1
|
Liu Y, Zhou Z, Lu G, Zhang X, Shi D, Tong L, Chen D, Tuan RS, Li ZA. Musculoskeletal organoids: An emerging toolkit for establishing personalized models of musculoskeletal disorders and developing regenerative therapies. Acta Biomater 2025:S1742-7061(25)00362-9. [PMID: 40381929 DOI: 10.1016/j.actbio.2025.05.037] [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: 01/01/2025] [Revised: 05/09/2025] [Accepted: 05/14/2025] [Indexed: 05/20/2025]
Abstract
Musculoskeletal (MSK) conditions are the primary cause of physical disability globally. These disorders are physically and mentally debilitating and severely impact the patients' quality of life. As the median age of the world's population increases, there has been an intensifying urgency of developing efficacious therapies for various orthopaedic conditions. Furthermore, the highly heterogeneous nature of MSK conditions calls for a personalized approach to studying disease mechanisms and developing regenerative treatments. Organoids have emerged as an advanced approach to generating functional tissue/organ mimics in vitro, which hold promise in MSK regeneration, disease modeling, and therapeutic development. Herein, we review the preparation, characterization, and application of various MSK organoids. We highlight the potential of patient-specific organoids in the development of personalized medicine and discuss the challenges and opportunities in the future development of MSK organoids. STATEMENT OF SIGNIFICANCE: Despite decades of research, translation of MSK research into clinical applications remains limited, partially attributed to our inadequate understanding of disease mechanisms. To advance therapeutic development, there are critical needs for MSK disease models with higher clinical relevance and predictive power. Additionally, engineered constructs that closely mimic the structural and functional features of native MSK tissues are highly desirable. MSK organoids have emerged as a promising approach to meet the above requirements. To unleash the full potential of MSK organoids necessitates a comprehensive understanding of their categories, construction, development, functions, applications, and challenges. This review aims to fulfill this crucial need, aiming to accelerate the clinical translation of MSK organoid platforms to benefit millions of patients afflicted with MSK conditions.
Collapse
Affiliation(s)
- Yuwei Liu
- Department of Orthopedics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Department of Sports Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, Guangdong, PR China
| | - Zhilong Zhou
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Gang Lu
- Institute for Tissue Engineering and Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong Special Administrative Region of China
| | - Xin Zhang
- Institute of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Beijing, 100191 PR China
| | - Dongquan Shi
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, PR China
| | - Liping Tong
- Research Center for Computer-aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China
| | - Di Chen
- Research Center for Computer-aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China; Department of Pharmacology, Faculty of Pharmaceutical Sciences, Shenzhen University of Advanced Technology, Shenzhen 518000, PR China.
| | - Rocky S Tuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Institute for Tissue Engineering and Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong Special Administrative Region of China.
| | - Zhong Alan Li
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Institute for Tissue Engineering and Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong Special Administrative Region of China; Peter Hung Pain Research Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region of China.
| |
Collapse
|
2
|
Michalak KP, Michalak AZ, Brenk-Krakowska A. Acute COVID-19 and LongCOVID syndrome - molecular implications for therapeutic strategies - review. Front Immunol 2025; 16:1582783. [PMID: 40313948 PMCID: PMC12043656 DOI: 10.3389/fimmu.2025.1582783] [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: 02/25/2025] [Accepted: 03/28/2025] [Indexed: 05/03/2025] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been recognized not only for its acute effects but also for its ability to cause LongCOVID Syndrome (LCS), a condition characterized by persistent symptoms affecting multiple organ systems. This review examines the molecular and immunological mechanisms underlying LCS, with a particular focus on autophagy inhibition, chronic inflammation, oxidative, nitrosative and calcium stress, viral persistence and autoimmunology. Potential pathophysiological mechanisms involved in LCS include (1) autoimmune activation, (2) latent viral persistence, where SARS-CoV-2 continues to influence host metabolism, (3) reactivation of latent pathogens such as Epstein-Barr virus (EBV) or cytomegalovirus (CMV), exacerbating immune and metabolic dysregulation, and (4) possible persistent metabolic and inflammatory dysregulation, where the body fails to restore post-infection homeostasis. The manipulation of cellular pathways by SARS-CoV-2 proteins is a critical aspect of the virus' ability to evade immune clearance and establish long-term dysfunction. Viral proteins such as NSP13, ORF3a and ORF8 have been shown to disrupt autophagy, thereby impairing viral clearance and promoting immune evasion. In addition, mitochondrial dysfunction, dysregulated calcium signaling, oxidative stress, chronic HIF-1α activation and Nrf2 inhibition create a self-sustaining inflammatory feedback loop that contributes to tissue damage and persistent symptoms. Therefore understanding the molecular basis of LCS is critical for the development of effective therapeutic strategies. Targeting autophagy and Nrf2 activation, glycolysis inhibition, and restoration calcium homeostasis may provide novel strategies to mitigate the long-term consequences of SARS-CoV-2 infection. Future research should focus on personalized therapeutic interventions based on the dominant molecular perturbations in individual patients.
Collapse
Affiliation(s)
- Krzysztof Piotr Michalak
- Laboratory of Vision Science and Optometry, Physics and Astronomy Faculty, Adam Mickiewicz University in Poznań, Poznań, Poland
| | | | - Alicja Brenk-Krakowska
- Laboratory of Vision Science and Optometry, Physics and Astronomy Faculty, Adam Mickiewicz University in Poznań, Poznań, Poland
| |
Collapse
|
3
|
Del Vecchio V, Sanchez-Pajares IR, Panda SK, Rehman A, De Falco V, Nigam A, Mosca L, Russo D, Arena C, Nicoletti MM, Desiderio V, Papaccio G, Mele L, Laino L. Xanthohumol modulate autophagy and ER stress to counteract stemness and enhance cisplatin efficacy in head and neck squamous cell carcinoma. Sci Rep 2025; 15:13137. [PMID: 40240816 PMCID: PMC12003764 DOI: 10.1038/s41598-025-98003-1] [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: 06/12/2024] [Accepted: 04/08/2025] [Indexed: 04/18/2025] Open
Abstract
Natural compounds have been increasingly investigated for their efficient anti-cancer activity. Xanthohumol (XN), a flavonoid derived from hops, has shown promise in preclinical studies for various cancers due to its unique biological properties. This study investigates the effects of XN and a cost-effective hop extract (HOP EX) on head and neck squamous cell carcinoma (HNSCC), focusing on their potential to modulate cancer stemness and enhance the efficacy of Cisplatin chemotherapy. Using a combination of flow cytometry, qPCR, and cellular assays, we assessed the impact of XN and HOP EX on cell viability, stemness, and chemoresistance in HNSCC cell lines. Further, we explored the underlying mechanisms by examining the induction of apoptosis, ER stress, and autophagy activation. Our findings demonstrate that both XN and HOP EX significantly decrease cell viability and stemness in HNSCC cells and enhance the cytotoxic effects of Cisplatin, suggesting a synergistic interaction. Mechanistically, we identified that the induction of ER stress and subsequent activation of the unfolded protein response (UPR) promote autophagy, leading to increased apoptosis. By modulating key cellular pathways such as ER stress and autophagy, these natural compounds could be developed into supportive treatments for HNSCC.
Collapse
Affiliation(s)
- Vitale Del Vecchio
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
- Department of Life Sciences, Health and Health Professions, Link Campus University, Via del Casale di San Pio V 4, Roma, 00165, Italia
| | | | - Sameer Kumar Panda
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
| | - Ayesha Rehman
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
| | - Vincenzo De Falco
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
| | - Aditya Nigam
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
| | - Laura Mosca
- Department of Life Sciences, Health and Health Professions, Link Campus University, Via del Casale di San Pio V 4, Roma, 00165, Italia
| | - Diana Russo
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "L. Vanvitelli", Via L. de Crecchio 6, Naples, 80138, Italy
| | - Claudia Arena
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "L. Vanvitelli", Via L. de Crecchio 6, Naples, 80138, Italy
| | - Maria Maddalena Nicoletti
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "L. Vanvitelli", Via L. de Crecchio 6, Naples, 80138, Italy
- Dermatology Unit, University of Campania "L.Vanvitelli", Naples, Italy
| | - Vincenzo Desiderio
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy.
| | - Gianpaolo Papaccio
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
| | - Luigi Mele
- Department of Health Sciences, University of Basilicata, Via dell'Ateneo Lucano 10, Potenza, 85100, Italy
| | - Luigi Laino
- Dermatology Unit, University of Campania "L.Vanvitelli", Naples, Italy
| |
Collapse
|
4
|
Soultsioti M, de Jong AWM, Blomberg N, Tas A, Giera M, Snijder EJ, Bárcena M. Perturbation of de novo lipogenesis hinders MERS-CoV assembly and release, but not the biogenesis of viral replication organelles. J Virol 2025; 99:e0228224. [PMID: 39976449 PMCID: PMC11915874 DOI: 10.1128/jvi.02282-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 01/20/2025] [Indexed: 02/21/2025] Open
Abstract
Coronaviruses hijack host cell metabolic pathways and resources to support their replication. They induce extensive host endomembrane remodeling to generate viral replication organelles and exploit host membranes for assembly and budding of their enveloped progeny virions. Because of the overall significance of host membranes, we sought to gain insight into the role of host factors involved in lipid metabolism in cells infected with Middle East respiratory syndrome coronavirus (MERS-CoV). We employed a single-cycle infection approach in combination with pharmacological inhibitors, biochemical assays, lipidomics, and light and electron microscopy. Pharmacological inhibition of acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN), key host factors in de novo fatty acid biosynthesis, led to pronounced inhibition of MERS-CoV particle release. Inhibition of ACC led to a profound metabolic switch in Huh7 cells, altering their lipidomic profile and inducing lipolysis. However, despite the extensive changes induced by the ACC inhibitor, the biogenesis of viral replication organelles remained unaffected. Instead, ACC inhibition appeared to affect the trafficking and post-translational modifications of the MERS-CoV envelope proteins. Electron microscopy revealed an accumulation of nucleocapsids in early budding stages, indicating that MERS-CoV assembly is adversely impacted by ACC inhibition. Notably, inhibition of palmitoylation resulted in similar effects, while supplementation of exogenous palmitic acid reversed the compound's inhibitory effects, possibly reflecting a crucial need for palmitoylation of the MERS-CoV spike and envelope proteins for their role in virus particle assembly.IMPORTANCEMiddle East respiratory syndrome coronavirus (MERS-CoV) is the etiological agent of a zoonotic respiratory disease of limited transmissibility between humans. However, MERS-CoV is still considered a high-priority pathogen and is closely monitored by WHO due to its high lethality rate of around 35% of laboratory-confirmed infections. Like other positive-strand RNA viruses, MERS-CoV relies on the host cell's endomembranes to support various stages of its replication cycle. However, in spite of this general reliance of MERS-CoV replication on host cell lipid metabolism, mechanistic insights are still very limited. In our study, we show that pharmacological inhibition of acetyl-CoA carboxylase (ACC), a key enzyme in the host cell's fatty acid biosynthesis pathway, significantly disrupts MERS-CoV particle assembly without exerting a negative effect on the biogenesis of viral replication organelles. Furthermore, our study highlights the potential of ACC as a target for the development of host-directed antiviral therapeutics against coronaviruses.
