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Valdez RM, Rivera BN, Chang Y, Pennington JM, Fischer KA, Löhr CV, Tilton SC. Assessing susceptibility for polycyclic aromatic hydrocarbon toxicity in an in vitro 3D respiratory model for asthma. FRONTIERS IN TOXICOLOGY 2024; 6:1287863. [PMID: 38706568 PMCID: PMC11066177 DOI: 10.3389/ftox.2024.1287863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
There is increased emphasis on understanding cumulative risk from the combined effects of chemical and non-chemical stressors as it relates to public health. Recent animal studies have identified pulmonary inflammation as a possible modifier and risk factor for chemical toxicity in the lung after exposure to inhaled pollutants; however, little is known about specific interactions and potential mechanisms of action. In this study, primary human bronchial epithelial cells (HBEC) cultured in 3D at the air-liquid interface (ALI) are utilized as a physiologically relevant model to evaluate the effects of inflammation on toxicity of polycyclic aromatic hydrocarbons (PAHs), a class of contaminants generated from incomplete combustion of fossil fuels. Normal HBEC were differentiated in the presence of IL-13 for 14 days to induce a profibrotic phenotype similar to asthma. Fully differentiated normal and IL-13 phenotype HBEC were treated with benzo[a]pyrene (BAP; 1-40 μg/mL) or 1% DMSO/PBS vehicle at the ALI for 48 h. Cells were evaluated for cytotoxicity, barrier integrity, and transcriptional biomarkers of chemical metabolism and inflammation by quantitative PCR. Cells with the IL-13 phenotype treated with BAP result in significantly (p < 0.05) decreased barrier integrity, less than 50% compared to normal cells. The effect of BAP in the IL-13 phenotype was more apparent when evaluating transcriptional biomarkers of barrier integrity in addition to markers of mucus production, goblet cell hyperplasia, type 2 asthmatic inflammation and chemical metabolism, which all resulted in dose-dependent changes (p < 0.05) in the presence of BAP. Additionally, RNA sequencing data showed that the HBEC with the IL-13 phenotype may have increased potential for uncontrolled proliferation and decreased capacity for immune response after BAP exposure compared to normal phenotype HBEC. These data are the first to evaluate the role of combined environmental factors associated with inflammation from pre-existing disease and PAH exposure on pulmonary toxicity in a physiologically relevant human in vitro model.
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Affiliation(s)
- Reese M. Valdez
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
- Superfund Research Program, Oregon State University, Corvallis, OR, United States
| | - Brianna N. Rivera
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
- Superfund Research Program, Oregon State University, Corvallis, OR, United States
| | - Yvonne Chang
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
- Superfund Research Program, Oregon State University, Corvallis, OR, United States
| | - Jamie M. Pennington
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
| | - Kay A. Fischer
- Oregon Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Christiane V. Löhr
- Oregon Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, United States
| | - Susan C. Tilton
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
- Superfund Research Program, Oregon State University, Corvallis, OR, United States
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Liu F, Zhao Y, Pei Y, Lian F, Lin H. Role of the NF-kB signalling pathway in heterotopic ossification: biological and therapeutic significance. Cell Commun Signal 2024; 22:159. [PMID: 38439078 PMCID: PMC10910758 DOI: 10.1186/s12964-024-01533-w] [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: 12/31/2023] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
Heterotopic ossification (HO) is a pathological process in which ectopic bone develops in soft tissues within the skeletal system. Endochondral ossification can be divided into the following types of acquired and inherited ossification: traumatic HO (tHO) and fibrodysplasia ossificans progressiva (FOP). Nuclear transcription factor kappa B (NF-κB) signalling is essential during HO. NF-κB signalling can drive initial inflammation through interactions with the NOD-like receptor protein 3 (NLRP3) inflammasome, Sirtuin 1 (SIRT1) and AMP-activated protein kinase (AMPK). In the chondrogenesis stage, NF-κB signalling can promote chondrogenesis through interactions with mechanistic target of rapamycin (mTOR), phosphatidylinositol-3-kinase (PI3K)/AKT (protein kinase B, PKB) and other molecules, including R-spondin 2 (Rspo2) and SRY-box 9 (Sox9). NF-κB expression can modulate osteoblast differentiation by upregulating secreted protein acidic and rich in cysteine (SPARC) and interacting with mTOR signalling, bone morphogenetic protein (BMP) signalling or integrin-mediated signalling under stretch stimulation in the final osteogenic stage. In FOP, mutated ACVR1-induced NF-κB signalling exacerbates inflammation in macrophages and can promote chondrogenesis and osteogenesis in mesenchymal stem cells (MSCs) through interactions with smad signalling and mTOR signalling. This review summarizes the molecular mechanism of NF-κB signalling during HO and highlights potential therapeutics for treating HO.
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Affiliation(s)
- Fangzhou Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Yike Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Yiran Pei
- Department of Pathophysiology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Fengyu Lian
- Department of Pathophysiology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Hui Lin
- Department of Pathophysiology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
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Li M, Gan C, Zhang R, Wang J, Wang Y, Zhu W, Liu L, Shang J, Zhao Q. TRAF5 regulates intestinal mucosal Th1/Th17 cell immune responses via Runx1 in colitis mice. Immunology 2023; 170:495-509. [PMID: 37575027 DOI: 10.1111/imm.13685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic gastrointestinal inflammatory disease associated with CD4+ Th1 and Th17 cell immune responses. Tumour necrosis factor-associated factor 5 (TRAF5) deficiency has been shown to aggravate DSS-induced colitis. However, the potential role of TRAF5 in regulating CD4+ T cell immune responses in the pathogenesis of IBD remains unclear. TRAF5-/- CD4+ CD45RBhigh T cells and WT CD4+ CD45RBhigh T cells were transferred to Rag2-/- mice via intravenous (i.v.) tail injection, respectively, to establish a chronic colitis model. Adeno-associated virus (AAV)-mediated gene knockout technique was used to knock out runt-associated transcription factor 1 (Runx1) expression in vivo. Specific cytokines of Th1 and Th17 cells were detected by quantitative RT-PCR, immunohistochemistry, ELISA, and flow cytometry. In T-cell transfer colitis mice, the Rag2-/- mice reconstituted with TRAF5-/- CD4+ CD45RBhigh T cells showed more severe intestinal inflammation than the WT control group, which was characterised by increased expression of INF-γ, TNF-α, IL-17a. Furthermore, we found that the INF-γ+ CD4+ , IL17a+ CD4+ , and INF-γ+ IL17a+ CD4+ T cells in the intestinal mucosa of Rag2-/- mice reconstituted with TRAF5-/- CD4+ CD45RBhigh T cells were significantly higher than those of the WT control group by flow cytometry. Mechanistically, knockout Runx1 inhibited the differentiation of TRAF5-/- CD4+ T cells into Th1 and Th17 cells in the intestinal mucosa of T-cell transfer colitis mice. TRAF5 regulates Th1 and Th17 cell differentiation and immune response through Runx1 to participate in the pathogenesis of colitis. Thus targeting TRAF5 in CD4+ T cells may be a novel treatment for IBD.
