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Zuo Z, Shi J, Wang Y, Yin Z, Wang Z, Yang Z, Jia B, Sun Y. The transcriptomic landscape of canonical activation of NLRP3 inflammasome from bone marrow-derived macrophages. Biochem Biophys Res Commun 2024; 694:149409. [PMID: 38141558 DOI: 10.1016/j.bbrc.2023.149409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
The NLRP3 inflammasome has gained significant attention due to its participation in diverse cellular processes. Nevertheless, the detailed framework of the canonical NLRP3 inflammasome assembly still remains unrevealed. This study aims to elucidate the transcriptomic landscape of the various stages involved in the canonical activation of the NLRP3 inflammasome in BMDMs by integrating RNA-seq, bioinformatics, and molecular dynamics analyses. The model for the canonical activation of the NLRP3 inflammasome was confirmed through morphological observations, functional assessments (ELISA and LDH), and protein detection (western blot). Subsequently, cells were subjected to RNA sequencing following three groups: control, priming (LPS 500 ng/ml, 4 h), and activation (LPS 500 ng/ml, 4 h; ATP 5 mM, 1 h). A total of 9116 differentially expressed genes (DEGs) were identified, which exerted regulatory effects on various pathways, including cell metabolism, ion fluxes, post-translational modifications, and organelles. Subsequently, six hub genes (Sirt3, Stat3, Syk, Trpm2, Tspo, and Txnip) were identified via integrating literature review and database screening. Finally, the three-dimensional structures of these six hub proteins were obtained using the MD-optimized RoseTTAFold and Gromacs simulations (at least 200 ns). In summary, our research offers novel insights into the transcriptomic-level understanding of the assembly of the canonical NLRP3 inflammasome.
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Affiliation(s)
- Zhuo Zuo
- School of Life Sciences, Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, Research Center of Special Environmental Biomechanics and Medical Engineering, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Jiajia Shi
- School of Life Sciences, Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, Research Center of Special Environmental Biomechanics and Medical Engineering, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Yaxing Wang
- School of Life Sciences, Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, Research Center of Special Environmental Biomechanics and Medical Engineering, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Zhongqian Yin
- School of Life Sciences, Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, Research Center of Special Environmental Biomechanics and Medical Engineering, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Zhe Wang
- School of Life Sciences, Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, Research Center of Special Environmental Biomechanics and Medical Engineering, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Zhouqi Yang
- School of Life Sciences, Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, Research Center of Special Environmental Biomechanics and Medical Engineering, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Bin Jia
- School of Life Sciences, Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, Research Center of Special Environmental Biomechanics and Medical Engineering, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Yulong Sun
- School of Life Sciences, Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, Research Center of Special Environmental Biomechanics and Medical Engineering, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China.
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Xin Q, Wang D, Wang S, Zhang L, Liang Q, Yan X, Fan K, Jiang B. Tackling Esophageal Squamous Cell Carcinoma with ITFn-Pt(IV): A Novel Fusion of PD-L1 Blockade, Chemotherapy, and T-cell Activation. Adv Healthc Mater 2023:e2303623. [PMID: 38142309 DOI: 10.1002/adhm.202303623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/07/2023] [Indexed: 12/25/2023]
Abstract
PD-1/PD-L1 blockade immunotherapy has gained approval for the treatment of a diverse range of tumors; however, its efficacy is constrained by the insufficient infiltration of T lymphocytes into the tumor microenvironment, resulting in suboptimal patient responses. Here, a pioneering immunotherapy ferritin nanodrug delivery system denoted as ITFn-Pt(IV) is introduced. This system orchestrates a synergistic fusion of PD-L1 blockade, chemotherapy, and T-cell activation, aiming to augment the efficacy of tumor immunotherapy. Leveraging genetic engineering approach and temperature-regulated channel-based drug loading techniques, the architecture of this intelligent responsive system is refined. It is adept at facilitating the precise release of T-cell activating peptide Tα1 in the tumor milieu, leading to an elevation in T-cell proliferation and activation. The integration of PD-L1 nanobody KN035 ensures targeted engagement with tumor cells and mediates the intracellular delivery of the encapsulated Pt(IV) drugs, culminating in immunogenic cell death and the subsequent dendritic cell maturation. Employing esophageal squamous cell carcinoma (ESCC) as tumor model, the potent antitumor efficacy of ITFn-Pt(IV) is elucidated, underscored by augmented T-cell infiltration devoid of systemic adverse effects. These findings accentuate the potential of ITFn-Pt(IV) for ESCC treatment and its applicability to other malignancies resistant to established PD-1/PD-L1 blockade therapies.