Collapse
Affiliation(s)
- M. Soultsioti
- Molecular Virology Laboratory, Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, the Netherlands
| | - A. W. M. de Jong
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - N. Blomberg
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - A. Tas
- Molecular Virology Laboratory, Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, the Netherlands
| | - M. Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - E. J. Snijder
- Molecular Virology Laboratory, Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, the Netherlands
| | - M. Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
5
|
Deguchi S, Yokoi F, Takayama K. Organoids and microphysiological systems for pharmaceutical research of viral respiratory infections. Drug Metab Pharmacokinet 2025; 60:101041. [PMID: 39847975 DOI: 10.1016/j.dmpk.2024.101041] [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: 08/29/2024] [Revised: 11/08/2024] [Accepted: 11/13/2024] [Indexed: 01/25/2025]
Abstract
In the pharmaceutical research of viral respiratory infections, cell culture models have traditionally been used to evaluate the therapeutic effects of candidate compounds. Although cell lines are easy to handle and cost-effective, they do not fully replicate the characteristics of human respiratory organs. Recently, organoids and microphysiological systems (MPS) have been employed to overcome this limitation for in vitro testing of drugs against viral respiratory infections. Advanced disease modeling using organoids, self-organized three-dimensional (3D) cell culture models derived from stem cells, or MPS, models for culturing multiple cell types in a microfluidic device and capable of recapitulating a physiological 3D dynamic environment, can accurately replicate the complex functions of respiratory organs, thus making them valuable tools for elucidating the organ damages caused by viral respiratory infections and evaluating the efficacy of candidate drugs against them. Recently, a wide range of organoids and MPS have been developed to model the complex pathophysiology caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and assess therapeutic drugs. In this review, we evaluate the latest pharmaceutical research on coronavirus disease 2019 (COVID-19) that utilizes organoids and MPS and discuss future perspectives of their applications.
Collapse
Affiliation(s)
- Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Fuki Yokoi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan; Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
| |
Collapse
|
6
|
Lee Y, Lee MK, Lee HR, Kim B, Kim M, Jung S. 3D-printed airway model as a platform for SARS-CoV-2 infection and antiviral drug testing. Biomaterials 2024; 311:122689. [PMID: 38944967 DOI: 10.1016/j.biomaterials.2024.122689] [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: 10/13/2023] [Revised: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
We present a bioprinted three-layered airway model with a physiologically relevant microstructure for the study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection dynamics. This model exhibited clear cell-cell junctions and mucus secretion with an efficient expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). Having infected air-exposed epithelial cells in the upper layer with a minimum multiplicity of infection of 0.01, the airway model showed a marked susceptibility to SARS-CoV-2 within one-day post-infection (dpi). Furthermore, the unique longevity allowed the observation of cytopathic effects and barrier degradation for 21 dpi. The in-depth transcriptomic analysis revealed dramatic changes in gene expression affecting the infection pathway, viral proliferation, and host immune response which are consistent with COVID-19 patient data. Finally, the treatment of antiviral agents, such as remdesivir and molnupiravir, through the culture medium underlying the endothelium resulted in a marked inhibition of viral replication within the epithelium. The bioprinted airway model can be used as a manufacturable physiological platform to study disease pathogeneses and drug efficacy.
Collapse
Affiliation(s)
- Yunji Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Myoung Kyu Lee
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea
| | - Hwa-Rim Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Byungil Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea
| | - Meehyein Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Sungjune Jung
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea; Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, 03722, Republic of Korea.
| |
Collapse
|
7
|
Mou X, Luo F, Zhang W, Cheng Q, Hepojoki J, Zhu S, Liu Y, Xiong H, Guo D, Yu J, Chen L, Li Y, Hou W, Chen S. SARS-CoV-2 NSP16 promotes IL-6 production by regulating the stabilization of HIF-1α. Cell Signal 2024; 124:111387. [PMID: 39251053 DOI: 10.1016/j.cellsig.2024.111387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 08/23/2024] [Accepted: 09/04/2024] [Indexed: 09/11/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of coronavirus disease 2019 (COVID-19). Severe and fatal COVID-19 cases often display cytokine storm i.e. significant elevation of pro-inflammatory cytokines and acute respiratory distress syndrome (ARDS) with systemic hypoxia. Understanding the mechanisms of these pathogenic manifestations would be essential for the prevention and especially treatment of COVID-19 patients. Here, using a dual luciferase reporter assay for hypoxia-response element (HRE), we initially identified SARS-CoV-2 nonstructural protein 5 (NSP5), NSP16, and open reading frame 3a (ORF3a) to upregulate hypoxia-inducible factor-1α (HIF-1α) signaling. Further experiments showed NSP16 to have the most prominent effect on HIF-1α, thus contributing to the induction of COVID-19 associated pro-inflammatory response. We demonstrate that NSP16 interrupts von Hippel-Lindau (VHL) protein interaction with HIF-1α, thereby inhibiting ubiquitin-dependent degradation of HIF-1α and allowing it to bind HRE region in the IL-6 promoter region. Taken together, the findings imply that SARS-CoV-2 NSP16 induces HIF-1α expression, which in turn exacerbates the production of IL-6.
Collapse
Affiliation(s)
- Xiaoli Mou
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China; Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China
| | - Fan Luo
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China; Department of Virology, Faculty of Medicine, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Weihao Zhang
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China
| | - Qi Cheng
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China
| | - Jussi Hepojoki
- Department of Virology, Faculty of Medicine, Medicum, University of Helsinki, 00290 Helsinki, Finland
| | - Shaowei Zhu
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China
| | - Yuanyuan Liu
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China
| | - Hairong Xiong
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China
| | - Deyin Guo
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China
| | - Jingyou Yu
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China
| | - Liangjun Chen
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Yirong Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Wei Hou
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China; School of Public Health, Wuhan University, Wuhan, Hubei 430071, China; School of Ecology and Environment, Tibet University, Lhasa, Tibet 850000, China; Shenzhen Research Institute, Wuhan University, Shenzhen, Guangdong 518057, China.
| | - Shuliang Chen
- State Key Laboratory of Virology, Institute of Medical Virology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, China; Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan, Hubei 430071, China.
| |
Collapse
|
8
|
Kang S, Chen EC, Cifuentes H, Co JY, Cole G, Graham J, Hsia R, Kiyota T, Klein JA, Kroll KT, Nieves Lopez LM, Norona LM, Peiris H, Potla R, Romero-Lopez M, Roth JG, Tseng M, Fullerton AM, Homan KA. Complex in vitromodels positioned for impact to drug testing in pharma: a review. Biofabrication 2024; 16:042006. [PMID: 39189069 DOI: 10.1088/1758-5090/ad6933] [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: 12/22/2023] [Accepted: 07/30/2024] [Indexed: 08/28/2024]
Abstract
Recent years have seen the creation and popularization of various complexin vitromodels (CIVMs), such as organoids and organs-on-chip, as a technology with the potential to reduce animal usage in pharma while also enhancing our ability to create safe and efficacious drugs for patients. Public awareness of CIVMs has increased, in part, due to the recent passage of the FDA Modernization Act 2.0. This visibility is expected to spur deeper investment in and adoption of such models. Thus, end-users and model developers alike require a framework to both understand the readiness of current models to enter the drug development process, and to assess upcoming models for the same. This review presents such a framework for model selection based on comparative -omics data (which we term model-omics), and metrics for qualification of specific test assays that a model may support that we term context-of-use (COU) assays. We surveyed existing healthy tissue models and assays for ten drug development-critical organs of the body, and provide evaluations of readiness and suggestions for improving model-omics and COU assays for each. In whole, this review comes from a pharma perspective, and seeks to provide an evaluation of where CIVMs are poised for maximum impact in the drug development process, and a roadmap for realizing that potential.
Collapse
Affiliation(s)
- Serah Kang
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Eugene C Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Helen Cifuentes
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Julia Y Co
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Gabrielle Cole
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Jessica Graham
- Product Quality & Occupational Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of Americaica
| | - Rebecca Hsia
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Tomomi Kiyota
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Jessica A Klein
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Katharina T Kroll
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Lenitza M Nieves Lopez
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Leah M Norona
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Heshan Peiris
- Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Ratnakar Potla
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Monica Romero-Lopez
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Julien G Roth
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Min Tseng
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Aaron M Fullerton
- Investigative Toxicology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| | - Kimberly A Homan
- Complex in vitro Systems Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America
| |
Collapse
|
9
|
Guarnieri JW, Lie T, Albrecht YES, Hewin P, Jurado KA, Widjaja GA, Zhu Y, McManus MJ, Kilbaugh TJ, Keith K, Potluri P, Taylor D, Angelin A, Murdock DG, Wallace DC. Mitochondrial antioxidants abate SARS-COV-2 pathology in mice. Proc Natl Acad Sci U S A 2024; 121:e2321972121. [PMID: 39008677 PMCID: PMC11287122 DOI: 10.1073/pnas.2321972121] [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] [Accepted: 06/07/2024] [Indexed: 07/17/2024] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection inhibits mitochondrial oxidative phosphorylation (OXPHOS) and elevates mitochondrial reactive oxygen species (ROS, mROS) which activates hypoxia-inducible factor-1alpha (HIF-1α), shifting metabolism toward glycolysis to drive viral biogenesis but also causing the release of mitochondrial DNA (mtDNA) and activation of innate immunity. To determine whether mitochondrially targeted antioxidants could mitigate these viral effects, we challenged mice expressing human angiotensin-converting enzyme 2 (ACE2) with SARS-CoV-2 and intervened using transgenic and pharmacological mitochondrially targeted catalytic antioxidants. Transgenic expression of mitochondrially targeted catalase (mCAT) or systemic treatment with EUK8 decreased weight loss, clinical severity, and circulating levels of mtDNA; as well as reduced lung levels of HIF-1α, viral proteins, and inflammatory cytokines. RNA-sequencing of infected lungs revealed that mCAT and Eukarion 8 (EUK8) up-regulated OXPHOS gene expression and down-regulated HIF-1α and its target genes as well as innate immune gene expression. These data demonstrate that SARS-CoV-2 pathology can be mitigated by catalytically reducing mROS, potentially providing a unique host-directed pharmacological therapy for COVID-19 which is not subject to viral mutational resistance.
