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Tavares e Silva J, Pessoa J, Nóbrega-Pereira S, Bernardes de Jesus B. The Impact of Long Noncoding RNAs in Tissue Regeneration and Senescence. Cells 2024; 13:119. [PMID: 38247811 PMCID: PMC10814083 DOI: 10.3390/cells13020119] [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: 11/14/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Overcoming senescence with tissue engineering has a promising impact on multiple diseases. Here, we provide an overview of recent studies in which cellular senescence was inhibited through the up/downregulation of specific lncRNAs. This approach prevented senescence in the bones, joints, nervous system, heart, and blood vessels, with a potential impact on regeneration and the prevention of osteoarthritis and osteoporosis, as well as neurodegenerative and cardiovascular diseases. Senescence of the skin and liver could also be prevented through the regulation of cellular levels of specific lncRNAs, resulting in the rejuvenation of cells from these organs and their potential protection from disease. From these exciting achievements, which support tissue regeneration and are not restricted to stem cells, we propose lncRNA regulation through RNA or gene therapies as a prospective preventive and therapeutic approach against aging and multiple aging-related diseases.
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Affiliation(s)
| | | | | | - Bruno Bernardes de Jesus
- Department of Medical Sciences and Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (J.T.e.S.); (J.P.); (S.N.-P.)
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Maharajan N, Lee CM, Vijayakumar KA, Cho GW. Oxymatrine Improves Oxidative Stress-Induced Senescence in HT22 Cells and Mice via the Activation of AMP-Activated Protein Kinase. Antioxidants (Basel) 2023; 12:2078. [PMID: 38136198 PMCID: PMC10741246 DOI: 10.3390/antiox12122078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/24/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
The accumulation of oxidative stress is one of the important factors causing cellular senescence. Oxymatrine (OM) is a natural quinolizidine alkaloid compound known for its antioxidant effects. This study aimed to investigate the anti-senescence potential of OM through oxidative stress-induced in vitro and in vivo models. By treating 600 μM of H2O2 to the HT22 mouse hippocampal neuronal cell line and by administering 150 mg/kg D-galactose to mice, we generated oxidative stress-induced senescence models. After providing 1, 2, and 4 μg/mL of OM to the HT22 mouse cell line and by administering 50 mg/kg OM to mice, we evaluated the enhancing effects. We evaluated different senescence markers, AMPK activity, and autophagy, along with DCFH-DA detection reaction and behavioral tests. In HT22 cells, OM showed a protective effect. OM, by reducing ROS and increasing p-AMPK expression, could potentially reduce oxidative stress-induced senescence. In the D-Gal-induced senescence mouse model, both the brain and heart tissues recovered AMPK activity, resulting in reduced levels of senescence. In neural tissue, to assess neurological recovery, including anxiety symptoms and exploration, we used a behavioral test. We also found that OM decreased the expression level of receptors for advanced glycation end products (RAGE). In heart tissue, we could observe the restoration of AMPK activity, which also increased the activity of autophagy. The results of our study suggest that OM ameliorates oxidative stress-induced senescence through its antioxidant action by restoring AMPK activity.
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Affiliation(s)
- Nagarajan Maharajan
- Department of Biological Science, College of Natural Sciences, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju 501759, Republic of Korea; (N.M.); (C.-M.L.); (K.A.V.)
| | - Chang-Min Lee
- Department of Biological Science, College of Natural Sciences, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju 501759, Republic of Korea; (N.M.); (C.-M.L.); (K.A.V.)
- BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Department of Integrative Biological Science, Chosun University, Gwangju 61452, Republic of Korea
| | - Karthikeyan A. Vijayakumar
- Department of Biological Science, College of Natural Sciences, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju 501759, Republic of Korea; (N.M.); (C.-M.L.); (K.A.V.)
| | - Gwang-Won Cho
- Department of Biological Science, College of Natural Sciences, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju 501759, Republic of Korea; (N.M.); (C.-M.L.); (K.A.V.)
- BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Department of Integrative Biological Science, Chosun University, Gwangju 61452, Republic of Korea
- The Basic Science Institute of Chosun University, Chosun University, Gwangju 61452, Republic of Korea
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Tang YF, Wang YZ, Wen GB, Jiang JJ. Prognostic model of kidney renal clear cell carcinoma using aging-related long noncoding RNA signatures identifies THBS1-IT1 as a potential prognostic biomarker for multiple cancers. Aging (Albany NY) 2023; 15:8630-8663. [PMID: 37708239 PMCID: PMC10522375 DOI: 10.18632/aging.204949] [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: 02/17/2023] [Accepted: 07/15/2023] [Indexed: 09/16/2023]
Abstract
Aging is responsible for the main intrinsic triggers of cancers; however, the studies of aging risk factors in cancer animal models and cancer patients are rare and insufficient to be represented in cancer clinical trials. For a better understanding of the complex regulatory networks of aging and cancers, 8 candidate aging related long noncoding RNAs (CarLncs) identified from the healthy aging models, centenarians and their offsprings, were selected and their association with kidney renal clear cell carcinoma (KIRC) was explored by series of cutting edge analyses such as support vector machine (SVM) and random forest (RF) algorithms. Using data downloaded from TCGA and GTEx databases, a regulatory network of CarLncs-miRNA-mRNA was constructed and five genes within the network were screened out as aging related feature genes for developing KIRC prognostic models. After a strict filtering pipeline for modeling, a formula using the transcript per million (TPM) values of feature genes "LncAging_score = 0.008* MMP11 + 0.066* THBS1-IT1 + (-0.014)* DYNLL2 + (-0.030)* RMND5A+ 0.008* PEG10" was developed. ROC analysis and nomogram suggest our model achieves a great performance in KIRC prognosis. Among the 8 CarLncs, we found that THBS1-IT1 was significantly dysregulated in 12 cancer types. A comprehensive pan-cancer analysis demonstrated that THBS1-IT1 is a potential prognostic biomarker in not only KIRC but also multiple cancers, such as LUSC, BLCA, GBM, LGG, MESO, PAAD, STAD and THCA, it was correlated with tumor microenvironment (TME) and tumor immune cell infiltration (TICI) and its high expression was related with poor survival.
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Affiliation(s)
- Yi-Fan Tang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yu-Zhi Wang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Gui-Biao Wen
- Department of Urology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jian-Jun Jiang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
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Zhou J, Tian G, Quan Y, Kong Q, Huang F, Li J, Wu W, Tang Y, Zhou Z, Liu X. The long noncoding RNA THBS1-AS1 promotes cardiac fibroblast activation in cardiac fibrosis by regulating TGFBR1. JCI Insight 2023; 8:160745. [PMID: 36787190 PMCID: PMC10070117 DOI: 10.1172/jci.insight.160745] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Cardiac fibrosis is associated with an adverse prognosis in cardiovascular disease that results in a decreased cardiac compliance and, ultimately, heart failure. Recent studies have identified the role of long noncoding RNA (lncRNA) in cardiac fibrosis. However, the functions of many lncRNAs in cardiac fibrosis remain to be characterized. Through a whole-transcriptome sequencing and bioinformatics analysis on a mouse model of pressure overload-induced cardiac fibrosis, we screened a key lncRNA termed thrombospondin 1 antisense 1 (THBS1-AS1), which was positively associated with cardiac fibrosis. In vitro functional studies demonstrated that the silencing of THBS1-AS1 ameliorated TGF-β1 effects on cardiac fibroblast (CF) activation, and the overexpression of THBS1-AS1 displayed the opposite effect. A mechanistic study revealed that THBS1-AS1 could sponge miR-221/222 to regulate the expression of TGFBR1. Moreover, under TGF-β1 stimulation, the forced expression of miR-221/222 or the knockdown TGFBR1 significantly reversed the THBS1-AS1 overexpression induced by further CF activation. In vivo, specific knockdown of THBS1-AS1 in activated CFs significantly alleviated transverse aorta constriction-induced (TAC-induced) cardiac fibrosis in mice. Finally, we demonstrated that the human THBS1-AS1 can also affect the activation of CFs by regulating TGFBR1. In conclusion, this study reveals that lncRNA THBS1-AS1 is a potentially novel regulator of cardiac fibrosis and may serve as a target for the treatment of cardiac fibrosis.