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Affiliation(s)
- Qi Xin
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Daji Wang
- Nanozyme Synthesis Center, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shenghui Wang
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Lirong Zhang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan, 450001, China
| | - Qian Liang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiyun Yan
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China
| | - Kelong Fan
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China
| | - Bing Jiang
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China
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Matteucci C, Nepravishta R, Argaw-Denboba A, Mandaliti W, Giovinazzo A, Petrone V, Balestrieri E, Sinibaldi-Vallebona P, Pica F, Paci M, Garaci E. Thymosin α1 interacts with Galectin-1 modulating the β-galactosides affinity and inducing alteration in the biological activity. Int Immunopharmacol 2023; 118:110113. [PMID: 37028279 DOI: 10.1016/j.intimp.2023.110113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 04/09/2023]
Abstract
The study of mechanism of action of Thymosin alpha 1 (Tα1) and the basis of the pleiotropic effect in health and disease, is one of the main focus of our ongoing research. Tα1 is a thymic peptide that demonstrates a peculiar ability to restore homeostasis in different physiological and pathological conditions (i.e., infections, cancer, immunodeficiency, vaccination, and aging) acting as multitasking protein depending on the host state of inflammation or immune dysfunction. However, few are the information about mechanisms of action mediated by specific Tα1-target protein interaction that could explain its pleiotropic effect. We investigated the interaction of Tα1 with Galectin-1 (Gal-1), a protein belonging to an oligosaccharide binding protein family involved in a variety of biological and pathological processes, including immunoregulation, infections, cancer progression and aggressiveness. Using molecular and cellular methodological approaches, we demonstrated the interaction between these two proteins. Tα1 specifically inhibited the hemagglutination activity of Gal-1, the Gal-1 dependent in vitro formation of endothelial cell tubular structures, and the migration of cancer cells in wound healing assay. Physico-chemical methods revealed the details of the molecular interaction of Tα1 with Gal-1. Hence, the study allowed the identification of the not known until now specific interaction between Tα1 and Gal-1, and unraveled a novel mechanism of action of Tα1 that could support understanding of its pleiotropic activity.
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Affiliation(s)
- Claudia Matteucci
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy.
| | - Ridvan Nepravishta
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome 00133, Italy
| | - Ayele Argaw-Denboba
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy; European Molecular Biology Laboratory, EMBL, Monterotondo, Rome 00015, Italy
| | - Walter Mandaliti
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome 00133, Italy
| | - Alessandro Giovinazzo
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy; Institute of Biochemistry and Cell Biology, IBBC-CNR, Monterotondo, Rome 00015, Italy
| | - Vita Petrone
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy; Institute of Translational Pharmacology, National Research Council, Rome 00133, Italy
| | - Francesca Pica
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome 00133, Italy
| | - Enrico Garaci
- IRCCS San Raffaele and IRCCS San Raffaele, Rome 00163, Italy; Medical and Experimental BioImaging Center, MEBIC Consortium, Rome 00166, Italy
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Antonella Minutolo, Vita Petrone, Marialaura Fanelli, Christian Maracchioni, Martina Giudice, Elisabetta Teti, Luigi Coppola, Chiara Sorace, Marco Iannetta, Martino Tony Miele, Sergio Bernardini, Antonio Mastino, Paola Sinibaldi Vallebona, Emanuela Balestrieri, Massimo Andreoni, Loredana Sarmati, Sandro Grelli, Enrico Garaci, Claudia Matteucci. Thymosin Alpha 1 Restores the Immune Homeostasis in lymphocytes during Post-Acute Sequelae of SARS-CoV-2 infection. Int Immunopharmacol 2023:110055. [PMID: 36989892 PMCID: PMC10030336 DOI: 10.1016/j.intimp.2023.110055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023]
Abstract
The complex alterations of the immune system and the immune-mediated multiorgan injury plays a key role in host response to SARS-CoV-2 infection and in the pathogenesis of COVID-19, being also associated with adverse outcomes. Thymosin alpha 1 (Tα1) is one of the molecules used in the treatment of COVID-19, as it is known to restore the homeostasis of the immune system during infections and cancer. The use of Tα1 in COVID-19 patients had been widely used in China and in COVID-19 patients, it has been shown to decrease hospitalization rate, especially in those with greater disease severity, and reduce mortality by restoring lymphocytopenia and more specifically, depleted T cells. Persistent dysregulation with depletion of naive B and T cell subpopulations and expansion of memory T cells suggest a chronic stimulation of the immune response in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC). Our data obtained from an ex vivo study, showed that in PASC individuals with a chronically altered immune response, Tα1 improve the restoration of an appropriate response, most evident in those with more severe illness and who need respiratory support during acute phase, and in those with specific systemic and psychiatric symptoms of PASC, confirming Tα1 treatment being more effective in compromised patients. The results obtained, along with promising reports on recent trials on Tα1 administration in patients with COVID-19, offer new insights into intervention also for those patients with long-lasting inflammation with post-infectious symptoms, some of which have a delayed onset.