Collapse
Affiliation(s)
- Joseph W. Guarnieri
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Timothy Lie
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
- University of Pennsylvania, Philadelphia, PA19104
| | - Yentli E. Soto Albrecht
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Peter Hewin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Kellie A. Jurado
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Gabrielle A. Widjaja
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Yi Zhu
- Department of Anesthesiology and Critical Care, Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Meagan J. McManus
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
- Department of Anesthesiology and Critical Care, Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Todd J. Kilbaugh
- Department of Anesthesiology and Critical Care, Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Kelsey Keith
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Prasanth Potluri
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Deanne Taylor
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Alessia Angelin
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
| | - Deborah G. Murdock
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
- Division of Human Genetics, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Douglas C. Wallace
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA19104
- Division of Human Genetics, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| |
Collapse
|
10
|
Chang CC, Wu CY, Wu CM, Wu CW, Wang YC, Lin GJ, Chien MS, Huang C. Cytotoxicity effect and transcriptome analysis of PCV3-infected cells revealed potential viral pathogenic mechanisms. Microb Pathog 2024; 192:106715. [PMID: 38810767 DOI: 10.1016/j.micpath.2024.106715] [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: 01/24/2024] [Revised: 05/10/2024] [Accepted: 05/25/2024] [Indexed: 05/31/2024]
Abstract
Porcine circovirus type 3 (PCV3) has become an important pathogen in the global swine industry and poses a threat to pig health, but its pathogenic mechanism remains unknown. In this study, we constructed an innovative, linear infectious clone of PCV3 for rescuing the virus, and explored the transcriptome of infected cells to gain insights into its pathogenic mechanisms. Subsequently, an in vivo experiment was conducted to evaluate the pathogenicity of the rescued virus in pig. PCV3 nucleic acid was distributed across various organs, indicating systemic circulation via the bloodstream and viremia. Immunohistochemical staining also revealed a significant presence of PCV3 antigens in the spleen, lungs, and lymph nodes, indicating that PCV3 had tropism for these organs. Transcriptome analysis of infected ST cells revealed differential expression of genes associated with apoptosis, immune responses, and cellular metabolism. Notably, upregulation of genes related to the hypoxia-inducible factor-1 pathway, glycolysis, and the AGE/RAGE pathway suggests activation of inflammatory responses, ultimately leading to onset of disease. These findings have expanded our understanding of PCV3 pathogenesis, and the interplay between PCV3 and host factors.
Collapse
Affiliation(s)
- Chia-Chun Chang
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Ching-Ying Wu
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Chi-Ming Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Ching-Wei Wu
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan; Research Center for Animal Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Yi-Chen Wang
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Guang-Jan Lin
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Maw-Sheng Chien
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan; Research Center for Animal Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan.
| | - Chienjin Huang
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan.
| |
Collapse
|
11
|
Guarnieri JW, Haltom JA, Albrecht YES, Lie T, Olali AZ, Widjaja GA, Ranshing SS, Angelin A, Murdock D, Wallace DC. SARS-CoV-2 mitochondrial metabolic and epigenomic reprogramming in COVID-19. Pharmacol Res 2024; 204:107170. [PMID: 38614374 DOI: 10.1016/j.phrs.2024.107170] [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: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
To determine the effects of SARS-CoV-2 infection on cellular metabolism, we conducted an exhaustive survey of the cellular metabolic pathways modulated by SARS-CoV-2 infection and confirmed their importance for SARS-CoV-2 propagation by cataloging the effects of specific pathway inhibitors. This revealed that SARS-CoV-2 strongly inhibits mitochondrial oxidative phosphorylation (OXPHOS) resulting in increased mitochondrial reactive oxygen species (mROS) production. The elevated mROS stabilizes HIF-1α which redirects carbon molecules from mitochondrial oxidation through glycolysis and the pentose phosphate pathway (PPP) to provide substrates for viral biogenesis. mROS also induces the release of mitochondrial DNA (mtDNA) which activates innate immunity. The restructuring of cellular energy metabolism is mediated in part by SARS-CoV-2 Orf8 and Orf10 whose expression restructures nuclear DNA (nDNA) and mtDNA OXPHOS gene expression. These viral proteins likely alter the epigenome, either by directly altering histone modifications or by modulating mitochondrial metabolite substrates of epigenome modification enzymes, potentially silencing OXPHOS gene expression and contributing to long-COVID.
Collapse
Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jeffrey A Haltom
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yentli E Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Timothy Lie
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arnold Z Olali
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sujata S Ranshing
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Deborah Murdock
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
12
|
Yang L, Kim TW, Han Y, Nair MS, Harschnitz O, Zhu J, Wang P, Koo SY, Lacko LA, Chandar V, Bram Y, Zhang T, Zhang W, He F, Pan C, Wu J, Huang Y, Evans T, van der Valk P, Titulaer MJ, Spoor JKH, Furler O'Brien RL, Bugiani M, D J Van de Berg W, Schwartz RE, Ho DD, Studer L, Chen S. SARS-CoV-2 infection causes dopaminergic neuron senescence. Cell Stem Cell 2024; 31:196-211.e6. [PMID: 38237586 PMCID: PMC10843182 DOI: 10.1016/j.stem.2023.12.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024]
Abstract
COVID-19 patients commonly present with signs of central nervous system and/or peripheral nervous system dysfunction. Here, we show that midbrain dopamine (DA) neurons derived from human pluripotent stem cells (hPSCs) are selectively susceptible and permissive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. SARS-CoV-2 infection of DA neurons triggers an inflammatory and cellular senescence response. High-throughput screening in hPSC-derived DA neurons identified several FDA-approved drugs that can rescue the cellular senescence phenotype by preventing SARS-CoV-2 infection. We also identified the inflammatory and cellular senescence signature and low levels of SARS-CoV-2 transcripts in human substantia nigra tissue of COVID-19 patients. Furthermore, we observed reduced numbers of neuromelanin+ and tyrosine-hydroxylase (TH)+ DA neurons and fibers in a cohort of severe COVID-19 patients. Our findings demonstrate that hPSC-derived DA neurons are susceptible to SARS-CoV-2, identify candidate neuroprotective drugs for COVID-19 patients, and suggest the need for careful, long-term monitoring of neurological problems in COVID-19 patients.
Collapse
Affiliation(s)
- Liuliu Yang
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Tae Wan Kim
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Yuling Han
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Jiajun Zhu
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - So Yeon Koo
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Neuroscience Graduate Program of Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lauretta A Lacko
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Vasuretha Chandar
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Tuo Zhang
- Genomic Resource Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Wei Zhang
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Feng He
- Genomic Resource Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chendong Pan
- Genomic Resource Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Junjie Wu
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Paul van der Valk
- Department of Pathology, Amsterdam University Medical Center, VU University Amsterdam, Amsterdam, the Netherlands
| | - Maarten J Titulaer
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jochem K H Spoor
- Department of Neurosurgery, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Robert L Furler O'Brien
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Marianna Bugiani
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Pathology, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Wilma D J Van de Berg
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands; Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy and Biobanking, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.
| |
Collapse
|
13
|
Chau CW, Sugimura R. Organoids in COVID-19: can we break the glass ceiling? J Leukoc Biol 2024; 115:85-99. [PMID: 37616269 DOI: 10.1093/jleuko/qiad098] [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: 01/30/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
COVID-19 emerged in September 2020 as a disease caused by the virus SARS-CoV-2. The disease presented as pneumonia at first but later was shown to cause multisystem infections and long-term complications. Many efforts have been put into discovering the exact pathogenesis of the disease. In this review, we aim to discuss an emerging tool in disease modeling, organoids, in the investigation of COVID-19. This review will introduce some methods and breakthroughs achieved by organoids and the limitations of this system.
Collapse
Affiliation(s)
- Chiu Wang Chau
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 21 Sassoon Rd, Pokfulam 99077, Hong Kong
| | - Ryohichi Sugimura
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 21 Sassoon Rd, Pokfulam 99077, Hong Kong
- Centre for Translational Stem Cell Biology, 17 Science Park W Ave, Science Park 999077, Hong Kong
| |
Collapse
|
14
|
Li M, Yuan Y, Zou T, Hou Z, Jin L, Wang B. Development trends of human organoid-based COVID-19 research based on bibliometric analysis. Cell Prolif 2023; 56:e13496. [PMID: 37218396 PMCID: PMC10693193 DOI: 10.1111/cpr.13496] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a catastrophic threat to human health worldwide. Human stem cell-derived organoids serve as a promising platform for exploring SARS-CoV-2 infection. Several review articles have summarized the application of human organoids in COVID-19, but the research status and development trend of this field have seldom been systematically and comprehensively studied. In this review, we use bibliometric analysis method to identify the characteristics of organoid-based COVID-19 research. First, an annual trend of publications and citations, the most contributing countries or regions and organizations, co-citation analysis of references and sources and research hotspots are determined. Next, systematical summaries of organoid applications in investigating the pathology of SARS-CoV-2 infection, vaccine development and drug discovery, are provided. Lastly, the current challenges and future considerations of this field are discussed. The present study will provide an objective angle to identify the current trend and give novel insights for directing the future development of human organoid applications in SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of BioengineeringChongqing UniversityChongqingChina
- Southwest Hospital/Southwest Eye HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Yuhan Yuan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of BioengineeringChongqing UniversityChongqingChina
| | - Ting Zou
- Southwest Hospital/Southwest Eye HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Zongkun Hou
- School of Basic Medical Sciences/School of Biology and Engineering (School of Modern Industry for Health and Medicine)Guizhou Medical UniversityGuiyangChina
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of BioengineeringChongqing UniversityChongqingChina
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of BioengineeringChongqing UniversityChongqingChina
| |
Collapse
|
15
|
Marongiu L, Burkard M, Helling T, Biendl M, Venturelli S. Modulation of the replication of positive-sense RNA viruses by the natural plant metabolite xanthohumol and its derivatives. Crit Rev Food Sci Nutr 2023; 65:429-443. [PMID: 37942943 DOI: 10.1080/10408398.2023.2275169] [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] [Indexed: 11/10/2023]
Abstract
The COVID-19 pandemic has highlighted the importance of identifying new potent antiviral agents. Nutrients as well as plant-derived substances are promising candidates because they are usually well tolerated by the human body and readily available in nature, and consequently mostly cheap to produce. A variety of antiviral effects have recently been described for the hop chalcone xanthohumol (XN), and to a lesser extent for its derivatives, making these hop compounds particularly attractive for further investigation. Noteworthy, mounting evidence indicated that XN can suppress a wide range of viruses belonging to several virus families, all of which share a common reproductive cycle. As a result, the purpose of this review is to summarize the most recent research on the antiviral properties of XN and its derivatives, with a particular emphasis on the positive-sense RNA viruses human hepatitis C virus (HCV), porcine reproductive and respiratory syndrome virus (PRRSV), and severe acute respiratory syndrome corona virus (SARS-CoV-2).
