vascular damage, immune dysregulation and viral persistence. Diagnosing long COVID involves medical evaluation by multidisciplinary team and assessment of persistent symptoms with scoring systems in development. Treatment strategies are symptom-focused, encompassing multidisciplinary care, rehabilitation and tailored exercise programmes. Pulmonary rehabilitation, an effective and critical component of long COVID management, has shown promise, particularly for patients with respiratory symptoms such as dyspnoea. These programmes, which combine exercise, breathing techniques, education and psychological support, improve symptoms, quality of life and overall recovery. Innovative technologies, such as telemedicine, wearable devices, telerehabilitation, are transforming long COVID management. Telemedicine facilitates consultations and interventions, eliminating healthcare access barriers. Wearable devices enable remote and continuous monitoring of patients during their rehabilitation activities. Telerehabilitation has proven to be safe and feasible and to have high potential for COVID-19 recovery. This review provides a concise overview of long COVID, encompassing its definition, prevalence, mechanisms, clinical manifestations, diagnosis and management approaches. It emphasizes the significance of multidisciplinary approach in diagnosis and treatment of long COVID, with focus on pulmonary rehabilitation and innovative technology advances to effectively address the management of long COVID.
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Affiliation(s)
- Allison Y. Li
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- College of EngineeringUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Willis X. Li
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jinghong Li
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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19
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Antia A, Alvarado DM, Zeng Q, Casorla-Perez LA, Davis DL, Sonnek NM, Ciorba MA, Ding S. SARS-CoV-2 Omicron BA.1 Variant Infection of Human Colon Epithelial Cells. Viruses 2024; 16:634. [PMID: 38675974 PMCID: PMC11055019 DOI: 10.3390/v16040634] [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: 03/05/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The Omicron variant of SARS-CoV-2, characterized by multiple subvariants including BA.1, XBB.1.5, EG.5, and JN.1, became the predominant strain in early 2022. Studies indicate that Omicron replicates less efficiently in lung tissue compared to the ancestral strain. However, the infectivity of Omicron in the gastrointestinal tract is not fully defined, despite the fact that 70% of COVID-19 patients experience digestive disease symptoms. Here, using primary human colonoids, we found that, regardless of individual variability, Omicron infects colon cells similarly or less effectively than the ancestral strain or the Delta variant. The variant induced limited type III interferon expression and showed no significant impact on epithelial integrity. Further experiments revealed inefficient cell-to-cell spread and spike protein cleavage in the Omicron spike protein, possibly contributing to its lower infectious particle levels. The findings highlight the variant-specific replication differences in human colonoids, providing insights into the enteric tropism of Omicron and its relevance to long COVID symptoms.
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Affiliation(s)
- Avan Antia
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.A.); (Q.Z.)
| | - David M. Alvarado
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Qiru Zeng
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.A.); (Q.Z.)
| | - Luis A. Casorla-Perez
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Deanna L. Davis
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Naomi M. Sonnek
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Matthew A. Ciorba
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (D.M.A.); (D.L.D.); (N.M.S.)
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.A.); (Q.Z.)
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20
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Hayashi T, Kobayashi S, Hirano J, Murakami K. Human norovirus cultivation systems and their use in antiviral research. J Virol 2024; 98:e0166323. [PMID: 38470106 PMCID: PMC11019851 DOI: 10.1128/jvi.01663-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Human norovirus (HuNoV) is a major cause of acute gastroenteritis and foodborne diseases, affecting all age groups. Despite its clinical needs, no approved antiviral therapies are available. Since the discovery of HuNoV in 1972, studies on anti-norovirals, mechanism of HuNoV infection, viral inactivation, etc., have been hampered by the lack of a robust laboratory-based cultivation system for HuNoV. A recent breakthrough in the development of HuNoV cultivation systems has opened opportunities for researchers to investigate HuNoV biology in the context of de novo HuNoV infections. A tissue stem cell-derived human intestinal organoid/enteroid (HIO) culture system is one of those that supports HuNoV replication reproducibly and, to our knowledge, is most widely distributed to laboratories worldwide to study HuNoV and develop therapeutic strategies. This review summarizes recently developed HuNoV cultivation systems, including HIO, and their use in antiviral studies.
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Affiliation(s)
- Tsuyoshi Hayashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sakura Kobayashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Junki Hirano
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Kosuke Murakami
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
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21
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Chau CW, To A, Au-Yeung RKH, Tang K, Xiang Y, Ruan D, Zhang L, Wong H, Zhang S, Au MT, Chung S, Song E, Choi DH, Liu P, Yuan S, Wen C, Sugimura R. SARS-CoV-2 infection activates inflammatory macrophages in vascular immune organoids. Sci Rep 2024; 14:8781. [PMID: 38627497 PMCID: PMC11021416 DOI: 10.1038/s41598-024-59405-9] [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: 12/07/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
SARS-CoV-2 provokes devastating tissue damage by cytokine release syndrome and leads to multi-organ failure. Modeling the process of immune cell activation and subsequent tissue damage is a significant task. Organoids from human tissues advanced our understanding of SARS-CoV-2 infection mechanisms though, they are missing crucial components: immune cells and endothelial cells. This study aims to generate organoids with these components. We established vascular immune organoids from human pluripotent stem cells and examined the effect of SARS-CoV-2 infection. We demonstrated that infections activated inflammatory macrophages. Notably, the upregulation of interferon signaling supports macrophages' role in cytokine release syndrome. We propose vascular immune organoids are a useful platform to model and discover factors that ameliorate SARS-CoV-2-mediated cytokine release syndrome.
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Affiliation(s)
- Chiu Wang Chau
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Alex To
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rex K H Au-Yeung
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yang Xiang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Degong Ruan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lanlan Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Hera Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Shihui Zhang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Man Ting Au
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | | | | | | | - Pentao Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Centre for Translational Stem Cell Biology, Sha Tin, Hong Kong
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Chunyi Wen
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.
| | - Ryohichi Sugimura
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
- Centre for Translational Stem Cell Biology, Sha Tin, Hong Kong.
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22
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Luo Y, Zhang Z, Ren J, Dou C, Wen J, Yang Y, Li X, Yan Z, Han Y. SARS-Cov-2 spike induces intestinal barrier dysfunction through the interaction between CEACAM5 and Galectin-9. Front Immunol 2024; 15:1303356. [PMID: 38686388 PMCID: PMC11056506 DOI: 10.3389/fimmu.2024.1303356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Background Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), as a typical tumor marker, has been found to exert immunomodulatory effects in many diseases. We previously reported the clinical and molecular evidences supporting that SARS-Cov-2 infected the gastrointestinal (GI) tract and found a reduction of CEACAM5 in COVID-19 patients' feces which associated with gut dysbiosis. Yet the role of CEACAM5 in GI infection is ill-defined. Methods Mice models were established through intraperitoneally injecting with recombinant viral spike-Fc to mimic the intestinal inflammation. We collected duodenum, jejunum, ileum and colon samples after 6h, 2 days, 4 days and 7 days of spike-Fc or control-Fc injection to perform proteomic analysis. Blood was collected from healthy donors and peripheral blood mononuclear cells (PBMC) were separated by density gradient centrifugation, then CD4+ T cells were isolated with magnetic beads and co-cultured with Caco-2 cells. Results In addition to intestinal CEACAM5, the expression of tight junction and the percent of CD4+ T lymphocytes were significantly decreased in spike-Fc group compared to control (p < 0.05), accompanied with increased level of inflammatory factors. The KEGG analysis revealed differentially expressed proteins were mainly enriched in the coronavirus disease (COVID-19), tight junction, focal adhesion, adherens junction and PI3K-Akt signaling pathway. Protein-protein interaction (PPI) network analysis identified the interaction between CEACAM5 and Galectin-9 that was also verified by molecular docking and co-IP assay. We further confirmed a reduction of CEACAM5 in SARS-CoV-2 spike stimulated enterocytes could promote the expression of Galectin-9 protein in CD4+T cells. Then it gave rise to the increasing release of inflammatory factors and increased apoptosis of CD4+T cells by inhibition of PI3K/AKT/mTOR pathway. Ultimately intestinal barrier dysfunction happened. Conclusion Our results indicated that CEACAM5 overexpression and Galectin-9 knockdown played a protective role in intestinal barrier injury upon spike-Fc stimulation. Collectively, our findings identified firstly that SARS-CoV-2 spike induced intestinal barrier dysfunction through the interaction between CEACAM5 and Galectin-9. The result provides potential therapeutic targets in intestinal barrier dysfunction for treating severe COVID patients.