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Affiliation(s)
- Mengting Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Caiqin Gan
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Runan Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Jiahui Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Youwei Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Weining Zhu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Lan Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Jian Shang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
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Shlykova O, Izmailova O, Kabaliei A, Palchyk V, Shynkevych V, Kaidashev I. PPARG stimulation restored lung mRNA expression of core clock, inflammation- and metabolism-related genes disrupted by reversed feeding in male mice. Physiol Rep 2023; 11:e15823. [PMID: 37704580 PMCID: PMC10499569 DOI: 10.14814/phy2.15823] [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: 06/19/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
The circadian rhythm system regulates lung function as well as local and systemic inflammations. The alteration of this rhythm might be induced by a change in the eating rhythm. Peroxisome proliferator-activated receptor gamma (PPARG) is a key molecule involved in circadian rhythm regulation, lung functions, and metabolic processes. We described the effect of the PPARG agonist pioglitazone (PZ) on the diurnal mRNA expression profile of core circadian clock genes (Arntl, Clock, Nr1d1, Cry1, Cry2, Per1, and Per2) and metabolism- and inflammation-related genes (Nfe2l2, Pparg, Rela, and Cxcl5) in the male murine lung disrupted by reversed feeding (RF). In mice, RF disrupted the diurnal expression pattern of core clock genes. It decreased Nfe2l2 and Pparg and increased Rela and Cxcl5 expression in lung tissue. There were elevated levels of IL-6, TNF-alpha, total cells, macrophages, and lymphocyte counts in bronchoalveolar lavage (BAL) with a significant increase in vascular congestion and cellular infiltrates in male mouse lung tissue. Administration of PZ regained the diurnal clock gene expression, increased Nfe2l2 and Pparg expression, and reduced Rela, Cxcl5 expression and IL-6, TNF-alpha, and cellularity in BAL. PZ administration at 7 p.m. was more efficient than at 7 a.m.
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Verma M, Verma D, Sripada AS, Sirohi K, Varma R, Sahu A, Alam R. NFκB1 inhibits memory formation and supports effector function of ILC2s in memory-driven asthma. Front Immunol 2023; 14:1217776. [PMID: 37575259 PMCID: PMC10415221 DOI: 10.3389/fimmu.2023.1217776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Background ILC2s are capable of generating memory. The mechanism of memory induction and memory-driven effector function (trained immunity) in ILC2s is unknown. Objective NFκB1 is preferentially expressed at a high level in ILC2s. We examined the role of NFkB1 in memory induction and memory-driven effector function in a mouse model of asthma. Methods Intranasal administration of Alternaria, flexivent, ELISA, histology, real-time PCR, western blot, flow cytometry and immunofluorescence staining. Results NFκB1 was essential for the effector phase of memory-driven asthma. NFκB1 was critical for IL33 production, ILC2 generation, and production of type-2 cytokines, which resulted in eosinophilic inflammation and other features of asthma. NFκB1 induction of type-2 cytokines in ILC2s was independent of GATA3. NFκB1 was important for allergen induction of ILC3s and FoxP3+ Tregs. NFκB1 did not affect Th2 cells or their cytokine production. In contrast to its protagonistic role in the effector phase, NFκB1 had an antagonistic role in the memory phase. NFκB1 inhibited allergen-induced upregulation of memory-associated repressor and preparedness genes in ILC2s. NFκB1 upregulated RUNX1. NFκB1 formed a heterodimer with RUNX1 in ILC2s. Conclusions NFκB1 positively regulated the effector phase but inhibited the induction phase of memory. The foregoing pointed to an interdependent antagonism between the memory induction and the memory effector processes. The NFκB1-RUNX1 heterodimer represented a non-canonical transcriptional activator of type-2 cytokines in ILC2s.
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Affiliation(s)
- Mukesh Verma
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Divya Verma
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Anand Santosh Sripada
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Kapil Sirohi
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Rangati Varma
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Anita Sahu
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Rafeul Alam
- Division of Allergy & Immunology, Department of Medicine, National Jewish Health, Denver, CO, United States
- School of Medicine, University of Colorado Denver, Denver, CO, United States
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Vázquez-Mera S, Martelo-Vidal L, Miguéns-Suárez P, Saavedra-Nieves P, Arias P, González-Fernández C, Mosteiro-Añón M, Corbacho-Abelaira MD, Blanco-Aparicio M, Méndez-Brea P, Salgado FJ, Nieto-Fontarigo JJ, González-Barcala FJ. Serum exosome inflamma-miRs are surrogate biomarkers for asthma phenotype and severity. Allergy 2023; 78:141-155. [PMID: 35971848 DOI: 10.1111/all.15480] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/20/2022] [Accepted: 07/31/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Asthma is a heterogeneous disease with several phenotypes, endotypes and severity degrees, in which different T-cell subpopulations are involved. These cells express specific miRNAs (i.e. inflamma-miRs) that can be released to serum in exosomes after activation and be used as biomarkers of underlying inflammation. Thus, we aim to evaluate specific T-cell miRNA signatures in serum exosomes from different subgroups of asthmatic patients. METHODS Samples from healthy donors (N = 30) and patients (N = 119) with different asthma endotypes (T2high -Atopic/T2high -Non-atopic/T2low ) and severity degrees (mild/MA and moderate-severe/MSA) were used. Demographic, clinical, haematological and biochemical characteristics were collected. Twelve miRNAs previously associated with different Th subsets were preselected and their levels in serum exosome samples were measured using RTqPCR. RESULTS We detected five miRNAs with high confidence in serum exosomes: miR-16-5p, miR-21-5p, miR-126-3p, miR146a-5p and miR-215-5p. All of them, except miR-16-5p were upregulated in MSA patients compared to MA. A logistic regression model including each of these miRNAs was created to discriminate both conditions, rendering a ROC curve AUC of 0.896 (0.830-0.961). miR-21-5p and miR-126-3p, both involved in Th1/Th2 differentiation, were specifically augmented in T2high -Atopic patients. Of note, all these changes were found in samples collected in autumn. On the contrary, IL-6high patients with MSA, which were more obese, older, with higher neutrophil and basophil counts and TNF levels, displayed a decrease of miR-21-5p, miR-126-3p and miR-146a-5p. CONCLUSION Immune-related miRNAs, including miR-21-5p, miR-126-3p, miR-146a-5p and miR-215-5p, can be used as clinically relevant non-invasive biomarkers of the phenotype/endotype and severity of asthma.