Collapse
Affiliation(s)
- Luigi Marongiu
- Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Markus Burkard
- Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
| | - Thomas Helling
- Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
| | - Martin Biendl
- HHV Hallertauer Hopfenveredelungsgesellschaft m.b.H, Mainburg, Germany
| | - Sascha Venturelli
- Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
- Department of Vegetative and Clinical Physiology, University Hospital of Tuebingen, Tuebingen, Germany
| |
Collapse
|
16
|
An Y, He Y, Ge N, Guo J, Yang F, Sun S. Organoids to Remodel SARS-CoV-2 Research: Updates, Limitations and Perspectives. Aging Dis 2023; 14:1677-1699. [PMID: 37196111 PMCID: PMC10529756 DOI: 10.14336/ad.2023.0209] [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: 01/11/2023] [Accepted: 02/09/2023] [Indexed: 05/19/2023] Open
Abstract
The novel COVID-19 pneumonia caused by the SARS-CoV-2 virus poses a significant threat to human health. Scientists have made significant efforts to control this virus, consequently leading to the development of novel research methods. Traditional animal and 2D cell line models might not be suitable for large-scale applications in SARS-CoV-2 research owing to their limitations. As an emerging modelling method, organoids have been applied in the study of various diseases. Their advantages include their ability to closely mirror human physiology, ease of cultivation, low cost, and high reliability; thus, they are considered to be a suitable choice to further the research on SARS-CoV-2. During the course of various studies, SARS-CoV-2 was shown to infect a variety of organoid models, exhibiting changes similar to those observed in humans. This review summarises the various organoid models used in SARS-CoV-2 research, revealing the molecular mechanisms of viral infection and exploring the drug screening tests and vaccine research that have relied on organoid models, hence illustrating the role of organoids in remodelling SARS-CoV-2 research.
Collapse
Affiliation(s)
- Yucheng An
- Department of Gastroenterology, Shengjing hospital of China Medical University, Shenyang, China
| | - Yanjie He
- Department of Surgery, New York University School of Medicine and NYU-Langone Medical Center, New York, NY, USA
| | - Nan Ge
- Department of Gastroenterology, Shengjing hospital of China Medical University, Shenyang, China
| | - Jintao Guo
- Department of Gastroenterology, Shengjing hospital of China Medical University, Shenyang, China
| | - Fan Yang
- Department of Gastroenterology, Shengjing hospital of China Medical University, Shenyang, China
| | - Siyu Sun
- Department of Gastroenterology, Shengjing hospital of China Medical University, Shenyang, China
| |
Collapse
|
17
|
Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Albrecht YS, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Zhang S, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Bram Y, Kidane Y, Priebe W, Emmett MR, Meller R, Demharter S, Stentoft-Hansen V, Salvatore M, Galeano D, Enguita FJ, Grabham P, Trovao NS, Singh U, Haltom J, Heise MT, Moorman NJ, Baxter VK, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts. Sci Transl Med 2023; 15:eabq1533. [PMID: 37556555 PMCID: PMC11624572 DOI: 10.1126/scitranslmed.abq1533] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/20/2023] [Indexed: 08/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed mitochondrial gene expression in nasopharyngeal and autopsy tissues from patients with coronavirus disease 2019 (COVID-19). In nasopharyngeal samples with declining viral titers, the virus blocked the transcription of a subset of nuclear DNA (nDNA)-encoded mitochondrial OXPHOS genes, induced the expression of microRNA 2392, activated HIF-1α to induce glycolysis, and activated host immune defenses including the integrated stress response. In autopsy tissues from patients with COVID-19, SARS-CoV-2 was no longer present, and mitochondrial gene transcription had recovered in the lungs. However, nDNA mitochondrial gene expression remained suppressed in autopsy tissue from the heart and, to a lesser extent, kidney, and liver, whereas mitochondrial DNA transcription was induced and host-immune defense pathways were activated. During early SARS-CoV-2 infection of hamsters with peak lung viral load, mitochondrial gene expression in the lung was minimally perturbed but was down-regulated in the cerebellum and up-regulated in the striatum even though no SARS-CoV-2 was detected in the brain. During the mid-phase SARS-CoV-2 infection of mice, mitochondrial gene expression was starting to recover in mouse lungs. These data suggest that when the viral titer first peaks, there is a systemic host response followed by viral suppression of mitochondrial gene transcription and induction of glycolysis leading to the deployment of antiviral immune defenses. Even when the virus was cleared and lung mitochondrial function had recovered, mitochondrial function in the heart, kidney, liver, and lymph nodes remained impaired, potentially leading to severe COVID-19 pathology.
Collapse
Affiliation(s)
- Joseph W. Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph M. Dybas
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Hossein Fazelinia
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Man S. Kim
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Justin Frere
- Icahn School of Medicine at Mount Sinai, New York, NY 10023, USA
| | - Yuanchao Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Yentli Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Deborah G. Murdock
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N. Singh
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Scott L. Weiss
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sonja M. Best
- COVID-19 International Research Team, Medford, MA 02155, USA
- Rocky Mountain Laboratory, National Institute of Allergy and Infectious Disease, NIH, Hamilton, MT 59840, USA
| | - Marie T. Lott
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Chicago, Chicago, IL 60615, USA
- Clever Research Lab, Springfield, IL 62704, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team, Medford, MA 02155, USA
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Yaron Bram
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Yared Kidane
- COVID-19 International Research Team, Medford, MA 02155, USA
- Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R. Emmett
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team, Medford, MA 02155, USA
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | | | | | - Diego Galeano
- COVID-19 International Research Team, Medford, MA 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Central, Paraguay
| | - Francisco J. Enguita
- COVID-19 International Research Team, Medford, MA 02155, USA
- Faculdade de Medicina, Universidade de Lisboa, Instituto de Medicina Molecular João Lobo Antunes, 1649-028 Lisboa, Portugal
| | - Peter Grabham
- College of Physicians and Surgeons, Columbia University, New York, NY 19103, USA
| | - Nidia S. Trovao
- COVID-19 International Research Team, Medford, MA 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Urminder Singh
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Jeffrey Haltom
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Mark T. Heise
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Emily A. Madden
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Wes A. Sanders
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Stephen B. Baylin
- COVID-19 International Research Team, Medford, MA 02155, USA
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Pedro M. Moraes-Vieira
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Campinas, Campinas, SP, Brazil
| | - Deanne Taylor
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Christopher E. Mason
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
- New York Genome Center, New York, NY 10013, USA
| | - Jonathan C. Schisler
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert E. Schwartz
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Division of Human Genetics, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
18
|
Ye C, Huang Y, Gao Y, Zhu S, Yuan J. Exploring the glycolytic cross-talk genes between inflammatory bowel disease and colorectal cancer. Funct Integr Genomics 2023; 23:230. [PMID: 37428395 PMCID: PMC10333365 DOI: 10.1007/s10142-023-01170-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
Patients with inflammatory bowel disease (IBD) have a higher risk of developing colorectal cancer (CRC). Glycolysis is involved in the development of both IBD and CRC. However, the mechanisms and outcomes of glycolysis shared between IBD and CRC remain unclear. This study aimed to explore the glycolytic cross-talk genes between IBD and CRC integrating bioinformatics and machine learning. With WGCNA, LASSO, COX, and SVM-RFE algorithms, P4HA1 and PMM2 were identified as glycolytic cross-talk genes. The independent risk signature of P4HA1 and PMM2 was constructed to predict the overall survival rate of patients with CRC. The risk signature correlated with clinical characteristics, prognosis, tumor microenvironment, immune checkpoint, mutants, cancer stemness, and chemotherapeutic drug sensitivity. CRC patients with high risk have increased microsatellite instability, tumor mutation burden. The nomogram integrating risk score, tumor stage, and age showed high accuracy for predicting overall survival rate. In addition, the diagnostic model for IBD based on P4HA1 and PMM2 showed excellent accuracy. Finally, immunohistochemistry results showed that P4HA1 and PMM2 were significantly upregulated in IBD and CRC. Our study reveals the presence of glycolytic cross-talk genes P4HA1 and PMM2 between IBD and CRC. This may prove to be beneficial in advancing research on the mechanism of development of IBD-associated CRC.
Collapse
Affiliation(s)
- Chenglin Ye
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yabing Huang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yuan Gao
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Sizhe Zhu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, People's Republic of China.
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China.
| |
Collapse
|
19
|
Chen P, Wu M, He Y, Jiang B, He ML. Metabolic alterations upon SARS-CoV-2 infection and potential therapeutic targets against coronavirus infection. Signal Transduct Target Ther 2023; 8:237. [PMID: 37286535 DOI: 10.1038/s41392-023-01510-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/18/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis, bringing enormous burden to our society. Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms. Although only a small proportion of patients progressed to severe COVID-19 with symptoms including acute respiratory distress syndrome (ARDS), disseminated coagulopathy, and cardiovascular disorders, severe COVID-19 is accompanied by high mortality rates with near 7 million deaths. Nowadays, effective therapeutic patterns for severe COVID-19 are still lacking. It has been extensively reported that host metabolism plays essential roles in various physiological processes during virus infection. Many viruses manipulate host metabolism to avoid immunity, facilitate their own replication, or to initiate pathological response. Targeting the interaction between SARS-CoV-2 and host metabolism holds promise for developing therapeutic strategies. In this review, we summarize and discuss recent studies dedicated to uncovering the role of host metabolism during the life cycle of SARS-CoV-2 in aspects of entry, replication, assembly, and pathogenesis with an emphasis on glucose metabolism and lipid metabolism. Microbiota and long COVID-19 are also discussed. Ultimately, we recapitulate metabolism-modulating drugs repurposed for COVID-19 including statins, ASM inhibitors, NSAIDs, Montelukast, omega-3 fatty acids, 2-DG, and metformin.
Collapse
Affiliation(s)
- Peiran Chen
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Binghua Jiang
- Cell Signaling and Proteomic Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China.
| |
Collapse
|
20
|
Afewerki S, Stocco TD, Rosa da Silva AD, Aguiar Furtado AS, Fernandes de Sousa G, Ruiz-Esparza GU, Webster TJ, Marciano FR, Strømme M, Zhang YS, Lobo AO. In vitro high-content tissue models to address precision medicine challenges. Mol Aspects Med 2023; 91:101108. [PMID: 35987701 PMCID: PMC9384546 DOI: 10.1016/j.mam.2022.101108] [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: 04/08/2022] [Revised: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 01/18/2023]
Abstract
The field of precision medicine allows for tailor-made treatments specific to a patient and thereby improve the efficiency and accuracy of disease prevention, diagnosis, and treatment and at the same time would reduce the cost, redundant treatment, and side effects of current treatments. Here, the combination of organ-on-a-chip and bioprinting into engineering high-content in vitro tissue models is envisioned to address some precision medicine challenges. This strategy could be employed to tackle the current coronavirus disease 2019 (COVID-19), which has made a significant impact and paradigm shift in our society. Nevertheless, despite that vaccines against COVID-19 have been successfully developed and vaccination programs are already being deployed worldwide, it will likely require some time before it is available to everyone. Furthermore, there are still some uncertainties and lack of a full understanding of the virus as demonstrated in the high number new mutations arising worldwide and reinfections of already vaccinated individuals. To this end, efficient diagnostic tools and treatments are still urgently needed. In this context, the convergence of bioprinting and organ-on-a-chip technologies, either used alone or in combination, could possibly function as a prominent tool in addressing the current pandemic. This could enable facile advances of important tools, diagnostics, and better physiologically representative in vitro models specific to individuals allowing for faster and more accurate screening of therapeutics evaluating their efficacy and toxicity. This review will cover such technological advances and highlight what is needed for the field to mature for tackling the various needs for current and future pandemics as well as their relevancy towards precision medicine.