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Affiliation(s)
- Yingshu Luo
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zhenling Zhang
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jiangnan Ren
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Chunxu Dou
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jiancheng Wen
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Yang Yang
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Xiaofeng Li
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zhixiang Yan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Yanzhi Han
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
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23
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Son R, Yamazawa K, Oguchi A, Suga M, Tamura M, Yanagita M, Murakawa Y, Kume S. Morphomics via next-generation electron microscopy. J Mol Cell Biol 2024; 15:mjad081. [PMID: 38148118 PMCID: PMC11167312 DOI: 10.1093/jmcb/mjad081] [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: 03/22/2022] [Revised: 10/02/2022] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
The living body is composed of innumerable fine and complex structures. Although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.
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Affiliation(s)
- Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kenji Yamazawa
- Advanced Manufacturing Support Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan
| | - Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Mitsuo Suga
- Multimodal Microstructure Analysis Unit, RIKEN–JEOL Collaboration Center, Kobe 650-0047, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- IFOM—The FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Satoshi Kume
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
- Center for Health Science Innovation, Osaka City University, Osaka 530-0011, Japan
- Osaka Electro-Communication University, Neyagawa 572-8530, Japan
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24
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Bigotti MG, Klein K, Gan ES, Anastasina M, Andersson S, Vapalahti O, Katajisto P, Erdmann M, Davidson AD, Butcher SJ, Collinson I, Ooi EE, Balistreri G, Brancaccio A, Yamauchi Y. The α-dystroglycan N-terminus is a broad-spectrum antiviral agent against SARS-CoV-2 and enveloped viruses. Antiviral Res 2024; 224:105837. [PMID: 38387750 DOI: 10.1016/j.antiviral.2024.105837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/20/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The COVID-19 pandemic has shown the need to develop effective therapeutics in preparedness for further epidemics of virus infections that pose a significant threat to human health. As a natural compound antiviral candidate, we focused on α-dystroglycan, a highly glycosylated basement membrane protein that links the extracellular matrix to the intracellular cytoskeleton. Here we show that the N-terminal fragment of α-dystroglycan (α-DGN), as produced in E. coli in the absence of post-translational modifications, blocks infection of SARS-CoV-2 in cell culture, human primary gut organoids and the lungs of transgenic mice expressing the human receptor angiotensin I-converting enzyme 2 (hACE2). Prophylactic and therapeutic administration of α-DGN reduced SARS-CoV-2 lung titres and protected the mice from respiratory symptoms and death. Recombinant α-DGN also blocked infection of a wide range of enveloped viruses including the four Dengue virus serotypes, influenza A virus, respiratory syncytial virus, tick-borne encephalitis virus, but not human adenovirus, a non-enveloped virus in vitro. This study establishes soluble recombinant α-DGN as a broad-band, natural compound candidate therapeutic against enveloped viruses.
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Affiliation(s)
- Maria Giulia Bigotti
- Bristol Heart Institute, Research Floor Level 7, Bristol Royal Infirmary, Bristol BS2 8HW, UK; School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Katja Klein
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Esther S Gan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Maria Anastasina
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Simon Andersson
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pekka Katajisto
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Solna, Sweden
| | - Maximilian Erdmann
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ian Collinson
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore; Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, 20 College Road, Singapore, 169856, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, Singapore, 117549, Singapore
| | - Giuseppe Balistreri
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland; Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Andrea Brancaccio
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK; Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC)-CNR, Rome, Italy.
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK; Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, 8093, Zurich, Switzerland; Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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25
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Liu W, Yang P, Yang P, Yang L, Jing H, Zhao L, Zhao R. Clinical characteristics and pharmacokinetics of PAXLOVID in COVID-19 patients with hematological tumor. MEDICAL REVIEW (2021) 2024; 4:169-171. [PMID: 38680682 PMCID: PMC11046570 DOI: 10.1515/mr-2023-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/06/2024] [Indexed: 05/01/2024]
Affiliation(s)
- Wei Liu
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
- Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, China
- NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing, China
- Institute for Drug Evaluation, Peking University Health Science Center, Beijing, China
| | - Ping Yang
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
- Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, China
- NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing, China
- Institute for Drug Evaluation, Peking University Health Science Center, Beijing, China
| | - Ping Yang
- Department of Hematology, Peking University Third Hospital, Beijing, China
| | - Li Yang
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
- Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, China
- NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing, China
- Institute for Drug Evaluation, Peking University Health Science Center, Beijing, China
| | - Hongmei Jing
- Department of Hematology, Peking University Third Hospital, Beijing, China
| | - Libo Zhao
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
- Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, China
- NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing, China
- Institute for Drug Evaluation, Peking University Health Science Center, Beijing, China
| | - Rongsheng Zhao
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
- Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, China
- NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing, China
- Institute for Drug Evaluation, Peking University Health Science Center, Beijing, China
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26
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Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
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Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
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27
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Zeng Z, Tang W. Gut microbiota: A potential player in psychiatric symptoms during COVID-19. World J Biol Psychiatry 2024; 25:267-280. [PMID: 38607962 DOI: 10.1080/15622975.2024.2342846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
OBJECTIVES This study aims to explore the potential interconnections among gut microbiota, COVID-19 infection, depression and anxiety disorder. Additionally, it tries to assess potential therapeutic interventions that may improve the dysbiosis of gut microbiota. METHODS To achieve these objectives, we reviewed existing literature, encompassing studies and critical reviews that intersect the domains of gut microbiota, COVID-19, depression and anxiety disorders. RESULTS The findings highlight a notable correlation between the dysbiosis of gut microbiota and psychiatric symptoms in the context of COVID-19. Specifically, there is a marked reduction in the populations of bacteria that generate anti-inflammatory short-chain fatty acids (SCFAs), alongside a rise in the prevalence of gut bacterial clusters linked to inflammatory processes. Furthermore, several potential treatment strategies were summarised for improving the dysbiosis. CONCLUSIONS Gut microbiota plays a significant role in psychiatric symptoms during COVID-19, which has significant implications for the study and prevention of psychiatric symptoms in major epidemic diseases.
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Affiliation(s)
- Zijie Zeng
- Department of Psychology, School of Public Health, Southern Medical University, Guangzhou, China
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28
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Chen B, Du C, Wang M, Guo J, Liu X. Organoids as preclinical models of human disease: progress and applications. MEDICAL REVIEW (2021) 2024; 4:129-153. [PMID: 38680680 PMCID: PMC11046574 DOI: 10.1515/mr-2023-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/28/2024] [Indexed: 05/01/2024]
Abstract
In the field of biomedical research, organoids represent a remarkable advancement that has the potential to revolutionize our approach to studying human diseases even before clinical trials. Organoids are essentially miniature 3D models of specific organs or tissues, enabling scientists to investigate the causes of diseases, test new drugs, and explore personalized medicine within a controlled laboratory setting. Over the past decade, organoid technology has made substantial progress, allowing researchers to create highly detailed environments that closely mimic the human body. These organoids can be generated from various sources, including pluripotent stem cells, specialized tissue cells, and tumor tissue cells. This versatility enables scientists to replicate a wide range of diseases affecting different organ systems, effectively creating disease replicas in a laboratory dish. This exciting capability has provided us with unprecedented insights into the progression of diseases and how we can develop improved treatments. In this paper, we will provide an overview of the progress made in utilizing organoids as preclinical models, aiding our understanding and providing a more effective approach to addressing various human diseases.
