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Liu M, Lu F, Feng J. Aging and homeostasis of the hypodermis in the age-related deterioration of skin function. Cell Death Dis 2024; 15:443. [PMID: 38914551 PMCID: PMC11196735 DOI: 10.1038/s41419-024-06818-z] [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: 02/22/2023] [Revised: 02/01/2024] [Accepted: 06/10/2024] [Indexed: 06/26/2024]
Abstract
Adipose tissues in the hypodermis, the crucial stem cell reservoir in the skin and the endocrine organ for the maintenance of skin homeostasis undergo significant changes during skin aging. Dermal white adipose tissue (dWAT) has recently been recognized as an important organ for both non-metabolic and metabolic health in skin regeneration and rejuvenation. Defective differentiation, adipogenesis, improper adipocytokine production, and immunological dissonance dysfunction in dWAT lead to age-associated clinical changes. Here, we review age-related alterations in dWAT across levels, emphasizing the mechanisms underlying the regulation of aging. We also discuss the pathogenic changes involved in age-related fat dysfunction and the unfavorable consequences of accelerated skin aging, such as chronic inflammaging, immunosenescence, delayed wound healing, and fibrosis. Research has shown that adipose aging is an early initiation event and a potential target for extending longevity. We believe that adipose tissues play an essential role in aging and form a potential therapeutic target for the treatment of age-related skin diseases. Further research is needed to improve our understanding of this phenomenon.
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Affiliation(s)
- Meiqi Liu
- Department of Plastic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Feng Lu
- Department of Plastic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Jingwei Feng
- Department of Plastic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, Guangdong, 510515, People's Republic of China.
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2
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Wang L, Fu Y, Yuan Z, Wang J, Guan Y. Identification and analysis of short-term and long-term salt-associated lncRNAs in the leaf of Avicennia marina. BMC PLANT BIOLOGY 2024; 24:500. [PMID: 38840244 PMCID: PMC11151563 DOI: 10.1186/s12870-024-05216-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
As a highly salt-resistant mangrove, Avicennia marina can thrive in the hypersaline water. The leaves of Avicennia marina play a crucial role in salinity stress adaptability by secreting salt. Although the functions of long non-coding RNAs (lncRNAs) in leaves remain unknown, they have emerged as regulators in leaf development, aging and salt response. In this study, we employed transcriptomic data of both short-term and long-term salt treated leaves to identify salt-associated lncRNAs of leaf tissue. As a result, 687 short-term and 797 long-term salt-associated lncRNAs were identified. Notably, both short-term and long-term salt-associated lncRNAs exhibited slightly longer lengths and larger exons, but smaller introns compared with salt-non-associated lncRNAs. Furthermore, salt-associated lncRNAs also displayed higher tissue-specificity than salt-non-associated lncRNAs. Most of the salt-associated lncRNAs were common to short- and long-term salt treatments. And about one fifth of the downregulated salt-associated lncRNAs identified both in two terms were leaf tissue-specific lncRNAs. Besides, these leaf-specific lncRNAs were found to be involved in the oxidation-reduction and photosynthesis processes, as well as several metabolic processes, suggesting the noticeable functions of salt-associated lncRNAs in regulating salt responses of Avicennia marina leaves.
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Affiliation(s)
- Lingling Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
| | - Yixuan Fu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Zixin Yuan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Jingyi Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Yali Guan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571158, China.
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Wang L, Yuan Z, Wang J, Guan Y. Genome-wide identification and functional profile analysis of long non-coding RNAs in Avicennia marina. THE PLANT GENOME 2024; 17:e20450. [PMID: 38600855 DOI: 10.1002/tpg2.20450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/29/2024] [Accepted: 03/15/2024] [Indexed: 04/12/2024]
Abstract
Avicennia marina, known for its remarkable adaptability to the challenging coastal environment, including high salinity, tide, and anaerobic soils, holds pivotal functions in safeguarding the coastal ecosystem. Long non-coding RNAs (lncRNAs) have emerged as significant players in various natural processes of plants such as development. However, lncRNAs in A. marina remain largely unknown and uncharacterized. Here, we employed the transcriptome datasets from multiple tissues, such as root, leaf, and seed, to detect and characterize the lncRNAs of A. marina. Analyzing synthetically, we finally identified 6333 lncRNAs in the A. marina. These lncRNAs exhibited distinct features compared to messenger RNAs, including larger exons, lower guanine-cytosine contents, lower expression levels, and higher tissue specificities. Moreover, we identified thousands of tissue-specific lncRNAs across the examined tissues and further found that these tissue-specific lncRNAs were significantly enriched in biological processes related to the major functions of their corresponding tissues. For instance, leaf-specific lncRNAs showed prominent enrichment in photosynthesis, oxidation-reduction processes, and light harvesting. By providing a comprehensive dataset and functional annotations for A. marina lncRNAs, this study offers a valuable overview of lncRNAs in A. marina and lays the fundamental foundation for further functional exploring of them.
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Affiliation(s)
- Lingling Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Zixin Yuan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jingyi Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yali Guan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, China
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4
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Yu L, Wan Q, Liu Q, Fan Y, Zhou Q, Skowronski AA, Wang S, Shao Z, Liao CY, Ding L, Kennedy BK, Zha S, Que J, LeDuc CA, Sun L, Wang L, Qiang L. IgG is an aging factor that drives adipose tissue fibrosis and metabolic decline. Cell Metab 2024; 36:793-807.e5. [PMID: 38378001 PMCID: PMC11070064 DOI: 10.1016/j.cmet.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 10/31/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Aging is underpinned by pronounced metabolic decline; however, the drivers remain obscure. Here, we report that IgG accumulates during aging, particularly in white adipose tissue (WAT), to impair adipose tissue function and metabolic health. Caloric restriction (CR) decreases IgG accumulation in WAT, whereas replenishing IgG counteracts CR's metabolic benefits. IgG activates macrophages via Ras signaling and consequently induces fibrosis in WAT through the TGF-β/SMAD pathway. Consistently, B cell null mice are protected from aging-associated WAT fibrosis, inflammation, and insulin resistance, unless exposed to IgG. Conditional ablation of the IgG recycling receptor, neonatal Fc receptor (FcRn), in macrophages prevents IgG accumulation in aging, resulting in prolonged healthspan and lifespan. Further, targeting FcRn by antisense oligonucleotide restores WAT integrity and metabolic health in aged mice. These findings pinpoint IgG as a hidden culprit in aging and enlighten a novel strategy to rejuvenate metabolic health.
