51
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Chen J, Zou Q, Lv D, Raza MA, Wang X, Chen Y, Xi X, Li P, Wen A, Zhu L, Tang G, Li M, Li X, Jiang Y. Comprehensive transcriptional profiling of aging porcine liver. PeerJ 2019; 7:e6949. [PMID: 31149403 PMCID: PMC6526898 DOI: 10.7717/peerj.6949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/09/2019] [Indexed: 01/04/2023] Open
Abstract
Background Aging is a major risk factor for the development of many diseases, and the liver, as the most important metabolic organ, is significantly affected by aging. It has been shown that the liver weight tends to increase in rodents and decrease in humans with age. Pigs have a genomic structure, with physiological as well as biochemical features that are similar to those of humans, and have therefore been used as a valuable model for studying human diseases. The molecular mechanisms of the liver aging of large mammals on a comprehensive transcriptional level remain poorly understood. The pig is an ideal model animal to clearly and fully understand the molecular mechanism underlying human liver aging. Methods In this study, four healthy female Yana pigs (an indigenous Chinese breed) were investigated: two young sows (180-days-old) and two old sows (8-years-old). High throughput RNA sequencing was performed to evaluate the expression profiles of messenger RNA, long non-coding RNAs, micro RNAs, and circular RNAs during the porcine liver aging process. Gene Ontology (GO) analysis was performed to investigate the biological functions of age-related genes. Results A number of age-related genes were identified in the porcine liver. GO annotation showed that up-regulated genes were mainly related to immune response, while the down-regulated genes were mainly related to metabolism. Moreover, several lncRNAs and their target genes were also found to be differentially expressed during liver aging. In addition, the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks were assessed during liver aging. Conclusions Numerous age-related genes were identified and circRNA-miRNA co-expression networks that are active during porcine liver aging were constructed. These findings contribute to the understanding of the transcriptional foundations of liver aging and also provide further references that clarify human liver aging at the molecular level.
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Affiliation(s)
- Jianning Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Daojun Lv
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd, Chengdu, Sichuan, China
| | - Muhammad Ali Raza
- Department of Crop Cultivation and Farming System, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xue Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Yan Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Xiaoyu Xi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Peilin Li
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd, Chengdu, Sichuan, China
| | - Anxiang Wen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
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52
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Lai RW, Lu R, Danthi PS, Bravo JI, Goumba A, Sampathkumar NK, Benayoun BA. Multi-level remodeling of transcriptional landscapes in aging and longevity. BMB Rep 2019. [PMID: 30526773 PMCID: PMC6386224 DOI: 10.5483/bmbrep.2019.52.1.296] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and gene expression has been observed to be deregulated with aging. In this review, we discuss the current knowledge on the transcriptional alterations that have been described to occur with age in metazoans. First, we discuss age-related transcriptional changes in protein-coding genes, the expected functional impact of such changes, and how known pro-longevity interventions impact these changes. Second, we discuss the changes and impact of emerging aspects of transcription in aging, including age-related changes in splicing, lncRNAs and circRNAs. Third, we discuss the changes and potential impact of transcription of transposable elements with aging. Fourth, we highlight small ncRNAs and their potential impact on the regulation of aging phenotypes. Understanding the aging transcriptome will be key to identify important regulatory targets, and ultimately slow-down or reverse aging and extend healthy lifespan in humans.
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Affiliation(s)
- Rochelle W Lai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexandre Goumba
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089; USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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53
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de Jong TV, Moshkin YM, Guryev V. Gene expression variability: the other dimension in transcriptome analysis. Physiol Genomics 2019; 51:145-158. [DOI: 10.1152/physiolgenomics.00128.2018] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Transcriptome sequencing is a powerful technique to study molecular changes that underlie the differences in physiological conditions and disease progression. A typical question that is posed in such studies is finding genes with significant changes between sample groups. In this respect expression variability is regarded as a nuisance factor that is primarily of technical origin and complicates the data analysis. However, it is becoming apparent that the biological variation in gene expression might be an important molecular phenotype that can affect physiological parameters. In this review we explore the recent literature on technical and biological variability in gene expression, sources of expression variability, (epi-)genetic hallmarks, and evolutionary constraints in genes with robust and variable gene expression. We provide an overview of recent findings on effects of external cues, such as diet and aging, on expression variability and on other biological phenomena that can be linked to it. We discuss metrics and tools that were developed for quantification of expression variability and highlight the importance of future studies in this direction. To assist the adoption of expression variability analysis, we also provide a detailed description and computer code, which can easily be utilized by other researchers. We also provide a reanalysis of recently published data to highlight the value of the analysis method.