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Affiliation(s)
- Sara Vázquez-Mera
- Department of Biochemistry and Molecular Biology, Faculty of Biology-Biological Research Centre (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Translational Research In Airway Diseases Group (TRIAD), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Laura Martelo-Vidal
- Department of Biochemistry and Molecular Biology, Faculty of Biology-Biological Research Centre (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Translational Research In Airway Diseases Group (TRIAD), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Pablo Miguéns-Suárez
- Department of Biochemistry and Molecular Biology, Faculty of Biology-Biological Research Centre (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Translational Research In Airway Diseases Group (TRIAD), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Paula Saavedra-Nieves
- Department of Statistics, Mathematical Analysis and Optimization, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Arias
- Department of Biochemistry and Molecular Biology, Faculty of Biology-Biological Research Centre (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Translational Research In Airway Diseases Group (TRIAD), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | | | - Mar Mosteiro-Añón
- Department of Respiratory Medicine, University Hospital Alvaro Cunqueiro, Vigo, Spain
| | | | | | - Paula Méndez-Brea
- Allergy Service, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco Javier Salgado
- Department of Biochemistry and Molecular Biology, Faculty of Biology-Biological Research Centre (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Translational Research In Airway Diseases Group (TRIAD), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Juan José Nieto-Fontarigo
- Translational Research In Airway Diseases Group (TRIAD), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Francisco Javier González-Barcala
- Translational Research In Airway Diseases Group (TRIAD), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain.,Department of Medicine, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Department of Respiratory Medicine, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain.,Spanish Biomedical Research Networking Centre in Respiratory Diseases (CIBERES), Barcelona, Spain
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Yang B, Qin Y, Zhang A, Wang P, Jiang H, Shi Y, You G, Shen D, Ni S, Guo L, Liu Y. Circular RNA CircSLC8A1 contributes to osteogenic differentiation in hBMSCs via CircSLC8A1/miR-144-3p/RUNX1 in periprosthetic osteolysis. J Cell Mol Med 2022; 27:189-203. [PMID: 36541023 PMCID: PMC9843530 DOI: 10.1111/jcmm.17633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/03/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) are often found in eukaryocyte and have a role in the pathogenesis of a variety of human disorders. Our related research has shown the differential expression of circRNAs in periprosthetic osteolysis (PPOL). However, the involvement of circRNAs in the exact process is yet unknown. CircSLC8A1 expression was evaluated in clinical samples and human bone marrow mesenchymal stem cells (hBMSCs) in this investigation using quantitative real-time PCR. In vitro and in vivo studies were conducted to explicate its functional role and pathway. We demonstrated CircSLC8A1 is involved in PPOL using gain- and loss-of-function methods. The association of CircSLC8A1 and miR-144-3p, along with miR-144-3p and RUNX1, was predicted using bioinformatics. RNA pull-down and luciferase assays confirmed it. The impact of CircSLC8A1 in the PPOL-mouse model was also investigated using adeno-associated virus. CircSLC8A1 was found to be downregulated in PPOL patients' periprosthetic tissues. Overexpression of CircSLC8A1 promoted osteogenic differentiation (OD) and inhibited apoptosis of hBMSCs in vitro. The osteogenic markers of RUNX1, osteopontin (OPN) and osteocalcin (OCN) were significantly upregulated in hBMSCs after miR-144-3p inhibitor was transferred. Mechanistic analysis demonstrated that CircSLC8A1 directly bound to miR-144-3p and participated in PPOL through the miR-144-3p/RUNX1 pathway in hBMSCs. Micro-CT and quantitative analysis showed that CircSLC8A1 markedly inhibited PPOL, and osteogenic markers (RUNX1, OPN and OCN) were significantly increased (P<0.05) in the mice model. Our findings prove that CircSLC8A1 exerted a regulatory role in promoting osteogenic differentiation in hBMSCs, and CircSLC8A1/miR-144-3p/RUNX1 pathway may provide a potential target for prevention of PPOL.
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Affiliation(s)
- Boning Yang
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Yu Qin
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Ao Zhang
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Penghao Wang
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Hua Jiang
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Yunyi Shi
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Guanchao You
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Dianlin Shen
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Shenghui Ni
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Lei Guo
- Department of Orthopedic Surgery, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
| | - Ying Liu
- Department of Nursing, First Affiliated HospitalChina Medical UniversityShenyangLiaoningChina
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Polyclonal evolution of Fanconi anemia to MDS and AML revealed at single cell resolution. Exp Hematol Oncol 2022; 11:64. [PMID: 36167633 PMCID: PMC9513989 DOI: 10.1186/s40164-022-00319-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
Background Fanconi anemia (FA) is a rare disease of bone marrow failure. FA patients are prone to develop myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). However, the molecular clonal evolution of the progression from FA to MDS/AML remains elusive. Methods Herein, we performed a comprehensive genomic analysis using an FA patient (P1001) sample that transformed to MDS and subsequently AML, together with other three FA patient samples at the MDS stage. Results Our finding showed the existence of polyclonal pattern in these cases at MDS stage. The clonal evolution analysis of FA case (P1001) showed the mutations of UBASH3A, SF3B1, RUNX1 and ASXL1 gradually appeared at the later stage of MDS, while the IDH2 alteration become the dominant clone at the leukemia stage. Moreover, single-cell sequencing analyses further demonstrated a polyclonal pattern was present at either MDS or AML stages, whereas IDH2 mutated cell clones appeared only at the leukemia stage. Conclusions We thus propose a clonal evolution model from FA to MDS and AML for this patient. The results of our study on the clonal evolution and mutated genes of the progression of FA to AML are conducive to understanding the progression of the disease that still perplexes us. Supplementary Information The online version contains supplementary material available at 10.1186/s40164-022-00319-5.
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Yang X, Li M, Ji Y, Lin Y, Xu L, Gu X, Sun H, Wang W, Shen Y, Liu H, Zhu J. Changes of Gene Expression Patterns of Muscle Pathophysiology-Related Transcription Factors During Denervated Muscle Atrophy. Front Physiol 2022; 13:923190. [PMID: 35812340 PMCID: PMC9263185 DOI: 10.3389/fphys.2022.923190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/07/2022] [Indexed: 12/11/2022] Open
Abstract
Peripheral nerve injury is common, and can lead to skeletal muscle atrophy and dysfunction. However, the underlying molecular mechanisms are not fully understood. The transcription factors have been proved to play a key role in denervated muscle atrophy. In order to systematically analyze transcription factors and obtain more comprehensive information of the molecular regulatory mechanisms in denervated muscle atrophy, a new transcriptome survey focused on transcription factors are warranted. In the current study, we used microarray to identify and analyze differentially expressed genes encoding transcription factors in denervated muscle atrophy in a rat model of sciatic nerve dissection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to explore the biological functions of differentially expressed transcription factors and their target genes related to skeletal muscle pathophysiology. We found that the differentially expressed transcription factors were mainly involved in the immune response. Based on correlation analysis and the expression trends of transcription factors, 18 differentially expressed transcription factors were identified. Stat3, Myod1, Runx1, Atf3, Junb, Runx2, Myf6, Stat5a, Tead4, Klf5, Myog, Mef2a, and Hes6 were upregulated. Ppargc1a, Nr4a1, Lhx2, Ppara, and Rxrg were downregulated. Functional network mapping revealed that these transcription factors are mainly involved in inflammation, development, aging, proteolysis, differentiation, regeneration, autophagy, oxidative stress, atrophy, and ubiquitination. These findings may help understand the regulatory mechanisms of denervated muscle atrophy and provide potential targets for future therapeutic interventions for muscle atrophy following peripheral nerve injury.
