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Li D, Donnelley M, Parsons D, Habgood MD, Schneider-Futschik EK. Extent of foetal exposure to maternal elexacaftor/tezacaftor/ivacaftor during pregnancy. Br J Pharmacol 2024; 181:2413-2428. [PMID: 38770951 DOI: 10.1111/bph.16417] [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: 10/24/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND AND PURPOSE Cystic fibrosis (CF) patients are living longer and healthier due to improved treatments, e.g. cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy elexacaftor/tezacaftor/ivacaftor (ETI), with treatment possibly occurring in pregnancy. The risk of ETI to foetuses remain unknown. Thus the effect of maternally administered ETI on foetal genetic and structural development was investigated. EXPERIMENTAL APPROACH Pregnant Sprague Dawley rats were orally treated with ETI (6.7 mg·kg-1·day-1 elexacaftor + 3.5 mg·kg-1·day-1 tezacaftor + 25 mg·kg-1·day-1 ivacaftor) for 7 days from E12 to E19. Tissue samples collected at E19 were analysed using histology and RNA sequencing. Histological changes and differentially expressed genes (DEG) were assessed. KEY RESULTS No overt structural abnormalities were found in foetal pancreas, liver, lung and small intestine after 7-day ETI exposure. Very few non-functionally associated DEG in foetal liver, lung and small intestine were identified using RNA-seq. 29 DEG were identified in thymus (27 up-regulated and two down-regulated) and most were functionally linked to each other. Gene ontology enrichment analysis revealed that multiple muscle-related terms were significantly enriched. Many more DEG were identified in cortex (44 up-regulated and four down-regulated) and a group of these were involved in central nervous system and brain development. CONCLUSION AND IMPLICATION Sub-chronic ETI treatment in late pregnancy does not appear to pose a significant risk to the genetic and structural development of many foetal tissues. However, significant gene changes in foetal thymic myoid cells and cortical neuronal development requires future follow-up studies to assess the risk to these organs.
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Affiliation(s)
- Danni Li
- Department of Biochemistry & Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Martin Donnelley
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - David Parsons
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Mark D Habgood
- Department of Biochemistry & Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Elena K Schneider-Futschik
- Department of Biochemistry & Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
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Yuan H, Chen S, Duncan MR, de Rivero Vaccari JP, Keane RW, Dalton Dietrich W, Chou TH, Benny M, Schmidt AF, Young K, Park KK, Porciatti V, Elizabeth Hartnett M, Wu S. IC100, a humanized therapeutic monoclonal anti-ASC antibody alleviates oxygen-induced retinopathy in mice. Angiogenesis 2024:10.1007/s10456-024-09917-9. [PMID: 38709389 DOI: 10.1007/s10456-024-09917-9] [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: 10/12/2023] [Accepted: 03/28/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Retinopathy of prematurity (ROP), which often presents with bronchopulmonary dysplasia (BPD), is among the most common morbidities affecting extremely premature infants and is a leading cause of severe vision impairment in children worldwide. Activations of the inflammasome cascade and microglia have been implicated in playing a role in the development of both ROP and BPD. Apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) is pivotal in inflammasome assembly. Utilizing mouse models of both oxygen-induced retinopathy (OIR) and BPD, this study was designed to test the hypothesis that hyperoxia induces ASC speck formation, which leads to microglial activation and retinopathy, and that inhibition of ASC speck formation by a humanized monoclonal antibody, IC100, directed against ASC, will ameliorate microglial activation and abnormal retinal vascular formation. METHODS We first tested ASC speck formation in the retina of ASC-citrine reporter mice expressing ASC fusion protein with a C-terminal citrine (fluorescent GFP isoform) using a BPD model that causes both lung and eye injury by exposing newborn mice to room air (RA) or 85% O2 from postnatal day (P) 1 to P14. The retinas were dissected on P14 and retinal flat mounts were used to detect vascular endothelium with AF-594-conjugated isolectin B4 (IB4) and citrine-tagged ASC specks. To assess the effects of IC100 on an OIR model, newborn ASC citrine reporter mice and wildtype mice (C57BL/6 J) were exposed to RA from P1 to P6, then 75% O2 from P7 to P11, and then to RA from P12 to P18. At P12 mice were randomized to the following groups: RA with placebo PBS (RA-PBS), O2 with PBS (O2-PBS), O2 + IC100 intravitreal injection (O2-IC100-IVT), and O2 + IC100 intraperitoneal injection (O2-IC100-IP). Retinal vascularization was evaluated by flat mount staining with IB4. Microglial activation was detected by immunofluorescence staining for allograft inflammatory factor 1 (AIF-1) and CD206. Retinal structure was analyzed on H&E-stained sections, and function was analyzed by pattern electroretinography (PERG). RNA-sequencing (RNA-seq) of the retinas was performed to determine the transcriptional effects of IC100 treatment in OIR. RESULTS ASC specks were significantly increased in the retinas by hyperoxia exposure and colocalized with the abnormal vasculature in both BPD and OIR models, and this was associated with increased microglial activation. Treatment with IC100-IVT or IC100-IP significantly reduced vaso-obliteration and intravitreal neovascularization. IC100-IVT treatment also reduced retinal microglial activation, restored retinal structure, and improved retinal function. RNA-seq showed that IC100 treatment corrected the induction of genes associated with angiogenesis, leukocyte migration, and VEGF signaling caused by O2. IC100 also corrected the suppression of genes associated with cell junction assembly, neuron projection, and neuron recognition caused by O2. CONCLUSION These data demonstrate the crucial role of ASC in the pathogenesis of OIR and the efficacy of a humanized therapeutic anti-ASC antibody in treating OIR mice. Thus, this anti-ASC antibody may potentially be considered in diseases associated with oxygen stresses and retinopathy, such as ROP.