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Affiliation(s)
- Lexiang Yu
- Naomi Berrie Diabetes Center, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Qianfen Wan
- Naomi Berrie Diabetes Center, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Qiongming Liu
- Naomi Berrie Diabetes Center, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Yong Fan
- Naomi Berrie Diabetes Center, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Qiuzhong Zhou
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
| | - Alicja A Skowronski
- Naomi Berrie Diabetes Center, Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Summer Wang
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Zhengping Shao
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Chen-Yu Liao
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Lei Ding
- Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Brian K Kennedy
- Buck Institute for Research on Aging, Novato, CA 94945, USA; Healthy Longevity Translational Research Programme, Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Centre for Health Longevity, National University Health System, Singapore, Singapore
| | - Shan Zha
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Jianwen Que
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Charles A LeDuc
- Naomi Berrie Diabetes Center, Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
| | - Liheng Wang
- Institute of Cardiovascular Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Department of Medicine, Division of Endocrinology, Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Li Qiang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; Naomi Berrie Diabetes Center, Department of Medicine, Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA.
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Hyeon J, Lee J, Kim E, Lee HM, Kim KP, Shin J, Park HS, Lee YI, Nam CH. Vutiglabridin exerts anti-ageing effects in aged mice through alleviating age-related metabolic dysfunctions. Exp Gerontol 2023; 181:112269. [PMID: 37567452 DOI: 10.1016/j.exger.2023.112269] [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: 03/31/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND Ageing alters the ECM, leading to mitochondrial dysfunction and oxidative stress, which triggers an inflammatory response that exacerbates with age. Age-related changes impact satellite cells, affecting muscle regeneration, and the balance of proteins. Furthermore, ageing causes a decline in NAD+ levels, and alterations in fat metabolism that impact our health. These various metabolic issues become intricately intertwined with ageing, leading to a variety of individual-level diseases and profoundly affecting individuals' healthspan. Therefore, we hypothesize that vutiglabridin capable of alleviating these metabolic abnormalities will be able to ameliorate many of the problems associated with ageing. METHOD The efficacy of vutiglabridin, which alleviates metabolic issues by enhancing mitochondrial function, was assessed in aged mice treated with vutiglabridin and compared to untreated elderly mice. On young mice, vutiglabridin-treated aged mice, and non-treated aged mice, the Senescence-associated beta-galactosidase staining and q-PCR for ageing marker genes were carried out. Bulk RNA-seq was carried out on GA muscle, eWAT, and liver from each group of mice to compare differences in gene expression in various gene pathways. Blood from each group of mice was used to compare and analyze the ageing lipid profile. RESULTS SA-β-gal staining of eWAT, liver, kidney, and spleen of ageing mice showed that vutiglabridin had anti-ageing effects compared to the control group, and q-PCR of ageing marker genes including Cdkn1a and Cdkn2a in each tissue showed that vutiglabridin reduced the ageing process. In aged mice treated with vutiglabridin, GA muscle showed improved homeostasis compared to controls, eWAT showed restored insulin sensitivity and prevented FALC-induced inflammation, and liver showed reduced inflammation levels due to prevented TLO formation, improved mitochondrial complex I assembly, resulting in reduced ROS formation. Furthermore, blood lipid analysis revealed that ageing-related lipid profile was relieved in ageing mice treated with vutiglabridin versus the control group. CONCLUSION Vutiglabridin slows metabolic ageing mechanisms such as decreased insulin sensitivity, increased inflammation, and altered NAD+ metabolism in adipose tissue in mice experiments, while also retaining muscle homeostasis, which is deteriorated with age. It also improves the lipid profile in the blood and restores mitochondrial function in the liver to reduce ROS generation.
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Affiliation(s)
- Jooseung Hyeon
- Aging and Immunity Laboratory, Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
| | - Jihan Lee
- Aging and Immunity Laboratory, Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
| | - Eunju Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea; Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea
| | - Hyeong Min Lee
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea; Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea; Glaceum Incorporation, Research Department, Suwon, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea; Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea
| | - Jaejin Shin
- Glaceum Incorporation, Research Department, Suwon, Republic of Korea
| | - Hyung Soon Park
- Glaceum Incorporation, Research Department, Suwon, Republic of Korea
| | - Yun-Il Lee
- Well Aging Research Center, Division of Biotechnology, Department of Interdisciplinary Studies, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Chang-Hoon Nam
- Aging and Immunity Laboratory, Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea.