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Affiliation(s)
- Xiaoming Yang
- School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Ming Li
- Department of Laboratory Medicine, Binhai County People’s Hospital affiliated to Kangda College of Nanjing Medical University, Yancheng, China
| | - Yanan Ji
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Yinghao Lin
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, China
| | - Lai Xu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Xiaosong Gu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Wei Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Yuntian Shen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
- *Correspondence: Yuntian Shen, ; Hua Liu, ; Jianwei Zhu,
| | - Hua Liu
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, Nantong, China
- *Correspondence: Yuntian Shen, ; Hua Liu, ; Jianwei Zhu,
| | - Jianwei Zhu
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Yuntian Shen, ; Hua Liu, ; Jianwei Zhu,
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10
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Ruan D, Wang Y, Li S, Zhang C, Zheng W, Yu C. Nalbuphine alleviates inflammation by down-regulating NF-κB in an acute inflammatory visceral pain rat model. BMC Pharmacol Toxicol 2022; 23:34. [PMID: 35642022 PMCID: PMC9158276 DOI: 10.1186/s40360-022-00573-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/24/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Nalbuphine can relieve patients’ inflammation response after surgery compared to other opioid drugs. However, its molecular mechanism has not been clear. Activation of NF-κB signaling pathway under oxidative stress and inflammation can maintain pain escalation. Methods We firstly investigated the effect of nalbuphine on writhing test and mechanical allodynia using a rat model of inflammatory visceral pain (acetic acid (AA) administrated). Cytokines (including tumor necrosis factor (TNF)-α, Interleukin (IL)-1β, IL-2, and IL-6 in plasma were tested with ELISA technology. Expression levels of TNF-α, IκBα and p-NF-κB p65 at the spinal cord (L3–5) were measured by western blot or RT-qPCR. Results We found that the paw withdrawal threshold (PWT) values of rats were reduced in the model group, while the numbers of writhing, levels of IL-1β, IL-2, IL-6, and TNF-α in plasma, and p-NF-κB protein and its gene expressions in the lumbar spinal cord were up-regulated. Subcutaneously injection of nalbuphine (10 μg/kg) or PDTC (NF-κB inhibitor) attenuated acetic acid-induced inflammatory pain, and this was associated with reversal of up-regulated IL-1β, IL-2, IL-6, and TNF-α in both plasma and spinal cord. Furthermore, acetic acid increased p-NF-κB and TNF-α protein levels in the white matter of the spinal cord, which was attenuated by nalbuphine. These results suggested that nalbuphine can significantly ameliorate inflammatory pain via modulating the expression of NF-κB p65 as well as inflammation factors level in the spinal cord. Conclusion In conclusion, nalbuphine inhibits inflammation through down-regulating NF-κB pathway at the spinal cord in a rat model of inflammatory visceral pain. Supplementary Information The online version contains supplementary material available at 10.1186/s40360-022-00573-7.
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Affiliation(s)
- Dijiao Ruan
- Department of Anesthesiology, Stomatological Hospital of Chongqing Medical University, 426 Songs North Road, Yubei District, Chongqing, China.,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China.,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Yuanyuan Wang
- Department of Anesthesiology, Stomatological Hospital of Chongqing Medical University, 426 Songs North Road, Yubei District, Chongqing, China.,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China.,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Sisi Li
- Department of Anesthesiology, Stomatological Hospital of Chongqing Medical University, 426 Songs North Road, Yubei District, Chongqing, China.,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China.,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Chao Zhang
- Department of Anesthesiology, Stomatological Hospital of Chongqing Medical University, 426 Songs North Road, Yubei District, Chongqing, China.,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China.,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Wenwen Zheng
- Department of Anesthesiology, Stomatological Hospital of Chongqing Medical University, 426 Songs North Road, Yubei District, Chongqing, China.,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China.,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Cong Yu
- Department of Anesthesiology, Stomatological Hospital of Chongqing Medical University, 426 Songs North Road, Yubei District, Chongqing, China. .,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China. .,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China.
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11
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Identification of key regulators in Sarcoidosis through multidimensional systems biological approach. Sci Rep 2022; 12:1236. [PMID: 35075176 PMCID: PMC8786862 DOI: 10.1038/s41598-022-05129-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 12/30/2021] [Indexed: 01/13/2023] Open
Abstract
Sarcoidosis is a multi-organ disorder where immunology, genetic and environmental factors play a key role in causing Sarcoidosis, but its molecular mechanism remains unclear. Identification of its genetics profiling that regulates the Sarcoidosis network will be one of the main challenges to understand its aetiology. We have identified differentially expressed genes (DEGs) by analyzing the gene expression profiling of Sarcoidosis and compared it with healthy control. Gene set enrichment analysis showed that these DEGs were mainly enriched in the inflammatory response, immune system, and pathways in cancer. Sarcoidosis protein interaction network was constructed by a total of 877 DEGs (up-down) and calculated its network topological properties, which follow hierarchical scale-free fractal nature up to six levels of the organization. We identified a large number of leading hubs that contain six key regulators (KRs) including ICOS, CTLA4, FLT3LG, CD33, GPR29 and ITGA4 are deeply rooted in the network from top to bottom, considering a backbone of the network. We identified the transcriptional factors (TFs) which are closely interacted with KRs. These genes and their TFs regulating the Sarcoidosis network are expected to be the main target for the therapeutic approaches and potential biomarkers. However, experimental validations of KRs needed to confirm their efficacy.
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12
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To Predict Anti-Inflammatory and Immunomodulatory Targets of Guizhi Decoction in Treating Asthma Based on Network Pharmacology, Molecular Docking, and Experimental Validation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:9033842. [PMID: 34966437 PMCID: PMC8712140 DOI: 10.1155/2021/9033842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/09/2021] [Accepted: 11/30/2021] [Indexed: 12/23/2022]
Abstract
Asthma, characterized by the continuous inflammatory response caused by a variety of immune cells, is one of the most common chronic respiratory diseases worldwide. Relevant clinical trials proved that the traditional Chinese medicine formula Guizhi Decoction (GZD) had multitarget and multichannel functions, which might be an effective drug for asthma. However, the effective ingredients and mechanisms of GZD against asthma are still unclear. Therefore, network pharmacology, molecular docking, and cell experiments were performed to explore the antiasthma effects and potential mechanisms of GZD. First, we applied the TCMSP database and literature to obtain the bioactivated ingredients in GZD. SwissTargetPrediction, TCMSP, GeneCards, OMIM, PharmGkb, TTD, DrugBank, and STRING database were used to get core genes. In addition, the key pathways were analyzed by the DAVID database. Molecular docking was used to predict whether the important components could act on the core target proteins directly. Finally, qPCR was carried out to verify the network pharmacology results and the possible mechanisms of GZD in the treatment of asthma. We collected 134 active ingredients in GZD, 959 drug targets, and 3223 disease targets. 431 intersection genes were screened for subsequent analysis. Through GO and KEGG analyses, enriched pathways related to inflammation and immune regulation were presented. Through the qPCR method to verify the role of essential genes, we found that GZD had an excellent anti-inflammatory effect. Direct or indirect inhibition of MAPK and NF-κB pathways might be one of the crucial mechanisms of GZD against asthma. GZD might be a promising potential drug for the treatment of asthma. This article provided a reference for the clinical application of GZD.