Collapse
Affiliation(s)
- Samson Afewerki
- Division of Nanotechnology and Functional Materials, Department of Materials Science and Engineering, Ångström Laboratory, Uppsala University, BOX 35, 751 03, Uppsala, Sweden
| | - Thiago Domingues Stocco
- Bioengineering Program, Technological and Scientific Institute, Brazil University, 08230-030, São Paulo, SP, Brazil; Faculty of Medical Sciences, Unicamp - State University of Campinas, 13083-877, Campinas, SP, Brazil
| | | | - André Sales Aguiar Furtado
- Interdisciplinary Laboratory for Advanced Materials, BioMatLab, Department of Materials Engineering, Federal University of Piauí (UFPI), Teresina, PI, Brazil
| | - Gustavo Fernandes de Sousa
- Interdisciplinary Laboratory for Advanced Materials, BioMatLab, Department of Materials Engineering, Federal University of Piauí (UFPI), Teresina, PI, Brazil
| | - Guillermo U Ruiz-Esparza
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA; Division of Health Sciences and Technology, Harvard University ‑ Massachusetts Institute of Technology, Boston, MA, 02115, USA
| | - Thomas J Webster
- Interdisciplinary Laboratory for Advanced Materials, BioMatLab, Department of Materials Engineering, Federal University of Piauí (UFPI), Teresina, PI, Brazil; Hebei University of Technology, Tianjin, China
| | - Fernanda R Marciano
- Department of Physics, Federal University of Piauí (UFPI), Teresina, PI, Brazil
| | - Maria Strømme
- Division of Nanotechnology and Functional Materials, Department of Materials Science and Engineering, Ångström Laboratory, Uppsala University, BOX 35, 751 03, Uppsala, Sweden
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA; Division of Health Sciences and Technology, Harvard University ‑ Massachusetts Institute of Technology, Boston, MA, 02115, USA.
| | - Anderson Oliveira Lobo
- Interdisciplinary Laboratory for Advanced Materials, BioMatLab, Department of Materials Engineering, Federal University of Piauí (UFPI), Teresina, PI, Brazil.
| |
Collapse
|
21
|
Yang S, Hu H, Kung H, Zou R, Dai Y, Hu Y, Wang T, Lv T, Yu J, Li F. Organoids: The current status and biomedical applications. MedComm (Beijing) 2023; 4:e274. [PMID: 37215622 PMCID: PMC10192887 DOI: 10.1002/mco2.274] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Organoids are three-dimensional (3D) miniaturized versions of organs or tissues that are derived from cells with stem potential and can self-organize and differentiate into 3D cell masses, recapitulating the morphology and functions of their in vivo counterparts. Organoid culture is an emerging 3D culture technology, and organoids derived from various organs and tissues, such as the brain, lung, heart, liver, and kidney, have been generated. Compared with traditional bidimensional culture, organoid culture systems have the unique advantage of conserving parental gene expression and mutation characteristics, as well as long-term maintenance of the function and biological characteristics of the parental cells in vitro. All these features of organoids open up new opportunities for drug discovery, large-scale drug screening, and precision medicine. Another major application of organoids is disease modeling, and especially various hereditary diseases that are difficult to model in vitro have been modeled with organoids by combining genome editing technologies. Herein, we introduce the development and current advances in the organoid technology field. We focus on the applications of organoids in basic biology and clinical research, and also highlight their limitations and future perspectives. We hope that this review can provide a valuable reference for the developments and applications of organoids.
Collapse
Affiliation(s)
- Siqi Yang
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Haijie Hu
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Hengchung Kung
- Krieger School of Arts and SciencesJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Ruiqi Zou
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Yushi Dai
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Yafei Hu
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Tiantian Wang
- Key Laboratory of Rehabilitation Medicine in Sichuan ProvinceWest China HospitalSichuan UniversityChengduSichuanChina
| | - Tianrun Lv
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Jun Yu
- Departments of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Departments of OncologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Fuyu Li
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| |
Collapse
|
22
|
Vandana JJ, Manrique C, Lacko LA, Chen S. Human pluripotent-stem-cell-derived organoids for drug discovery and evaluation. Cell Stem Cell 2023; 30:571-591. [PMID: 37146581 PMCID: PMC10775018 DOI: 10.1016/j.stem.2023.04.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/27/2023] [Accepted: 04/11/2023] [Indexed: 05/07/2023]
Abstract
Human pluripotent stem cells (hPSCs) and three-dimensional organoids have ushered in a new era for disease modeling and drug discovery. Over the past decade, significant progress has been in deriving functional organoids from hPSCs, which have been applied to recapitulate disease phenotypes. In addition, these advancements have extended the application of hPSCs and organoids for drug screening and clinical-trial safety evaluations. This review provides an overview of the achievements and challenges in using hPSC-derived organoids to conduct relevant high-throughput, high-contentscreens and drug evaluation. These studies have greatly enhanced our knowledge and toolbox for precision medicine.
Collapse
Affiliation(s)
- J Jeya Vandana
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer, New York, NY, USA
| | - Cassandra Manrique
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY, USA
| | - Lauretta A Lacko
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
23
|
Ostermann PN, Schaal H. Human brain organoids to explore SARS-CoV-2-induced effects on the central nervous system. Rev Med Virol 2023; 33:e2430. [PMID: 36790825 DOI: 10.1002/rmv.2430] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). In less than three years, an estimated 600 million infections with SARS-CoV-2 occurred worldwide, resulting in a pandemic with tremendous impact especially on economic and health sectors. Initially considered a respiratory disease, COVID-19, along with its long-term sequelae (long-COVID) rather is a systemic disease. Neurological symptoms like dementia or encephalopathy were reported early during the pandemic as concomitants of the acute phase and as characteristics of long-COVID. An excessive inflammatory immune response is hypothesized to play a major role in this context. However, direct infection of neural cells may also contribute to the neurological aspects of (long)-COVID-19. To mainly explore such direct effects of SARS-CoV-2 on the central nervous system, human brain organoids provide a useful platform. Infecting these three-dimensional tissue cultures allows the study of viral neurotropism as well as of virus-induced effects on single cells or even the complex cellular network within the organoid. In this review, we summarize the experimental studies that used SARS-CoV-2-infected human brain organoids to unravel the complex nature of (long)-COVID-19-related neurological manifestations.
Collapse
Affiliation(s)
- Philipp Niklas Ostermann
- Institute of Virology, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
24
|
Tang X, Xue D, Zhang T, Nilsson-Payant BE, Carrau L, Duan X, Gordillo M, Tan AY, Qiu Y, Xiang J, Schwartz RE, tenOever BR, Evans T, Chen S. A multi-organoid platform identifies CIART as a key factor for SARS-CoV-2 infection. Nat Cell Biol 2023; 25:381-389. [PMID: 36918693 PMCID: PMC10014579 DOI: 10.1038/s41556-023-01095-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 01/25/2023] [Indexed: 03/16/2023]
Abstract
COVID-19 is a systemic disease involving multiple organs. We previously established a platform to derive organoids and cells from human pluripotent stem cells to model SARS-CoV-2 infection and perform drug screens1,2. This provided insight into cellular tropism and the host response, yet the molecular mechanisms regulating SARS-CoV-2 infection remain poorly defined. Here we systematically examined changes in transcript profiles caused by SARS-CoV-2 infection at different multiplicities of infection for lung airway organoids, lung alveolar organoids and cardiomyocytes, and identified several genes that are generally implicated in controlling SARS-CoV-2 infection, including CIART, the circadian-associated repressor of transcription. Lung airway organoids, lung alveolar organoids and cardiomyocytes derived from isogenic CIART-/- human pluripotent stem cells were significantly resistant to SARS-CoV-2 infection, independently of viral entry. Single-cell RNA-sequencing analysis further validated the decreased levels of SARS-CoV-2 infection in ciliated-like cells of lung airway organoids. CUT&RUN, ATAC-seq and RNA-sequencing analyses showed that CIART controls SARS-CoV-2 infection at least in part through the regulation of NR4A1, a gene also identified from the multi-organoid analysis. Finally, transcriptional profiling and pharmacological inhibition led to the discovery that the Retinoid X Receptor pathway regulates SARS-CoV-2 infection downstream of CIART and NR4A1. The multi-organoid platform identified the role of circadian-clock regulation in SARS-CoV-2 infection, which provides potential therapeutic targets for protection against COVID-19 across organ systems.
Collapse
Affiliation(s)
- Xuming Tang
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin E Nilsson-Payant
- Department of Microbiology, New York University, New York, NY, USA
- TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Lucia Carrau
- Department of Microbiology, New York University, New York, NY, USA
| | - Xiaohua Duan
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Miriam Gordillo
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Adrian Y Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Yunping Qiu
- Stable Isotope and Metabolomics Core Facility, The Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | | | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
25
|
Yang W, Li Y, Shi F, Liu H. Human lung organoid: Models for respiratory biology and diseases. Dev Biol 2023; 494:26-34. [PMID: 36470449 DOI: 10.1016/j.ydbio.2022.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/23/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
The human respiratory system, consisting of the airway and alveoli, is one of the most complex organs directly interfaced with the external environment. The diverse epithelial cells lining the surface are usually the first cell barrier that comes into contact with pathogens that could lead to deadly pulmonary disease. There is an urgent need to understand the mechanisms of self-renewal and protection of these epithelial cells against harmful pathogens, such as SARS-CoV-2. Traditional models, including cell lines and mouse models, have extremely limited native phenotypic features. Therefore, in recent years, to mimic the complexity of the lung, airway and alveoli organoid technology has been developed and widely applied. TGF-β/BMP/SMAD, FGF and Wnt/β-catenin signaling have been proven to play a key role in lung organoid expansion and differentiation. Thus, we summarize the current novel lung organoid culture strategies and discuss their application for understanding the lung biological features and pathophysiology of pulmonary diseases, especially COVID-19. Lung organoids provide an excellent in vitro model and research platform.
