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Wetthasinghe L, Ng HF, Ngeow YF, Chew KS, Lee WS. Navigating the intricacies of RT-qPCR data analysis in gene expression studies. Funct Integr Genomics 2024; 24:115. [PMID: 38910215 DOI: 10.1007/s10142-024-01393-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Affiliation(s)
- Linah Wetthasinghe
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
| | - Hien Fuh Ng
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia.
| | - Yun Fong Ngeow
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Persekutuan, Kuala Lumpur, 50603, Malaysia
| | - Way Seah Lee
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
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Listyoko AS, Okazaki R, Harada T, Inui G, Yamasaki A. Impact of obesity on airway remodeling in asthma: pathophysiological insights and clinical implications. FRONTIERS IN ALLERGY 2024; 5:1365801. [PMID: 38562155 PMCID: PMC10982419 DOI: 10.3389/falgy.2024.1365801] [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: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
The prevalence of obesity among asthma patients has surged in recent years, posing a significant risk factor for uncontrolled asthma. Beyond its impact on asthma severity and patients' quality of life, obesity is associated with reduced lung function, increased asthma exacerbations, hospitalizations, heightened airway hyperresponsiveness, and elevated asthma-related mortality. Obesity may lead to metabolic dysfunction and immune dysregulation, fostering chronic inflammation characterized by increased pro-inflammatory mediators and adipocytokines, elevated reactive oxygen species, and reduced antioxidant activity. This chronic inflammation holds the potential to induce airway remodeling in individuals with asthma and obesity. Airway remodeling encompasses structural and pathological changes, involving alterations in the airway's epithelial and subepithelial layers, hyperplasia and hypertrophy of airway smooth muscle, and changes in airway vascularity. In individuals with asthma and obesity, airway remodeling may underlie heightened airway hyperresponsiveness and increased asthma severity, ultimately contributing to the development of persistent airflow limitation, declining lung function, and a potential increase in asthma-related mortality. Despite efforts to address the impact of obesity on asthma outcomes, the intricate mechanisms linking obesity to asthma pathophysiology, particularly concerning airway remodeling, remain incompletely understood. This comprehensive review discusses current research investigating the influence of obesity on airway remodeling, to enhance our understanding of obesity's role in the context of asthma airway remodeling.
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Affiliation(s)
- Aditya Sri Listyoko
- Division of Respiratory Medicine and Rheumatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
- Pulmonology and Respiratory Medicine Department, Faculty of Medicine, Brawijaya University-Dr. Saiful Anwar General Hospital, Malang, Indonesia
| | - Ryota Okazaki
- Division of Respiratory Medicine and Rheumatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Tomoya Harada
- Division of Respiratory Medicine and Rheumatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Genki Inui
- Division of Respiratory Medicine and Rheumatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Akira Yamasaki
- Division of Respiratory Medicine and Rheumatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
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Choi M, Kwon H, Pak Y. Caveolin-2 in association with nuclear lamina controls adipocyte hypertrophy. FASEB J 2023; 37:e22745. [PMID: 36637913 DOI: 10.1096/fj.202201028rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 01/14/2023]
Abstract
Here, we identify that Caveolin-2 (Cav-2), an integral membrane protein, controls adipocyte hypertrophy in association with nuclear lamina. In the hypertrophy stage of adipogenesis, pY19-Cav-2 association with lamin A/C facilitated the disengagement of CCAAT/enhancer-binding protein α (C/EBPα) and peroxisome proliferator-activated receptor γ (PPARγ) from lamin A/C and repressed Cav-2 promoter at the nuclear periphery for epigenetic activation of Cav-2, and thereby promoted C/EBPα and PPARγ-induced adipocyte hypertrophy. Stable expression of Cav-2 was required and retained by phosphorylation, deubiquitination, and association with lamin A/C for the adipocyte hypertrophy. However, obese adipocytes exhibited augmented Cav-2 stability resulting from the up-regulation of lamin A/C over lamin B1, protein tyrosine phosphatase 1B (PTP1B), and nuclear deubiquitinating enzyme (DUB), Uchl5. Our findings show a novel epigenetic regulatory mechanism of adipocyte hypertrophy by Cav-2 at the nuclear periphery.