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Liu M, Feng J. Association between adiposity and facial aging: results from a Mendelian randomization study. Eur J Med Res 2023; 28:350. [PMID: 37715292 PMCID: PMC10503104 DOI: 10.1186/s40001-023-01236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/16/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Skin, as a sociologically meaningful interface, has psychological implications different from other organs, particularly in the context of the global population aging. Growing evidence suggests that facial aging is associated with an increased risk of adiposity. Existing research, however, were observational, and while they may find some correlations, it is difficult to simply disentangle non-causal or reverse-causal links because these associations may be confounded or fail to accurately reflect true causative linkages. OBJECTIVES We conducted a 2-sample Mendelian randomization (MR) study to examine the potential effect of facial aging on the risk of broad obesity and its three major adiposity indicators, including body mass index (BMI), body fat percentage (BF%) and waist circumference (WC). METHODS Genetic instruments from IEU OpenGWAS project, one of the largest available genome-wide association studies (GWAS) for facial aging (423,999 samples) were used to investigate the relation to broad obesity (32,858 cases, 65,839 controls). Using the inverse-variance weighted (IVW) technique, single nucleotide polymorphisms (SNPs) associated with adiposity indicators (BMI (461,460 samples), BF% (454,633 samples), and WC (462,166 samples)) were investigated in relationship to facial aging. Further sensitivity analyses were performed, including Mendelian randomization-Egger (MR-Egger), weighted median estimates, and leave-one-out analysis, to evaluate the consistency of the results and related potential issues in MR studies. RESULTS We identified strong and significant correlations between adiposity and facial aging in the 17 broad obesity-associated SNPs (IVW estimate of odds ratio OR = 1.020, 95% CI 1.010-1.029, P = 7.303e - 05), 458 BMI-associated SNPs (IVW estimate of odds ratio OR = 1.047, 95% CI 1.0357-1.058, P = 1.154e - 16),for the 395 BF%-associated SNPs (OR = 1.056, 95%CI 1.040-1.072,P = 7.617e - 12), or for the 374 WC-associated SNPs (OR = 1.072, 95% CI 1057-1.087,P = 1.229e - 23). A range of complementary methodologies have been employed to evaluate horizontal pleiotropy and related potential caveats occurring in MR research. CONCLUSIONS Using Mendelian randomization as an alternative approach to investigate causality, we found a causal relationship between adiposity and facial aging, which was statistically strong and significant.
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Affiliation(s)
- Meiqi Liu
- Department of Plastic and Cosmetic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jingwei Feng
- Department of Plastic and Cosmetic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, Guangdong, People's Republic of China.
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Zhou Q, Yu L, Cook JR, Qiang L, Sun L. Deciphering the decline of metabolic elasticity in aging and obesity. Cell Metab 2023; 35:1661-1671.e6. [PMID: 37625407 PMCID: PMC10528724 DOI: 10.1016/j.cmet.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 05/04/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023]
Abstract
Organisms must adapt to fluctuating nutrient availability to maintain energy homeostasis. Here, we term the capacity for such adaptation and restoration "metabolic elasticity" and model it through ad libitum-fasting-refeeding cycles. Metabolic elasticity is achieved by coordinate versatility in gene expression, which we call "gene elasticity." We have developed the gene elasticity score as a systematic method to quantify the elasticity of the transcriptome across metabolically active tissues in mice and non-human primates. Genes involved in lipid and carbohydrate metabolism show high gene elasticity, and their elasticity declines with age, particularly with PPARγ dysregulation in adipose tissue. Synchronizing PPARγ activity with nutrient conditions through feeding-timed agonism optimizes their metabolic benefits and safety. We further broaden the conceptual scope of metabolic and gene elasticity to dietary challenges, revealing declines in diet-induced obesity similar to those in aging. Altogether, our findings provide a dynamic perspective on the dysmetabolic consequences of aging and obesity.
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Affiliation(s)
- Qiuzhong Zhou
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
| | - Lexiang Yu
- Naomi Berrie Diabetes Center and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA; Department of Medicine, Columbia University, New York, NY, USA
| | - Joshua R Cook
- Department of Medicine, Columbia University, New York, NY, USA
| | - Li Qiang
- Naomi Berrie Diabetes Center and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA; Department of Medicine, Columbia University, New York, NY, USA.
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore.
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Liu HJ, Miao H, Yang JZ, Liu F, Cao G, Zhao YY. Deciphering the role of lipoproteins and lipid metabolic alterations in ageing and ageing-associated renal fibrosis. Ageing Res Rev 2023; 85:101861. [PMID: 36693450 DOI: 10.1016/j.arr.2023.101861] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/07/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
Fibrosis is the ultimate pathological feature of many chronic diseases, and ageing a major risk factor for fibrotic diseases. Current therapies are limited to those that reduce the rate of functional decline in patients with mild to moderate disease, but few interventions are available to specifically target the pathogenesis of fibrosis. In this context, new treatments that can significantly improve survival time and quality of life for these patients are urgently needed. In this review, we outline both the synthesis and metabolism of lipids and lipoproteins associated with ageing-associated renal fibrosis and the prominent contribution of lipids and lipidomics in the discovery of biomarkers that can be used for the prevention, diagnosis, and treatment of renal ageing and fibrosis. Next, we describe the effect of dyslipidaemia on ageing-related renal fibrosis and the pathophysiological changes in the kidney caused by dyslipidaemia. We then summarize the enzymes, transporters, transcription factors, and RNAs that contribute to dysregulated lipid metabolism in renal fibrosis and discuss their role in renal fibrosis in detail. We conclude by discussing the progress in research on small molecule therapeutic agents that prevent and treat ageing and ageing-associated renal fibrosis by modulating lipid metabolism. A growing number of studies suggest that restoring aberrant lipid metabolism may be a novel and promising therapeutic strategy to combat ageing and ageing-associated renal fibrosis.
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Affiliation(s)
- Hong-Jiao Liu
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China
| | - Hua Miao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China
| | - Jun-Zheng Yang
- Guangdong Nephrotic Drug Engineering Technology Research Center, Institute of Consun Co. for Chinese Medicine in Kidney Diseases, Guangdong Consun Pharmaceutical Group, No. 71 Dongpeng Avenue, Guangzhou, Guangdong 510530, China
| | - Fei Liu
- Department of Urology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 South of Panjiayuan, Beijing 100021, China.
| | - Gang Cao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China.
| | - Ying-Yong Zhao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China.