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Affiliation(s)
- Huijun Yuan
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute and Holtz Children's Hospital, University of Miami Miller School of Medicine, P. O. Box 016960, Miami, FL, 33101, USA
| | - Shaoyi Chen
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute and Holtz Children's Hospital, University of Miami Miller School of Medicine, P. O. Box 016960, Miami, FL, 33101, USA
| | - Matthew R Duncan
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute and Holtz Children's Hospital, University of Miami Miller School of Medicine, P. O. Box 016960, Miami, FL, 33101, USA
| | - Juan Pablo de Rivero Vaccari
- The Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Robert W Keane
- The Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - W Dalton Dietrich
- The Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tsung-Han Chou
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Merline Benny
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute and Holtz Children's Hospital, University of Miami Miller School of Medicine, P. O. Box 016960, Miami, FL, 33101, USA
| | - Augusto F Schmidt
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute and Holtz Children's Hospital, University of Miami Miller School of Medicine, P. O. Box 016960, Miami, FL, 33101, USA
| | - Karen Young
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute and Holtz Children's Hospital, University of Miami Miller School of Medicine, P. O. Box 016960, Miami, FL, 33101, USA
| | - Kevin K Park
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vittorio Porciatti
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Shu Wu
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute and Holtz Children's Hospital, University of Miami Miller School of Medicine, P. O. Box 016960, Miami, FL, 33101, USA.
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Cheng Y, Zhang M, Xu R, Fu L, Xue M, Xu C, Tang C, Fang T, Liu X, Sun B, Chen L. p53 accelerates endothelial cell senescence in diabetic retinopathy by enhancing FoxO3a ubiquitylation and degradation via UBE2L6. Exp Gerontol 2024; 188:112391. [PMID: 38437929 DOI: 10.1016/j.exger.2024.112391] [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: 04/22/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Diabetic retinopathy (DR) is the most common ocular fundus disease in diabetic patients. Chronic hyperglycemia not only promotes the development of diabetes and its complications, but also aggravates the occurrence of senescence. Previous studies have shown that DR is associated with senescence, but the specific mechanism has not been fully elucidated. Here, we first detected the differentially expressed genes (DEGs) and cellular senescence level of db/db mouse retinas by bulk RNA sequencing. Then, we used single-cell sequencing (scRNA-seq) to identify the main cell types in the retina and analyzed the DEGs in each cluster. We demonstrated that p53 expression was significantly increased in retinal endothelial cell cluster of db/db mice. Inhibition of p53 can reduce the expression of SA-β-Gal and the senescence-associated secretory phenotype (SASP) in HRMECs. Finally, we found that p53 can promote FoxO3a ubiquitination and degradation by increasing the expression of the ubiquitin-conjugating enzyme UBE2L6. Overall, our results demonstrate that p53 can accelerate the senescence process of endothelial cells and aggravate the development of DR. These data reveal new targets and insights that may be used to treat DR.
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Affiliation(s)
- Ying Cheng
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Man Zhang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Rong Xu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Lingli Fu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Mei Xue
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Chaofei Xu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Chao Tang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Ting Fang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Xiaohuan Liu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China
| | - Bei Sun
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China.
| | - Liming Chen
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300134, China.