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Affiliation(s)
- Moonjeong Choi
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Hayeong Kwon
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Yunbae Pak
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, South Korea
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Lu Z, Meng L, Sun Z, Shi X, Shao W, Zheng Y, Yao X, Song J. Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People. Front Genet 2021; 12:620740. [PMID: 34093637 PMCID: PMC8175074 DOI: 10.3389/fgene.2021.620740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/15/2021] [Indexed: 12/20/2022] Open
Abstract
As the prevalence of obesity increases, so does the occurrence of obesity-related complications, such as cardiovascular and cerebrovascular diseases, diabetes, and some cancers. Increased adipose tissue is the main cause of harm in obesity. To better understand obesity and its related complications, we analyzed the mRNA expression profiles of adipose tissues from 126 patients with obesity and 275 non-obese controls. Using an integrated bioinformatics method, we explored the functions of 113 differentially expressed genes (DEGs) between them. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses revealed that upregulated DEGs were enriched in immune cell chemotaxis, complement-related cascade activation, and various inflammatory signaling pathways, while downregulated DEGs enriched in nutrient metabolism. The CIBERSORT algorithm indicated that an increase in macrophages may be the main cause of adipose tissue inflammation, while decreased γδ T cells reduce sympathetic action, leading to dysregulation of adipocyte thermogenesis. A protein-protein interaction network was constructed using the STRING database, and the top 10 hub genes were identified using the cytoHubba plug-in in Cytoscape. All were confirmed to be obesity-related using a separate dataset. In addition, we identified chemicals related to these hub genes that may contribute to obesity. In conclusion, we have successfully identified several hub genes in the development of obesity, which provide insights into the possible mechanisms controlling obesity and its related complications, as well as potential biomarkers and therapeutic targets for further research.
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Affiliation(s)
- Zhenhua Lu
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lingbing Meng
- Department of Cardiology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Zhen Sun
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaolei Shi
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Weiwei Shao
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yangyang Zheng
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinglei Yao
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jinghai Song
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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Ma X, Sun J, Zhu S, Du Z, Li D, Li W, Li Z, Tian Y, Kang X, Sun G. MiRNAs and mRNAs Analysis during Abdominal Preadipocyte Differentiation in Chickens. Animals (Basel) 2020; 10:ani10030468. [PMID: 32168898 PMCID: PMC7143929 DOI: 10.3390/ani10030468] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/02/2020] [Accepted: 03/07/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary We sequenced the miRNAs and mRNAs of preabdominal fat cells and differentiated adipocytes, and target genes of miRNA combined with mRNA transcriptome data jointly. We found that the MAPK signal pathway, insulin signal pathway, fatty acid metabolism, ECM( extracellular matrix)–receptor interaction, and other signal pathways were involved in the differentiation of preabdominal fat cells. In addition, we found that some miRNAs–mRNAs combinations were strongly related to the differentiation of fat cells (miR-214−ACSBG2, NFKB2, CAMK2A, ACLY, CCND3, PLK3, ITGB2; miR-148a-5p−ROCK2; miR-10a-5p−ELOVL5; miR-146b-5p−LAMA4; miR-6615-5p−FLNB; miR-1774−COL6A1). Our findings provide important resources for the study of adipocyte differentiation. Abstract The excessive deposition of abdominal fat has become an important factor in restricting the production efficiency of chickens, so reducing abdominal fat deposition is important for improving growth rate. It has been proven that miRNAs play an important role in regulating many physiological processes of organisms. In this study, we constructed a model of adipogenesis by isolating preadipocytes (Ab-Pre) derived from abdominal adipose tissue and differentiated adipocytes (Ab-Ad) in vitro. Deep sequencing of miRNAs and mRNAs expressed in Ab-Pre and Ab-Ad groups was conducted to explore the effect of miRNAs and mRNAs on fat deposition. We identified 80 differentially expressed miRNAs (DEMs) candidates, 58 of which were up-regulated and 22 down-regulated. Furthermore, six miRNAs and six mRNAs were verified by qRT-PCR, and the results showed that the expression of the DEMs and differentially expressed genes (DEGs) in the two groups was consistent with our sequencing results. When target genes of miRNA were combined with mRNA transcriptome data, a total of 891 intersection genes were obtained, we predicted the signal pathways of cross genes enrichment to the MAPK signal pathway, insulin signal pathway, fatty acid metabolism, and ECM–receptor interaction. Meanwhile, we constructed miRNA and negatively correlated mRNA target networks, including 12 miRNA–mRNAs pairs, which showed a strong association with the abdominal adipocyte differentiation (miR-214−ACSBG2, NFKB2, CAMK2A, ACLY, CCND3, PLK3, ITGB2; miR-148a-5p−ROCK2; miR-10a-5p−ELOVL5; miR-146b-5p−LAMA4; miR-6615-5p−FLNB; miR-1774−COL6A1). Overall, these findings provide a background for further research on lipid metabolism. Thus, we can better understand the molecular genetic mechanism of chicken abdominal fat deposition.