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13
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Qin Y, Wang Y, Zhao H, Yang Z, Kang Y. Aberrant miRNA-mRNA regulatory network in polycystic ovary syndrome is associated with markers of insulin sensitivity and inflammation. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1405. [PMID: 34733957 PMCID: PMC8506717 DOI: 10.21037/atm-21-1288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022]
Abstract
Background Polycystic ovary syndrome (PCOS) is a common multifactorial metabolic and endocrine disorder in women of reproductive age. Increasingly, evidence indicates that the microRNA (miRNA)-mRNA axis contributes to the development of PCOS. Methods To investigate the molecular mechanisms through which miRNA-mRNA expression affects hyperandrogenism, ovarian tissue samples from prenatally androgenized (PNA) mice were subjected to miRNA-seq and RNA-seq analysis. Analyses were performed to identify differentially expressed microRNAs (DEmiRs) and differentially expressed genes (DEGs). In combination with our previous data obtained from clinical samples, we have performed an integrated miRNA-mRNA analysis of PNA mice and granulosa cells (GCs) from patients with PCOS. The changes in expression were validated by RT-qPCR in more mouse models and clinical samples. Results In total, 3,432 genes and 16 miRNAs were differentially expressed in PNA mice compared with the control mice. We investigated the regulation pattern of miRNAs-mRNAs and observed a total of 12 miRNA-mRNA pairs involved in negative regulation. Functional analysis concentrated on insulin resistance, the T cell receptor signaling pathway, and other inflammation-related pathways. Verification of these results by RT-qPCR showed that the expression of miR-106-5p and miR-155-5p in clinical GCs was consistent with that in PNA mice. After predicting the target genes of miR-106-5p and miR-155-5p and performing negative regulation analysis, six target genes were obtained in GCs. The integration analysis showed that the network of miR-106-5p/miR-155-5p targets was mostly concentrated in pathway related to insulin resistance and inflammation. In addition, the upregulation of the inflammatory genes Il18/IL18 and Socs3/SOCS3 was validated in the PNA mice and GCs from patients compared with the appropriate control sample. The in vitro experiments showed that the regulatory relationship observed may be related to the direct stimulation of DHT. Conclusions Our results showed that the miRNA-mRNA regulatory network in PCOS was associated with markers of insulin sensitivity and inflammation. Our study provides a new genetic basis and novel insight regarding the pathogenesis of PCOS.
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Affiliation(s)
- Yulan Qin
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yuhuan Wang
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Zhao
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
| | - Zhaoxia Yang
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yani Kang
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
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14
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Francavilla A, Gagliardi A, Piaggeschi G, Tarallo S, Cordero F, Pensa RG, Impeduglia A, Caviglia GP, Ribaldone DG, Gallo G, Grioni S, Ferrero G, Pardini B, Naccarati A. Faecal miRNA profiles associated with age, sex, BMI, and lifestyle habits in healthy individuals. Sci Rep 2021; 11:20645. [PMID: 34667192 PMCID: PMC8526833 DOI: 10.1038/s41598-021-00014-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
For their stability and detectability faecal microRNAs represent promising molecules with potential clinical interest as non-invasive diagnostic and prognostic biomarkers. However, there is no evidence on how stool miRNA profiles change according to an individual’s age, sex, and body mass index (BMI) or how lifestyle habits influence the expression levels of these molecules. We explored the relationship between the stool miRNA levels and common traits (sex, age, BMI, and menopausal status) or lifestyle habits (physical activity, smoking status, coffee, and alcohol consumption) as derived by a self-reported questionnaire, using small RNA-sequencing data of samples from 335 healthy subjects. We detected 151 differentially expressed miRNAs associated with one variable and 52 associated with at least two. Differences in miR-638 levels were associated with age, sex, BMI, and smoking status. The highest number of differentially expressed miRNAs was associated with BMI (n = 92) and smoking status (n = 84), with several miRNAs shared between them. Functional enrichment analyses revealed the involvement of the miRNA target genes in pathways coherent with the analysed variables. Our findings suggest that miRNA profiles in stool may reflect common traits and lifestyle habits and should be considered in relation to disease and association studies based on faecal miRNA expression.
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Affiliation(s)
- Antonio Francavilla
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Amedeo Gagliardi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Giulia Piaggeschi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | | | - Ruggero G Pensa
- Department of Computer Science, University of Turin, Turin, Italy
| | | | - Gian Paolo Caviglia
- Division of Gastroenterology, Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Gaetano Gallo
- Department of Medical and Surgical Sciences, University of Catanzaro, Catanzaro, Italy
| | - Sara Grioni
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale Dei Tumori Di Milano, Milan, Italy
| | - Giulio Ferrero
- Department of Computer Science, University of Turin, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy. .,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.
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15
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Ahmed MM, Johnson NR, Boyd TD, Coughlan C, Chial HJ, Potter H. Innate Immune System Activation and Neuroinflammation in Down Syndrome and Neurodegeneration: Therapeutic Targets or Partners? Front Aging Neurosci 2021; 13:718426. [PMID: 34603007 PMCID: PMC8481947 DOI: 10.3389/fnagi.2021.718426] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
Innate immune system activation and inflammation are associated with and may contribute to clinical outcomes in people with Down syndrome (DS), neurodegenerative diseases such as Alzheimer's disease (AD), and normal aging. In addition to serving as potential diagnostic biomarkers, innate immune system activation and inflammation may play a contributing or causal role in these conditions, leading to the hypothesis that effective therapies should seek to dampen their effects. However, recent intervention studies with the innate immune system activator granulocyte-macrophage colony-stimulating factor (GM-CSF) in animal models of DS, AD, and normal aging, and in an AD clinical trial suggest that activating the innate immune system and inflammation may instead be therapeutic. We consider evidence that DS, AD, and normal aging are accompanied by innate immune system activation and inflammation and discuss whether and when during the disease process it may be therapeutically beneficial to suppress or promote such activation.
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Affiliation(s)
- Md. Mahiuddin Ahmed
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Alzheimer’s and Cognition Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Noah R. Johnson
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Alzheimer’s and Cognition Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Timothy D. Boyd
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Alzheimer’s and Cognition Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Partner Therapeutics, Inc., Lexington, MA, United States
| | - Christina Coughlan
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Alzheimer’s and Cognition Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Heidi J. Chial
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Alzheimer’s and Cognition Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Huntington Potter
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Alzheimer’s and Cognition Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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16
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Gerstner N, Kehl T, Lenhof K, Eckhart L, Schneider L, Stöckel D, Backes C, Meese E, Keller A, Lenhof HP. GeneTrail: A Framework for the Analysis of High-Throughput Profiles. Front Mol Biosci 2021; 8:716544. [PMID: 34604304 PMCID: PMC8481803 DOI: 10.3389/fmolb.2021.716544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/01/2021] [Indexed: 12/05/2022] Open
Abstract
Experimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are required to gain novel insights into the biological processes under investigation. Here, we present an overview of the GeneTrail tool suite that offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles. Our framework enables the analysis of standard bulk, time-series, and single-cell measurements and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes. We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms. GeneTrail can be accessed freely and without login requirements at http://genetrail.bioinf.uni-sb.de.