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Winsky-Sommerer R, King HA, Iadevaia V, Möller-Levet C, Gerber AP. A post-transcriptional regulatory landscape of aging in the female mouse hippocampus. Front Aging Neurosci 2023; 15:1119873. [PMID: 37122377 PMCID: PMC10135431 DOI: 10.3389/fnagi.2023.1119873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2023] Open
Abstract
Aging is associated with substantial physiological changes and constitutes a major risk factor for neurological disorders including dementia. Alterations in gene expression upon aging have been extensively studied; however, an in-depth characterization of post-transcriptional regulatory events remains elusive. Here, we profiled the age-related changes of the transcriptome and translatome in the female mouse hippocampus by RNA sequencing of total RNA and polysome preparations at four ages (3-, 6-, 12-, 20-month-old); and we implemented a variety of bioinformatics approaches to unravel alterations in transcript abundance, alternative splicing, and polyadenylation site selection. We observed mostly well-coordinated transcriptome and translatome expression signatures across age including upregulation of transcripts related to immune system processes and neuroinflammation, though transcripts encoding ribonucleoproteins or associated with mitochondrial functions, calcium signaling and the cell-cycle displayed substantial discordant profiles, suggesting translational control associated with age-related deficits in hippocampal-dependent behavior. By contrast, alternative splicing was less preserved, increased with age and was associated with distinct functionally-related transcripts encoding proteins acting at synapses/dendrites, RNA-binding proteins; thereby predicting regulatory roles for RBM3 and CIRBP. Only minor changes in polyadenylation site selection were identified, indicating pivotal 3'-end selection in young adults compared to older groups. Overall, our study provides a comprehensive resource of age-associated post-transcriptional regulatory events in the mouse hippocampus, enabling further examination of the molecular features underlying age-associated neurological diseases.
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10
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Yang W, Lyu Y, Xiang R, Yang J. Long Noncoding RNAs in the Pathogenesis of Insulin Resistance. Int J Mol Sci 2022; 23:ijms232416054. [PMID: 36555704 PMCID: PMC9785789 DOI: 10.3390/ijms232416054] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Insulin resistance (IR), designated as the blunted response of insulin target tissues to physiological level of insulin, plays crucial roles in the development and progression of diabetes, nonalcoholic fatty liver disease (NAFLD) and other diseases. So far, the distinct mechanism(s) of IR still needs further exploration. Long non-coding RNA (lncRNA) is a class of non-protein coding RNA molecules with a length greater than 200 nucleotides. LncRNAs are widely involved in many biological processes including cell differentiation, proliferation, apoptosis and metabolism. More recently, there has been increasing evidence that lncRNAs participated in the pathogenesis of IR, and the dysregulated lncRNA profile played important roles in the pathogenesis of metabolic diseases including obesity, diabetes and NAFLD. For example, the lncRNAs MEG3, H19, MALAT1, GAS5, lncSHGL and several other lncRNAs have been shown to regulate insulin signaling and glucose/lipid metabolism in various tissues. In this review, we briefly introduced the general features of lncRNA and the methods for lncRNA research, and then summarized and discussed the recent advances on the roles and mechanisms of lncRNAs in IR, particularly focused on liver, skeletal muscle and adipose tissues.
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Affiliation(s)
- Weili Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yixiang Lyu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Rui Xiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Jichun Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
- Correspondence:
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Wang L, Wang J, Chen H, Hu B. Genome-wide identification, characterization, and functional analysis of lncRNAs in Hevea brasiliensis. FRONTIERS IN PLANT SCIENCE 2022; 13:1012576. [PMID: 36275565 PMCID: PMC9581277 DOI: 10.3389/fpls.2022.1012576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Natural rubber (NR) is an essential industrial raw material widely used in our life. Hevea brasiliensis (Reyan7-33-97) is an economic plant producing natural rubber. Long non-coding RNAs (lncRNAs) are emerging as crucial regulators in numerous biological processes while the characterization and analysis of lncRNAs in Hevea brasiliensis are still largely unrevealed. We integrated the transcriptome datasets from multiple tissues to identify rubber lncRNAs. As a result, 12,029 lncRNAs were found and characterized with notably distinctive features such as longer exon, lower expression levels and GC content, and more tissue specificity in comparison with mRNAs. We discovered thousands of tissue-specific lncRNAs in rubber root, latex, bark, leaf, flower, and seed tissues. The functional enrichment result reveals that tissue-specific lncRNAs are potentially referred to particular functions of tissues, while the non-tissue specific is related to the translation and metabolic processes. In the present study, a comprehensive lncRNA dataset was identified and its functional profile in Hevea brasiliensis was explored, which provides an annotation resource and important clues to understand the biological functions of lncRNAs in Hevea brasiliensis.
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Affiliation(s)
- Lingling Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jingyi Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Hui Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Bin Hu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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12
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Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development. Int J Mol Sci 2022; 23:ijms231911547. [PMID: 36232849 PMCID: PMC9569805 DOI: 10.3390/ijms231911547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.
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13
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Liu J, Chen S, Liu M, Chen Y, Fan W, Lee S, Xiao H, Kudrna D, Li Z, Chen X, Peng Y, Tian K, Zhang B, Wing RA, Zhang J, Wang X. Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max. Int J Mol Sci 2022; 23:7371. [PMID: 35806374 PMCID: PMC9266934 DOI: 10.3390/ijms23137371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/25/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Alternative splicing (AS) is a ubiquitous phenomenon among eukaryotic intron-containing genes, which greatly contributes to transcriptome and proteome diversity. Here we performed the isoform sequencing (Iso-Seq) of soybean underground tissues inoculated and uninoculated with Rhizobium and obtained 200,681 full-length transcripts covering 26,183 gene loci. It was found that 80.78% of the multi-exon loci produced more than one splicing variant. Comprehensive analysis of these identified 7874 differentially splicing events with highly diverse splicing patterns during nodule development, especially in defense and transport-related processes. We further profiled genes with differential isoform usage and revealed that 2008 multi-isoform loci underwent stage-specific or simultaneous major isoform switches after Rhizobium inoculation, indicating that AS is a vital way to regulate nodule development. Moreover, we took the lead in identifying 1563 high-confidence long non-coding RNAs (lncRNAs) in soybean, and 157 of them are differentially expressed during nodule development. Therefore, our study uncovers the landscape of AS during the soybean-Rhizobium interaction and provides systematic transcriptomic data for future study of multiple novel directions in soybean.