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Mohamad Nor NS, Ambak R, Mohd Zaki N, Abdul Aziz NS, Cheong SM, Abd Razak MA, Yusof M, Ahmad MH, Baharuddin A, Megat Radzi MR, Wan Kozil WNK, Ishak IH, Aris T. An update on obesity research pattern among adults in Malaysia: a scoping review. BMC WOMENS HEALTH 2018; 18:114. [PMID: 30066661 PMCID: PMC6069511 DOI: 10.1186/s12905-018-0590-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background Obesity is a global health burden in the non-communicable diseases and much efforts have been implemented in the past decade in response to the rise of obesity prevalence among the Malaysian population. These include the development of the national policies, health programmes and research activities. The main aim of the scoping review was to identify obesity research pattern among adults in Malaysia in terms of the scopes, topics and the research designs. Methods The scoping review was conducted based on the framework by Arksey and O’Malley. The Preferred Reporting Items for Systematic Reviews and Meta Analysis (PRISMA) diagram was used as a guide to record the review process. Articles from year 2008 until 2017 on overweight and obesity among adults aged 18 years and above were retrieved based on the keywords using electronic databases (Embase/Ovid, Pubmed, Cochrane library and Google Scholar). Local journals, Nutrition Research in Malaysia Biblography (2011 and 2016), online local theses databases, virtual library databases were also included in the searches. Consultations with relevant key informants from the National Institutes of Health and local universities were also conducted. Search activities were managed using Endnote software and MS Excelsheet. Results The characteristics of the results were described based on the objectives of the review. A total of 2004 articles and reports were retrieved, and 188 articles related to obesity in Malaysia were included in the final review. Scopes and topics of obesity research based on the Nutrition Research Priorities in Malaysia (NRPM) for 11th Malaysia Plan were obesity prevalence, weight loss intervention, association of physical activities and dietary factors with obesity. The majority of obesity research among adults in Malaysia was cross sectional studies and only a small number of intervention studies, qualitative studies and systematic review were indentified. Research gaps were identified in order to make useful recommendations to the stakeholders. Conclusions In the past decade, there has been an emerging evidence on obesity research among adults in Malaysia. More obesity research needs to be conducted particularly on obesity intervention among specific gender, qualitative studies, economic cost and genetic factors of obesity. Electronic supplementary material The online version of this article (10.1186/s12905-018-0590-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Noor Safiza Mohamad Nor
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia.
| | - Rashidah Ambak
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Norazian Mohd Zaki
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Nur Shahida Abdul Aziz
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Siew Man Cheong
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Mohamad Aznuddin Abd Razak
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Muslimah Yusof
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Mohamad Hasnan Ahmad
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Azli Baharuddin
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Megat Rusydi Megat Radzi
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | | | - Intan Hafizah Ishak
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Tahir Aris
- Institute for Public Health, National Institutes for Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
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