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Affiliation(s)
- Tristan V. de Jong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Yuri M. Moshkin
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
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54
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Bink DI, Lozano-Vidal N, Boon RA. Long Non-Coding RNA in Vascular Disease and Aging. Noncoding RNA 2019; 5:ncrna5010026. [PMID: 30893946 PMCID: PMC6468806 DOI: 10.3390/ncrna5010026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Cardiovascular diseases are the most prominent cause of death in Western society, especially in the elderly. With the increasing life expectancy, the number of patients with cardiovascular diseases will rise in the near future, leading to an increased healthcare burden. There is a need for new therapies to treat this growing number of patients. The discovery of long non-coding RNAs has led to a novel group of molecules that could be considered for their potential as therapeutic targets. This review presents an overview of long non-coding RNAs that are regulated in vascular disease and aging and which might therefore give insight into new pathways that could be targeted to diagnose, prevent, and/or treat vascular diseases.
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Affiliation(s)
- Diewertje I Bink
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, VU University, 1081HV Amsterdam, The Netherlands.
| | - Noelia Lozano-Vidal
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, VU University, 1081HV Amsterdam, The Netherlands.
| | - Reinier A Boon
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, VU University, 1081HV Amsterdam, The Netherlands.
- Institute of Cardiovascular Regeneration, Goethe University, 60596 Frankfurt am Main, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, 13347 Berlin, Germany.
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55
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Benayoun BA, Pollina EA, Singh PP, Mahmoudi S, Harel I, Casey KM, Dulken BW, Kundaje A, Brunet A. Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses. Genome Res 2019; 29:697-709. [PMID: 30858345 PMCID: PMC6442391 DOI: 10.1101/gr.240093.118] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/25/2019] [Indexed: 12/20/2022]
Abstract
Aging is accompanied by the functional decline of tissues. However, a systematic study of epigenomic and transcriptomic changes across tissues during aging is missing. Here, we generated chromatin maps and transcriptomes from four tissues and one cell type from young, middle-aged, and old mice—yielding 143 high-quality data sets. We focused on chromatin marks linked to gene expression regulation and cell identity: histone H3 trimethylation at lysine 4 (H3K4me3), a mark enriched at promoters, and histone H3 acetylation at lysine 27 (H3K27ac), a mark enriched at active enhancers. Epigenomic and transcriptomic landscapes could easily distinguish between ages, and machine-learning analysis showed that specific epigenomic states could predict transcriptional changes during aging. Analysis of data sets from all tissues identified recurrent age-related chromatin and transcriptional changes in key processes, including the up-regulation of immune system response pathways such as the interferon response. The up-regulation of the interferon response pathway with age was accompanied by increased transcription and chromatin remodeling at specific endogenous retroviral sequences. Pathways misregulated during mouse aging across tissues, notably innate immune pathways, were also misregulated with aging in other vertebrate species—African turquoise killifish, rat, and humans—indicating common signatures of age across species. To date, our data set represents the largest multitissue epigenomic and transcriptomic data set for vertebrate aging. This resource identifies chromatin and transcriptional states that are characteristic of young tissues, which could be leveraged to restore aspects of youthful functionality to old tissues.
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Affiliation(s)
- Bérénice A Benayoun
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Salah Mahmoudi
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Itamar Harel
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ben W Dulken
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, California 94305, USA
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56
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Moskalev A, Guvatova Z, Shaposhnikov M, Lashmanova E, Proshkina E, Koval L, Zhavoronkov A, Krasnov G, Kudryavtseva A. The Neuronal Overexpression of Gclc in Drosophila melanogaster Induces Life Extension With Longevity-Associated Transcriptomic Changes in the Thorax. Front Genet 2019; 10:149. [PMID: 30891062 PMCID: PMC6411687 DOI: 10.3389/fgene.2019.00149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 02/12/2019] [Indexed: 01/24/2023] Open
Abstract
Some effects of aging in animals are tissue-specific. In D. melanogaster neuronal overexpression of Gclc increases lifespan and improves certain physiological parameters associated with health benefits such as locomotor activity, circadian rhythmicity, and stress resistance. Our previous transcriptomic analyses of Drosophila heads, primarily composed of neuronal tissue, revealed significant changes in expression levels of genes involved in aging-related signaling pathways (Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta), translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity, and transmission. Considering that various tissues age differently and age-related gene expression changes are tissue-specific, we investigated the effects of neuronal Gclc overexpression on gene expression levels in the imago thorax, which is primarily composed of muscles. A total of 58 genes were found to be differentially expressed between thoraces of control and Gclc overexpressing flies. The Gclc level demonstrated associations with expression of genes involved in the circadian rhythmicity, the genes in categories related to the muscle system process and the downregulation of genes involved in proteolysis. Most of the functional categories altered by Gclc overexpression related to metabolism including Drug metabolism, Metabolism of xenobiotics by cytochrome P450, Glutathione metabolism, Starch and sucrose metabolism, Citrate cycle (TCA cycle), One carbon pool by folate. Thus, the transcriptomic changes caused by neuron-specific Gclc overexpression in the thorax were less pronounced than in the head and affected pathways also differed from previous results. Although these pathways don't belong to the canonical longevity pathways, we suggest that they could participate in the delay of aging of Gclc overexpressing flies.