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Duarte PM, Gurgel BCDV, Miranda TS, Sardenberg J, Gu T, Aukhil I. Distinctive genes and signaling pathways associated with type 2 diabetes-related periodontitis: Preliminary study. PLoS One 2024; 19:e0296925. [PMID: 38241313 PMCID: PMC10798476 DOI: 10.1371/journal.pone.0296925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/22/2023] [Indexed: 01/21/2024] Open
Abstract
The biological mechanisms underlying the pathogenesis of type 2 diabetes (T2DM)-related periodontitis remain unclear. This cross-sectional study evaluated the distinctive transcriptomic changes between tissues with periodontal health and with periodontitis in patients with T2DM. In this cross-sectional study, whole transcriptome sequencing was performed on gingival biopsies from non-periodontitis and periodontitis tissues from non-diabetic and diabetic patients. A differentially expressed gene (DEG) analysis and Ingenuity Pathway Analysis (IPA) assessed the genes and signaling pathways associated with T2DM-related periodontitis. Immunohistochemistry was performed to validate selected DEGs possibly involved in T2DM-related periodontitis. Four hundred and twenty and one thousand five hundred and sixty-three DEGs (fold change ≥ 2) were uniquely identified in the diseased tissues of non-diabetic and diabetic patients, respectively. The IPA predicted the activation of Phagosome Formation, Cardiac β-adrenergic, tRNA Splicing, and PI3K/AKT pathways. The IPA also predicted the inhibition of Cholesterol Biosynthesis, Adrenomedullin, and Inositol Phosphate Compounds pathways in T2DM-related periodontitis. Validation of DEGs confirmed changes in protein expression of PTPN2, PTPN13, DHCR24, PIK3R2, CALCRL, IL1RN, IL-6R and ITGA4 in diseased tissues in diabetic subjects. Thus, these preliminary findings indicate that there are specific genes and functional pathways that may be involved in the pathogenesis of T2DM-related periodontitis.
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Affiliation(s)
- Poliana Mendes Duarte
- Department of Periodontology, University of Florida College of Dentistry, Gainesville, FL, United States of America
| | | | | | - Juliana Sardenberg
- Department of Periodontology, University of Florida College of Dentistry, Gainesville, FL, United States of America
| | - Tongjun Gu
- ICBR Bioinformatics, University of Florida, Gainesville, FL, United States of America
| | - Ikramuddin Aukhil
- ECU School of Dental Medicine, East Carolina University, Greenville, NC, United States of America
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Li J, Chen K, Li X, Zhang X, Zhang L, Yang Q, Xia Y, Xie C, Wang X, Tong J, Shen Y. Mechanistic insights into the alterations and regulation of the AKT signaling pathway in diabetic retinopathy. Cell Death Discov 2023; 9:418. [PMID: 37978169 PMCID: PMC10656479 DOI: 10.1038/s41420-023-01717-2] [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: 08/20/2023] [Revised: 11/05/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023] Open
Abstract
In the early stages of diabetic retinopathy (DR), diabetes-related hyperglycemia directly inhibits the AKT signaling pathway by increasing oxidative stress or inhibiting growth factor expression, which leads to retinal cell apoptosis, nerve proliferation and fundus microvascular disease. However, due to compensatory vascular hyperplasia in the late stage of DR, the vascular endothelial growth factor (VEGF)/phosphatidylinositol 3 kinase (PI3K)/AKT cascade is activated, resulting in opposite levels of AKT regulation compared with the early stage. Studies have shown that many factors, including insulin, insulin-like growth factor-1 (IGF-1), VEGF and others, can regulate the AKT pathway. Disruption of the insulin pathway decreases AKT activation. IGF-1 downregulation decreases the activation of AKT in DR, which abrogates the neuroprotective effect, upregulates VEGF expression and thus induces neovascularization. Although inhibiting VEGF is the main treatment for neovascularization in DR, excessive inhibition may lead to apoptosis in inner retinal neurons. AKT pathway substrates, including mammalian target of rapamycin (mTOR), forkhead box O (FOXO), glycogen synthase kinase-3 (GSK-3)/nuclear factor erythroid 2-related factor 2 (Nrf2), and nuclear factor kappa-B (NF-κB), are a research focus. mTOR inhibitors can delay or prevent retinal microangiopathy, whereas low mTOR activity can decrease retinal protein synthesis. Inactivated AKT fails to inhibit FOXO and thus causes apoptosis. The GSK-3/Nrf2 cascade regulates oxidation and inflammation in DR. NF-κB is activated in diabetic retinas and is involved in inflammation and apoptosis. Many pathways or vital activities, such as the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) and mitogen-activated protein kinase (MAPK) signaling pathways, interact with the AKT pathway to influence DR development. Numerous regulatory methods can simultaneously impact the AKT pathway and other pathways, and it is essential to consider both the connections and interactions between these pathways. In this review, we summarize changes in the AKT signaling pathway in DR and targeted drugs based on these potential sites.
