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Fan JH, Li XM. Mesangial cell-derived CircRNAs in chronic glomerulonephritis: RNA sequencing and bioinformatics analysis. Ren Fail 2024; 46:2371059. [PMID: 38946402 PMCID: PMC467094 DOI: 10.1080/0886022x.2024.2371059] [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: 05/01/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) have been shown to play critical roles in the initiation and progression of chronic glomerulonephritis (CGN), while their role from mesangial cells in contributing to the pathogenesis of CGN is rarely understood. Our study aims to explore the potential functions of mesangial cell-derived circRNAs using RNA sequencing (RNA-seq) and bioinformatics analysis. METHODS Mouse mesangial cells (MMCs) were stimulated by lipopolysaccharide (LPS) to establish an in vitro model of CGN. Pro-inflammatory cytokines and cell cycle stages were detected by Enzyme-linked immunosorbent assay (ELISA) and Flow Cytometry experiment, respectively. Subsequently, differentially expressed circRNAs (DE-circRNAs) were identified by RNA-seq. GEO microarrays were used to identify differentially expressed mRNAs (DE-mRNAs) between CGN and healthy populations. Weighted co-expression network analysis (WGCNA) was utilized to explore clinically significant modules of CGN. CircRNA-associated CeRNA networks were constructed by bioinformatics analysis. The hub mRNAs from CeRNA network were identified using LASSO algorithms. Furthermore, utilizing protein-protein interaction (PPI), gene ontology (GO), pathway enrichment (KEGG), and GSEA analyses to explore the potential biological function of target genes from CeRNA network. In addition, we investigated the relationships between immune cells and hub mRNAs from CeRNA network using CIBERSORT. RESULTS The expression of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α was drastically increased in LPS-induced MMCs. The number of cells decreased significantly in the G1 phase but increased significantly in the S/G2 phase. A total of 6 DE-mRNAs were determined by RNA-seq, including 4 up-regulated circRNAs and 2 down-regulated circRNAs. WGCNA analysis identified 1747 DE-mRNAs of the turquoise module from CGN people in the GEO database. Then, the CeRNA networks, including 6 circRNAs, 38 miRNAs, and 80 mRNAs, were successfully constructed. The results of GO and KEGG analyses revealed that the target mRNAs were mainly enriched in immune, infection, and inflammation-related pathways. Furthermore, three hub mRNAs (BOC, MLST8, and HMGCS2) from the CeRNA network were screened using LASSO algorithms. GSEA analysis revealed that hub mRNAs were implicated in a great deal of immune system responses and inflammatory pathways, including IL-5 production, MAPK signaling pathway, and JAK-STAT signaling pathway. Moreover, according to an evaluation of immune infiltration, hub mRNAs have statistical correlations with neutrophils, plasma cells, monocytes, and follicular helper T cells. CONCLUSIONS Our findings provide fundamental and novel insights for further investigations into the role of mesangial cell-derived circRNAs in CGN pathogenesis.
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Affiliation(s)
- Ji Hui Fan
- Department of Nephrology, Huaibei People’s Hospital, Huaibei, China
| | - Xiao Min Li
- Department of Nephrology, Huaibei People’s Hospital, Huaibei, China
- Department of Traditional Chinese Medicine, Huaibei People’s Hospital, Huaibei, China
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Bukhari QUA, Della Pelle F, Alvarez-Diduk R, Scroccarello A, Nogués C, Careta O, Compagnone D, Merkoci A. Laser-assembled conductive 3D nanozyme film-based nitrocellulose sensor for real-time detection of H 2O 2 released from cancer cells. Biosens Bioelectron 2024; 262:116544. [PMID: 38963952 DOI: 10.1016/j.bios.2024.116544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]
Abstract
In this work, a nanostructured conductive film possessing nanozyme features was straightforwardly produced via laser-assembling and integrated into complete nitrocellulose sensors; the cellulosic substrate allows to host live cells, while the nanostructured film nanozyme activity ensures the enzyme-free real-time detection of hydrogen peroxide (H2O2) released by the sames. In detail, a highly exfoliated reduced graphene oxide 3D film decorated with naked platinum nanocubes was produced using a CO2-laser plotter via the simultaneous reduction and patterning of graphene oxide and platinum cations; the nanostructured film was integrated into a nitrocellulose substrate and the complete sensor was manufactured using an affordable semi-automatic printing approach. The linear range for the direct H2O2 determination was 0.5-80 μM (R2 = 0.9943), with a limit of detection of 0.2 μM. Live cell measurements were achieved by placing the sensor in the culture medium, ensuring their adhesion on the sensors' surface; two cell lines were used as non-tumorigenic (Vero cells) and tumorigenic (SKBR3 cells) models, respectively. Real-time detection of H2O2 released by cells upon stimulation with phorbol ester was carried out; the nitrocellulose sensor returned on-site and real-time quantitative information on the H2O2 released proving useful sensitivity and selectivity, allowing to distinguish tumorigenic cells. The proposed strategy allows low-cost in-series semi-automatic production of paper-based point-of-care devices using simple benchtop instrumentation, paving the way for the easy and affordable monitoring of the cytopathology state of cancer cells.