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Affiliation(s)
- Nico Gerstner
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Kerstin Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Lea Eckhart
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Lara Schneider
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Daniel Stöckel
- Healthcare Digital & Data, Merck Healthcare KGaA, Darmstadt, Germany
| | - Christina Backes
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, United States
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
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17
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Tripathi DM, Rohilla S, Kaur I, Siddiqui H, Rawal P, Juneja P, Kumar V, Kumari A, Naidu VGM, Ramakrishna S, Banerjee S, Puria R, Sarin SK, Kaur S. Immunonano-Lipocarrier-Mediated Liver Sinusoidal Endothelial Cell-Specific RUNX1 Inhibition Impedes Immune Cell Infiltration and Hepatic Inflammation in Murine Model of NASH. Int J Mol Sci 2021; 22:ijms22168489. [PMID: 34445195 PMCID: PMC8395158 DOI: 10.3390/ijms22168489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Runt-related transcription factor (RUNX1) regulates inflammation in non-alcoholic steatohepatitis (NASH). Methods: We performed in vivo targeted silencing of the RUNX1 gene in liver sinusoidal endothelial cells (LSECs) by using vegfr3 antibody tagged immunonano-lipocarriers encapsulated RUNX1 siRNA (RUNX1 siRNA) in murine models of methionine choline deficient (MCD) diet-induced NASH. MCD mice given nanolipocarriers-encapsulated negative siRNA were vehicle, and mice with standard diet were controls. Results: Liver RUNX1 expression was increased in the LSECs of MCD mice in comparison to controls. RUNX1 protein expression was decreased by 40% in CD31-positive LSECs of RUNX1 siRNA mice in comparison to vehicle, resulting in the downregulation of adhesion molecules, ICAM1 expression, and VCAM1 expression in LSECs. There was a marked decrease in infiltrated T cells and myeloid cells along with reduced inflammatory cytokines in the liver of RUNX1 siRNA mice as compared to that observed in the vehicle. Conclusions: In vivo LSEC-specific silencing of RUNX1 using immunonano-lipocarriers encapsulated siRNA effectively reduces its expression of adhesion molecules, infiltrate on of immune cells in liver, and inflammation in NASH.
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Affiliation(s)
- Dinesh Mani Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India; (D.M.T.); (I.K.); (H.S.); (P.J.); (A.K.); (S.K.S.)
| | - Sumati Rohilla
- School of Biotechnology, Gautam Buddha University, Greater Noida 201312, India; (S.R.); (P.R.); (R.P.)
| | - Impreet Kaur
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India; (D.M.T.); (I.K.); (H.S.); (P.J.); (A.K.); (S.K.S.)
| | - Hamda Siddiqui
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India; (D.M.T.); (I.K.); (H.S.); (P.J.); (A.K.); (S.K.S.)
| | - Preety Rawal
- School of Biotechnology, Gautam Buddha University, Greater Noida 201312, India; (S.R.); (P.R.); (R.P.)
| | - Pinky Juneja
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India; (D.M.T.); (I.K.); (H.S.); (P.J.); (A.K.); (S.K.S.)
| | - Vikash Kumar
- Stem Cell Biology Laboratory, National Institute of Immunology, New Delhi 110067, India;
| | - Anupama Kumari
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India; (D.M.T.); (I.K.); (H.S.); (P.J.); (A.K.); (S.K.S.)
| | - Vegi Ganga Modi Naidu
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Guwahati 781122, India; (V.G.M.N.); (S.B.)
| | - Seeram Ramakrishna
- Department of Mechanical Engineering, National University of Singapore, Singapore 117575, Singapore;
| | - Subham Banerjee
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Guwahati 781122, India; (V.G.M.N.); (S.B.)
| | - Rekha Puria
- School of Biotechnology, Gautam Buddha University, Greater Noida 201312, India; (S.R.); (P.R.); (R.P.)
| | - Shiv K. Sarin
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India; (D.M.T.); (I.K.); (H.S.); (P.J.); (A.K.); (S.K.S.)
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Savneet Kaur
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India; (D.M.T.); (I.K.); (H.S.); (P.J.); (A.K.); (S.K.S.)
- Correspondence:
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18
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Thomas AL, Marsman J, Antony J, Schierding W, O’Sullivan JM, Horsfield JA. Transcriptional Regulation of RUNX1: An Informatics Analysis. Genes (Basel) 2021; 12:1175. [PMID: 34440349 PMCID: PMC8395016 DOI: 10.3390/genes12081175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/04/2023] Open
Abstract
The RUNX1/AML1 gene encodes a developmental transcription factor that is an important regulator of haematopoiesis in vertebrates. Genetic disruptions to the RUNX1 gene are frequently associated with acute myeloid leukaemia. Gene regulatory elements (REs), such as enhancers located in non-coding DNA, are likely to be important for Runx1 transcription. Non-coding elements that modulate Runx1 expression have been investigated over several decades, but how and when these REs function remains poorly understood. Here we used bioinformatic methods and functional data to characterise the regulatory landscape of vertebrate Runx1. We identified REs that are conserved between human and mouse, many of which produce enhancer RNAs in diverse tissues. Genome-wide association studies detected single nucleotide polymorphisms in REs, some of which correlate with gene expression quantitative trait loci in tissues in which the RE is active. Our analyses also suggest that REs can be variant in haematological malignancies. In summary, our analysis identifies features of the RUNX1 regulatory landscape that are likely to be important for the regulation of this gene in normal and malignant haematopoiesis.
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Affiliation(s)
- Amarni L. Thomas
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (A.L.T.); (J.A.)
| | - Judith Marsman
- Department of Cardiology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands;
| | - Jisha Antony
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (A.L.T.); (J.A.)
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - William Schierding
- Liggins Institute, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - Justin M. O’Sullivan
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
- Liggins Institute, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton SO17 1BJ, UK
| | - Julia A. Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (A.L.T.); (J.A.)
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
- Genetics Otago Research Centre, University of Otago, Dunedin 9054, New Zealand
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19
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Meikle CKS, Creeden JF, McCullumsmith C, Worth RG. SSRIs: Applications in inflammatory lung disease and implications for COVID-19. Neuropsychopharmacol Rep 2021; 41:325-335. [PMID: 34254465 PMCID: PMC8411309 DOI: 10.1002/npr2.12194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/17/2021] [Accepted: 07/02/2021] [Indexed: 12/15/2022] Open
Abstract
Selective serotonin reuptake inhibitors (SSRIs) have anti-inflammatory properties that may have clinical utility in treating severe pulmonary manifestations of COVID-19. SSRIs exert anti-inflammatory effects at three mechanistic levels: (a) inhibition of proinflammatory transcription factor activity, including NF-κB and STAT3; (b) downregulation of lung tissue damage and proinflammatory cell recruitment via inhibition of cytokines, including IL-6, IL-8, TNF-α, and IL-1β; and (c) direct suppression inflammatory cells, including T cells, macrophages, and platelets. These pathways are implicated in the pathogenesis of COVID-19. In this review, we will compare the pathogenesis of lung inflammation in pulmonary diseases including COVID-19, ARDS, and chronic obstructive pulmonary disease (COPD), describe the anti-inflammatory properties of SSRIs, and discuss the applications of SSRIS in treating COVID-19-associated inflammatory lung disease.