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Affiliation(s)
- Jiayuan Li
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
- Department of Cardiology, The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Kuangqi Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiang Li
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xuhong Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Liyue Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Qianjie Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Yutong Xia
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Chen Xie
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiawei Wang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianping Tong
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China.
| | - Ye Shen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China.
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Padovani-Claudio DA, Ramos CJ, Capozzi ME, Penn JS. Elucidating glial responses to products of diabetes-associated systemic dyshomeostasis. Prog Retin Eye Res 2023; 94:101151. [PMID: 37028118 PMCID: PMC10683564 DOI: 10.1016/j.preteyeres.2022.101151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 04/08/2023]
Abstract
Diabetic retinopathy (DR) is a leading cause of blindness in working age adults. DR has non-proliferative stages, characterized in part by retinal neuroinflammation and ischemia, and proliferative stages, characterized by retinal angiogenesis. Several systemic factors, including poor glycemic control, hypertension, and hyperlipidemia, increase the risk of DR progression to vision-threatening stages. Identification of cellular or molecular targets in early DR events could allow more prompt interventions pre-empting DR progression to vision-threatening stages. Glia mediate homeostasis and repair. They contribute to immune surveillance and defense, cytokine and growth factor production and secretion, ion and neurotransmitter balance, neuroprotection, and, potentially, regeneration. Therefore, it is likely that glia orchestrate events throughout the development and progression of retinopathy. Understanding glial responses to products of diabetes-associated systemic dyshomeostasis may reveal novel insights into the pathophysiology of DR and guide the development of novel therapies for this potentially blinding condition. In this article, first, we review normal glial functions and their putative roles in the development of DR. We then describe glial transcriptome alterations in response to systemic circulating factors that are upregulated in patients with diabetes and diabetes-related comorbidities; namely glucose in hyperglycemia, angiotensin II in hypertension, and the free fatty acid palmitic acid in hyperlipidemia. Finally, we discuss potential benefits and challenges associated with studying glia as targets of DR therapeutic interventions. In vitro stimulation of glia with glucose, angiotensin II and palmitic acid suggests that: 1) astrocytes may be more responsive than other glia to these products of systemic dyshomeostasis; 2) the effects of hyperglycemia on glia are likely to be largely osmotic; 3) fatty acid accumulation may compound DR pathophysiology by promoting predominantly proinflammatory and proangiogenic transcriptional alterations of macro and microglia; and 4) cell-targeted therapies may offer safer and more effective avenues for DR treatment as they may circumvent the complication of pleiotropism in retinal cell responses. Although several molecules previously implicated in DR pathophysiology are validated in this review, some less explored molecules emerge as potential therapeutic targets. Whereas much is known regarding glial cell activation, future studies characterizing the role of glia in DR and how their activation is regulated and sustained (independently or as part of retinal cell networks) may help elucidate mechanisms of DR pathogenesis and identify novel drug targets for this blinding disease.
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Affiliation(s)
- Dolly Ann Padovani-Claudio
- Department of Ophthalmology and Visual Sciences, Vanderbilt University School of Medicine, B3321A Medical Center North, 1161 21st Avenue South, Nashville, TN, 37232-0011, USA.
| | - Carla J Ramos
- Department of Ophthalmology and Visual Sciences, Vanderbilt University School of Medicine, AA1324 Medical Center North, 1161 21st Avenue South, Nashville, TN, 37232-0011, USA.
| | - Megan E Capozzi
- Duke Molecular Physiology Institute, Duke University School of Medicine, 300 North Duke Street, Durham, NC, 27701, USA.
| | - John S Penn
- Department of Ophthalmology and Visual Sciences, Vanderbilt University School of Medicine, B3307 Medical Center North, 1161 21st Avenue South, Nashville, TN, 37232-0011, USA.