Collapse
Affiliation(s)
- Wenhao Yang
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children Sichuan University, Ministry of Education, Chengdu, China; NHC Key Laboratory of Chronobiology Sichuan University, Chengdu, China; The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, China; Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yingna Li
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children Sichuan University, Ministry of Education, Chengdu, China; NHC Key Laboratory of Chronobiology Sichuan University, Chengdu, China; The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, China; Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Fang Shi
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children Sichuan University, Ministry of Education, Chengdu, China; NHC Key Laboratory of Chronobiology Sichuan University, Chengdu, China; The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, China; Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Hanmin Liu
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children Sichuan University, Ministry of Education, Chengdu, China; NHC Key Laboratory of Chronobiology Sichuan University, Chengdu, China; The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, China; Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China.
| |
Collapse
|
26
|
Liu D, Xu C, Jiang L, Zhu X. Pulmonary endogenous progenitor stem cell subpopulation: Physiology, pathogenesis, and progress. JOURNAL OF INTENSIVE MEDICINE 2023; 3:38-51. [PMID: 36789358 PMCID: PMC9924023 DOI: 10.1016/j.jointm.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/09/2022] [Accepted: 08/13/2022] [Indexed: 06/18/2023]
Abstract
Lungs are structurally and functionally complex organs consisting of diverse cell types from the proximal to distal axis. They have direct contact with the external environment and are constantly at risk of various injuries. Capable to proliferate and differentiate, pulmonary endogenous progenitor stem cells contribute to the maintenance of lung structure and function both under homeostasis and following injuries. Discovering candidate pulmonary endogenous progenitor stem cell types and underlying regenerative mechanisms provide insights into therapeutic strategy development for lung diseases. In this review, we reveal their compositions, roles in lung disease pathogenesis and injury repair, and the underlying mechanisms. We further underline the advanced progress in research approach and potential therapy for lung regeneration. We also demonstrate the feasibility and prospects of pulmonary endogenous stem cell transplantation for lung disease treatment.
Collapse
Affiliation(s)
- Di Liu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Chufan Xu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Xiaoyan Zhu
- Department of Physiology, Navy Medical University, 800 Xiangyin Road, Shanghai 200433, China
| |
Collapse
|
27
|
Novelli G, Spitalieri P, Murdocca M, Centanini E, Sangiuolo F. Organoid factory: The recent role of the human induced pluripotent stem cells (hiPSCs) in precision medicine. Front Cell Dev Biol 2023; 10:1059579. [PMID: 36699015 PMCID: PMC9869172 DOI: 10.3389/fcell.2022.1059579] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
During the last decades, hiPSC-derived organoids have been extensively studied and used as in vitro models for several applications among which research studies. They can be considered as organ and tissue prototypes, especially for those difficult to obtain. Moreover, several diseases can be accurately modeled and studied. Hence, patient-derived organoids (PDOs) can be used to predict individual drug responses, thus paving the way toward personalized medicine. Lastly, by applying tissue engineering and 3D printing techniques, organoids could be used in the future to replace or regenerate damaged tissue. In this review, we will focus on hiPSC-derived 3D cultures and their ability to model human diseases with an in-depth analysis of gene editing applications, as well as tumor models. Furthermore, we will highlight the state-of-the-art of organoid facilities that around the world offer know-how and services. This is an increasing trend that shed the light on the need of bridging the publicand the private sector. Hence, in the context of drug discovery, Organoid Factories can offer biobanks of validated 3D organoid models that can be used in collaboration with pharmaceutical companies to speed up the drug screening process. Finally, we will discuss the limitations and the future development that will lead hiPSC-derived technology from bench to bedside, toward personalized medicine, such as maturity, organoid interconnections, costs, reproducibility and standardization, and ethics. hiPSC-derived organoid technology is now passing from a proof-of-principle to real applications in the clinic, also thanks to the applicability of techniques, such as CRISPR/Cas9 genome editing system, material engineering for the scaffolds, or microfluidic systems. The benefits will have a crucial role in the advance of both basic biological and translational research, particularly in the pharmacological field and drug development. In fact, in the near future, 3D organoids will guide the clinical decision-making process, having validated patient-specific drug screening platforms. This is particularly important in the context of rare genetic diseases or when testing cancer treatments that could in principle have severe side effects. Therefore, this technology has enabled the advancement of personalized medicine in a way never seen before.
Collapse
Affiliation(s)
- Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- IRCCS Neuromed, Pozzilli, IS, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, United States
| | - Paola Spitalieri
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Michela Murdocca
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Eleonora Centanini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, CS, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| |
Collapse
|
28
|
Gautam LK, Harriott NC, Caceres AM, Ryan AL. Basic Science Perspective on Engineering and Modeling the Large Airways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1413:73-106. [PMID: 37195527 DOI: 10.1007/978-3-031-26625-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The airway epithelium provides a physical and biochemical barrier playing a key role in protecting the lung from infiltration of pathogens and irritants and is, therefore, crucial in maintaining tissue homeostasis and regulating innate immunity. Due to continual inspiration and expiration of air during breathing, the epithelium is exposed to a plethora of environmental insults. When severe or persistent, these insults lead to inflammation and infection. The effectiveness of the epithelium as a barrier is reliant upon its capacity for mucociliary clearance, immune surveillance, and regeneration upon injury. These functions are accomplished by the cells that comprise the airway epithelium and the niche in which they reside. Engineering of new physiological and pathological models of the proximal airways requires the generation of complex structures comprising the surface airway epithelium, submucosal gland epithelium, extracellular matrix, and niche cells, including smooth muscle cells, fibroblasts, and immune cells. This chapter focuses on the structure-function relationships in the airways and the challenges of developing complex engineered models of the human airway.
Collapse
Affiliation(s)
- Lalit K Gautam
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Noa C Harriott
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Adrian M Caceres
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Amy L Ryan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
29
|
Ni K, Che B, Yang C, Qin Y, Gu R, Wang C, Luo M, Deng L. Emerging toolset of three-dimensional pulmonary cell culture models for simulating lung pathophysiology towards mechanistic elucidation and therapeutic treatment of SARS-COV-2 infection. Front Pharmacol 2022; 13:1033043. [PMID: 36578545 PMCID: PMC9790924 DOI: 10.3389/fphar.2022.1033043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses a never before seen challenge to human health and the world economy. However, it is difficult to widely use conventional animal and cell culture models in understanding the underlying pathological mechanisms of COVID-19, which in turn hinders the development of relevant therapeutic treatments, including drugs. To overcome this challenge, various three-dimensional (3D) pulmonary cell culture models such as organoids are emerging as an innovative toolset for simulating the pathophysiology occurring in the respiratory system, including bronchial airways, alveoli, capillary network, and pulmonary interstitium, which provide a robust and powerful platform for studying the process and underlying mechanisms of SARS-CoV-2 infection among the potential primary targets in the lung. This review introduces the key features of some of these recently developed tools, including organoid, lung-on-a-chip, and 3D bioprinting, which can recapitulate different structural compartments of the lung and lung function, in particular, accurately resembling the human-relevant pathophysiology of SARS-CoV-2 infection in vivo. In addition, the recent progress in developing organoids for alveolar and airway disease modeling and their applications for discovering drugs against SARS-CoV-2 infection are highlighted. These innovative 3D cell culture models together may hold the promise to fully understand the pathogenesis and eventually eradicate the pandemic of COVID-19.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Mingzhi Luo
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou, Jiangsu, China
| | - Linhong Deng
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou, Jiangsu, China
| |
Collapse
|
30
|
Chen J, Na F. Organoid technology and applications in lung diseases: Models, mechanism research and therapy opportunities. Front Bioeng Biotechnol 2022; 10:1066869. [PMID: 36568297 PMCID: PMC9772457 DOI: 10.3389/fbioe.2022.1066869] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
The prevalency of lung disease has increased worldwide, especially in the aging population. It is essential to develop novel disease models, that are superior to traditional models. Organoids are three-dimensional (3D) in vitro structures that produce from self-organizing and differentiating stem cells, including pluripotent stem cells (PSCs) or adult stem cells (ASCs). They can recapitulate the in vivo cellular heterogeneity, genetic characteristics, structure, and functionality of original tissues. Drug responses of patient-derived organoids (PDOs) are consistent with that of patients, and show correlations with genetic alterations. Thus, organoids have proven to be valuable in studying the biology of disease, testing preclinical drugs and developing novel therapies. In recent years, organoids have been successfully applied in studies of a variety of lung diseases, such as lung cancer, influenza, cystic fibrosis, idiopathic pulmonary fibrosis, and the recent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. In this review, we provide an update on the generation of organoid models for these diseases and their applications in basic and translational research, highlighting these signs of progress in pathogenesis study, drug screening, personalized medicine and immunotherapy. We also discuss the current limitations and future perspectives in organoid models of lung diseases.
Collapse
Affiliation(s)
| | - Feifei Na
- State Key Laboratory of Biotherapy and Cancer Center, Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
31
|
Cable J, Lutolf MP, Fu J, Park SE, Apostolou A, Chen S, Song CJ, Spence JR, Liberali P, Lancaster M, Meier AB, Pek NMQ, Wells JM, Capeling MM, Uzquiano A, Musah S, Huch M, Gouti M, Hombrink P, Quadrato G, Urenda JP. Organoids as tools for fundamental discovery and translation-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1518:196-208. [PMID: 36177906 PMCID: PMC11293861 DOI: 10.1111/nyas.14874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Complex three-dimensional in vitro organ-like models, or organoids, offer a unique biological tool with distinct advantages over two-dimensional cell culture systems, which can be too simplistic, and animal models, which can be too complex and may fail to recapitulate human physiology and pathology. Significant progress has been made in driving stem cells to differentiate into different organoid types, though several challenges remain. For example, many organoid models suffer from high heterogeneity, and it can be difficult to fully incorporate the complexity of in vivo tissue and organ development to faithfully reproduce human biology. Successfully addressing such limitations would increase the viability of organoids as models for drug development and preclinical testing. On April 3-6, 2022, experts in organoid development and biology convened at the Keystone Symposium "Organoids as Tools for Fundamental Discovery and Translation" to discuss recent advances and insights from this relatively new model system into human development and disease.