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Affiliation(s)
- Claire Kyung Sun Meikle
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Justin Fortune Creeden
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA.,Department of Psychiatry, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Cheryl McCullumsmith
- Department of Psychiatry, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Randall G Worth
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
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20
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Xin Y, Zefeng K, Ling L, Ruijuan G. Association between NF-kB polymorphism and age-related macular degeneration in a high-altitude population. PLoS One 2021; 16:e0251931. [PMID: 34101738 PMCID: PMC8186772 DOI: 10.1371/journal.pone.0251931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/05/2021] [Indexed: 12/02/2022] Open
Abstract
Objective To investigate the association between the nuclear factor kappa B (NF-kB) gene polymorphism and age-related macular degeneration (AMD) in a high-altitude population. Methods Fifty-five patients with AMD and 57 control subjects were recruited from the Qinghai Provincial People’s Hospital, China. Genomic DNA was extracted from the blood sample of each participant. Four NF-kB polymorphisms (rs3774959, rs3774932, rs3774937, and rs230526) were genotyped using a MassARRAY system. The genotype and allele frequencies were compared between the case and control groups using the chi-squared test or Fisher’s exact test. Results There was no significant difference in sex, age, hypertension, diabetes, blood lipid level or smoking and drinking status between the AMD and control groups (P > 0.05). The genotype distributions of four NF-kB polymorphisms were in accordance with Hardy-Weinberg equilibrium in the control group (P > 0.05). The frequencies of genotype AA of rs3774932 and genotype CC of rs3774937 were nominally significantly higher in the AMD group than in the control group (P = 0.046 and 0.023, respectively), although these associations did not survive the Bonferroni correction (corrected P > 0.05). Genotype distributions of rs3774959 and rs230526 were not significantly different between the two groups (P = 0.08 and 0.16, respectively). No significant difference in the allele frequencies of the four polymorphisms was found between the AMD and control groups (P > 0.05). Conclusions Genotype AA of rs3774932 and genotype CC of rs3774937 in NF-kB might be risk factors for AMD.
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Affiliation(s)
- Yan Xin
- Medical College of Qinghai University, Xining, Qinghai Province, China
| | - Kang Zefeng
- Ophthalmic Hospital, Chinese Academy of Traditional Chinese Medicine, Beijing, China
- * E-mail: (GR); (KZ)
| | - Li Ling
- Department of Ophthalmology, Qinghai Provincial People’s Hospital, Xining, Qinghai Province, China
| | - Guan Ruijuan
- Department of Ophthalmology, Qinghai Provincial People’s Hospital, Xining, Qinghai Province, China
- * E-mail: (GR); (KZ)
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21
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Wu S, Guo T, Qi W, Li Y, Gu J, Liu C, Sha Y, Yang B, Hu S, Zong X. Curcumin ameliorates ischemic stroke injury in rats by protecting the integrity of the blood-brain barrier. Exp Ther Med 2021; 22:783. [PMID: 34055082 PMCID: PMC8145684 DOI: 10.3892/etm.2021.10215] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/16/2021] [Indexed: 12/16/2022] Open
Abstract
The blood-brain barrier (BBB) is critical for proper cerebral homeostasis and its dysfunction during ischemic stroke can result in significant neurological injury. The major goal of the present study was to identify whether curcumin pretreatment possessed protective effects on BBB integrity during the 24 h of acute ischemic brain injury. To investigate the protective effects of curcumin, male Sprague-Dawley rats were divided into multiple groups, including sham, middle cerebral artery occlusion/reperfusion (MCAO/R) vehicle and curcumin pretreated MCAO/R groups. The effects of curcumin were measured by analyzing neurological deficits, infarct size, BBB permeability and expression levels of permeability-related proteins in the brain. It was found that curcumin pretreatment significantly improved neurological scores, decreased infarct size, and protected synaptic remodeling of hippocampal neurons and upregulated the protein expression level of tight junction proteins, ZO-1, occludin and claudin-5 in ischemic rat brains. Furthermore, curcumin pretreatment before stroke was shown to downregulate the phosphorylation of NF-κB and MMP-9, which are central mediators of inflammation. The results from the present study indicated that curcumin pretreatment ameliorated ischemic stroke injury by protecting BBB integrity and synaptic remodeling, as well as inhibiting inflammatory responses.
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Affiliation(s)
- Shuguang Wu
- Department of Anesthesiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 313000, P.R. China
| | - Ting Guo
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Wenxuan Qi
- Jiangsu Provincial Institute of Health Emergency, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Yuyu Li
- Jiangsu Provincial Institute of Health Emergency, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Jie Gu
- Jiangsu Provincial Institute of Health Emergency, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Cui Liu
- Jiangsu Provincial Institute of Health Emergency, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Yuehong Sha
- Department of Emergency, First People's Hospital, Pizhou, Jiangsu 221300, P.R. China
| | - Baocheng Yang
- Jiangsu Provincial Institute of Health Emergency, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Emergency Center of The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Shuqun Hu
- Jiangsu Provincial Institute of Health Emergency, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Emergency Center of The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Xuemei Zong
- Jiangsu Provincial Institute of Health Emergency, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Emergency Center of The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
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22
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Senevirathna JDM, Asakawa S. Multi-Omics Approaches and Radiation on Lipid Metabolism in Toothed Whales. Life (Basel) 2021; 11:364. [PMID: 33923876 PMCID: PMC8074237 DOI: 10.3390/life11040364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/09/2021] [Accepted: 04/17/2021] [Indexed: 11/25/2022] Open
Abstract
Lipid synthesis pathways of toothed whales have evolved since their movement from the terrestrial to marine environment. The synthesis and function of these endogenous lipids and affecting factors are still little understood. In this review, we focused on different omics approaches and techniques to investigate lipid metabolism and radiation impacts on lipids in toothed whales. The selected literature was screened, and capacities, possibilities, and future approaches for identifying unusual lipid synthesis pathways by omics were evaluated. Omics approaches were categorized into the four major disciplines: lipidomics, transcriptomics, genomics, and proteomics. Genomics and transcriptomics can together identify genes related to unique lipid synthesis. As lipids interact with proteins in the animal body, lipidomics, and proteomics can correlate by creating lipid-binding proteome maps to elucidate metabolism pathways. In lipidomics studies, recent mass spectroscopic methods can address lipid profiles; however, the determination of structures of lipids are challenging. As an environmental stress, the acoustic radiation has a significant effect on the alteration of lipid profiles. Radiation studies in different omics approaches revealed the necessity of multi-omics applications. This review concluded that a combination of many of the omics areas may elucidate the metabolism of lipids and possible hazards on lipids in toothed whales by radiation.