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Exploration of the Potential Link, Hub Genes, and Potential Drugs for Coronavirus Disease 2019 and Lung Cancer Based on Bioinformatics Analysis. JOURNAL OF ONCOLOGY 2022; 2022:8124673. [PMID: 36199786 PMCID: PMC9529395 DOI: 10.1155/2022/8124673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022]
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) has a huge influence on global public health and the economy. Lung cancer is one of the high-risk factors of COVID-19, but the molecular mechanism of lung cancer and COVID-19 is still unclear, and further research is needed. Therefore, we used the transcriptome information of the public database and adopted bioinformatics methods to identify the common pathways and molecular biomarkers of lung cancer and COVID-19 to further understand the connection between them. The two RNA-seq data sets in this study—GSE147507 (COVID-19) and GSE33532 (lung cancer)—were both derived from the Gene Expression Omnibus (GEO) database and identified differentially expressed genes (DEGs) for lung cancer and COVID-19 patients. We conducted Gene Ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis and found some common features between lung cancer and COVID-19. We also performed TFs-gene, miRNAs-gene, and gene-drug analyses. In total, 32 DEGs were found. A protein-protein interaction (PPI) network was constructed by DEGs, and 10 hub genes were screened. Finally, the identified drugs may be helpful for COVID-19 treatment.
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Zhao H, Kong H, Wang B, Wu S, Chen T, Cui Y. RNA-Binding Proteins and Alternative Splicing Genes Are Coregulated in Human Retinal Endothelial Cells Treated with High Glucose. J Diabetes Res 2022; 2022:7680513. [PMID: 35308095 PMCID: PMC8926481 DOI: 10.1155/2022/7680513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 01/10/2023] Open
Abstract
To explore the relevant RNA-binding proteins (RBPs) and alternative splicing events (ASEs) in diabetic retinopathy (DR). We devised a comprehensive work to integrate analyses of the differentially expressed genes, including differential RBPs, and variable splicing characteristics related to DR in human retinal endothelial cells induced by low glucose and high glucose in dataset GSE117238. A total of 2320 differentially expressed genes (DEGs) were identified, including 1228 upregulated genes and 1092 downregulated genes. Further analysis screened out 232 RBP genes, and 42 AS genes overlapped DEGs. We selected high expression and consistency six RBP genes (FUS, HNRNPA2B1, CANX, EIF1, CALR, and POLR2A) for coexpression analysis. Through analysis, we found eight RASGs (MDM2, GOLGA2P7, NFE2L1, KDM4A, FAM111A, CIRBP, IDH1, and MCM7) that could be regulated by RBP. The coexpression network was conducted to further elucidate the regulatory and interaction relationship between RBPs and AS. Apoptotic progress, protein phosphorylation, and NF-kappaB cascade revealed by the functional enrichment analysis of RASGs regulated by RBPs were closely related to diabetic retinopathy. Furthermore, the expression of differentially expressed RBPs was validated by qRT-PCR in mouse retinal microvascular endothelial cells and retinas from the streptozotocin mouse model. The results showed that Fus, Hnrnpa2b1, Canx, Calr, and Polr2a were remarkedly difference in high-glucose-treated retinal microvascular endothelial cells and Fus, Hnrnpa2b1, Canx, and Calr were remarkedly difference in retinas from streptozotocin-induced diabetic mice compared to control. The regulatory network between identified RBPs and RASGs suggests the presence of several signaling pathways possibly involved in the pathogenesis of DR. The verified RBPs should be further addressed by future studies investigating associations between RBPs and the downstream of AS, as they could serve as potential biomarkers and targets for DR.
