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Tenfen L, Simon Machado R, Mathias K, Piacentini N, Joaquim L, Bonfante S, Danielski LG, Engel NA, da Silva MR, Rezin GT, de Quadros RW, Gava FF, Petronilho F. Short-term hyperoxia induced mitochondrial respiratory chain complexes dysfunction and oxidative stress in lung of rats. Inhal Toxicol 2024; 36:174-188. [PMID: 38449063 DOI: 10.1080/08958378.2024.2322497] [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: 05/31/2023] [Accepted: 02/18/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Oxygen therapy is an alternative for many patients with hypoxemia. However, this practice can be dangerous as oxygen is closely associated with the development of oxidative stress. METHODS Male Wistar rats were exposed to hyperoxia with a 40% fraction of inspired oxygen (FIO2) and hyperoxia (FIO2 = 60%) for 120 min. Blood and lung tissue samples were collected for gas, oxidative stress, and inflammatory analyses. RESULTS Hyperoxia (FIO2 = 60%) increased PaCO2 and PaO2, decreased blood pH and caused thrombocytopenia and lymphocytosis. In lung tissue, neutrophil infiltration, nitric oxide concentration, carbonyl protein formation and the activity of complexes I and II of the mitochondrial respiratory chain increased. FIO2 = 60% decreased SOD activity and caused several histologic changes. CONCLUSION In conclusion, we have experimentally demonstrated that short-term exposure to high FIO2 can cause oxidative stress in the lung.
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Affiliation(s)
- Leonardo Tenfen
- Graduate Program in Health Sciences, Health Sciences Unit, University of South Santa Catarina, Tubarão, Brazil
| | - Richard Simon Machado
- Graduate Program in Health Sciences, Health Sciences Unit, University of South Santa Catarina, Tubarão, Brazil
| | - Khiany Mathias
- Graduate Program in Health Sciences, Health Sciences Unit, University of South Santa Catarina, Tubarão, Brazil
| | - Natalia Piacentini
- Laboratory of Experimental Neurology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Brazil
| | - Larissa Joaquim
- Graduate Program in Health Sciences, Health Sciences Unit, University of South Santa Catarina, Tubarão, Brazil
| | - Sandra Bonfante
- Graduate Program in Health Sciences, Health Sciences Unit, University of South Santa Catarina, Tubarão, Brazil
| | - Lucineia Gainski Danielski
- Laboratory of Experimental Neurology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Brazil
| | - Nicole Alessandra Engel
- Graduate Program in Health Sciences, Health Sciences Unit, University of South Santa Catarina, Tubarão, Brazil
| | - Mariella Reinol da Silva
- Graduate Program in Health Sciences, Health Sciences Unit, University of South Santa Catarina, Tubarão, Brazil
| | - Gislaine Tezza Rezin
- Graduate Program in Health Sciences, Health Sciences Unit, University of South Santa Catarina, Tubarão, Brazil
| | | | - Fernanda Frederico Gava
- Laboratory of Experimental Neurology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Brazil
| | - Fabricia Petronilho
- Laboratory of Experimental Neurology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Brazil
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Deng X, Thompson JA. An R package for Survival-based Gene Set Enrichment Analysis. RESEARCH SQUARE 2023:rs.3.rs-3367968. [PMID: 37841872 PMCID: PMC10571627 DOI: 10.21203/rs.3.rs-3367968/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Functional enrichment analysis is usually used to assess the effects of experimental differences. However, researchers sometimes want to understand the relationship between transcriptomic variation and health outcomes like survival. Therefore, we suggest the use of Survival-based Gene Set Enrichment Analysis (SGSEA) to help determine biological functions associated with a disease's survival. We developed an R package and corresponding Shiny App called SGSEA for this analysis and presented a study of kidney renal clear cell carcinoma (KIRC) to demonstrate the approach. In Gene Set Enrichment Analysis (GSEA), the log-fold change in expression between treatments is used to rank genes, to determine if a biological function has a non-random distribution of altered gene expression. SGSEA is a variation of GSEA using the hazard ratio instead of a log fold change. Our study shows that pathways enriched with genes whose increased transcription is associated with mortality (NES > 0, adjusted p-value < 0.15) have previously been linked to KIRC survival, helping to demonstrate the value of this approach. This approach allows researchers to quickly identify disease variant pathways for further research and provides supplementary information to standard GSEA, all within a single R package or through using the convenient app.