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Affiliation(s)
- Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Zulfiya Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | - Ekaterina Lashmanova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ekaterina Proshkina
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | - Liubov Koval
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | | | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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57
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Mahmoudi E, Cairns MJ. Circular RNAs are temporospatially regulated throughout development and ageing in the rat. Sci Rep 2019; 9:2564. [PMID: 30796328 PMCID: PMC6385508 DOI: 10.1038/s41598-019-38860-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/10/2019] [Indexed: 01/16/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently closed structural isoforms of linear mRNA which have been observed across a broad range of species and tissues. Here, we provide a comprehensive circRNAs expression catalogue for the rat including 8 organs of both sexes during 4 developmental stages using a public RNAseq dataset. These analyses revealed thousands of circular RNA species, many expressed in an organ-specific manner along with their host genes which were enriched with tissue-specific biological functions. A large number of circRNAs also displayed a developmental-dependent expression pattern and are accumulated during ageing. CircRNAs also displayed some sexually dimorphic expression, with gender associated differences observed in various tissues and developmental stages. These observations suggest that circRNAs are dynamically expressed in a spatial-, temporal- and gender-specific manner in mammals, and may have important biological function in differentiation, development and aging.
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Affiliation(s)
- E Mahmoudi
- School of Biomedical Sciences and Pharmacy, the University of Newcastle, Callaghan, NSW, 2308, Australia.,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, Newcastle, Australia
| | - M J Cairns
- School of Biomedical Sciences and Pharmacy, the University of Newcastle, Callaghan, NSW, 2308, Australia. .,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW, 2308, Australia. .,Hunter Medical Research Institute, Newcastle, Australia.
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58
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Sousa-Victor P, Neves J, Cedron-Craft W, Ventura PB, Liao CY, Riley RR, Soifer I, van Bruggen N, Kolumam GA, Villeda SA, Lamba DA, Jasper H. MANF regulates metabolic and immune homeostasis in ageing and protects against liver damage. Nat Metab 2019; 1:276-290. [PMID: 31489403 PMCID: PMC6727652 DOI: 10.1038/s42255-018-0023-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aging is accompanied by altered intercellular communication, deregulated metabolic function, and inflammation. Interventions that restore a youthful state delay or reverse these processes, prompting the search for systemic regulators of metabolic and immune homeostasis. Here we identify MANF, a secreted stress-response protein with immune modulatory properties, as an evolutionarily conserved regulator of systemic and in particular liver metabolic homeostasis. We show that MANF levels decline with age in flies, mice and humans, and MANF overexpression extends lifespan in flies. MANF deficient flies exhibit enhanced inflammation and shorter lifespans, and MANF heterozygous mice exhibit inflammatory phenotypes in various tissues, as well as progressive liver damage, fibrosis, and steatosis. We show that immune cell-derived MANF protects against liver inflammation and fibrosis, while hepatocyte-derived MANF prevents hepatosteatosis. Liver rejuvenation by heterochronic parabiosis in mice further depends on MANF, while MANF supplementation ameliorates several hallmarks of liver aging, prevents hepatosteatosis induced by diet, and improves age-related metabolic dysfunction. Our findings identify MANF as a systemic regulator of homeostasis in young animals, suggesting a therapeutic application for MANF in age-related metabolic diseases.
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Affiliation(s)
- Pedro Sousa-Victor
- Paul F. Glenn Center for Biology of Aging Research, Buck Institute for Research on Aging, Novato, CA, USA
| | - Joana Neves
- Paul F. Glenn Center for Biology of Aging Research, Buck Institute for Research on Aging, Novato, CA, USA
| | - Wendy Cedron-Craft
- Paul F. Glenn Center for Biology of Aging Research, Buck Institute for Research on Aging, Novato, CA, USA
| | - P Britten Ventura
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Chen-Yu Liao
- Paul F. Glenn Center for Biology of Aging Research, Buck Institute for Research on Aging, Novato, CA, USA
| | - Rebeccah R Riley
- Paul F. Glenn Center for Biology of Aging Research, Buck Institute for Research on Aging, Novato, CA, USA
| | - Ilya Soifer
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | | | - Saul A Villeda
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Deepak A Lamba
- Paul F. Glenn Center for Biology of Aging Research, Buck Institute for Research on Aging, Novato, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Heinrich Jasper
- Paul F. Glenn Center for Biology of Aging Research, Buck Institute for Research on Aging, Novato, CA, USA.