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Affiliation(s)
- Baodan Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cijie Du
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengfei Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Guo
- Innovation Centre for Advanced Interdisciplinary Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
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29
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Miyakawa K, Machida M, Kawasaki T, Kakizaki M, Kimura Y, Sugiyama M, Hasegawa H, Umezawa A, Akutsu H, Ryo A. Replication Efficiency of SARS-CoV-2 Omicron Subvariants BA.2.75, BA.5, and XBB.1 in Human Mini-Gut Organoids. Cell Mol Gastroenterol Hepatol 2024; 17:1066-1068. [PMID: 38494057 PMCID: PMC11127620 DOI: 10.1016/j.jcmgh.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024]
Affiliation(s)
- Kei Miyakawa
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Tokyo, Japan; Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan.
| | - Masakazu Machida
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoyuki Kawasaki
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Masatoshi Kakizaki
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Masaya Sugiyama
- Department of Viral Pathogenesis and Controls, National Center for Global Health and Medicine, Chiba, Japan
| | - Hideki Hasegawa
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan.
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan; Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan.
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30
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Liao Z, Wang C, Tang X, Yang M, Duan Z, Liu L, Lu S, Ma L, Cheng R, Wang G, Liu H, Yang S, Xu J, Tadese DA, Mwangi J, Kamau PM, Zhang Z, Yang L, Liao G, Zhao X, Peng X, Lai R. Human transferrin receptor can mediate SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2024; 121:e2317026121. [PMID: 38408250 DOI: 10.1073/pnas.2317026121] [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: 10/09/2023] [Accepted: 01/08/2024] [Indexed: 02/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been detected in almost all organs of coronavirus disease-19 patients, although some organs do not express angiotensin-converting enzyme-2 (ACE2), a known receptor of SARS-CoV-2, implying the presence of alternative receptors and/or co-receptors. Here, we show that the ubiquitously distributed human transferrin receptor (TfR), which binds to diferric transferrin to traffic between membrane and endosome for the iron delivery cycle, can ACE2-independently mediate SARS-CoV-2 infection. Human, not mouse TfR, interacts with Spike protein with a high affinity (KD ~2.95 nM) to mediate SARS-CoV-2 endocytosis. TfR knock-down (TfR-deficiency is lethal) and overexpression inhibit and promote SARS-CoV-2 infection, respectively. Humanized TfR expression enables SARS-CoV-2 infection in baby hamster kidney cells and C57 mice, which are known to be insusceptible to the virus infection. Soluble TfR, Tf, designed peptides blocking TfR-Spike interaction and anti-TfR antibody show significant anti-COVID-19 effects in cell and monkey models. Collectively, this report indicates that TfR is a receptor/co-receptor of SARS-CoV-2 mediating SARS-CoV-2 entry and infectivity by likely using the TfR trafficking pathway.
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Affiliation(s)
- Zhiyi Liao
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaoming Wang
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaopeng Tang
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Mengli Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming 650118, China
| | - Zilei Duan
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
| | - Lei Liu
- Laboratory of Animal Tumor Models, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming 650118, China
| | - Lei Ma
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming 650118, China
| | - Ruomei Cheng
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
| | - Gan Wang
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
| | - Hongqi Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming 650118, China
| | - Shuo Yang
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingwen Xu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming 650118, China
| | - Dawit Adisu Tadese
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - James Mwangi
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peter Muiruri Kamau
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiye Zhang
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
| | - Lian Yang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Guoyang Liao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming 650118, China
| | - Xudong Zhao
- Laboratory of Animal Tumor Models, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming 650118, China
| | - Ren Lai
- Engineering Laboratory of Peptides of Chinese Academy of Sciences, Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), and Sino-African Joint Research Center, New Cornerstone Science Laboratory, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650201, China
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31
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Walocha R, Kim M, Wong-Ng J, Gobaa S, Sauvonnet N. Organoids and organ-on-chip technology for investigating host-microorganism interactions. Microbes Infect 2024:105319. [PMID: 38447861 DOI: 10.1016/j.micinf.2024.105319] [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: 10/03/2023] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024]
Abstract
Recent advances in organoid and organ-on-chip (OoC) technologies offer an unprecedented level of tissue mimicry. These models can recapitulate the diversity of cellular composition, 3D organization, and mechanical stimulation. These approaches are intensively used to understand complex diseases. This review focuses on the latest advances in this field to study host-microorganism interactions.
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Affiliation(s)
- Remigiusz Walocha
- Tissue Homeostasis Group, Biomaterials and Microfluidics Core Facility, Institut Pasteur, Université Paris Cité, Paris, France; Biomaterials and Microfluidics Core Facility, Institut Pasteur, Université Paris Cité, Paris, France
| | - MinHee Kim
- Biomaterials and Microfluidics Core Facility, Institut Pasteur, Université Paris Cité, Paris, France
| | - Jérôme Wong-Ng
- Biomaterials and Microfluidics Core Facility, Institut Pasteur, Université Paris Cité, Paris, France
| | - Samy Gobaa
- Biomaterials and Microfluidics Core Facility, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nathalie Sauvonnet
- Tissue Homeostasis Group, Biomaterials and Microfluidics Core Facility, Institut Pasteur, Université Paris Cité, Paris, France; Biomaterials and Microfluidics Core Facility, Institut Pasteur, Université Paris Cité, Paris, France.
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32
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Norese C, Nicosia E, Cortese K, Gentili V, Rizzo R, Rizzo S, Grasselli E, De Negri Atanasio G, Gagliani MC, Tiso M, Zinni M, Pulliero A, Izzotti A. SARS-CoV-2 presence in recreational seawater and evaluation of intestine permeability: experimental evidence of low impact on public health. Front Public Health 2024; 12:1326453. [PMID: 38500723 PMCID: PMC10944960 DOI: 10.3389/fpubh.2024.1326453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction Coastal seawater pollution poses a public health risk due to the potential ingestion of contaminated water during recreational activities. Wastewater-based epidemiology has revealed the abundant presence of SARS-CoV-2 in seawater emitted from wastewater outlets. The objective of this research was to investigate the impact of seawater on SARS-CoV-2 infectivity to assess the safety of recreational activities in seawater. Methods Wild SARS-CoV-2 was collected from oral swabs of COVID-19 affected patients and incubated for up to 90 min using the following solutions: (a) standard physiological solution (control), (b) reconstructed seawater (3.5% NaCl), and (c) authentic seawater (3.8%). Samples were then exposed to two different host systems: (a) Vero E6 cells expressing the ACE2 SARS-CoV-2 receptor and (b) 3D multi-tissue organoids reconstructing the human intestine. The presence of intracellular virus inside the host systems was determined using plaque assay, quantitative real-time PCR (qPCR), and transmission electron microscopy. Results Ultrastructural examination of Vero E6 cells revealed the presence of virus particles at the cell surface and in replicative compartments inside cells treated with seawater and/or reconstituted water only for samples incubated up to 2 min. After a 90-min incubation, the presence of the virus and its infectivity in Vero E6 cells was reduced by 90%. Ultrastructural analysis performed in 3D epi-intestinal tissue did not reveal intact viral particles or infection signs, despite the presence of viral nucleic acid detected by qPCR. Indeed, viral genes (Orf1ab and N) were found in the intestinal luminal epithelium but not in the enteric capillaries. These findings suggest that the intestinal tissue is not a preferential entry site for SARS-CoV-2 in the human body. Additionally, the presence of hypertonic saline solution did not increase the susceptibility of the intestinal epithelium to virus penetration; rather, it neutralized its infectivity. Conclusion Our results indicate that engaging in recreational activities in a seawater environment does not pose a significant risk for COVID-19 infection, despite the possible presence of viral nucleic acid deriving from degraded and fragmented viruses.