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Salaveria K, Smith S, Liu YH, Bagshaw R, Ott M, Stewart A, Law M, Carter A, Hanson J. The Applicability of Commonly Used Severity of Illness Scores to Tropical Infections in Australia. Am J Trop Med Hyg 2022; 106:257-267. [PMID: 34662860 PMCID: PMC8733535 DOI: 10.4269/ajtmh.21-0615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/31/2021] [Indexed: 01/03/2023] Open
Abstract
Many patients with leptospirosis, melioidosis, and rickettsial infection require intensive care unit (ICU) admission in tropical Australia every year. The multi-organ dysfunction associated with these infections results in significantly elevated severity of illness (SOI) scores. However, the accuracy of these SOI scores in predicting death from these tropical infections is incompletely defined. This retrospective study was performed at Cairns Hospital, a tertiary-referral hospital in tropical Australia. All patients admitted to ICU with laboratory-confirmed leptospirosis, melioidosis, and rickettsial disease between January 1, 1999 and June 30, 2020, were eligible for the study. The ability of Acute Physiology and Chronic Health Evaluation (APACHE) II, APACHE III, Simplified Acute Physiology Scores (SAPS) II, and Sequential Organ Failure Assessment (SOFA) scores to predict death before ICU discharge was evaluated. Overall, 18 (12.1%) of the 149 included patients died: 15/74 (20.3%) with melioidosis, 2/54 (3.7%) with leptospirosis and 1/21 (4.8%) with rickettsial disease. However, the APACHE II, APACHE III, SAPS II, and SOFA scores significantly overestimated the case-fatality rate of all the infections; the disparity between the predicted and observed mortality was most marked in the cases of leptospirosis and rickettsial disease. Commonly used SOI scores significantly overestimate the case-fatality rate of melioidosis, leptospirosis, and rickettsial infections in Australian ICU patients. This may be at least partly explained by the unique pathophysiology of these infections, particularly leptospirosis and rickettsial disease. However, SOI scores may still be useful in facilitating the comparison of disease severity in clinical trials that examine patients with these pathogens.
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Affiliation(s)
- Kris Salaveria
- Department of Intensive Care, Cairns Hospital, Cairns, Queensland, Australia
| | - Simon Smith
- Department of Medicine, Cairns Hospital, Cairns, Queensland, Australia
| | - Yu-Hsuan Liu
- Department of Intensive Care, Cairns Hospital, Cairns, Queensland, Australia
| | - Richard Bagshaw
- Department of Medicine, Cairns Hospital, Cairns, Queensland, Australia
| | - Markus Ott
- Department of Intensive Care, Cairns Hospital, Cairns, Queensland, Australia
| | | | - Matthew Law
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Angus Carter
- Department of Intensive Care, Cairns Hospital, Cairns, Queensland, Australia;,James Cook University, Cairns Campus, Cairns, Queensland, Australia
| | - Josh Hanson
- Department of Medicine, Cairns Hospital, Cairns, Queensland, Australia;,Kirby Institute, University of New South Wales, Sydney, Australia;,Address correspondence to Josh Hanson, Kirby Institute, Level 6, Wallace Wurth Building, High Street, UNSW, Kensington NSW 2052, Australia. E-mail:
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Zhu N, Hou J, Ma G, Guo S, Zhao C, Chen B. Co-expression network analysis identifies a gene signature as a predictive biomarker for energy metabolism in osteosarcoma. Cancer Cell Int 2020; 20:259. [PMID: 32581649 PMCID: PMC7310058 DOI: 10.1186/s12935-020-01352-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/15/2020] [Indexed: 02/08/2023] Open
Abstract
Background Osteosarcoma (OS) is a common malignant bone tumor originating in the interstitial tissues and occurring mostly in adolescents and young adults. Energy metabolism is a prerequisite for cancer cell growth, proliferation, invasion, and metastasis. However, the gene signatures associated with energy metabolism and their underlying molecular mechanisms that drive them are unknown. Methods Energy metabolism-related genes were obtained from the TARGET database. We applied the “NFM” algorithm to classify putative signature gene into subtypes based on energy metabolism. Key genes related to progression were identified by weighted co-expression network analysis (WGCNA). Based on least absolute shrinkage and selection operator (LASSO) Cox proportional regression hazards model analyses, a gene signature for the predication of OS progression and prognosis was established. Robustness and estimation evaluations and comparison against other models were used to evaluate the prognostic performance of our model. Results Two subtypes associated with energy metabolism was determined using the “NFM” algorithm, and significant modules related to energy metabolism were identified by WGCNA. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) suggested that the genes in the significant modules were enriched in kinase, immune metabolism processes, and metabolism-related pathways. We constructed a seven-gene signature consisting of SLC18B1, RBMXL1, DOK3, HS3ST2, ATP6V0D1, CCAR1, and C1QTNF1 to be used for OS progression and prognosis. Upregulation of CCAR1, and C1QTNF1 was associated with augmented OS risk, whereas, increases in the expression SCL18B1, RBMXL1, DOK3, HS3ST2, and ATP6VOD1 was correlated with a diminished risk of OS. We confirmed that the seven-gene signature was robust, and was superior to the earlier models evaluated; therefore, it may be used for timely OS diagnosis, treatment, and prognosis. Conclusions The seven-gene signature related to OS energy metabolism developed here could be used in the early diagnosis, treatment, and prognosis of OS.
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Affiliation(s)
- Naiqiang Zhu
- Department of Minimally Invasive Spinal Surgery, The Affiliated Hospital of Chengde Medical College, Chengde, 067000 China
| | - Jingyi Hou
- Chengde Medical College, Chengde, 067000 China
| | - Guiyun Ma
- Department of Minimally Invasive Spinal Surgery, The Affiliated Hospital of Chengde Medical College, Chengde, 067000 China
| | - Shuai Guo
- Department of Minimally Invasive Spinal Surgery, The Affiliated Hospital of Chengde Medical College, Chengde, 067000 China
| | - Chengliang Zhao
- Department of Minimally Invasive Spinal Surgery, The Affiliated Hospital of Chengde Medical College, Chengde, 067000 China
| | - Bin Chen
- Department of Minimally Invasive Spinal Surgery, The Affiliated Hospital of Chengde Medical College, Chengde, 067000 China
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