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Affiliation(s)
- Qurat U A Bukhari
- Nanobioelectronics & Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, Barcelona, Spain; Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Campus "Aurelio Saliceti" Via R. Balzarini 1, 64100, Teramo, Italy
| | - Flavio Della Pelle
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Campus "Aurelio Saliceti" Via R. Balzarini 1, 64100, Teramo, Italy
| | - Ruslan Alvarez-Diduk
- Nanobioelectronics & Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, Barcelona, Spain.
| | - Annalisa Scroccarello
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Campus "Aurelio Saliceti" Via R. Balzarini 1, 64100, Teramo, Italy
| | - Carme Nogués
- Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Biociencies, Universitat Autonoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Oriol Careta
- Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Biociencies, Universitat Autonoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Dario Compagnone
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Campus "Aurelio Saliceti" Via R. Balzarini 1, 64100, Teramo, Italy.
| | - Arben Merkoci
- Nanobioelectronics & Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, Barcelona, Spain; ICREA Institució Catalana de Recerca i Estudis Avançats, Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.
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Jin Y, Minten C, Jenkins M, Jones L, Gorbet M. Investigation of the rhythmic recruitment of tear neutrophils to the ocular surface and their phenotypes. Sci Rep 2024; 14:7061. [PMID: 38528025 DOI: 10.1038/s41598-024-57311-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/17/2024] [Indexed: 03/27/2024] Open
Abstract
Hundreds of thousands of polymorphonuclear neutrophils (PMNs) are collected from the ocular surface upon waking, while few are harvested during daytime. This study aimed to investigate potential factors contributing to the circadian infiltration of tear PMNs, including changes in IL-8 and C5a in tears, and their phenotypes across different time points in a 24-h cycle. Tear PMNs were collected using a gentle eyewash after 2-h and 7-h of sleep (eye closure, EC) at night, after 2-h EC during the day, and towards the end of the afternoon. Significantly fewer cells were collected after 2-h EC during the day compared to 2-h EC at night. A positive correlation between IL-8 and PMN numbers existed, but not with C5a. Tear PMNs collected after 2-h EC at night were less degranulated and possessed a larger activation potential compared to 7-h EC. Tear PMNs from 7-h EC at night exhibited hyper-segmented nuclei and more NETosis compared to 2 h EC night, indicating an aged and activated phenotype. The diurnal-nocturnal recruitment pattern of tear PMNs may be driven by increased IL-8 in nighttime tears. Higher degranulation and NETs point to the significant activation of tear PMNs on the ocular surface during prolonged eye closure at night.
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Affiliation(s)
- Yutong Jin
- School of Optometry and Vision Science, University of Waterloo, Waterloo, Canada
- Centre for Ocular Research and Education, University of Waterloo, Waterloo, Canada
| | - Ceili Minten
- Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada
| | - Mara Jenkins
- Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada
| | - Lyndon Jones
- School of Optometry and Vision Science, University of Waterloo, Waterloo, Canada
- Centre for Ocular Research and Education, University of Waterloo, Waterloo, Canada
| | - Maud Gorbet
- School of Optometry and Vision Science, University of Waterloo, Waterloo, Canada.
- Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada.
- Centre for Ocular Research and Education, University of Waterloo, Waterloo, Canada.