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Affiliation(s)
- Hongran Zhao
- Department of Ophthalmology, Qilu Hospital of Shandong University, Shandong University, Jinan, Shandong Province, China
- School of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Hui Kong
- School of Medicine, Shandong University, Jinan, Shandong Province, China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Bozhao Wang
- Department of Ophthalmology, Qilu Hospital of Shandong University, Shandong University, Jinan, Shandong Province, China
- School of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Sihui Wu
- Department of Ophthalmology, Qilu Hospital of Shandong University, Shandong University, Jinan, Shandong Province, China
- School of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Tianran Chen
- School of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Yan Cui
- Department of Ophthalmology, Qilu Hospital of Shandong University, Shandong University, Jinan, Shandong Province, China
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Li M, Wu M, Qin Y, Liu H, Tu C, Shen B, Xu X, Chen H. Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics. PeerJ 2020; 8:e9971. [PMID: 33194371 PMCID: PMC7646293 DOI: 10.7717/peerj.9971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/26/2020] [Indexed: 12/31/2022] Open
Abstract
Background Although asthma is one of the most common chronic, noncommunicable diseases worldwide, the pathogenesis of childhood asthma is not yet clear. Genetic factors and environmental factors may lead to airway immune-inflammation responses and an imbalance of airway nerve regulation. The aim of the present study was to determine which serum proteins are differentially expressed between children with or without asthma and to ascertain the potential roles that these differentially expressed proteins (DEPs) may play in the pathogenesis of childhood asthma. Methods Serum samples derived from four children with asthma and four children without asthma were collected. The DEPs were identified by using isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses. Using biological information technology, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Cluster of Orthologous Groups of Proteins (COG) databases and analyses, we determined the biological processes associated with these DEPs. Key protein glucose-6-phosphate dehydrogenase (G6PD) was verified by enzyme linked immunosorbent assay (ELISA). Results We found 46 DEPs in serum samples of children with asthma vs. children without asthma. Among these DEPs, 12 proteins were significantly (>1.5 fold change) upregulated and 34 proteins were downregulated. The results of GO analyses showed that the DEPs were mainly involved in binding, the immune system, or responding to stimuli or were part of a cellular anatomical entity. In the KEGG signaling pathway analysis, most of the downregulated DEPs were associated with cardiomyopathy, phagosomes, viral infections, and regulation of the actin cytoskeleton. The results of a COG analysis showed that the DEPs were primarily involved in signal transduction mechanisms and posttranslational modifications. These DEPs were associated with and may play important roles in the immune response, the inflammatory response, extracellular matrix degradation, and the nervous system. The downregulated of G6PD in the asthma group was confirmed using ELISA experiment. Conclusion After bioinformatics analyses, we found numerous DEPs that may play important roles in the pathogenesis of childhood asthma. Those proteins may be novel biomarkers of childhood asthma and may provide new clues for the early clinical diagnosis and treatment of childhood asthma.
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Affiliation(s)
- Ming Li
- Department of Neonatology, Maternal and Child Health Hospital, the Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Mingzhu Wu
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital, the Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Qin
- School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Huaqing Liu
- Department of Neonatology, Maternal and Child Health Hospital, the Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Chengcheng Tu
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital, the Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Bing Shen
- School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Xiaohong Xu
- Department of Clinical Laboratory, Maternal and Child Health Hospital, the Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Hongbo Chen
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital, the Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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Xing X, Jiang Y, Wang H, Zhang Y, Niu T, Qu Y, Wang C, Wang H, Liu K. Identification of novel differentially expressed genes in retinas of STZ-induced long-term diabetic rats through RNA sequencing. Mol Genet Genomic Med 2020; 8:e1115. [PMID: 31958216 PMCID: PMC7057111 DOI: 10.1002/mgg3.1115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/08/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The aim of this research was to investigate the retinal transcriptome changes in long-term streptozotocin (STZ)-induced rats' retinas using RNA sequencing (RNA-seq), to explore the molecular mechanisms of diabetic retinopathy (DR), and to identify novel targets for the treatment of DR by comparing the gene expression profile we obtained. METHODS In this study, 6 healthy male SD rats were randomly divided into wild-type (WT) group and streptozotocin (STZ)-induced group, 3 rats each group. After 6 months, 3 normal retina samples and 3 DM retina samples (2 retinas from the same rat were considered as 1 sample) were tested and differentially expressed genes (DEGs) were measured by RNA-seq technology. Then, we did Gene Ontology (GO) enrichment analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis and validated the results of RNA-seq through qRT-PCR. RESULTS A total of 118 DEGs were identified, of which 72 were up-regulated and 46 were down-regulated. The enriched GO terms showed that 3 most significant enrichment terms were binding (molecular function), cell part (cellular component), and biological regulation (biological process). The results of the KEGG pathway analysis revealed a significant enrichment in cell adhesion molecules, PI3K-Akt signaling pathway, and allograft rejection, etc. CONCLUSION: Our research has identified specific DEGs and also speculated their potential functions, which will provide novel targets to explore the molecular mechanisms of DR.
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Affiliation(s)
- Xindan Xing
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yan Jiang
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hanying Wang
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuan Zhang
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Tian Niu
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuan Qu
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chingyi Wang
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Haiyan Wang
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Kun Liu
- Department of OphthalmologyShanghai General HospitalNational Clinical Research Center for Eye DiseasesShanghai Key Laboratory of Ocular Fundus DiseasesShanghai Engineering Center for Visual Science and PhotomedicineShanghai Engineering Center for Precise Diagnosis and Treatment of Eye DiseasesShanghai Jiao Tong University School of MedicineShanghaiChina
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