Collapse
Affiliation(s)
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Lausanne, Switzerland
- Institute of Chemical Sciences and Engineering, School of Basic Science (SB), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Roche Institute for Translational Bioengineering (ITB), Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sunghee Estelle Park
- Department of Bioengineering and NSF Science and Technology Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Athanasia Apostolou
- Emulate Inc, Boston, Massachusetts, USA
- Department of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York City, New York, USA
| | - Cheng Jack Song
- Keck Medicine of University of Southern California, Los Angeles, California, USA
| | - Jason R Spence
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI) and University of Basel, Basel, Switzerland
| | | | - Anna B Meier
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Nicole Min Qian Pek
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati, Ohio, USA
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - James M Wells
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati, Ohio, USA
- Division of Developmental Biology and Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Ana Uzquiano
- Department of Stem Cell and Regenerative Biology, Harvard University
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samira Musah
- Developmental and Stem Cell Biology Program and Division of Nephrology, Department of Medicine and Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Center for Biomolecular and Tissue Engineering, Durham, North Carolina, USA
- Department of Biomedical Engineering, Pratt School of Engineering, Durham, North Carolina, USA
- Duke Regeneration Center, Duke University, Durham, North Carolina, USA
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mina Gouti
- Stem Cell Modelling of Development & Disease Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Pleun Hombrink
- University Medical Center Utrecht and HUB Organoids, Utrecht, Netherlands
| | - Giorgia Quadrato
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine and Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California, USA
| | - Jean-Paul Urenda
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine and Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
32
|
Rodenburg LW, Delpiano L, Railean V, Centeio R, Pinto MC, Smits SMA, van der Windt IS, van Hugten CFJ, van Beuningen SFB, Rodenburg RNP, van der Ent CK, Amaral MD, Kunzelmann K, Gray MA, Beekman JM, Amatngalim GD. Drug Repurposing for Cystic Fibrosis: Identification of Drugs That Induce CFTR-Independent Fluid Secretion in Nasal Organoids. Int J Mol Sci 2022; 23:12657. [PMID: 36293514 PMCID: PMC9603984 DOI: 10.3390/ijms232012657] [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: 09/13/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Individuals with cystic fibrosis (CF) suffer from severe respiratory disease due to a genetic defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which impairs airway epithelial ion and fluid secretion. New CFTR modulators that restore mutant CFTR function have been recently approved for a large group of people with CF (pwCF), but ~19% of pwCF cannot benefit from CFTR modulators Restoration of epithelial fluid secretion through non-CFTR pathways might be an effective treatment for all pwCF. Here, we developed a medium-throughput 384-well screening assay using nasal CF airway epithelial organoids, with the aim to repurpose FDA-approved drugs as modulators of non-CFTR-dependent epithelial fluid secretion. From a ~1400 FDA-approved drug library, we identified and validated 12 FDA-approved drugs that induced CFTR-independent fluid secretion. Among the hits were several cAMP-mediating drugs, including β2-adrenergic agonists. The hits displayed no effects on chloride conductance measured in the Ussing chamber, and fluid secretion was not affected by TMEM16A, as demonstrated by knockout (KO) experiments in primary nasal epithelial cells. Altogether, our results demonstrate the use of primary nasal airway cells for medium-scale drug screening, target validation with a highly efficient protocol for generating CRISPR-Cas9 KO cells and identification of compounds which induce fluid secretion in a CFTR- and TMEM16A-indepent manner.
Collapse
Affiliation(s)
- Lisa W. Rodenburg
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Livia Delpiano
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Violeta Railean
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Raquel Centeio
- Physiological Institute, University of Regensburg, D-93053 Regensburg, Germany
| | - Madalena C. Pinto
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Shannon M. A. Smits
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Isabelle S. van der Windt
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Casper F. J. van Hugten
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Sam F. B. van Beuningen
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB Utrecht, The Netherlands
| | - Remco N. P. Rodenburg
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Cornelis K. van der Ent
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
| | - Margarida D. Amaral
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Karl Kunzelmann
- Physiological Institute, University of Regensburg, D-93053 Regensburg, Germany
| | - Michael A. Gray
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jeffrey M. Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB Utrecht, The Netherlands
| | - Gimano D. Amatngalim
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| |
Collapse
|
33
|
Han Y, Tan L, Zhou T, Yang L, Carrau L, Lacko LA, Saeed M, Zhu J, Zhao Z, Nilsson-Payant BE, Lira Neto FT, Cahir C, Giani AM, Chai JC, Li Y, Dong X, Moroziewicz D, Paull D, Zhang T, Koo S, Tan C, Danziger R, Ba Q, Feng L, Chen Z, Zhong A, Wise GJ, Xiang JZ, Wang H, Schwartz RE, tenOever BR, Noggle SA, Rice CM, Qi Q, Evans T, Chen S. A human iPSC-array-based GWAS identifies a virus susceptibility locus in the NDUFA4 gene and functional variants. Cell Stem Cell 2022; 29:1475-1490.e6. [PMID: 36206731 PMCID: PMC9550219 DOI: 10.1016/j.stem.2022.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 06/09/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022]
Abstract
Population-based studies to identify disease-associated risk alleles typically require samples from a large number of individuals. Here, we report a human-induced pluripotent stem cell (hiPSC)-based screening strategy to link human genetics with viral infectivity. A genome-wide association study (GWAS) identified a cluster of single-nucleotide polymorphisms (SNPs) in a cis-regulatory region of the NDUFA4 gene, which was associated with susceptibility to Zika virus (ZIKV) infection. Loss of NDUFA4 led to decreased sensitivity to ZIKV, dengue virus, and SARS-CoV-2 infection. Isogenic hiPSC lines carrying non-risk alleles of SNPs or deletion of the cis-regulatory region lower sensitivity to viral infection. Mechanistic studies indicated that loss/reduction of NDUFA4 causes mitochondrial stress, which leads to the leakage of mtDNA and thereby upregulation of type I interferon signaling. This study provides proof-of-principle for the application of iPSC arrays in GWAS and identifies NDUFA4 as a previously unknown susceptibility locus for viral infection.
Collapse
Affiliation(s)
- Yuling Han
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Lei Tan
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ting Zhou
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Liuliu Yang
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Lucia Carrau
- Department of Microbiology, New York University, 430 E 29th Street, New York, NY 10016, USA
| | - Lauretta A Lacko
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Jiajun Zhu
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Zeping Zhao
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | | | | | - Clare Cahir
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; The Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Alice Maria Giani
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Jin Chou Chai
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Yang Li
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Xue Dong
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Dorota Moroziewicz
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Tuo Zhang
- Genomic Resource Core Facility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Soyeon Koo
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Christina Tan
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Ron Danziger
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Qian Ba
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingling Feng
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, China
| | - Zhengming Chen
- Department of Population Health Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Aaron Zhong
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Gilbert J Wise
- Department of Urology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Jenny Z Xiang
- Genomic Resource Core Facility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Benjamin R tenOever
- Department of Microbiology, New York University, 430 E 29th Street, New York, NY 10016, USA
| | - Scott A Noggle
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
34
|
Duan X, Lacko LA, Chen S. Druggable targets and therapeutic development for COVID-19. Front Chem 2022; 10:963701. [PMID: 36277347 PMCID: PMC9581228 DOI: 10.3389/fchem.2022.963701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease (COVID-19), which is caused by SARS-CoV-2, is the biggest challenge to the global public health and economy in recent years. Until now, only limited therapeutic regimens have been available for COVID-19 patients, sparking unprecedented efforts to study coronavirus biology. The genome of SARS-CoV-2 encodes 16 non-structural, four structural, and nine accessory proteins, which mediate the viral life cycle, including viral entry, RNA replication and transcription, virion assembly and release. These processes depend on the interactions between viral polypeptides and host proteins, both of which could be potential therapeutic targets for COVID-19. Here, we will discuss the potential medicinal value of essential proteins of SARS-CoV-2 and key host factors. We summarize the most updated therapeutic interventions for COVID-19 patients, including those approved clinically or in clinical trials.
Collapse
|
35
|
Zhu JY, Wang G, Huang X, Lee H, Lee JG, Yang P, van de Leemput J, Huang W, Kane MA, Yang P, Han Z. SARS-CoV-2 Nsp6 damages Drosophila heart and mouse cardiomyocytes through MGA/MAX complex-mediated increased glycolysis. Commun Biol 2022; 5:1039. [PMID: 36180527 PMCID: PMC9523645 DOI: 10.1038/s42003-022-03986-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/13/2022] [Indexed: 12/01/2022] Open
Abstract
SARS-CoV-2 infection causes COVID-19, a severe acute respiratory disease associated with cardiovascular complications including long-term outcomes. The presence of virus in cardiac tissue of patients with COVID-19 suggests this is a direct, rather than secondary, effect of infection. Here, by expressing individual SARS-CoV-2 proteins in the Drosophila heart, we demonstrate interaction of virus Nsp6 with host proteins of the MGA/MAX complex (MGA, PCGF6 and TFDP1). Complementing transcriptomic data from the fly heart reveal that this interaction blocks the antagonistic MGA/MAX complex, which shifts the balance towards MYC/MAX and activates glycolysis-with similar findings in mouse cardiomyocytes. Further, the Nsp6-induced glycolysis disrupts cardiac mitochondrial function, known to increase reactive oxygen species (ROS) in heart failure; this could explain COVID-19-associated cardiac pathology. Inhibiting the glycolysis pathway by 2-deoxy-D-glucose (2DG) treatment attenuates the Nsp6-induced cardiac phenotype in flies and mice. These findings point to glycolysis as a potential pharmacological target for treating COVID-19-associated heart failure.
Collapse
Affiliation(s)
- Jun-Yi Zhu
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Guanglei Wang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Xiaohu Huang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Hangnoh Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Jin-Gu Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Penghua Yang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
- University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Peixin Yang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
| |
Collapse
|
36
|
Wang T, Cao Y, Zhang H, Wang Z, Man CH, Yang Y, Chen L, Xu S, Yan X, Zheng Q, Wang Y. COVID-19 metabolism: Mechanisms and therapeutic targets. MedComm (Beijing) 2022; 3:e157. [PMID: 35958432 PMCID: PMC9363584 DOI: 10.1002/mco2.157] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dysregulates antiviral signaling, immune response, and cell metabolism in human body. Viral genome and proteins hijack host metabolic network to support viral biogenesis and propagation. However, the regulatory mechanism of SARS-CoV-2-induced metabolic dysfunction has not been elucidated until recently. Multiomic studies of coronavirus disease 2019 (COVID-19) revealed an intensive interaction between host metabolic regulators and viral proteins. SARS-CoV-2 deregulated cellular metabolism in blood, intestine, liver, pancreas, fat, and immune cells. Host metabolism supported almost every stage of viral lifecycle. Strikingly, viral proteins were found to interact with metabolic enzymes in different cellular compartments. Biochemical and genetic assays also identified key regulatory nodes and metabolic dependencies of viral replication. Of note, cholesterol metabolism, lipid metabolism, and glucose metabolism are broadly involved in viral lifecycle. Here, we summarized the current understanding of the hallmarks of COVID-19 metabolism. SARS-CoV-2 infection remodels host cell metabolism, which in turn modulates viral biogenesis and replication. Remodeling of host metabolism creates metabolic vulnerability of SARS-CoV-2 replication, which could be explored to uncover new therapeutic targets. The efficacy of metabolic inhibitors against COVID-19 is under investigation in several clinical trials. Ultimately, the knowledge of SARS-CoV-2-induced metabolic reprogramming would accelerate drug repurposing or screening to combat the COVID-19 pandemic.