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Affiliation(s)
- Jing Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Shengcai Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Min Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
| | - Yimian Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Wei Fan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Han Xiao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Zixin Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
| | - Xu Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Yaqi Peng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Kewei Tian
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Bao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Rod A. Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
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Jusic A, Thomas PB, Wettinger SB, Dogan S, Farrugia R, Gaetano C, Tuna BG, Pinet F, Robinson EL, Tual-Chalot S, Stellos K, Devaux Y. Noncoding RNAs in age-related cardiovascular diseases. Ageing Res Rev 2022; 77:101610. [PMID: 35338919 DOI: 10.1016/j.arr.2022.101610] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/28/2022] [Accepted: 03/15/2022] [Indexed: 11/01/2022]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality in the adult population worldwide and represent a severe economic burden and public health concern. The majority of human genes do not code for proteins. However, noncoding transcripts play important roles in ageing that significantly increases the risk for CVDs. Noncoding RNAs (ncRNAs) are critical regulators of multiple biological processes related to ageing such as oxidative stress, mitochondrial dysfunction and chronic inflammation. NcRNAs are also involved in pathophysiological developments within the cardiovascular system including arrhythmias, cardiac hypertrophy, fibrosis, myocardial infarction and heart failure. In this review article, we cover the roles of ncRNAs in cardiovascular ageing and disease as well as their potential therapeutic applications in CVDs.
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15
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Navarro-Corcuera A, Sehrawat TS, Jalan-Sakrikar N, Gibbons HR, Pirius NE, Khanal S, Hamdan FH, Aseem SO, Cao S, Banales JM, Kang N, Faubion WA, LaRusso NF, Shah VH, Huebert RC. Long non-coding RNA ACTA2-AS1 promotes ductular reaction by interacting with the p300/ELK1 complex. J Hepatol 2022; 76:921-933. [PMID: 34953958 PMCID: PMC8934273 DOI: 10.1016/j.jhep.2021.12.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 11/01/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Biliary disease is associated with a proliferative/fibrogenic ductular reaction (DR). p300 is an epigenetic regulator that acetylates lysine 27 on histone 3 (H3K27ac) and is activated during fibrosis. Long non-coding RNAs (lncRNAs) are aberrantly expressed in cholangiopathies, but little is known about how they recruit epigenetic complexes and regulate DR. We investigated epigenetic complexes, including transcription factors (TFs) and lncRNAs, contributing to p300-mediated transcription during fibrosis. METHODS We evaluated p300 in vivo using tamoxifen-inducible, cholangiocyte-selective, p300 knockout (KO) coupled with bile duct ligation (BDL) and Mdr KO mice treated with SGC-CBP30. Primary cholangiocytes and liver tissue were analyzed for expression of Acta2-as1 lncRNA by qPCR and RNA in situ hybridization. In vitro, we performed RNA-sequencing in human cholangiocytes with a p300 inhibitor. Cholangiocytes were exposed to lipopolysaccharide (LPS) as an injury model. We confirmed formation of a p300/ELK1 complex by immunoprecipitation (IP). RNA IP was used to examine interactions between ACTA2-AS1 and p300. Chromatin IP assays were used to evaluate p300/ELK1 occupancy and p300-mediated H3K27ac. Organoids were generated from ACTA2-AS1-depleted cholangiocytes. RESULTS BDL-induced DR and fibrosis were reduced in Krt19-CreERT/p300fl/fl mice. Similarly, Mdr KO mice were protected from DR and fibrosis after SGC-CBP30 treatment. In vitro, depletion of ACTA2-AS1 reduced expression of proliferative/fibrogenic markers, reduced LPS-induced cholangiocyte proliferation, and impaired organoid formation. ACTA2-AS1 regulated transcription by facilitating p300/ELK1 binding to the PDGFB promoter after LPS exposure. Correspondingly, LPS-induced H3K27ac was mediated by p300/ELK1 and was reduced in ACTA2-AS1-depleted cholangiocytes. CONCLUSION Cholangiocyte-selective p300 KO or p300 inhibition attenuate DR/fibrosis in mice. ACTA2-AS1 influences recruitment of p300/ELK1 to specific promoters to drive H3K27ac and epigenetic activation of proliferative/fibrogenic genes. This suggests that cooperation between epigenetic co-activators and lncRNAs facilitates DR/fibrosis in biliary diseases. LAY SUMMARY We identified a three-part complex containing an RNA molecule, a transcription factor, and an epigenetic enzyme. The complex is active in injured bile duct cells and contributes to activation of genes involved in proliferation and fibrosis.
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Affiliation(s)
- Amaia Navarro-Corcuera
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Tejasav S Sehrawat
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Nidhi Jalan-Sakrikar
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Nicholas E Pirius
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States
| | - Shalil Khanal
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Sayed Obaidullah Aseem
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Sheng Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Ningling Kang
- The Hormel Institute, University of Minnesota, Austin, MN, United States
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Nicholas F LaRusso
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States
| | - Vijay H Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States
| | - Robert C Huebert
- Division of Gastroenterology and Hepatology, Mayo Clinic and Foundation, Rochester, MN, United States; Gastroenterology Research Unit; Mayo Clinic and Foundation, Rochester, MN, United States.