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Oliynyk Z, Rudyk M, Dovbynchuk T, Dzubenko N, Tolstanova G, Skivka L. Inflammatory hallmarks in 6-OHDA- and LPS-induced Parkinson's disease in rats. Brain Behav Immun Health 2023; 30:100616. [PMID: 37096171 PMCID: PMC10121378 DOI: 10.1016/j.bbih.2023.100616] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease, affecting more than 1% of aged people. PD, which was previously identified as movement disorder, now is recognized as a multi-factorial systemic disease with important pathogenetic and pathophysiological role of inflammation. Reproducing local and systemic inflammation, which is inherent in PD, in animal models is essential for maximizing the translation of their potential to the clinic, as well as for developing putative anti-inflammatory neuroprotective agents. This study was aimed to compare activation patterns of microglia/macrophage population and systemic inflammation indices in rats with 6-Hydroxydopamine (6-OHDA)- and Lipopolysaccharide (LPS)-induced PD. Metabolic and phenotypic characteristics of microglia/macrophage population were examined by flow cytometry, systemic inflammatory markers were calculated using hematological parameters in 6-OHDA- and LPS-lesioned Wistar rats 29 days after the surgery. Microglia/macrophages from rats in both models exhibited pro-inflammatory metabolic shift. Nevertheless, in LPS-lesioned animals, highly increased proportion of CD80/86+ cells in microglia/macrophage population was registered alongside increased values of systemic inflammatory indices: neutrophil to lymphocyte ratio (NLR), derived neutrophil to lymphocyte ratio (dNLR), platelet to lymphocyte ratio and systemic immune inflammation index (SII). There was significant positive correlation between the count of CD80/86+ cells and systemic inflammatory indices in these animals. Microglia/macrophages from 6-OHDA-lesioned rats were characterized by the increased fraction of CD206+ cells alongside decreased proportion of CD80/86+ cells. No signs of systemic inflammation were observed. Negative correlation between quantitation characteristics of CD80/86+ cells and values of systemic inflammatory indices was registered. Collectively, our data show that LPS-PD model unlike 6-OHDA-PD replicates crosstalk between local and systemic inflammatory responses, which is inherent in PD pathogenesis and pathophysiology.
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Affiliation(s)
- Zhanna Oliynyk
- Educational and Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 2, Hlushkov Avenue, Kyiv, 03022, Ukraine
| | - Mariia Rudyk
- Educational and Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 2, Hlushkov Avenue, Kyiv, 03022, Ukraine
- Corresponding author. Microbiology and Immunology Department, ESC “Institute of Biology and Medicine”, Taras Shevchenko Kyiv National University, Kyiv, 2, Hlushkov Avenue, Kyiv, 03022, Ukraine.
| | - Taisa Dovbynchuk
- Educational and Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 2, Hlushkov Avenue, Kyiv, 03022, Ukraine
| | - Nataliia Dzubenko
- Educational and Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 2, Hlushkov Avenue, Kyiv, 03022, Ukraine
| | - Ganna Tolstanova
- Educational and Scientific Institute of High Technologies, Taras Shevchenko University of Kyiv, 4g, Hlushkova Avenue, Kyiv, 03022, Ukraine
| | - Larysa Skivka
- Educational and Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 2, Hlushkov Avenue, Kyiv, 03022, Ukraine
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Mun S, Han K, Hyun JK. The Time Sequence of Gene Expression Changes after Spinal Cord Injury. Cells 2022; 11:cells11142236. [PMID: 35883679 PMCID: PMC9324287 DOI: 10.3390/cells11142236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/15/2022] [Accepted: 07/17/2022] [Indexed: 02/01/2023] Open
Abstract
Gene expression changes following spinal cord injury (SCI) are time-dependent, and an accurate understanding of these changes can be crucial in determining time-based treatment options in a clinical setting. We performed RNA sequencing of the contused spinal cord of rats at five different time points from the very acute to chronic stages (1 hour, 1 day, 1 week, 1 month, and 3 months) following SCI. We identified differentially expressed genes (DEGs) and Gene Ontology (GO) terms at each time point, and 14,257 genes were commonly expressed at all time points. The biological process of the inflammatory response was increased at 1 hour and 1 day, and the cellular component of the integral component of the synaptic membrane was increased at 1 day. DEGs associated with cell activation and the innate immune response were highly enriched at 1 week and 1 month, respectively. A total of 2841 DEGs were differentially expressed at any of the five time points, and 18 genes (17 upregulated and 1 downregulated) showed common expression differences at all time points. We found that interleukin signaling, neutrophil degranulation, eukaryotic translation, collagen degradation, LGI–ADAM interactions, GABA receptor, and L1CAM-ankyrin interactions were prominent after SCI depending on the time post injury. We also performed gene–drug network analysis and found several potential antagonists and agonists which can be used to treat SCI. We expect to discover effective treatments in the clinical field through further studies revealing the efficacy and safety of potential drugs.
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Affiliation(s)
- Seyoung Mun
- Department of Nanobiomedical Science & BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea;
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea;
| | - Kyudong Han
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea;
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Jung Keun Hyun
- Department of Nanobiomedical Science & BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea;
- Department of Rehabilitation Medicine, College of Medicine, Dankook University, Cheonan 31116, Korea
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea
- Correspondence: ; Tel.: +82-10-2293-3415
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