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Affiliation(s)
- Clelia Norese
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Elena Nicosia
- Regione Liguria, Environmental Department, Ligurian Region, Genoa, Italy
| | - Katia Cortese
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
- LTTA, Clinical Research Center, University of Ferrara, Ferrara, Italy
| | - Sabrina Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Elena Grasselli
- Department of Earth, Environmental, and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Giulia De Negri Atanasio
- Department of Earth, Environmental, and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | | | - Micaela Tiso
- MICAMO, Spin-Off Department of Earth Sciences, University of Genoa, Genoa, Italy
| | - Matteo Zinni
- MICAMO, Spin-Off Department of Earth Sciences, University of Genoa, Genoa, Italy
| | | | - Alberto Izzotti
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
- HSM, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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Matsubara Y, Kiyohara H, Mikami Y, Nanki K, Namkoong H, Chubachi S, Tanaka H, Azekawa S, Sugimoto S, Yoshimatsu Y, Sujino T, Takabayashi K, Hosoe N, Sato T, Ishii M, Hasegawa N, Okada Y, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Fukunaga K, Kanai T. Gastrointestinal symptoms in COVID-19 and disease severity: a Japanese registry-based retrospective cohort study. J Gastroenterol 2024; 59:195-208. [PMID: 38270615 DOI: 10.1007/s00535-023-02071-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/24/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND Research on whether gastrointestinal symptoms correlate with the severity of Coronavirus Disease 2019 (COVID-19) has been inconclusive. This study aimed to clarify any associations between gastrointestinal symptoms and the prognosis of COVID-19. METHODS We collected data from the Japanese nationwide registry for COVID-19 to conduct a retrospective cohort study. Data from 3498 Japanese COVID-19 patients, diagnosed at 74 facilities between February 2020 and August 2022, were analyzed in this study. Hospitalized patients were followed up until discharge or transfer to another hospital. Outpatients were observed until the end of treatment. Associations between gastrointestinal symptoms and clinical outcomes were investigated using multivariable-adjusted logistic regression models. RESULTS The prevalence of diarrhea, nausea/vomiting, abdominal pain, and melena were 16.6% (581/3498), 8.9% (311/3498), 3.5% (121/3498), and 0.7% (23/3498), respectively. In the univariable analysis, admission to intensive care unit (ICU) and requirement for mechanical ventilation were less common in patients with diarrhea than those without (ICU, 15.7% vs. 20.6% (p = 0.006); mechanical ventilation, 7.9% vs. 11.4% (p = 0.013)). In the multivariable-adjusted analysis, diarrhea was associated with lower likelihood of ICU admission (adjusted odds ratio (aOR), 0.70; 95% confidence interval (CI), 0.53-0.92) and mechanical ventilation (aOR, 0.61; 95% CI, 0.42-0.89). Similar results were obtained in a sensitivity analysis with another logistic regression model that adjusted for 14 possible covariates with diarrhea (ICU; aOR, 0.70; 95% CI, 0.53-0.93; mechanical ventilation; aOR 0.62; 95% CI, 0.42-0.92). CONCLUSIONS Diarrhea was associated with better clinical outcomes in COVID-19 patients.
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Affiliation(s)
- Yuta Matsubara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Hiroki Kiyohara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan.
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Kosaku Nanki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Shotaro Chubachi
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hiromu Tanaka
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shuhei Azekawa
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shinya Sugimoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Yusuke Yoshimatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Kaoru Takabayashi
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Hosoe
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Toshiro Sato
- Department of Integrative Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Makoto Ishii
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Ryuji Koike
- Health Science Research and Development Center (HeRD), Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
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MacCann R, Ghosh TS, Garcia Leon AA, Li J, Negi R, Gaillard C, Saini G, Tinago W, Feeney ER, Yousif O, Cotter AG, de Barra E, Sadlier C, Doran P, Landay A, O'Toole PW, Mallon PW. Associations between host microbiome and inflammation suggest role for host microbiome in driving COVID-19 disease severity. Microbes Infect 2024; 26:105247. [PMID: 37944587 DOI: 10.1016/j.micinf.2023.105247] [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: 04/12/2023] [Revised: 09/04/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Systemic inflammation and innate immune activation are associated with COVID-19 disease severity. Knowledge gaps remain in the relationships between microbiome, inflammation and COVID-19 disease severity. To better characterise these associations, we performed 16SrDNA analysis of stool samples in COVID-19 subjects to explore diversity and taxanomic composition. We correlated these to host inflammatory profiles, derived from soluble plasma biomarkers measured by bead-based fluorescence and electrochemiluminescence immunoassays. Associations of microbial diversity and inflammatory biomarkers on maximal COVID-19 severity (mild, moderate v severe/critical) was explored using logistic regression and weighted gene correlation network analysis (WGCNA). Of 79 subjects, 58% were male and 88% were Caucasian with 36% experiencing mild disease, 22% moderate disease and 40% critical/severe COVID-19. Hierarchical clustering and principal component analysis (PCo) revealed distinct inflammatory clusters that were found to correlate with 4 modules of microbiome profiles. Modules 3 and 4 were associated with both older age and severe/critical disease outcomes. These modules were enriched in pathogenic and inflammatory bacteria that mapped to a pro-inflammatory biomarker cluster. In contrast, module 1 exhibited enrichment of anti-inflammatory bacteria, was associated with younger age and mild/moderate disease outcomes and mapped to a less-inflamed biomarker cluster. This study provides further insights into links between host microbiome, inflammatory responses to SARS-CoV-2 infection and clinical COVID-19 disease severity, suggesting a role for the microbiome in shaping distinct host inflammatory responses to infection.
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Affiliation(s)
- Rachel MacCann
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Department of Infectious Diseases, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland; Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Alejandro Abner Garcia Leon
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin 4, Ireland
| | - Junhui Li
- APC Microbiome Ireland, Cork, Ireland
| | - Riya Negi
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin 4, Ireland
| | - Colette Gaillard
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin 4, Ireland
| | - Gurvin Saini
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin 4, Ireland
| | - Willard Tinago
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin 4, Ireland
| | - Eoin R Feeney
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Department of Infectious Diseases, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Obada Yousif
- Endocrinology Department, Wexford General Hospital, Carricklawn, Wexford, Ireland
| | - Aoife G Cotter
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin 4, Ireland; Department of Infectious Diseases, Mater Misericordiae University Hospital, Eccles St, Dublin 7, Ireland
| | - Eoghan de Barra
- Department of Infectious Diseases, Beaumont Hospital, Beaumont, Dublin 9, Ireland; Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Corinna Sadlier
- Department of Infectious Diseases, Cork University Hospital, Wilton, Co Cork, Ireland
| | - Peter Doran
- Clinical Trials Institute, University of Galway
| | - Alan Landay
- Department of Internal Medicine, Rush University, Chicago, IL, USA
| | | | - Patrick W Mallon
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Department of Infectious Diseases, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland; Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Belfield, Dublin 4, Ireland
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35
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Ribó-Molina P, van Nieuwkoop S, Mykytyn AZ, van Run P, Lamers MM, Haagmans BL, Fouchier RAM, van den Hoogen BG. Human metapneumovirus infection of organoid-derived human bronchial epithelium represents cell tropism and cytopathology as observed in in vivo models. mSphere 2024; 9:e0074323. [PMID: 38265200 PMCID: PMC10900881 DOI: 10.1128/msphere.00743-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Human metapneumovirus (HMPV), a member of the Pneumoviridae family, causes upper and lower respiratory tract infections in humans. In vitro studies with HMPV have mostly been performed in monolayers of undifferentiated epithelial cells. In vivo studies in cynomolgus macaques and cotton rats have shown that ciliated epithelial cells are the main target of HMPV infection, but these observations cannot be studied in monolayer systems. Here, we established an organoid-derived bronchial culture model that allows physiologically relevant studies on HMPV. Inoculation with multiple prototype HMPV viruses and recent clinical virus isolates led to differences in replication among HMPV isolates. Prolific HMPV replication in this model caused damage to the ciliary layer, including cilia loss at advanced stages post-infection. These cytopathic effects correlated with those observed in previous in vivo studies with cynomolgus macaques. The assessment of the innate immune responses in three donors upon HMPV and RSV inoculation highlighted the importance of incorporating multiple donors to account for donor-dependent variation. In conclusion, these data indicate that the organoid-derived bronchial cell culture model resembles in vivo findings and is therefore a suitable and robust model for future HMPV studies. IMPORTANCE Human metapneumovirus (HMPV) is one of the leading causative agents of respiratory disease in humans, with no treatment or vaccine available yet. The use of primary epithelial cultures that recapitulate the tissue morphology and biochemistry of the human airways could aid in defining more relevant targets to prevent HMPV infection. For this purpose, this study established the first primary organoid-derived bronchial culture model suitable for a broad range of HMPV isolates. These bronchial cultures were assessed for HMPV replication, cellular tropism, cytopathology, and innate immune responses, where the observations were linked to previous in vivo studies with HMPV. This study exposed an important gap in the HMPV field since extensively cell-passaged prototype HMPV B viruses did not replicate in the bronchial cultures, underpinning the need to use recently isolated viruses with a controlled passage history. These results were reproducible in three different donors, supporting this model to be suitable to study HMPV infection.