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Key Words
- post-acute sars-cov-2 symptoms
- thymosin alpha 1
- immune regulation
- anti-inflammatory response
- a-cov, acute covid-19
- aa, ambient air
- cdc, center for desease control and prevention
- em, effector memory
- tfh, follicular helper lymphocytes
- hd, healthy donors
- pasc, post-acute sequelae of sars-cov-2 infection
- pcc, post-covid conditions
- pd-1, programmed cell death-1
- ards, respiratory stress syndrome
- resp sup, respiratory support
- rpmi, roswell park memorial institute
- sev, severe acute phase of infection
- tem, terminal effector memory
- tα1, thymosin alpha 1
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Sun Y, Kuang Y, Zuo Z. Transcriptomic Changes in Mouse Bone Marrow-Derived Macrophages Exposed to Neuropeptide FF. Genes (Basel) 2021; 12:705. [PMID: 34065092 DOI: 10.3390/genes12050705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 12/27/2022] Open
Abstract
Neuropeptide FF (NPFF) is a neuropeptide that regulates various biological activities. Currently, the regulation of NPFF on the immune system is an emerging field. However, the influence of NPFF on the transcriptome of primary macrophages has not been fully elucidated. In this study, the effect of NPFF on the transcriptome of mouse bone marrow-derived macrophages (BMDMs) was explored by RNA sequencing, bioinformatics, and molecular simulation. BMDMs were treated with 1 nM NPFF for 18 h, followed by RNA sequencing. Differentially expressed genes (DEGs) were obtained, followed by GO, KEGG, and PPI analysis. A total of eight qPCR-validated DEGs were selected as hub genes. Subsequently, the three-dimensional (3-D) structures of the eight hub proteins were constructed by Modeller and Rosetta. Next, the molecular dynamics (MD)-optimized 3-D structure of hub protein was acquired with Gromacs. Finally, the binding modes between NPFF and hub proteins were studied by Rosetta. A total of 2655 DEGs were obtained (up-regulated 1442 vs. down-regulated 1213), and enrichment analysis showed that NPFF extensively regulates multiple functional pathways mediated by BMDMs. Moreover, the 3-D structure of the hub protein was obtained after MD-optimization. Finally, the docking modes of NPFF-hub proteins were predicted. Besides, NPFFR2 was expressed on the cell membrane of BMDMs, and NPFF 1 nM significantly activated NPFFR2 protein expression. In summary, instead of significantly inhibiting the expression of the immune-related gene transcriptome of RAW 264.7 cells, NPFF simultaneously up-regulated and down-regulated the gene expression profile of a large number of BMDMs, hinting that NPFF may profoundly affect a variety of cellular processes dominated by BMDMs. Our work provides transcriptomics clues for exploring the influence of NPFF on the physiological functions of BMDMs.