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Affiliation(s)
- Junteng Zhou
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
- Health Management Center, General Practice Medical Center, and
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
| | - Geer Tian
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Yue Quan
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Qihang Kong
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Fangyang Huang
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
| | - Junli Li
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Wenchao Wu
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Yong Tang
- International Joint Research Centre on Purinergic Signaling, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhichao Zhou
- Division of Cardiology, Department of Medicine Solna, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Xiaojing Liu
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
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Luo YM, Yang SD, Wen MY, Wang B, Liu JH, Li ST, Li YY, Cheng H, Zhao LL, Li SM, Jiang JJ. Insights into the mechanisms of triptolide nephrotoxicity through network pharmacology-based analysis and RNA-seq. FRONTIERS IN PLANT SCIENCE 2023; 14:1144583. [PMID: 36959927 PMCID: PMC10027700 DOI: 10.3389/fpls.2023.1144583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Triptolide (TPL) is a promising plant-derived compound for clinical therapy of multiple human diseases; however, its application was limited considering its toxicity. METHODS To explore the underlying molecular mechanism of TPL nephrotoxicity, a network pharmacology based approach was utilized to predict candidate targets related with TPL toxicity, followed by deep RNA-seq analysis to characterize the features of three transcriptional elements include protein coding genes (PCGs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) as well as their associations with nephrotoxicity in rats with TPL treatment. RESULTS & DISCUSSION Although the deeper mechanisms of TPL nephrotoxcity remain further exploration, our results suggested that c-Jun is a potential target of TPL and Per1 related circadian rhythm signaling is involved in TPL induced renal toxicity.
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Affiliation(s)
- Yue-Ming Luo
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Shu-Dong Yang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Miao-Yu Wen
- Department of Geriatrics, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Bing Wang
- Department of Nephrology, Shenzhen Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jia-Hui Liu
- Department of Nephrology, Shenzhen Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Si-Ting Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yu-Yan Li
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Hong Cheng
- Department of Geriatrics, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Li-Li Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Graduate school of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Shun-Min Li
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jian-Jun Jiang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
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Frankowska N, Bryl E, Fulop T, Witkowski JM. Longevity, Centenarians and Modified Cellular Proteodynamics. Int J Mol Sci 2023; 24:ijms24032888. [PMID: 36769212 PMCID: PMC9918038 DOI: 10.3390/ijms24032888] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
We have shown before that at least one intracellular proteolytic system seems to be at least as abundant in the peripheral blood lymphocytes of centenarians as in the same cells of young individuals (with the cells of the elderly population showing a significant dip compared to both young and centenarian cohorts). Despite scarce published data, in this review, we tried to answer the question how do different types of cells of longevous people-nonagenarians to (semi)supercentenarians-maintain the quality and quantity of their structural and functional proteins? Specifically, we asked if more robust proteodynamics participate in longevity. We hypothesized that at least some factors controlling the maintenance of cellular proteomes in centenarians will remain at the "young" level (just performing better than in the average elderly). In our quest, we considered multiple aspects of cellular protein maintenance (proteodynamics), including the quality of transcribed DNA, its epigenetic changes, fidelity and quantitative features of transcription of both mRNA and noncoding RNAs, the process of translation, posttranslational modifications leading to maturation and functionalization of nascent proteins, and, finally, multiple facets of the process of elimination of misfolded, aggregated, and otherwise dysfunctional proteins (autophagy). We also included the status of mitochondria, especially production of ATP necessary for protein synthesis and maintenance. We found that with the exception of the latter and of chaperone function, practically all of the considered aspects did show better performance in centenarians than in the average elderly, and most of them approached the levels/activities seen in the cells of young individuals.
