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López-Martínez A, Santos-Álvarez JC, Velázquez-Enríquez JM, Ramírez-Hernández AA, Vásquez-Garzón VR, Baltierrez-Hoyos R. lncRNA-mRNA Co-Expression and Regulation Analysis in Lung Fibroblasts from Idiopathic Pulmonary Fibrosis. Noncoding RNA 2024; 10:26. [PMID: 38668384 PMCID: PMC11054336 DOI: 10.3390/ncrna10020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease marked by abnormal accumulation of extracellular matrix (ECM) due to dysregulated expression of various RNAs in pulmonary fibroblasts. This study utilized RNA-seq data meta-analysis to explore the regulatory network of hub long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in IPF fibroblasts. The meta-analysis unveiled 584 differentially expressed mRNAs (DEmRNA) and 75 differentially expressed lncRNAs (DElncRNA) in lung fibroblasts from IPF. Among these, BCL6, EFNB1, EPHB2, FOXO1, FOXO3, GNAI1, IRF4, PIK3R1, and RXRA were identified as hub mRNAs, while AC008708.1, AC091806.1, AL442071.1, FAM111A-DT, and LINC01989 were designated as hub lncRNAs. Functional characterization revealed involvement in TGF-β, PI3K, FOXO, and MAPK signaling pathways. Additionally, this study identified regulatory interactions between sequences of hub mRNAs and lncRNAs. In summary, the findings suggest that AC008708.1, AC091806.1, FAM111A-DT, LINC01989, and AL442071.1 lncRNAs can regulate BCL6, EFNB1, EPHB2, FOXO1, FOXO3, GNAI1, IRF4, PIK3R1, and RXRA mRNAs in fibroblasts bearing IPF and contribute to fibrosis by modulating crucial signaling pathways such as FoxO signaling, chemical carcinogenesis, longevity regulatory pathways, non-small cell lung cancer, and AMPK signaling pathways.
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Affiliation(s)
- Armando López-Martínez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Jovito Cesar Santos-Álvarez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Juan Manuel Velázquez-Enríquez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Alma Aurora Ramírez-Hernández
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
| | - Verónica Rocío Vásquez-Garzón
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
- CONACYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico
| | - Rafael Baltierrez-Hoyos
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico; (A.L.-M.); (J.C.S.-Á.); (J.M.V.-E.); (A.A.R.-H.); (V.R.V.-G.)
- CONACYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca C.P. 68020, Mexico
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Shankar DA, Walkey AJ, Hawkins FJ, Bosch NA, Peterson D, Law AC. Hospital-level variation in practices and outcomes for patients with severe acute exacerbations of idiopathic pulmonary fibrosis: a retrospective multicentre cohort study. BMJ Open Respir Res 2023; 10:e001593. [PMID: 37076251 PMCID: PMC10124258 DOI: 10.1136/bmjresp-2022-001593] [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: 12/19/2022] [Accepted: 03/17/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND In the absence of evidence-based strategies to improve patient outcomes, the management of patients with severe idiopathic pulmonary fibrosis (IPF) exacerbations may vary widely across centres. We assessed between-hospital variation in practices and mortality for patients with severe IPF exacerbations. METHODS Using the Premier Healthcare Database from 1 October 2015 to 31 December 2020, we identified patients admitted to intensive care unit (ICU) or intermediate care unit with an IPF exacerbation. We assessed idiosyncratic, between-hospital variation in ICU practices (invasive mechanical ventilation (IMV), non-invasive mechanical ventilation (NIMV), corticosteroid use, and immunosuppressive and/or antioxidant use) and hospital mortality by determining median risk-adjusted hospital rates and intraclass correlation coefficients (ICCs) from hierarchical multivariable regression models. A priori, an ICC>15% was deemed 'high variation'. RESULTS We identified 5256 critically ill patients with a severe IPF exacerbation at 385 US hospitals. Hospital median risk-adjusted rates of practices were: IMV (14% (IQR: 8.3%-26%)), NIMV (42% (31%-54%)), corticosteroid use (89% (84%-93%)), and immunosuppressive and/or antioxidant use (3.3% (1.9%-5.8%)). Model ICCs were: IMV (19% (95% CI: 18% to 21%)), NIMV (15% (13% to 16%)), corticosteroid use (9.8% (8.3% to 11%)), and immunosuppressive and/or antioxidant use (8.5% (7.1% to 9.9%)). The median risk-adjusted hospital mortality was 16% (IQR: 11%-24%) with an ICC of 7.5% (95% CI: 6.2% to 8.9%). INTERPRETATION We observed high variation in the use of IMV and NIMV, and less variation in corticosteroid and immunosuppressant and/or antioxidant use among patients hospitalised with severe IPF exacerbations. Further research is needed to guide the decisions surrounding initiation of IMV and role of NIMV and to understand the effectiveness of corticosteroids among patients with severe IPF exacerbations.
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Affiliation(s)
- Divya A Shankar
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Allan J Walkey
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Finn J Hawkins
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Nicholas A Bosch
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Daniel Peterson
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Anica C Law
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
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Chertok Shacham E, Ishay A. New insights on Effects of Glucocorticoids in SARS-CoV-2 infection. Endocr Pract 2022; 28:1100-1106. [PMID: 35870803 PMCID: PMC9300587 DOI: 10.1016/j.eprac.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 01/08/2023]
Abstract
Objective Since January 2020, the highly contagious novel coronavirus SARS-CoV-2 has caused a global pandemic. Severe COVID-19 leads to a massive release of proinflammatory mediators, leading to diffuse damage to the lung parenchyma, and the development of acute respiratory distress syndrome. Treatment with the highly potent glucocorticoid (GC) dexamethasone was found to be effective in reducing mortality in severely affected patients. Methods To review the effects of glucocorticoids in the context of COVID-19 we performed a literature search in the PubMed database using the terms COVID-19 and glucocorticoid treatment. We identified 1429 article publications related to COVID-19 and glucocorticoid published from 1.1.2020 to the present including 238 review articles and 36 Randomized Controlled Trials. From these studies, we retrieved 13 Randomized Controlled Trials and 86 review articles that were relevant to our review topics. We focused on the recent literature dealing with glucocorticoid metabolism in critically ill patients and investigating the effects of glucocorticoid therapy on the immune system in COVID-19 patients with severe lung injury. Results In our review, we have discussed the regulation of the hypothalamic-pituitary-adrenal axis in patients with critical illness, selection of a specific GC for critical illness-related GC insufficiency, and recent studies that investigated hypothalamic-pituitary-adrenal dysfunction in patients with COVID-19. We have also addressed the specific activation of the immune system with chronic endogenous glucocorticoid excess, as seen in patients with Cushing syndrome, and, finally, we have discussed immune activation due to coronavirus infection and the possible mechanisms leading to improved outcomes in patients with COVID-19 treated with GCs. Conclusion For clinical endocrinologists prescribing GCs for their patients, a precise understanding of both the molecular- and cellular-level mechanisms of endogenous and exogenous GCs is imperative, including timing of administration, dosage, duration of treatment, and specific formulations of GCs.
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Affiliation(s)
| | - Avraham Ishay
- Endocrinology Unit, HaEmek Medical Center, Afula, Israel; Faculty of medicine, Technion - Israel Institute of Technology, Haifa, Israel
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