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Affiliation(s)
- Pau Ribó-Molina
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Anna Z. Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M. Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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36
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Wang Y, Yi Y, Zhang F, Yao YY, Chen YX, Wu CM, Wang RY, Yan M. Lung Ultrasound Score as a Predictor of Failure to Wean COVID-19 Elderly Patients off Mechanical Ventilation: A Prospective Observational Study. Clin Interv Aging 2024; 19:313-322. [PMID: 38404479 PMCID: PMC10887876 DOI: 10.2147/cia.s438714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
Background The lung ultrasound score was developed for rapidly assessing the extent of lung ventilation, and it can predict failure to wean various types of patients off mechanical ventilation. Whether it is also effective for COVID-19 patients is unclear. Methods This single-center, prospective, observational study was conducted to assess the ability of the 12-region lung ultrasound score to predict failure to wean COVID-19 patients off ventilation. In parallel, we assessed whether right hemidiaphragmatic excursion or previously published predictors of weaning failure can apply to these patients. Predictive ability was assessed in terms of the area under the receiver operating characteristic curve (AUC). Results The mean age of the 35 patients in the study was (75 ± 9) years and 12 patients (37%) could not be weaned off mechanical ventilation. The lung ultrasound score predicted these failures with an AUC of 0.885 (95% CI 0.770-0.999, p < 0.001), and a threshold score of 10 provided specificity of 72.7% and sensitivity of 92.3%. AUCs were lower for previously published predictors of weaning failure, and right hemidiaphragmatic excursion did not differ significantly between the two groups. Conclusion The lung ultrasound score can accurately predict failure to wean critically ill COVID-19 patients off mechanical ventilation, whereas assessment of right hemidiaphragmatic excursion does not appear helpful in this regard. Trial Registration https://clinicaltrials.gov/ct2/show/NCT05706441.
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Affiliation(s)
- Ying Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
| | - Yu Yi
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
| | - Fan Zhang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
| | - Yuan-Yuan Yao
- Department of Anesthesiology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310016, People’s Republic of China
| | - Yue-Xiu Chen
- Department of Anesthesiology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310016, People’s Republic of China
| | - Chao-Min Wu
- Department of Anesthesiology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310016, People’s Republic of China
| | - Rui-Yu Wang
- Department of Anesthesiology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310016, People’s Republic of China
| | - Min Yan
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
- Department of Anesthesiology, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310016, People’s Republic of China
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37
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Isaguliants MG, Ivanov AV, Buonaguro FM. Chronic Viral Infections and Cancer, Openings for Therapies and Vaccines. Cancers (Basel) 2024; 16:818. [PMID: 38398209 PMCID: PMC10886681 DOI: 10.3390/cancers16040818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 02/25/2024] Open
Abstract
Infections are responsible for approximately one out of six cases of cancer worldwide [...].
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Affiliation(s)
- Maria G. Isaguliants
- Institute of Microbiology and Virology, Riga Stradins University, LV-1007 Riga, Latvia
| | - Alexander V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Franco M. Buonaguro
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Naples, Italy;
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38
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Sun J, Zhang H, Yang Z. A retrospective analysis of children with mild and asymptomatic Omicron infections under 14: A single-center study. Medicine (Baltimore) 2024; 103:e37149. [PMID: 38363889 PMCID: PMC10869072 DOI: 10.1097/md.0000000000037149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/11/2024] [Indexed: 02/18/2024] Open
Abstract
Omicron BA.5 subvariant has been proven to be more transmissible than other Omicron subvariants. But the studies on the spread of the Omicron BA.5 subvariant in children are still limited. This study aimed to analyze the clinical features of children infected with Omicron BA.5.2 variant in the mobile cabin hospital and the influence factors of the infections. Children with mild and asymptomatic Omicron infections under 14 years old who were admitted to the mobile cabin hospital from October 30 to December 7, 2022 were retrospectively collected. A total of 741 children, 424 boys (57.2%) and 317 girls (42.8%) were enrolled, including 145 asymptomatic cases (22.7%) and 493 (77.3%) mild cases. Upper respiratory tract infection was the dominant manifestation. Fever was the most common presenting symptom (80.7%), followed by cough (52.5%). The average time to symptom disappearance was 3.76 days, and the average negative conversion time of nucleic acid was 12.3 days. Univariate analysis showed that the negative conversion time of nucleic acid differed significantly across the age groups. The multivariate analysis showed that the older the age, the longer the negative conversion time of nucleic acid. Among those with the negative conversion time of nucleic acid longer than 12 days, age was positively correlated to the negative conversion time of nucleic acid, while the number of vaccine doses received was negatively correlated to the negative conversion time of nucleic acid. Omicron infection occurred in children of any age group, with good prospect for recovery. Age and number of vaccine doses received were risk factors influencing the negative conversion time of nucleic acid.
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Affiliation(s)
- Jing Sun
- Department of Pediatrics, Lanzhou Chengguan District People’s Hospital, Lanzhou City, China
| | - Haiyan Zhang
- Department of Pediatrics, Lanzhou Chengguan District People’s Hospital, Lanzhou City, China
| | - Zhen Yang
- Department of Pediatrics, Lanzhou Maternal and Child Health Care Hospital, Lanzhou City, China
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39
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Yang X, Zheng X, Zhu Y, Zhao X, Liu J, Xun J, Yuan S, Chen J, Pan H, Yang J, Wang J, Liang Z, Shen X, Liang Y, Lin Q, Liang H, Li M, Peng F, Lu D, Xu J, Lu H, Jiang S, Zhao P, Zhu H. Asialoglycoprotein receptor 1 promotes SARS-CoV-2 infection of human normal hepatocytes. Signal Transduct Target Ther 2024; 9:42. [PMID: 38355848 PMCID: PMC10866945 DOI: 10.1038/s41392-024-01754-y] [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: 08/29/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes multi-organ damage, which includes hepatic dysfunction, as observed in over 50% of COVID-19 patients. Angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 (ACE2) is the primary receptor for SARS-CoV-2 entry into host cells, and studies have shown the presence of intracellular virus particles in human hepatocytes that express ACE2, but at extremely low levels. Consequently, we asked if hepatocytes might express receptors other than ACE2 capable of promoting the entry of SARS-CoV-2 into cells. To address this question, we performed a genome-wide CRISPR-Cas9 activation library screening and found that Asialoglycoprotein receptor 1 (ASGR1) promoted SARS-CoV-2 pseudovirus infection of HeLa cells. In Huh-7 cells, simultaneous knockout of ACE2 and ASGR1 prevented SARS-CoV-2 pseudovirus infection. In the immortalized THLE-2 hepatocyte cell line and primary hepatic parenchymal cells, both of which barely expressed ACE2, SARS-CoV-2 pseudovirus could successfully establish an infection. However, after treatment with ASGR1 antibody or siRNA targeting ASGR1, the infection rate significantly dropped, suggesting that SARS-CoV-2 pseudovirus infects hepatic parenchymal cells mainly through an ASGR1-dependent mechanism. We confirmed that ASGR1 could interact with Spike protein, which depends on receptor binding domain (RBD) and N-terminal domain (NTD). Finally, we also used Immunohistochemistry and electron microscopy to verify that SARS-CoV-2 could infect primary hepatic parenchymal cells. After inhibiting ASGR1 in primary hepatic parenchymal cells by siRNA, the infection efficiency of the live virus decreased significantly. Collectively, these findings indicate that ASGR1 is a candidate receptor for SARS-CoV-2 that promotes infection of hepatic parenchymal cells.