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Affiliation(s)
- Natalia Frankowska
- Department of Physiopathology, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Ewa Bryl
- Department of Pathology and Experimental Rheumatology, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Tamas Fulop
- Research Center on Aging, Geriatric Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Jacek M. Witkowski
- Department of Physiopathology, Medical University of Gdansk, 80-211 Gdansk, Poland
- Correspondence: ; Tel.: +48-58-349-1510
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Drekolia MK, Talyan S, Cordellini Emídio R, Boon RA, Guenther S, Looso M, Dumbović G, Bibli SI. Unravelling the impact of aging on the human endothelial lncRNA transcriptome. Front Genet 2022; 13:1035380. [PMID: 36338971 PMCID: PMC9634578 DOI: 10.3389/fgene.2022.1035380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/06/2022] [Indexed: 11/21/2022] Open
Abstract
The incidence and prevalence of cardiovascular disease is highest among the elderly. There is a need to further understand the mechanisms behind endothelial cell aging in order to achieve vascular rejuvenation and minimize the onset of age-related vascular diseases. Long non-coding RNAs (lncRNAs) have been proposed to regulate numerous processes in the human genome, yet their function in vascular aging and their therapeutic potential remain largely unknown. This is primarily because the majority of studies investigating the impact of aging on lncRNA expression heavily rely on in vitro studies based on replicative senescence. Here, using a unique collection of young and aged endothelial cells isolated from native human arteries, we sought to characterize the age-related alterations in lncRNA expression profiles. We were able to detect a total of 4463 lncRNAs expressed in the human endothelium from which ∼17% (798) were altered in advanced age. One of the most affected lncRNAs in aging was the primate-specific, Prostate Cancer Associated Transcript (PCAT) 14. In our follow up analysis, using single molecule RNA FISH, we showed that PCAT14 is relatively abundant, localized almost exclusively in the nucleus of young endothelial cells, and silenced in the aged endothelium. Functionally, our studies proposed that downregulation of PCAT14 alters endothelial cell transcription profile and cell functions including endothelial cell migration, sprouting and inflammatory responses in vitro. Taken together, our data highlight that endothelial cell aging correlates with altered expression of lncRNAs, which could impair the endothelial regenerative capacity and enhance inflammatory phenotypes.
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Affiliation(s)
- Maria-Kyriaki Drekolia
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt, Germany
| | - Sweta Talyan
- Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | - Reinier Abraham Boon
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Rhein/Main, Frankfurt, Germany
| | - Stefan Guenther
- Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Center for Cardiovascular Research (DZHK), partner site Rhein/Main, Frankfurt, Germany
| | - Mario Looso
- Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Center for Cardiovascular Research (DZHK), partner site Rhein/Main, Frankfurt, Germany
| | - Gabrijela Dumbović
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
- *Correspondence: Sofia-Iris Bibli, ; Gabrijela Dumbović,
| | - Sofia-Iris Bibli
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Rhein/Main, Frankfurt, Germany
- *Correspondence: Sofia-Iris Bibli, ; Gabrijela Dumbović,
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The landscape of aging. SCIENCE CHINA LIFE SCIENCES 2022; 65:2354-2454. [PMID: 36066811 PMCID: PMC9446657 DOI: 10.1007/s11427-022-2161-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023]
Abstract
Aging is characterized by a progressive deterioration of physiological integrity, leading to impaired functional ability and ultimately increased susceptibility to death. It is a major risk factor for chronic human diseases, including cardiovascular disease, diabetes, neurological degeneration, and cancer. Therefore, the growing emphasis on “healthy aging” raises a series of important questions in life and social sciences. In recent years, there has been unprecedented progress in aging research, particularly the discovery that the rate of aging is at least partly controlled by evolutionarily conserved genetic pathways and biological processes. In an attempt to bring full-fledged understanding to both the aging process and age-associated diseases, we review the descriptive, conceptual, and interventive aspects of the landscape of aging composed of a number of layers at the cellular, tissue, organ, organ system, and organismal levels.