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16
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Gupta A, Shamsi F, Altemose N, Dorlhiac GF, Cypess AM, White AP, Yosef N, Patti ME, Tseng YH, Streets A. Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages. Genome Res 2022; 32:242-257. [PMID: 35042723 PMCID: PMC8805720 DOI: 10.1101/gr.275509.121] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 12/10/2021] [Indexed: 02/02/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) enables molecular characterization of complex biological tissues at high resolution. The requirement of single-cell extraction, however, makes it challenging for profiling tissues such as adipose tissue, for which collection of intact single adipocytes is complicated by their fragile nature. For such tissues, single-nucleus extraction is often much more efficient and therefore single-nucleus RNA sequencing (snRNA-seq) presents an alternative to scRNA-seq. However, nuclear transcripts represent only a fraction of the transcriptome in a single cell, with snRNA-seq marked with inherent transcript enrichment and detection biases. Therefore, snRNA-seq may be inadequate for mapping important transcriptional signatures in adipose tissue. In this study, we compare the transcriptomic landscape of single nuclei isolated from preadipocytes and mature adipocytes across human white and brown adipocyte lineages, with whole-cell transcriptome. We show that snRNA-seq is capable of identifying the broad cell types present in scRNA-seq at all states of adipogenesis. However, we also explore how and why the nuclear transcriptome is biased and limited, as well as how it can be advantageous. We robustly characterize the enrichment of nuclear-localized transcripts and adipogenic regulatory lncRNAs in snRNA-seq, while also providing a detailed understanding for the preferential detection of long genes upon using this technique. To remove such technical detection biases, we propose a normalization strategy for a more accurate comparison of nuclear and cellular data. Finally, we show successful integration of scRNA-seq and snRNA-seq data sets with existing bioinformatic tools. Overall, our results illustrate the applicability of snRNA-seq for the characterization of cellular diversity in the adipose tissue.
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Affiliation(s)
- Anushka Gupta
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
| | - Farnaz Shamsi
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicolas Altemose
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
| | - Gabriel F Dorlhiac
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, USA
| | - Aaron M Cypess
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andrew P White
- Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, California 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California at Berkeley, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA
| | | | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Aaron Streets
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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17
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Nwadiugwu M. RNA-seq analysis of phagocytic cells from murine epididymal white adipose tissue shows immunosenescence and age-related phosphorus metabolism. Hum Cell 2022; 35:572-582. [PMID: 35032296 DOI: 10.1007/s13577-021-00663-4] [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: 11/02/2021] [Accepted: 12/15/2021] [Indexed: 12/01/2022]
Abstract
The underlying state of alterations in adipose tissue is hypothesized to be as a result of age-related changes. Young and aged mice have been documented to show distinct gene expression and distinct macrophage-specific adipose tissue regulation. However, more biological understanding is required to know the processes associated with these conditions in relation to the aging process. Transcriptional profiling with RNA-seq analysis was used to determine differentially expressed genes in young (2 months old) and aged (20 months old) mice macrophage-enriched phagocytic stromal vascular fractions of pooled epididymal white adipose tissue using data obtained from gene expression omnibus. Results showed distinct differentially expressed genes in young and aged mice with a p value cutoff of 0.05 and dissimilarities in the young and aged epididymal white adipose tissue phagocytic cells. Functional enrichment showed activation of cytokine-cytokine receptor interaction pathways, phosphorus metabolic processes and inflammatory pathways such as IL-17, TNF, NF-kappa B, and TGF-β, while AMPK, PPAR and oxidative phosphorylation were suppressed. The analysis showed that aging is linked with phagocytic cell decline, accumulated cellular damages, inflammation, immunosenescence and increased phosphorus metabolism. Interventions that reduce phosphate-containing compound could improve phosphorus metabolism in old age to prolong lifespan and better health.
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Affiliation(s)
- Martin Nwadiugwu
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA.
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18
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Abstract
Biology of aging is an active and rapidly expanding area of biomedical research. Over the years, focus of work in this field has been gradually shifting from studying the effects and symptoms of aging to searching for mechanisms of the aging process. Progress of this work led to an additional shift from looking for “the mechanism” of aging and formulating the corresponding “theories of aging” to appreciation that aging represents a net result of multiple physiological changes and their intricate interactions. It was also shown that mechanisms of aging include nutrient-dependent signaling pathways which have been remarkably conserved in the course of the evolution. Another important development in this field is increased emphasis on searching for pharmacological and environmental interventions that can extend healthspan or influence other aspects of aging. Progress in understanding the key role of aging as a risk factor for chronic disease provides impetus for these studies. Data from the recent pandemic provided additional evidence for the impact of age on resilience. Progress of work in this area also was influenced by major analytical and technological advances, including greatly improved methods for the study of gene expression, protein, lipids, and metabolites profiles, enhanced ability to produce various genetic modifications and novel approaches to assessment of biological age. Progress in research on the biology of aging provides reasons for optimism about the chances that safe and widely applicable anti-aging interventions with significant benefits for both individual and public health will be developed in the not too distant future.
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Affiliation(s)
- Andrzej Bartke
- Department of Internal Medicine, Southern Illinois University School of Medicine, 801 N. Rutledge St., P. O. Box 19628, Springfield, IL, 62794-9628, USA.
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19
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Ferreira M, Francisco S, Soares AR, Nobre A, Pinheiro M, Reis A, Neto S, Rodrigues AJ, Sousa N, Moura G, Santos MAS. Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues. Aging (Albany NY) 2021; 13:18150-18190. [PMID: 34330884 PMCID: PMC8351669 DOI: 10.18632/aging.203379] [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: 02/19/2021] [Accepted: 07/21/2021] [Indexed: 02/06/2023]
Abstract
Gene expression alterations occurring with aging have been described for a multitude of species, organs, and cell types. However, most of the underlying studies rely on static comparisons of mean gene expression levels between age groups and do not account for the dynamics of gene expression throughout the lifespan. These studies also tend to disregard the pairwise relationships between gene expression profiles, which may underlie commonly altered pathways and regulatory mechanisms with age. To overcome these limitations, we have combined segmented regression analysis with weighted gene correlation network analysis (WGCNA) to identify high-confidence signatures of aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice in a publicly available RNA-Seq dataset (GSE132040). Functional enrichment analysis of the overlap of genes identified in both approaches showed that immune- and inflammation-related responses are prominently altered in the brain and the liver, while in the heart and the muscle, aging affects amino and fatty acid metabolism, and tissue regeneration, respectively, which reflects an age-related global loss of tissue function. We also explored sexual dimorphism in the aging mouse transcriptome and found the liver and the muscle to have the most pronounced gender differences in gene expression throughout the lifespan, particularly in proteostasis-related pathways. While the data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, which we highlight as important features of murine tissue physiological aging.