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Affiliation(s)
- Xinyi Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Xu Zheng
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China
| | - Yuqi Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Xiaying Zhao
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jun Liu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jiangna Xun
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Songhua Yuan
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Chen
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hanyu Pan
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jinlong Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jing Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Zhimin Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Xiaoting Shen
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Yue Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Qinru Lin
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Huitong Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Min Li
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Fei Peng
- Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jianqing Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hongzhou Lu
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases and Nursing Research Institution, National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, Shenzhen, Guangdong, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ping Zhao
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China.
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Rosas-Murrieta NH, Rodríguez-Enríquez A, Herrera-Camacho I, Millán-Pérez-Peña L, Santos-López G, Rivera-Benítez JF. Comparative Review of the State of the Art in Research on the Porcine Epidemic Diarrhea Virus and SARS-CoV-2, Scope of Knowledge between Coronaviruses. Viruses 2024; 16:238. [PMID: 38400014 PMCID: PMC10892376 DOI: 10.3390/v16020238] [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: 12/13/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
This review presents comparative information corresponding to the progress in knowledge of some aspects of infection by the porcine epidemic diarrhea virus (PEDV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronaviruses. PEDV is an alphacoronavirus of great economic importance due to the million-dollar losses it generates in the pig industry. PEDV has many similarities to the SARS-CoV-2 betacoronavirus that causes COVID-19 disease. This review presents possible scenarios for SARS-CoV-2 based on the collected literature on PEDV and the tools or strategies currently developed for SARS-CoV-2 that would be useful in PEDV research. The speed of the study of SARS-CoV-2 and the generation of strategies to control the pandemic was possible due to the knowledge derived from infections caused by other human coronaviruses such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS). Therefore, from the information obtained from several coronaviruses, the current and future behavior of SARS-CoV-2 could be inferred and, with the large amount of information on the virus that causes COVID-19, the study of PEDV could be improved and probably that of new emerging and re-emerging coronaviruses.
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Affiliation(s)
- Nora H. Rosas-Murrieta
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Alan Rodríguez-Enríquez
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
- Posgrado en Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Irma Herrera-Camacho
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Lourdes Millán-Pérez-Peña
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Gerardo Santos-López
- Centro de Investigación Biomédica de Oriente, Laboratorio de Biología Molecular y Virología, Instituto Mexicano del Seguro Social (IMSS), Metepec 74360, Mexico;
| | - José F. Rivera-Benítez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ciudad de México 38110, Mexico;
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41
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Tian S, Huang W. The causal relationship between gut microbiota and COVID-19: A two-sample Mendelian randomization analysis. Medicine (Baltimore) 2024; 103:e36493. [PMID: 38306556 PMCID: PMC10843424 DOI: 10.1097/md.0000000000036493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/15/2023] [Indexed: 02/04/2024] Open
Abstract
Recent studies have shown that gut microbiota is associated with coronavirus disease 2019 (COVID-19). However, the causal impact of the gut microbiota on COVID-19 remains unclear. We performed a bidirectional Mendelian randomization. The summary statistics on the gut microbiota from the MiBioGen consortium. Summary statistics for COVID-19 were obtained from the 6th round of the COVID-19 Host Genetics Initiative genome-wide association study meta-analysis. Inverse variance weighting was used as the main method to test the causal relationship between gut microbiota and COVID-19. Reverse Mendelian randomization analysis was performed. Mendelian randomization analysis showed that Intestinimas.id.2062 was associated with an increased risk of severe COVID-19. Bifidobacterium.id.436, LachnospiraceaeUCG010.id.11330, RikenellaceaeRC9gutgroup.id.11191 increase the risk of hospitalized COVID-19. RuminococcaceaeUCG014.id.11371 shows the positive protection on hospitalized COVID-19. There is no causal relationship between gut microbiota and infection with COVID-19. According to the results of reverse Mendelian randomization analysis, no significant causal effect of COVID-19 on gut microbiota was found. The study found that gut microbiota with COVID-19 has a causal relationship. This study provides a basis for the theory of the gut-lung axis. Further randomized controlled trials are needed to clarify the protective effect of probiotics against COVID-19 and the specific protective mechanisms. This study has important implications for gut microbiota as a nondrug intervention for COVID-19.
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Affiliation(s)
- Siyu Tian
- Proctology Department, School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wenhui Huang
- Cardiothoracic Surgery Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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42
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Hua S, Latha K, Marlin R, Benmeziane K, Bossevot L, Langlois S, Relouzat F, Dereuddre-Bosquet N, Le Grand R, Cavarelli M. Intestinal immunological events of acute and resolved SARS-CoV-2 infection in non-human primates. Mucosal Immunol 2024; 17:25-40. [PMID: 37827377 DOI: 10.1016/j.mucimm.2023.10.001] [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: 07/19/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
SARS-CoV-2 infection has been associated with intestinal mucosal barrier damage, leading to microbial and endotoxin translocation, heightened inflammatory responses, and aggravated disease outcomes. This study aimed to investigate the immunological mechanisms associated with impaired intestinal barrier function. We conducted a comprehensive analysis of gut damage and inflammation markers and phenotypic characterization of myeloid and lymphoid populations in the ileum and colon of SARS-CoV-2-exposed macaques during both the acute and resolved infection phases. Our findings revealed a significant accumulation of terminally differentiated and activated CD4+ and CD8+ T cells, along with memory B cells, within the gastrointestinal tract up to 43 days after exposure to SARS-CoV-2. This robust infection-induced immune response was accompanied by a notable depletion of plasmacytoid dendritic cells, myeloid dendritic cells, and macrophages, particularly affecting the colon during the resolved infection phase. Additionally, we identified a population of CX3CR1Low inflammatory macrophages associated with intestinal damage during active viral replication. Elevated levels of immune activation and gut damage markers, and perturbation of macrophage homeostasis, persisted even after the resolution of the infection, suggesting potential long-term clinical sequelae. These findings enhance our understanding of gastrointestinal immune pathology following SARS-CoV-2 infection and provide valuable information for developing and testing medical countermeasures.
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Affiliation(s)
- Stéphane Hua
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Krishna Latha
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Romain Marlin
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Keltouma Benmeziane
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Laetitia Bossevot
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Sébastien Langlois
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Francis Relouzat
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Mariangela Cavarelli
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France.
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McCoy R, Oldroyd S, Yang W, Wang K, Hoven D, Bulmer D, Zilbauer M, Owens RM. In Vitro Models for Investigating Intestinal Host-Pathogen Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306727. [PMID: 38155358 PMCID: PMC10885678 DOI: 10.1002/advs.202306727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Indexed: 12/30/2023]
Abstract
Infectious diseases are increasingly recognized as a major threat worldwide due to the rise of antimicrobial resistance and the emergence of novel pathogens. In vitro models that can adequately mimic in vivo gastrointestinal physiology are in high demand to elucidate mechanisms behind pathogen infectivity, and to aid the design of effective preventive and therapeutic interventions. There exists a trade-off between simple and high throughput models and those that are more complex and physiologically relevant. The complexity of the model used shall be guided by the biological question to be addressed. This review provides an overview of the structure and function of the intestine and the models that are developed to emulate this. Conventional models are discussed in addition to emerging models which employ engineering principles to equip them with necessary advanced monitoring capabilities for intestinal host-pathogen interrogation. Limitations of current models and future perspectives on the field are presented.