Collapse
Affiliation(s)
- Tianshi Wang
- Shanghai Key Laboratory for Tumor Microenvironment and InflammationDepartment of Biochemistry and Molecular Cell BiologyShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Ying Cao
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteRenji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Haiyan Zhang
- Bai Jia Obstetrics and Gynecology HospitalShanghaiChina
| | - Zihao Wang
- Fudan University Shanghai Cancer CenterKey Laboratory of Breast Cancer in ShanghaiShanghai Key Laboratory of Radiation OncologyCancer Instituteand The Shanghai Key Laboratory of Medical EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- The International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghaiChina
| | - Cheuk Him Man
- Division of HematologyDepartment of MedicineUniversity of Hong KongPokfulamHong Kong, China
| | - Yunfan Yang
- Department of Cell BiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanChina
| | - Lingchao Chen
- Department of NeurosurgeryHuashan HospitalShanghai Medical CollegeFudan UniversityNational Center for Neurological DisordersShanghai Key Laboratory of Brain Function and Restoration and Neural RegenerationNeurosurgical Institute of Fudan UniversityShanghai Clinical Medical Center of NeurosurgeryShanghaiChina
| | - Shuangnian Xu
- Department of HematologySouthwest HospitalArmy Medical UniversityChongqingChina
| | - Xiaojing Yan
- Department of HematologyThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Quan Zheng
- Center for Single‐Cell OmicsSchool of Public HealthShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yi‐Ping Wang
- Fudan University Shanghai Cancer CenterKey Laboratory of Breast Cancer in ShanghaiShanghai Key Laboratory of Radiation OncologyCancer Instituteand The Shanghai Key Laboratory of Medical EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- The International Co‐laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghaiChina
| |
Collapse
|
37
|
Rubio-Casillas A, Redwan EM, Uversky VN. SARS-CoV-2: A Master of Immune Evasion. Biomedicines 2022; 10:1339. [PMID: 35740361 PMCID: PMC9220273 DOI: 10.3390/biomedicines10061339] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 02/07/2023] Open
Abstract
Viruses and their hosts have coevolved for a long time. This coevolution places both the pathogen and the human immune system under selective pressure; on the one hand, the immune system has evolved to combat viruses and virally infected cells, while viruses have developed sophisticated mechanisms to escape recognition and destruction by the immune system. SARS-CoV-2, the pathogen that is causing the current COVID-19 pandemic, has shown a remarkable ability to escape antibody neutralization, putting vaccine efficacy at risk. One of the virus's immune evasion strategies is mitochondrial sabotage: by causing reactive oxygen species (ROS) production, mitochondrial physiology is impaired, and the interferon antiviral response is suppressed. Seminal studies have identified an intra-cytoplasmatic pathway for viral infection, which occurs through the construction of tunneling nanotubes (TNTs), hence enhancing infection and avoiding immune surveillance. Another method of evading immune monitoring is the disruption of the antigen presentation. In this scenario, SARS-CoV-2 infection reduces MHC-I molecule expression: SARS-CoV-2's open reading frames (ORF 6 and ORF 8) produce viral proteins that specifically downregulate MHC-I molecules. All of these strategies are also exploited by other viruses to elude immune detection and should be studied in depth to improve the effectiveness of future antiviral treatments. Compared to the Wuhan strain or the Delta variant, Omicron has developed mutations that have impaired its ability to generate syncytia, thus reducing its pathogenicity. Conversely, other mutations have allowed it to escape antibody neutralization and preventing cellular immune recognition, making it the most contagious and evasive variant to date.
Collapse
Affiliation(s)
- Alberto Rubio-Casillas
- Biology Laboratory, Autlán Regional Preparatory School, University of Guadalajara, Autlán 48900, Jalisco, Mexico
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia;
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria 21934, Egypt
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| |
Collapse
|
38
|
Vollbracht C, Kraft K. Oxidative Stress and Hyper-Inflammation as Major Drivers of Severe COVID-19 and Long COVID: Implications for the Benefit of High-Dose Intravenous Vitamin C. Front Pharmacol 2022; 13:899198. [PMID: 35571085 PMCID: PMC9100929 DOI: 10.3389/fphar.2022.899198] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 12/25/2022] Open
Abstract
Oxidative stress is a pivotal point in the pathophysiology of COVID-19 and presumably also in Long-COVID. Inflammation and oxidative stress are mutually reinforcing each other, thus contributing to the systemic hyperinflammatory state and coagulopathy which are cardinal pathological mechanisms of severe stages. COVID-19 patients, like other critically ill patients e.g. with pneumonia, very often show severe deficiency of the antioxidant vitamin C. So far, it has not been investigated how long this deficiency lasts or whether patients with long COVID symptoms also suffer from deficiencies. A vitamin C deficit has serious pathological consequences because vitamin C is one of the most effective antioxidants, but also co-factor of many enzymatic processes that affect the immune and nervous system, blood circulation and energy metabolism. Because of its anti-oxidative, anti-inflammatory, endothelial-restoring, and immunomodulatory effects the supportive intravenous (iv) use of supraphysiological doses has been investigated so far in 12 controlled or observational studies with altogether 1578 inpatients with COVID-19. In these studies an improved oxygenation, a decrease in inflammatory markers and a faster recovery were observed. In addition, early treatment with iv high dose vitamin C seems to reduce the risks of severe courses of the disease such as pneumonia and also mortality. Persistent inflammation, thrombosis and a dysregulated immune response (auto-immune phenomena and/or persistent viral load) seem to be major contributors to Long-COVID. Oxidative stress and inflammation are involved in the development and progression of fatigue and neuro-psychiatric symptoms in various diseases by disrupting tissue (e.g. autoantibodies), blood flow (e.g. immune thrombosis) and neurotransmitter metabolism (e.g. excitotoxicity). In oncological diseases, other viral infections and autoimmune diseases, which are often associated with fatigue, cognitive disorders, pain and depression similar to Long-COVID, iv high dose vitamin C was shown to significantly relieve these symptoms. Supportive iv vitamin C in acute COVID-19 might therefore reduce the risk of severe courses and also the development of Long-COVID.
Collapse
Affiliation(s)
- Claudia Vollbracht
- Medical Science Department, Pascoe Pharmazeutische Präparate GmbH, Giessen, Germany
| | - Karin Kraft
- Chair of Naturopathy, University Medicine Rostock, Rostock, Germany
| |
Collapse
|
39
|
Huckestein BR, Alcorn JF. Improving Mitochondrial Function in Viral Infection: Targeting Cellular Metabolism. Am J Respir Cell Mol Biol 2022; 66:598-600. [PMID: 35442855 PMCID: PMC9163644 DOI: 10.1165/rcmb.2022-0096ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Brydie R Huckestein
- Children's Hospital of Pittsburgh of UPMC, 6619, Pittsburgh, Pennsylvania, United States
| | - John F Alcorn
- Children's Hospital of Pittsburgh of UPMC, Pediatrics, Pittsburgh, Pennsylvania, United States;
| |
Collapse
|
40
|
Synthesis of Human Phase I and Phase II Metabolites of Hop (Humulus lupulus) Prenylated Flavonoids. Metabolites 2022; 12:metabo12040345. [PMID: 35448532 PMCID: PMC9030851 DOI: 10.3390/metabo12040345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 12/12/2022] Open
Abstract
Hop prenylated flavonoids have been investigated for their in vivo activities due to their broad spectrum of positive health effects. Previous studies on the metabolism of xanthohumol using untargeted methods have found that it is first degraded into 8-prenylnaringenin and 6-prenylnaringenin, by spontaneous cyclisation into isoxanthohumol, and subsequently demethylated by gut bacteria. Further combinations of metabolism by hydroxylation, sulfation, and glucuronidation result in an unknown number of isomers. Most investigations involving the analysis of prenylated flavonoids used surrogate or untargeted approaches in metabolite identification, which is prone to errors in absolute identification. Here, we present a synthetic approach to obtaining reference standards for the identification of human xanthohumol metabolites. The synthesised metabolites were subsequently analysed by qTOF LC-MS/MS, and some were matched to a human blood sample obtained after the consumption of 43 mg of micellarised xanthohumol. Additionally, isomers of the reference standards were identified due to their having the same mass fragmentation pattern and different retention times. Overall, the methods unequivocally identified the metabolites of xanthohumol that are present in the blood circulatory system. Lastly, in vitro bioactive testing should be applied using metabolites and not original compounds, as free compounds are scarcely found in human blood.
Collapse
|
41
|
Human organoid models to study SARS-CoV-2 infection. Nat Methods 2022; 19:418-428. [PMID: 35396481 DOI: 10.1038/s41592-022-01453-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/08/2022] [Indexed: 12/11/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest pandemics in history. SARS-CoV-2 not only infects the respiratory tract, but also causes damage to many organs. Organoids, which can self-renew and recapitulate the various physiology of different organs, serve as powerful platforms to model COVID-19. In this Perspective, we overview the current effort to apply both human pluripotent stem cell-derived organoids and adult organoids to study SARS-CoV-2 tropism, host response and immune cell-mediated host damage, and perform drug discovery and vaccine development. We summarize the technologies used in organoid-based COVID-19 research, discuss the remaining challenges and provide future perspectives in the application of organoid models to study SARS-CoV-2 and future emerging viruses.
Collapse
|
42
|
Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Albrecht YS, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Kidane YH, Priebe W, Emmett MR, Meller R, Singh U, Bram Y, tenOever BR, Heise MT, Moorman NJ, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baxter VK, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. TARGETED DOWN REGULATION OF CORE MITOCHONDRIAL GENES DURING SARS-COV-2 INFECTION. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.19.481089. [PMID: 35233572 PMCID: PMC8887073 DOI: 10.1101/2022.02.19.481089] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.
Collapse
Affiliation(s)
- Joseph W. Guarnieri
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Joseph M. Dybas
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Hossein Fazelinia
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Man S. Kim
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | | | - Yuanchao Zhang
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Yentli Soto Albrecht
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | | | - Alessia Angelin
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Larry N. Singh
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Scott L. Weiss
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Sonja M. Best
- COVID-19 International Research Team
- Rocky Mountain Laboratories NIAID, Hamilton, MT 59840
| | - Marie T. Lott
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Viktorija Zaksas
- COVID-19 International Research Team
- University of Chicago, Chicago, IL, 60615, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | | | | | - Yared H. Kidane
- COVID-19 International Research Team
- Scottish Rite for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team
- University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark R. Emmett
- COVID-19 International Research Team
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Urminder Singh
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | | | - Mark T. Heise
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | - Emily A. Madden
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Wes A. Sanders
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Stephen B. Baylin
- COVID-19 International Research Team
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | - Deanne Taylor
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Christopher E. Mason
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
- New York Genome Center, NY, USA
| | - Jonathan C. Schisler
- COVID-19 International Research Team
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Robert E. Schwartz
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- KBR, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Douglas C. Wallace
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- University of Pennsylvania, Philadelphia, PA 19104 USA
| |
Collapse
|
43
|
Duan X, Wang H, Ho DD, Schwartz RE, Evans T, Chen S. Comments on 'An airway organoid-based screen identifies a role for the HIF1α‒glycolysis axis in SARS-CoV-2 infection'. J Mol Cell Biol 2021; 14:6446811. [PMID: 34850919 PMCID: PMC8690227 DOI: 10.1093/jmcb/mjab075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Xiaohua Duan
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.,State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA
| |
Collapse
|