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Sun Y, Zuo Z, Kuang Y. Prolactin-Releasing Peptide Differentially Regulates Gene Transcriptomic Profiles in Mouse Bone Marrow-Derived Macrophages. Int J Mol Sci 2021; 22:ijms22094456. [PMID: 33923285 PMCID: PMC8123224 DOI: 10.3390/ijms22094456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 01/24/2023] Open
Abstract
Prolactin-releasing Peptide (PrRP) is a neuropeptide whose receptor is GPR10. Recently, the regulatory role of PrRP in the neuroendocrine field has attracted increasing attention. However, the influence of PrRP on macrophages, the critical housekeeper in the neuroendocrine field, has not yet been fully elucidated. Here, we investigated the effect of PrRP on the transcriptome of mouse bone marrow-derived macrophages (BMDMs) with RNA sequencing, bioinformatics, and molecular simulation. BMDMs were exposed to PrRP (18 h) and were subjected to RNA sequencing. Differentially expressed genes (DEGs) were acquired, followed by GO, KEGG, and PPI analysis. Eight qPCR-validated DEGs were chosen as hub genes. Next, the three-dimensional structures of the proteins encoded by these hub genes were modeled by Rosetta and Modeller, followed by molecular dynamics simulation by the Gromacs program. Finally, the binding modes between PrRP and hub proteins were investigated with the Rosetta program. PrRP showed no noticeable effect on the morphology of macrophages. A total of 410 DEGs were acquired, and PrRP regulated multiple BMDM-mediated functional pathways. Besides, the possible docking modes between PrRP and hub proteins were investigated. Moreover, GPR10 was expressed on the cell membrane of BMDMs, which increased after PrRP exposure. Collectively, PrRP significantly changed the transcriptome profile of BMDMs, implying that PrRP may be involved in various physiological activities mastered by macrophages.
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Affiliation(s)
- Yulong Sun
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China; (Z.Z.); (Y.K.)
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
- Correspondence: ; Tel.: +86-29-8846-0332
| | - Zhuo Zuo
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China; (Z.Z.); (Y.K.)
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Yuanyuan Kuang
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China; (Z.Z.); (Y.K.)
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
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Sun Y, Kuang Y, Zuo Z, Zhang J, Ma X, Xing X, Liu L, Miao Y, Ren T, Li H, Mei Q. Cellular processes involved in RAW 264.7 macrophages exposed to NPFF: A transcriptional study. Peptides 2021; 136:170469. [PMID: 33309723 DOI: 10.1016/j.peptides.2020.170469] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/25/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022]
Abstract
Neuropeptide FF (NPFF) is a neuropeptide that modulates various physiological processes. The regulatory role of NPFF in the immune and inflammatory response is currently being revealed. However, the effect of NPFF at the transcriptome level in macrophages has not been fully elucidated. Here, the impact of NPFF on gene expression at the transcriptome level of RAW 264.7 cells was investigated by RNA-seq. RAW 264.7 macrophages were treated with NPFF (1 nM) for 18 h, followed by RNA-seq examination. Differentially expressed genes (DEGs) were acquired, followed by GO, KEGG, and PPI analysis. A total of eight qPCR-verified DEGs were obtained. Next, three-dimensional models of the eight hub proteins were constructed by using homology modeling with Modeller (9v23). Finally, molecular dynamics simulation (300 ns) was performed with GROMACS 2018.2 to investigate the structural characteristics of these hub proteins. NPFF had no detectable effect on the morphology of RAW264.7 cells. A total of 211 DEGs were acquired, and an enrichment study demonstrated that the immune response-related pathway was significantly inhibited by NPFF. Moreover, the molecular dynamics optimized-protein models of the hub proteins were obtained. Collectively, NPFF inhibited the expression of immune-related genes in RAW 264.7 cells at the transcriptome level, which suggested a negative relationship between NPFF and this set of immune-related genes in RAW 264.7 macrophages. Therefore, our data may provide direct evidence of the role of NPFF in peripheral or central inflammatory diseases.