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Affiliation(s)
- Margarida Ferreira
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Stephany Francisco
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana R. Soares
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana Nobre
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Andreia Reis
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Sonya Neto
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana João Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Gabriela Moura
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Manuel A. S. Santos
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
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20
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Lu X, Zhou Q, Liu J, Sun L. Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging. STAR Protoc 2021; 2:100397. [PMID: 33786463 PMCID: PMC7994534 DOI: 10.1016/j.xpro.2021.100397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Comprehensive analyses of lncRNAs in aging have been lacking because previous studies have mainly focused on the protein-coding genes during aging. Here, we describe a protocol for the organism-wide analysis of murine lncRNAs during aging. We provide step-by-step instructions to identify lncRNAs that contribute to aging and to determine their underlying functions in each tissue. We further describe methods to compare the lncRNA expression patterns and dynamic changes among multiple tissues. For complete details on the use and execution of this protocol, please refer to Zhou et al. (2020).
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Affiliation(s)
- Xinyue Lu
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Qiuzhong Zhou
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jin Liu
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore 169857, Singapore
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21
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Ma W, Liu Y, Ma H, Ren Z, Yan J. Cis-acting: A pattern of lncRNAs for gene regulation in induced pluripotent stem cells from patients with Down syndrome determined by integrative analysis of lncRNA and mRNA profiling data. Exp Ther Med 2021; 22:701. [PMID: 34007310 PMCID: PMC8120638 DOI: 10.3892/etm.2021.10133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
Down syndrome (DS), caused by the trisomy of chromosome 21, is one of the common chromosomal disorders, the main clinical manifestations of which are delayed nervous development and intellectual disability. Long non-coding RNAs (lncRNAs) have critical roles in various biological processes, including cell growth, cell cycle regulation and differentiation. The roles of abnormally expressed lncRNAs have been previously reported; however, the biological functions and regulatory patterns of lncRNAs in DS have remained largely elusive. The aim of the present study was to perform a whole-genome-wide identification of lncRNAs and mRNAs associated with DS. In addition, global expression profiling analysis of DS-induced pluripotent stem cells was performed and differentially expressed (DE) lncRNAs and mRNAs were screened. Furthermore, the target genes and functions of the DE lncRNAs were predicted using Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analysis. The results revealed that the majority of the lncRNAs exerted functions in DS via cis-acting target genes. In addition, the results of the enrichment analysis indicated that these target genes were mainly involved in nervous and muscle development in DS. In conclusion, this integrative analysis using lncRNA and mRNA profiling provided novel insight into the pathogenesis of DS and it may promote the diagnosis and development of novel therapeutics for this disease.
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Affiliation(s)
- Wenbo Ma
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, P.R. China
| | - Yanna Liu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, P.R. China
| | - Houshi Ma
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, P.R. China
| | - Zhaorui Ren
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, P.R. China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, P.R. China
| | - Jingbin Yan
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, P.R. China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, P.R. China
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22
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Kim S, Kim C. Transcriptomic Analysis of Cellular Senescence: One Step Closer to Senescence Atlas. Mol Cells 2021; 44:136-145. [PMID: 33795532 PMCID: PMC8019598 DOI: 10.14348/molcells.2021.2239] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 12/19/2022] Open
Abstract
Senescent cells that gradually accumulate during aging are one of the leading causes of aging. While senolytics can improve aging in humans as well as mice by specifically eliminating senescent cells, the effect of the senolytics varies in different cell types, suggesting variations in senescence. Various factors can induce cellular senescence, and the rate of accumulation of senescent cells differ depending on the organ. In addition, since the heterogeneity is due to the spatiotemporal context of senescent cells, in vivo studies are needed to increase the understanding of senescent cells. Since current methods are often unable to distinguish senescent cells from other cells, efforts are being made to find markers commonly expressed in senescent cells using bulk RNA-sequencing. Moreover, single-cell RNA (scRNA) sequencing, which analyzes the transcripts of each cell, has been utilized to understand the in vivo characteristics of the rare senescent cells. Recently, transcriptomic cell atlases for each organ using this technology have been published in various species. Novel senescent cells that do not express previously established marker genes have been discovered in some organs. However, there is still insufficient information on senescent cells due to the limited throughput of the scRNA sequencing technology. Therefore, it is necessary to improve the throughput of the scRNA sequencing technology or develop a way to enrich the rare senescent cells. The in vivo senescent cell atlas that is established using rapidly developing single-cell technologies will contribute to the precise rejuvenation by specifically removing senescent cells in each tissue and individual.
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Affiliation(s)
- Sohee Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Chuna Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
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23
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Yang J, Shi BY. Dickkopf (Dkk)-2 is a beige fat-enriched adipokine to regulate adipogenesis. Biochem Biophys Res Commun 2021; 548:211-216. [PMID: 33647798 DOI: 10.1016/j.bbrc.2021.02.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 02/16/2021] [Indexed: 01/15/2023]
Abstract
In the past decades, remarkable efforts have been made to unravel the regulation of adipose tissue metabolism, given the increasing prevalence of obesity and its huge impact on human health. Wnt signaling pathway is closely involved in this entity. As extracellular inhibitors to Wnt signaling, secreted protein Dickkopfs (Dkks) may be potential targets to combat obesity and related metabolic disorders. In this study, we showed that Dkk2 was a beige fat-enriched adipokine to regulate adipogenesis. Dkk2 was strikingly expressed in beige fat depot compared to classic white, brown, and subcutaneous fat. Dkk2 treatment inhibited adipogenesis in 3T3-L1 pre-adipocytes, C3H10T1/2 mesenchymal stem cells, and primary bone marrow mesenchymal stromal cells. Activation of the master adipogenic factor PPARγ by the synthetic Thiazolidinedione ligand rosiglitazone largely rescued the inhibition of adipogenesis by Dkk2. Furthermore, adenoviral overexpression of Dkk2 in the liver to mimic its gain-of-function showed minimal effect on whole-body metabolism. These results collectively suggest that Dkk2 is a first-in-class beige fat adipokine and functions mainly through a paracrine manner to inhibit adipogenesis rather than as an endocrine factor. Our findings aid a better understanding of beige fat function and regulation and further, provide a potential therapeutic target for treating obesity.