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Affiliation(s)
- Reece McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Sophie Oldroyd
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Woojin Yang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Kaixin Wang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Darius Hoven
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - David Bulmer
- Department of PharmacologyUniversity of CambridgeCambridgeCB2 1PDUK
| | - Matthias Zilbauer
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Róisín M. Owens
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
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Costigan D, Fenn J, Yen S, Ilott N, Bullers S, Hale J, Greenhalf W, Conibear E, Koycheva A, Madon K, Jahan I, Huang M, Badhan A, Parker E, Rosadas C, Jones K, McClure M, Tedder R, Taylor G, Baillie KJ, Semple MG, Openshaw PJM, Pearson C, Johnson J, Lalvani A, Thornton EE. A pro-inflammatory gut mucosal cytokine response is associated with mild COVID-19 disease and superior induction of serum antibodies. Mucosal Immunol 2024; 17:111-123. [PMID: 37995912 PMCID: PMC10884467 DOI: 10.1016/j.mucimm.2023.11.005] [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: 07/07/2023] [Revised: 10/25/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
The relationship between gastrointestinal tract infection, the host immune response, and the clinical outcome of disease is not well understood in COVID-19. We sought to understand the effect of intestinal immune responses to SARS-CoV-2 on patient outcomes including the magnitude of systemic antibody induction. Combining two prospective cohort studies, International Severe Acute Respiratory and emerging Infections Consortium Comprehensive Clinical Characterisations Collaboration (ISARIC4C) and Integrated Network for Surveillance, Trials and Investigations into COVID-19 Transmission (INSTINCT), we acquired samples from 88 COVID-19 cases representing the full spectrum of disease severity and analysed viral RNA and host gut cytokine responses in the context of clinical and virological outcome measures. There was no correlation between the upper respiratory tract and faecal viral loads. Using hierarchical clustering, we identified a group of fecal cytokines including Interleukin-17A, Granulocyte macrophage colony-stimulating factor, Tumor necrosis factorα, Interleukin-23, and S100A8, that were transiently elevated in mild cases and also correlated with the magnitude of systemic anti-Spike-receptor-binding domain antibody induction. Receiver operating characteristic curve analysis showed that expression of these gut cytokines at study enrolment in hospitalised COVID-19 cases was associated negatively with overall clinical severity implicating a protective role in COVID-19. This suggests that a productive intestinal immune response may be beneficial in the response to a respiratory pathogen and a biomarker of a successful barrier response.
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Affiliation(s)
- Dana Costigan
- MRC Translational Immune Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Joe Fenn
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK.
| | - Sandi Yen
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Nicholas Ilott
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Samuel Bullers
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK; Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Jessica Hale
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - William Greenhalf
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Emily Conibear
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK
| | | | - Kieran Madon
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK
| | - Ishrat Jahan
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Ming Huang
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Anjna Badhan
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Eleanor Parker
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Carolina Rosadas
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Kelsey Jones
- Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Myra McClure
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Richard Tedder
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Taylor
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Kenneth J Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Peter J M Openshaw
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK
| | - Claire Pearson
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK; Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Jethro Johnson
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Ajit Lalvani
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK
| | - Emily E Thornton
- MRC Translational Immune Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK; Nuffield Department of Medicine, University of Oxford, UK.
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Li Z, Chen X, Ma C, Du X, Zhang Y. Angiotensin converting enzyme 2 does not facilitate porcine epidemic diarrhea virus entry into porcine intestinal epithelial cells and inhibits it-induced inflammatory injury by promoting STAT1 phosphorylation. Virus Res 2024; 340:199300. [PMID: 38092254 PMCID: PMC10761916 DOI: 10.1016/j.virusres.2023.199300] [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: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
ACE2 has been confirmed to be a functional receptor for SARS-CoV and SARS-CoV-2, but research on animal coronaviruses, especially PEDV, are still unknown. The present study investigated whether ACE2 plays a role in receptor recognition and subsequent infection during PEDV invasion of host cells. IPEC-J2 cells stably expressing porcine ACE2 did not increase the production of PEDV-N but inhibited its expression. Porcine ACE2 knockout cells was generated by CRISPR/Cas9 genome editing in IPEC-J2 cells. The expression of PEDV-N did not decrease but slightly increased. The Co-IP results showed that there was no significant association between ACE2 and PEDV-S. There were no obvious interaction between PEDV-S, PEDV-E, PEDV-M and porcine ACE2 promoters, but PEDV-N could inhibit the activity of ACE2 promoters. PEDV-N degraded STAT1 and prevented its phosphorylation, thereby inhibiting the expression of interferon-stimulated genes. Repeated infection of PEDV further confirmed the above results. PEDV activated ACE-Ang II-AT1R axis, while ACE2-Ang (1-7)-MasR axis activity was decreased and inflammatory response was intensified. However, excess ACE2 can reverse this reaction. These results reveal that ACE2 does not facilitate PEDV entry into cells, but relieves PEDV-induced inflammation by promoting STAT1 phosphorylation.
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Affiliation(s)
- Zhiqiang Li
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xueqing Chen
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chang Ma
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyu Du
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanshu Zhang
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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Liu C, Huang W, He X, Feng Z, Chen Q. Research Advances on Swine Acute Diarrhea Syndrome Coronavirus. Animals (Basel) 2024; 14:448. [PMID: 38338091 PMCID: PMC10854734 DOI: 10.3390/ani14030448] [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: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a virulent pathogen that causes acute diarrhea in piglets. The virus was first discovered in Guangdong Province, China, in 2017 and has since emerged in Jiangxi, Fujian, and Guangxi Provinces. The outbreak exhibited a localized and sporadic pattern, with no discernable temporal continuity. The virus can infect human progenitor cells and demonstrates considerable potential for cross-species transmission, representing a potential risk for zoonotic transmission. Therefore, continuous surveillance of and comprehensive research on SADS-CoV are imperative. This review provides an overview of the temporal and evolutionary features of SADS-CoV outbreaks, focusing on the structural characteristics of the virus, which serve as the basis for discussing its potential for interspecies transmission. Additionally, the review summarizes virus-host interactions, including the effects on host cells, as well as apoptotic and autophagic behaviors, and discusses prevention and treatment modalities for this viral infection.
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Affiliation(s)
- Chuancheng Liu
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Weili Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Xinyan He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Zhihua Feng
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Qi Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
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Demyashkin G, Gorokhov K, Shchekin V, Vadyukhin M, Matevosyan A, Rudavina A, Pilipchuk A, Pilipchuk A, Kochetkova S, Atiakshin D, Shegay P, Kaprin A. Features of Appendix and the Characteristics of Appendicitis Development in Children with COVID-19. Biomedicines 2024; 12:312. [PMID: 38397914 PMCID: PMC10886907 DOI: 10.3390/biomedicines12020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Research on the subject of the influence of SARS-CoV-2 mechanisms on human homeostasis remains an actual problem. Particular interest is the study of pathomorphological changes in the appendix in children with COVID-19. OBJECTIVES Aim of this study: morphological and molecular biological evaluation of the appendix in children of different age groups with COVID-19. METHODS Groups were formed on the basis of anamnestic, clinical, and morphological data: I (n = 42; aged 2 to 18 years, average age-10.8 ± 4.79)-with an established clinical diagnosis: coronavirus infection (COVID-19; PCR+); II (n = 55; aged 2 to 18 years, average age-9.7 ± 4.77)-with a confirmed clinical diagnosis of acute appendicitis; collected before the onset of the COVID-19 pandemic in 2017-2019; and III (n = 38; aged 2 to 18 years, average age-10.3 ± 4.62)-the control group. Histological and immunohistochemical studies were conducted using primary antibodies to CD3, CD4, CD68, CD163, CD20, and CD138 and to pro-inflammatory (IL-1, IL-6) and anti-inflammatory (IL-4, IL-10) cytokines. RESULTS In most samples of appendixes in children with COVID-19, signs of destructive phlegmonous-ulcerative and gangrenous appendicitis were discovered. An increase in CD3+, CD4+, CD68+, CD163+, and CD20+ CD138+ immunocompetent cells was found in the appendix of children with COVID-19. As well, there was an increase in pro-inflammatory (IL-1, IL-6) and anti-inflammatory (IL-4, IL-10) cytokines. CONCLUSIONS The aforementioned pathological and immunohistochemical changes were more pronounced in the group of children aged 6-12 years (childhood).
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Affiliation(s)
- Grigory Demyashkin
- Department of Pathomorphology, National Medical Research Centre of Radiology, Ministry of Health of Russia, 249036 Obninsk, Russia; (K.G.); (P.S.); (A.K.)