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Affiliation(s)
- Yulong Sun
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China.
| | - Yuanyuan Kuang
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Zhuo Zuo
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an, Shaanxi Province, 710049, China
| | - Xiaolong Ma
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Xiaoyu Xing
- School of Humanities, Economics and Laws, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Lingyi Liu
- School of Physical Science and Technology, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Yuchen Miao
- School of Physical Science and Technology, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Tao Ren
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
| | - Hui Li
- Hong-Hui Hospital, Xi'an Jiaotong University College of Medicine, South Door Slightly Friendship Road 555, Xi'an, Shaanxi Province, 710054, China
| | - Qibing Mei
- Key Laboratory for Space Biosciences & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi Province, 710072, China
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Matteucci C, Minutolo A, Balestrieri E, Petrone V, Fanelli M, Malagnino V, Ianetta M, Giovinazzo A, Barreca F, Di Cesare S, De Marco P, Miele MT, Toschi N, Mastino A, Sinibaldi Vallebona P, Bernardini S, Rogliani P, Sarmati L, Andreoni M, Grelli S, Garaci E. Thymosin Alpha 1 Mitigates Cytokine Storm in Blood Cells From Coronavirus Disease 2019 Patients. Open Forum Infect Dis 2020; 8:ofaa588. [PMID: 33506065 PMCID: PMC7798699 DOI: 10.1093/ofid/ofaa588] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) is characterized by immune-mediated lung injury and complex alterations of the immune system, such as lymphopenia and cytokine storm, that have been associated with adverse outcomes underlining a fundamental role of host response in severe acute respiratory syndrome coronavirus 2 infection and the pathogenesis of the disease. Thymosin alpha 1 (Tα1) is one of the molecules used in the management of COVID-19, because it is known to restore the homeostasis of the immune system during infections and cancer. Methods In this study, we captured the interconnected biological processes regulated by Tα1 in CD8+ T cells under inflammatory conditions. Results Genes associated with cytokine signaling and production were upregulated in blood cells from patients with COVID-19, and the ex vivo treatment with Tα1-mitigated cytokine expression, and inhibited lymphocyte activation in a CD8+ T-cell subset specifically. Conclusion These data suggest the potential role of Tα1 in modulating the immune response homeostasis and the cytokine storm in vivo.
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Affiliation(s)
- Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Antonella Minutolo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Vita Petrone
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Marialaura Fanelli
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Vincenzo Malagnino
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | - Marco Ianetta
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | | | - Filippo Barreca
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | - Silvia Di Cesare
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Unit of Immune and Infectious Diseases, Academic Department of Pediatrics, Bambino Gesù Childrens' Hospital-Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
| | - Patrizia De Marco
- Respiratory Medicine Unit, University Hospital Policlinico Tor Vergata, Rome, Italy
| | - Martino Tony Miele
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Nicola Toschi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Athinoula A. Martinos Center for Biomedical Imaging, Harvard Medical School, Boston, Massachusetts, USA
| | - Antonio Mastino
- Institute of Translational Pharmacology, National Research Council, Rome, Italy.,Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Paola Sinibaldi Vallebona
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Institute of Translational Pharmacology, National Research Council, Rome, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Paola Rogliani
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Respiratory Medicine Unit, University Hospital Policlinico Tor Vergata, Rome, Italy
| | - Loredana Sarmati
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Virology Unit, Policlinic of Tor Vergata, Rome, Italy
| | - Enrico Garaci
- University San Raffaele, Rome, Italy.,IRCCS San Raffaele Pisana, Rome, Italy
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Li H, Liu S, Du Y, Tan J, Luo J, Sun Y. Hub Proteins Involved in RAW 264.7 Macrophages Exposed to Direct Current Electric Field. Int J Mol Sci 2020; 21:E4505. [PMID: 32599940 DOI: 10.3390/ijms21124505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023] Open
Abstract
At present, studies on macrophage proteins mainly focus on biological stimuli, with less attention paid to the responses of macrophage proteins to physical stimuli, such as electric fields. Here, we exploited the electric field-sensitive hub proteins of macrophages. RAW 264.7 macrophages were treated with a direct current electric field (dcEF) (200 mV/mm) for four hours, followed by RNA-Seq analysis. Differentially expressed genes (DEGs) were obtained, followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and protein–protein interaction (PPI) analysis. Eight qPCR-verified DEGs were selected. Subsequently, three-dimensional protein models of DEGs were modeled by Modeller and Rosetta, followed by molecular dynamics simulation for 200 ns with GROMACS. Finally, dcEFs (10, 50, and 500 mV/mm) were used to simulate the molecular dynamics of DEG proteins for 200 ns, followed by trajectory analysis. The dcEF has no obvious effect on RAW 264.7 morphology. A total of 689 DEGs were obtained, and enrichment analysis showed that the steroid biosynthesis pathway was most affected by the dcEF. Moreover, the three-dimensional protein structures of hub proteins were constructed, and trajectory analysis suggested that the dcEF caused an increase in the atomic motion of the protein in a dcEF-intensity-dependent manner. Overall, we provide new clues and a basis for investigating the hub proteins of macrophages in response to electric field stimulation.