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Affiliation(s)
- Jing Yang
- The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta Western Road, Xi'an, Shaanxi, 710061, PR China
| | - Bing-Yin Shi
- Department of Endocrinology, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta Western Road, Xi'an, Shaanxi, 710061, PR China.
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24
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Wang YN, Yang CE, Zhang DD, Chen YY, Yu XY, Zhao YY, Miao H. Long non-coding RNAs: A double-edged sword in aging kidney and renal disease. Chem Biol Interact 2021; 337:109396. [PMID: 33508306 DOI: 10.1016/j.cbi.2021.109396] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/18/2020] [Accepted: 01/22/2021] [Indexed: 01/23/2023]
Abstract
Aging as one of intrinsic biological processes is a risk factor for many chronic diseases. Kidney disease is a global problem and health care burden worldwide. The diagnosis of kidney disease is currently based on serum creatinine and urea levels. Novel biomarkers may improve diagnostic accuracy, thereby allowing early prevention and treatment. Over the past few years, advances in genome analyses have identified an emerging class of noncoding RNAs that play critical roles in the regulation of gene expression and epigenetic reprogramming. Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome and could bind DNA, RNA and protein. Emerging evidence has demonstrated that lncRNAs played an important role in all stages of kidney disease. To date, only some lncRNAs were well identified and characterized, but the complexity of multilevel regulation of transcriptional programs involved in these processes remains undefined. In this review, we summarized the lncRNA expression profiling of large-scale identified lncRNAs on kidney diseases including acute kidney injury, chronic kidney disease, diabetic nephropathy and kidney transplantation. We further discussed a number of annotated lncRNAs linking with complex etiology of kidney diseases. Finally, several lncRNAs were highlighted as diagnostic biomarkers and therapeutic targets. Targeting lncRNAs may represent a precise therapeutic strategy for progressive renal fibrosis.
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Affiliation(s)
- Yan-Ni Wang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Chang-E Yang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Dan-Dan Zhang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Yuan-Yuan Chen
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Xiao-Yong Yu
- Department of Nephrology, Shaanxi Traditional Chinese Medicine Hospital, No. 2 Xihuamen, Xi'an, Shaanxi, 710003, China.
| | - Ying-Yong Zhao
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China.
| | - Hua Miao
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China.
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25
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Abstract
Long noncoding RNAs are defined as transcripts longer than 200 nt with no protein coding potential. Most lncRNAs are expressed in a tissue-specific manner and barring a few, their absolute expression is lower compared to most coding transcripts. Differential expression studies have contributed the most to the functional characterisation of the lncRNAs we know. Sensitive and specific quantification of lncRNA expression is crucial for such studies. SYBR Green dye based real time quantitative PCR is a simple and affordable method of quantitative PCR, wherein the specific binding of the dye to double stranded DNA amplicon emits fluorescence proportionate to the amount of PCR products. Here we describe a detailed protocol for successful lncRNA quantitation by reverse transcription followed by SYBR Green chemistry-based real-time PCR.
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26
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Forrester JV, Kuffova L, Delibegovic M. The Role of Inflammation in Diabetic Retinopathy. Front Immunol 2020; 11:583687. [PMID: 33240272 PMCID: PMC7677305 DOI: 10.3389/fimmu.2020.583687] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Inflammation is central to pathogenic processes in diabetes mellitus and the metabolic syndrome and particularly implicates innate immunity in the development of complications. Inflammation is a primary event in Type 1 diabetes where infectious (viral) and/or autoimmune processes initiate disease; in contrast, chronic inflammation is typical in Type 2 diabetes and is considered a sequel to increasing insulin resistance and disturbed glucose metabolism. Diabetic retinopathy (DR) is perceived as a vascular and neurodegenerative disease which occurs after some years of poorly controlled diabetes. However, many of the clinical features of DR are late events and reflect the nature of the retinal architecture and its cellular composition. Retinal microvascular disease is, in fact, an early event pathogenetically, induced by low grade, persistent leukocyte activation which causes repeated episodes of capillary occlusion and, progressive, attritional retinal ischemia. The later, overt clinical signs of DR are a consequence of the retinal ischemia. Metabolic dysregulation involving both lipid and glucose metabolism may lead to leukocyte activation. On a molecular level, we have shown that macrophage-restricted protein tyrosine phosphatase 1B (PTP1B) is a key regulator of inflammation in the metabolic syndrome involving insulin resistance and it is possible that PTP1B dysregulation may underlie retinal microvascular disease. We have also shown that adherent CCR5+CD11b+ monocyte macrophages appear to be selectively involved in retinal microvascular occlusion. In this review, we discuss the relationship between early leukocyte activation and the later features of DR, common pathogenetic processes between diabetic microvascular disease and other vascular retinopathies, the mechanisms whereby leukocyte activation is induced in hyperglycemia and dyslipidemia, the signaling mechanisms involved in diabetic microvascular disease, and possible interventions which may prevent these retinopathies. We also address a possible role for adaptive immunity in DR. Although significant improvements in treatment of DR have been made with intravitreal anti-VEGF therapy, a sizeable proportion of patients, particularly with sight-threatening macular edema, fail to respond. Alternative therapies targeting inflammatory processes may offer an advantage.
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Affiliation(s)
- John V Forrester
- Institute of Medical Sciences, University of Aberdeen, Scotland, United Kingdom
| | - Lucia Kuffova
- Institute of Medical Sciences, University of Aberdeen, Scotland, United Kingdom.,Eye Clinic, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Mirela Delibegovic
- Institute of Medical Sciences, University of Aberdeen, Scotland, United Kingdom
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