- Laboratory of Histology and Immunohistochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (G.D.); (M.V.); (A.M.); (A.R.); (A.P.); (A.P.); (S.K.)
| | - Konstantin Gorokhov
- Department of Pathomorphology, National Medical Research Centre of Radiology, Ministry of Health of Russia, 249036 Obninsk, Russia; (K.G.); (P.S.); (A.K.)
| | - Vladimir Shchekin
- Laboratory of Histology and Immunohistochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (G.D.); (M.V.); (A.M.); (A.R.); (A.P.); (A.P.); (S.K.)
| | - Matvey Vadyukhin
- Laboratory of Histology and Immunohistochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (G.D.); (M.V.); (A.M.); (A.R.); (A.P.); (A.P.); (S.K.)
| | - Artem Matevosyan
- Laboratory of Histology and Immunohistochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (G.D.); (M.V.); (A.M.); (A.R.); (A.P.); (A.P.); (S.K.)
| | - Arina Rudavina
- Laboratory of Histology and Immunohistochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (G.D.); (M.V.); (A.M.); (A.R.); (A.P.); (A.P.); (S.K.)
| | - Anna Pilipchuk
- Laboratory of Histology and Immunohistochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (G.D.); (M.V.); (A.M.); (A.R.); (A.P.); (A.P.); (S.K.)
| | - Alina Pilipchuk
- Laboratory of Histology and Immunohistochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (G.D.); (M.V.); (A.M.); (A.R.); (A.P.); (A.P.); (S.K.)
| | - Svetlana Kochetkova
- Laboratory of Histology and Immunohistochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia; (G.D.); (M.V.); (A.M.); (A.R.); (A.P.); (A.P.); (S.K.)
| | - Dmitrii Atiakshin
- Research and Educational Resource Center for Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis Innovative Technologies, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia;
| | - Petr Shegay
- Department of Pathomorphology, National Medical Research Centre of Radiology, Ministry of Health of Russia, 249036 Obninsk, Russia; (K.G.); (P.S.); (A.K.)
| | - Andrey Kaprin
- Department of Pathomorphology, National Medical Research Centre of Radiology, Ministry of Health of Russia, 249036 Obninsk, Russia; (K.G.); (P.S.); (A.K.)
- Research and Educational Resource Center for Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis Innovative Technologies, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia;
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Kwon O, Lee H, Jung J, Son YS, Jeon S, Yoo WD, Son N, Jung KB, Choi E, Lee IC, Kwon HJ, Kim C, Lee MO, Cho HS, Kim DS, Son MY. Chemically-defined and scalable culture system for intestinal stem cells derived from human intestinal organoids. Nat Commun 2024; 15:799. [PMID: 38280855 PMCID: PMC10821882 DOI: 10.1038/s41467-024-45103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
Three-dimensional human intestinal organoids (hIO) are widely used as a platform for biological and biomedical research. However, reproducibility and challenges for large-scale expansion limit their applicability. Here, we establish a human intestinal stem cell (ISC) culture method expanded under feeder-free and fully defined conditions through selective enrichment of ISC populations (ISC3D-hIO) within hIO derived from human pluripotent stem cells. The intrinsic self-organisation property of ISC3D-hIO, combined with air-liquid interface culture in a minimally defined medium, forces ISC3D-hIO to differentiate into the intestinal epithelium with cellular diversity, villus-like structure, and barrier integrity. Notably, ISC3D-hIO is an ideal cell source for gene editing to study ISC biology and transplantation for intestinal diseases. We demonstrate the intestinal epithelium differentiated from ISC3D-hIO as a model system to study severe acute respiratory syndrome coronavirus 2 viral infection. ISC3D-hIO culture technology provides a biological tool for use in regenerative medicine and disease modelling.
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Affiliation(s)
- Ohman Kwon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hana Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jaeeun Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Ye Seul Son
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sojeong Jeon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Won Dong Yoo
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Naeun Son
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Kwang Bo Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eunho Choi
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - In-Chul Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
- KRIBB, Korea Preclinical Evaluation Center, Jeongeup, 56212, Republic of Korea
| | - Hyung-Jun Kwon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
- KRIBB, Korea Preclinical Evaluation Center, Jeongeup, 56212, Republic of Korea
| | - Chuna Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
- KRIBB, Aging Convergence Research Center, Daejeon, 34141, Republic of Korea
| | - Mi-Ok Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Dae Soo Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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Negrut N, Menegas G, Kampioti S, Bourelou M, Kopanyi F, Hassan FD, Asowed A, Taleouine FZ, Ferician A, Marian P. The Multisystem Impact of Long COVID: A Comprehensive Review. Diagnostics (Basel) 2024; 14:244. [PMID: 38337760 PMCID: PMC10855167 DOI: 10.3390/diagnostics14030244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
(1) Background: COVID-19 was responsible for the latest pandemic, shaking and reshaping healthcare systems worldwide. Its late clinical manifestations make it linger in medical memory as a debilitating illness over extended periods. (2) Methods: the recent literature was systematically analyzed to categorize and examine the symptomatology and pathophysiology of Long COVID across various bodily systems, including pulmonary, cardiovascular, gastrointestinal, neuropsychiatric, dermatological, renal, hematological, and endocrinological aspects. (3) Results: The review outlines the diverse clinical manifestations of Long COVID across multiple systems, emphasizing its complexity and challenges in diagnosis and treatment. Factors such as pre-existing conditions, initial COVID-19 severity, vaccination status, gender, and age were identified as influential in the manifestation and persistence of Long COVID symptoms. This condition is highlighted as a debilitating disease capable of enduring over an extended period and presenting new symptoms over time. (4) Conclusions: Long COVID emerges as a condition with intricate multi-systemic involvement, complicating its diagnosis and treatment. The findings underscore the necessity for a nuanced understanding of its diverse manifestations to effectively manage and address the evolving nature of this condition over time.
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Affiliation(s)
- Nicoleta Negrut
- Department of Psycho-Neuroscience and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Georgios Menegas
- Department of Orthopaedics, Achillopouleio General Hospital of Volos, Polymeri 134, 38222 Volos, Greece;
| | - Sofia Kampioti
- Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania (M.B.); (F.D.H.)
| | - Maria Bourelou
- Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania (M.B.); (F.D.H.)
| | - Francesca Kopanyi
- Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania (M.B.); (F.D.H.)
| | - Faiso Dahir Hassan
- Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania (M.B.); (F.D.H.)
| | - Anamaria Asowed
- Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania (M.B.); (F.D.H.)
| | - Fatima Zohra Taleouine
- University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK;
| | - Anca Ferician
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (A.F.)
| | - Paula Marian
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (A.F.)
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50
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Piazzesi A, Pane S, Del Chierico F, Romani L, Campana A, Palma P, Putignani L. The pediatric gut bacteriome and virome in response to SARS-CoV-2 infection. Front Cell Infect Microbiol 2024; 14:1335450. [PMID: 38318164 PMCID: PMC10839054 DOI: 10.3389/fcimb.2024.1335450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Since the beginning of the SARS-CoV-2 pandemic in early 2020, it has been apparent that children were partially protected from both infection and the more severe forms of the disease. Many different mechanisms have been proposed to explain this phenomenon, including children's frequent exposure to other upper respiratory infections and vaccines, and which inflammatory cytokines they are more likely to produce in response to infection. Furthermore, given the presence of SARS-CoV-2 in the intestine and its ability to infect enterocytes, combined with the well described immunomodulatory capabilities of the microbiome, another potential contributing factor may be the presence of certain protective microbial members of the gut microbiota (GM). Methods We performed shotgun metagenomic sequencing and profiled both the bacteriome and virome of the GM of pediatric SARS-CoV-2 patients compared to healthy, age-matched subjects. Results We found that, while pediatric patients do share some pro-inflammatory microbial signatures with adult patients, they also possess a distinct microbial signature of protective bacteria previously found to be negatively correlated with SARS-CoV-2 infectivity and COVID-19 severity. COVID-19 was also associated with higher fecal Cytomegalovirus load, and with shifts in the relative abundances of bacteriophages in the GM. Furthermore, we address how the preventative treatment of COVID-19 patients with antibiotics, a common practice especially in the early days of the pandemic, affected the bacteriome and virome, as well as the abundances of antimicrobial resistance and virulence genes in these patients. Discussion To our knowledge, this is the first study to address the bacteriome, virome, and resistome of pediatric patients in response to COVID-19 and to preventative antibiotics use.
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Affiliation(s)
- Antonia Piazzesi
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefania Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | - Lorenza Romani
- Infectious Diseases Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Campana
- Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Paolo Palma
- Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Chair of Pediatrics, Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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