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Affiliation(s)
- Jayan D. M. Senevirathna
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
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23
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Xiu MX, Liu ZT, Tang J. Screening and identification of key regulatory connections and immune cell infiltration characteristics for lung transplant rejection using mucosal biopsies. Int Immunopharmacol 2020; 87:106827. [PMID: 32791489 PMCID: PMC7417178 DOI: 10.1016/j.intimp.2020.106827] [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: 04/20/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
This study aimed to explore key regulatory connections underlying lung transplant rejection. The differentially expressed genes (DEGs) between rejection and stable lung transplantation (LTx) samples were screened using R package limma, followed by functional enrichment analysis and protein-protein interaction network construction. Subsequently, a global triple network, including miRNAs, mRNAs, and transcription factors (TFs), was constructed. Furthermore, immune cell infiltration characteristics were analyzed to investigate the molecular immunology of lung transplant rejection. Finally, potential drug-target interactions were generated. In brief, 739 DEGs were found between rejection and stable LTx samples. PTPRC, IL-6, ITGAM, CD86, TLR8, TYROBP, CXCL10, ITGB2, and CCR5 were defined as hub genes. Eight TFs, including STAT1, SPIB, NFKB1, SPI1, STAT5A, RUNX1, VENTX, and BATF, and five miRNAs, including miR-335-5p, miR-26b-5p, miR-124-3p, miR-1-3p, and miR-155-5p, were involved in regulating hub genes. The immune cell infiltration analysis revealed higher proportions of activated memory CD4 T cells, follicular helper T cells, γδ T cells, monocytes, M1 and M2 macrophages, and eosinophils in rejection samples, besides lower proportions of resting memory CD4 T cells, regulatory T cells, activated NK cells, M0 macrophages, and resting mast cells. This study provided a comprehensive perspective of the molecular co-regulatory network underlying lung transplant rejection.
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Affiliation(s)
- Meng-Xi Xiu
- Medical School of Nanchang University, Nanchang, PR China
| | - Zu-Ting Liu
- Medical School of Nanchang University, Nanchang, PR China
| | - Jian Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China.
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24
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Silencing of SPARC represses heterotopic ossification via inhibition of the MAPK signaling pathway. Biosci Rep 2020; 39:BSR20191805. [PMID: 31548362 PMCID: PMC6851515 DOI: 10.1042/bsr20191805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 09/08/2019] [Accepted: 09/18/2019] [Indexed: 11/17/2022] Open
Abstract
Heterotopic ossification (HO), the pathologic formation of extraskeletal bone, can be disabling and lethal. However, the underlying molecular mechanisms were largely unknown. The present study aimed to clarify the involvement of secreted protein acidic and rich in cysteine (SPARC) and the underlying mechanism in rat model of HO. The mechanistic investigation on roles of SPARC in HO was examined through gain- and loss-of-function approaches of SPARC, with alkaline-phosphatase (ALP) activity, mineralized nodules, and osteocalcin (OCN) content measured. To further confirm the regulatory role of SPARC, levels of mitogen-activated protein kinase (MAPK) signaling pathways-related proteins (extracellular signal-regulated kinase (ERK), c-jun N-terminal kinase (JNK), p38, nuclear factor κ-B (NF-κB), and IkB kinase β (IKKβ)) were determined. Bone marrow mesenchymal stem cells were treated with pathway inhibitor to investigate the relationship among SPARC, MAPK signaling pathway, and HO. The results suggested that SPARC expression was up-regulated in Achilles tendon tissues of HO rats. Silencing of SPARC could decrease phosphorylation of ERK, JNK, p38, NF-κB, and IKKβ. Additionally, silencing of SPARC or inhibition of MAPK signaling pathway could reduce the ALP activity, the number of mineralized nodules, and OCN content, thus impeding HO. To sum up, our study identifies the inhibitory role of SPARC gene silencing in HO via the MAPK signaling pathway, suggesting SPARC presents a potential target for HO therapy.
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25
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Riddell A, McBride M, Braun T, Nicklin SA, Cameron E, Loughrey CM, Martin TP. RUNX1: an emerging therapeutic target for cardiovascular disease. Cardiovasc Res 2020; 116:1410-1423. [PMID: 32154891 PMCID: PMC7314639 DOI: 10.1093/cvr/cvaa034] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/18/2019] [Accepted: 02/03/2020] [Indexed: 12/12/2022] Open
Abstract
Runt-related transcription factor-1 (RUNX1), also known as acute myeloid leukaemia 1 protein (AML1), is a member of the core-binding factor family of transcription factors which modulate cell proliferation, differentiation, and survival in multiple systems. It is a master-regulator transcription factor, which has been implicated in diverse signalling pathways and cellular mechanisms during normal development and disease. RUNX1 is best characterized for its indispensable role for definitive haematopoiesis and its involvement in haematological malignancies. However, more recently RUNX1 has been identified as a key regulator of adverse cardiac remodelling following myocardial infarction. This review discusses the role RUNX1 plays in the heart and highlights its therapeutic potential as a target to limit the progression of adverse cardiac remodelling and heart failure.
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Affiliation(s)
- Alexandra Riddell
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular & Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK
| | - Martin McBride
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular & Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Stuart A Nicklin
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular & Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK
| | - Ewan Cameron
- School of Veterinary Medicine, University of Glasgow, Garscube Campus, Glasgow G61 1BD, UK
| | - Christopher M Loughrey
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular & Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK
| | - Tamara P Martin
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular & Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK
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26
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Deng J, Hou G, Fang Z, Liu J, Lv XD. Distinct expression and prognostic value of OTU domain-containing proteins in non-small-cell lung cancer. Oncol Lett 2019; 18:5417-5427. [PMID: 31612050 PMCID: PMC6781715 DOI: 10.3892/ol.2019.10883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-proteasome pathway is an important protein degradation regulatory system in cells. This pathway is also a reversible process that is strictly regulated, and the regulation of deubiquitinating enzymes (DUBs) represents an important facet of the process. Ovarian tumor-associated proteases domain-containing proteins (OTUDs), as a subfamily within the DUB family, serve an important role in regulatory mechanisms of several biological processes, through the regulation of gene transcription, cell cycle, immune response, inflammation and tumor growth processes, and may be important in the diagnosis of various diseases and constitute novel drug targets. However, the role of OTUDs in non-small-cell lung cancer (NSCLC) has not been fully elucidated. In the present study, the Oncomine database was used to examine gene expression in NSCLC, and the prognostic value of each gene was analyzed by Kaplan-Meier analysis. The results indicated that high mRNA expression levels of OTUD1, OTUD3, OTUD4 and putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 were associated with improved prognosis in all NSCLC and adenocarcinoma, but not in squamous cell carcinoma. By contrast, high expression levels of OTUD2 mRNA were associated with poorer overall survival in patients with NSCLC. These data suggested that these OTUD isozymes may be a potential drug target for NSCLC.
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Affiliation(s)
- Jingjing Deng
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Gouxin Hou
- Department of Oncology, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Zhixian Fang
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Jialiang Liu
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Xiao-Dong Lv
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
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27
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RUNX family: Oncogenes or tumor suppressors (Review). Oncol Rep 2019; 42:3-19. [PMID: 31059069 PMCID: PMC6549079 DOI: 10.3892/or.2019.7149] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Runt-related transcription factor (RUNX) proteins belong to a transcription factors family known as master regulators of important embryonic developmental programs. In the last decade, the whole family has been implicated in the regulation of different oncogenic processes and signaling pathways associated with cancer. Furthermore, a suppressor tumor function has been also reported, suggesting the RUNX family serves key role in all different types of cancer. In this review, the known biological characteristics, specific regulatory abilities and experimental evidence of RUNX proteins will be analyzed to demonstrate their oncogenic potential and tumor suppressor abilities during oncogenic processes, suggesting their importance as biomarkers of cancer. Additionally, the importance of continuing with the molecular studies of RUNX proteins' and its dual functions in cancer will be underlined in order to apply it in the future development of specific diagnostic methods and therapies against different types of cancer.
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