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Wang G, Li M, Wang Y, Wang B, Pu H, Mao J, Zhang S, Zhou S, Luo P. Characterization of differentially expressed and lipid metabolism-related lncRNA-mRNA interaction networks during the growth of liver tissue through rabbit models. Front Vet Sci 2022; 9:998796. [PMID: 36118359 PMCID: PMC9477072 DOI: 10.3389/fvets.2022.998796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundCharacterization the long non-coding RNAs (lncRNAs) and their regulated mRNAs involved in lipid metabolism during liver growth and development is of great value for discovering new genomic biomarkers and therapeutic targets for fatty liver and metabolic syndrome.Materials and methodsLiver samples from sixteen rabbit models during the four growth stages (birth, weaning, sexual maturity, and somatic maturity) were used for RNA-seq and subsequent bioinformatics analyses. Differentially expressed (DE) lncRNAs and mRNAs were screened, and the cis/trans-regulation target mRNAs of DE lncRNAs were predicted. Then the function enrichment analyses of target mRNAs were performed through Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. The target protein interaction (PPI) and lncRNA-mRNA co-expression networks were constructed using string version 11.0 platform and R Stats. Finally, six lncRNAs and six mRNAs were verified taking RT-qPCR.ResultsLiver Oil Red O detection found that the liver showed time-dependent accumulation of lipid droplets. 41,095 lncRNAs, 30,744 mRNAs, and amount to 3,384 DE lncRNAs and 2980 DE mRNAs were identified from 16 cDNA sequencing libraries during the growth of liver. 689 out of all DE lncRNAs corresponded to 440 DE mRNAs by cis-regulation and all DE mRNAs could be regulated by DE lncRNAs by trans-regulation. GO enrichment analysis showed significant enrichment of 892 GO terms, such as protein binding, cytosol, extracellular exsome, nucleoplasm, and oxidation-reduction process. Besides, 52 KEGG pathways were significantly enriched, including 11 pathways of lipid metabolism were found, like Arachidonic acid metabolism, PPAR signaling pathway and Biosynthesis of unsaturated fatty acids. After the low expression DE mRNAs and lncRNAs were excluded, we further obtained the 54 mRNAs were regulated by 249 lncRNAs. 351 interaction pairs were produced among 38 mRNAs and 215 lncRNAs through the co-expression analysis. The PPI network analysis found that 10 mRNAs such as 3β-Hydroxysteroid-Δ24 Reductase (DHCR24), lathosterol 5-desaturase (SC5D), and acetyl-CoA synthetase 2 (ACSS2) were highly interconnected hub protein-coding genes. Except for MSTRG.43041.1, the expression levels of the 11 genes by RT-qPCR were the similar trends to the RNA-seq results.ConclusionThe study revealed lncRNA-mRNA interation networks that regulate lipid metabolism during liver growth, providing potential research targets for the prophylaxis and treatment of related diseases caused by liver lipid metabolism disorders.
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Affiliation(s)
- Guoze Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, China
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Maolin Li
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, China
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yi Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, China
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Binbin Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, China
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Hanxu Pu
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, China
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jinxin Mao
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Shuai Zhang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, China
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shi Zhou
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- *Correspondence: Shi Zhou
| | - Peng Luo
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, China
- Peng Luo
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Specific Gain and Loss of Co-Expression Modules in Long-Lived Individuals Indicate a Role of circRNAs in Human Longevity. Genes (Basel) 2022; 13:genes13050749. [PMID: 35627134 PMCID: PMC9140997 DOI: 10.3390/genes13050749] [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: 03/25/2022] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022] Open
Abstract
Deep RNA sequencing of 164 blood samples collected from long-lived families was performed to investigate the expression patterns of circular RNAs (circRNAs). Unlike that observed in previous studies, circRNA expression in long-lived elderly individuals (98.3 ± 3.4 year) did not exhibit an age-accumulating pattern. Based on weighted circRNA co-expression network analysis, we found that longevous elders specifically gained eight but lost seven conserved circRNA-circRNA co-expression modules (c-CCMs) compared with normal elder controls (spouses of offspring of long-lived individuals, age = 59.3 ± 5.8 year). Further analysis showed that these modules were associated with healthy aging-related pathways. These results together suggest an important role of circRNAs in regulating human lifespan extension.
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