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Li H, Liu S, Yang X, Du Y, Luo J, Tan J, Sun Y. Cellular processes involved in lung cancer cells exposed to direct current electric field. Sci Rep 2020; 10:5289. [PMID: 32210363 DOI: 10.1038/s41598-020-62332-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/06/2020] [Indexed: 11/08/2022] Open
Abstract
With the rapid breakthrough of electrochemical treatment of tumors, electric field (EF)-sensitive genes, previously rarely exploited, have become an emerging field recently. Here, we reported our work for the identification of EF-sensitive genes in lung cancer cells. The gene expression profile (GSE33845), in which the human lung cancer CL1-0 cells were treated with a direct current electric field (dcEF) (300 mV/mm) for 2 h, was retrieved from GEO database. Differentially expressed genes (DEGs) were acquired, followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and protein-protein interaction (PPI) analysis. Hub genes were acquired and analyzed by various tools including the Human Protein Atlas, Kaplan-Meier analysis, Cytoscape, FunRich, Oncomine and cBioPortal. Subsequently, three-dimensional protein models of hub genes were modeled by Modeller 9.20 and Rosetta 3.9. Finally, a 100 ns molecular dynamics simulation for each hub protein was performed with GROMACS 2018.2. A total of 257 DEGs were acquired and analyzed by GO, KEGG and PPI. Then, 10 hub genes were obtained, and the signal pathway analysis showed that two inflammatory pathways were activated: the FoxO signaling pathway and the AGE-RAGE signaling pathway. The molecular dynamic analysis including RMSD and the radius of gyration hinted that the 3D structures of hub proteins were built. Overall, our work identified EF-sensitive genes in lung cancer cells and identified that the inflammatory state of tumor cells may be involved in the feedback mechanism of lung cancer cells in response to electric field stimulation. In addition, qualified three-dimensional protein models of hub genes were also constructed, which will be helpful in understanding the complex effects of dcEF on human lung cancer CL1-0 cells.
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Li H, Liu S, Yang X, Du Y, Luo J, Tan J, Sun Y. Cellular Processes Involved in Jurkat Cells Exposed to Nanosecond Pulsed Electric Field. Int J Mol Sci 2019; 20:E5847. [PMID: 31766457 DOI: 10.3390/ijms20235847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 12/11/2022] Open
Abstract
Recently, nanosecond pulsed electric field (nsPEF) has been considered as a new tool for tumor therapy, but its molecular mechanism of function remains to be fully elucidated. Here, we explored the cellular processes of Jurkat cells exposed to nanosecond pulsed electric field. Differentially expressed genes (DEGs) were acquired from the GEO2R, followed by analysis with a series of bioinformatics tools. Subsequently, 3D protein models of hub genes were modeled by Modeller 9.21 and Rosetta 3.9. Then, a 100 ns molecular dynamics simulation for each hub protein was performed with GROMACS 2018.2. Finally, three kinds of nsPEF voltages (0.01, 0.05, and 0.5 mV/mm) were used to simulate the molecular dynamics of hub proteins for 100 ns. A total of 1769 DEGs and eight hub genes were obtained. Molecular dynamic analysis, including root mean square deviation (RMSD), root mean square fluctuation (RMSF), and the Rg, demonstrated that the 3D structure of hub proteins was built, and the structural characteristics of hub proteins under different nsPEFs were acquired. In conclusion, we explored the effect of nsPEF on Jurkat cell signaling pathway from the perspective of molecular informatics, which will be helpful in understanding the complex effects of nsPEF on acute T-cell leukemia Jurkat cells.
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