- Immunology Discovery, Genentech, South San Francisco, CA, USA.
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59
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Chen J, Zou Q, Lv D, Raza MA, Wang X, Li P, Chen Y, Xi X, Wen A, Zhu L, Tang G, Li M, Li X, Jiang Y. Comprehensive transcriptional profiling of porcine brain aging. Gene 2019; 693:1-9. [PMID: 30695714 DOI: 10.1016/j.gene.2019.01.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/27/2018] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
Abstract
The brain as an important organ can be affected largely by aging, and the comprehensive transcriptional underpinnings of brain aging remain poorly understood. Here, we performed a high throughput RNA sequencing to evaluate the expression profiles of messenger RNA (mRNA), long non-coding RNAs (lncRNAs), micro RNAs (miRNAs), and circular RNAs (circRNAs) in porcine brain. We have identified 714 mRNAs, 38lncRNAs, 41miRNAs, and 148circRNAs were age-related genes in the porcine cerebral cortex. The lncRNAs, miRNAs and circRNAs have effect on the age of porcine brain due to the much changes of expression level as noncoding RNAs. The up-regulated genes were significantly enriched for stress response, reproductive regulatory process, immune response and metabolic process, and the down-regulated genes were related to neurologic function, stress response and signaling pathway. The synaptic transmission pathway may be the key role in aging of porcine brain that it was co-enriched for in both differentially expressed mRNAs and lncRNAs. Moreover, some lncRNAs and their target genes were also differentially expressed during brain aging. We further assessed the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks during brain aging. We also selected 2 mRNAs, 2 lncRNAs, 2 miRNAs, and 1 circRNAs to perform the q-PCR, and the expression patterns were highly consistent between the two methods confirming the high reproducibility and reliability of the gene expression profiling in our study. In conclusion, our findings will contribute to understand the transcriptional underpinnings of brain aging and provide a foundation for future studies on the molecular mechanisms underlying brain aging.
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Affiliation(s)
- Jianning Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Daojun Lv
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd., Chengdu, Sichuan 611130, China
| | - Muhammad Ali Raza
- Department of Crop Cultivation and Farming System, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xue Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Peilin Li
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd., Chengdu, Sichuan 611130, China
| | - Yan Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xiaoyu Xi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Anxiang Wen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China.
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60
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Huang K, Chen W, Zhu F, Li PWL, Kapahi P, Bai H. RiboTag translatomic profiling of Drosophila oenocytes under aging and induced oxidative stress. BMC Genomics 2019; 20:50. [PMID: 30651069 PMCID: PMC6335716 DOI: 10.1186/s12864-018-5404-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Aging is accompanied with loss of tissue homeostasis and accumulation of cellular damages. As one of the important metabolic centers, liver shows age-related dysregulation of lipid metabolism, impaired detoxification pathway, increased inflammation and oxidative stress response. However, the mechanisms for these age-related changes still remain unclear. In the fruit fly, Drosophila melanogaster, liver-like functions are controlled by two distinct tissues, fat body and oenocytes. Compared to fat body, little is known about how oenocytes age and what are their roles in aging regulation. To characterize age- and stress-regulated gene expression in oenocytes, we performed cell-type-specific ribosome profiling (RiboTag) to examine the impacts of aging and oxidative stress on oenocyte translatome in Drosophila. RESULTS We show that aging and oxidant paraquat significantly increased the levels of reactive oxygen species (ROS) in adult oenocytes of Drosophila, and aged oenocytes exhibited reduced sensitivity to paraquat treatment. Through RiboTag sequencing, we identified 3324 and 949 differentially expressed genes in oenocytes under aging and paraquat treatment, respectively. Aging and paraquat exhibit both shared and distinct regulations on oenocyte translatome. Among all age-regulated genes, oxidative phosphorylation, ribosome, proteasome, fatty acid metabolism, and cytochrome P450 pathways were down-regulated, whereas DNA replication and immune response pathways were up-regulated. In addition, most of the peroxisomal genes were down-regulated in aged oenocytes, including genes involved in peroxisomal biogenesis factors and fatty acid beta-oxidation. Many age-related mRNA translational changes in oenocytes are similar to aged mammalian liver, such as up-regulation of innate immune response and Ras/MAPK signaling pathway and down-regulation of peroxisome and fatty acid metabolism. Furthermore, oenocytes highly expressed genes involving in liver-like processes (e.g., ketogenesis). CONCLUSIONS Our oenocyte-specific translatome analysis identified many genes and pathways that are shared between Drosophila oenocytes and mammalian liver, highlighting the molecular and functional similarities between the two tissues. Many of these genes were altered in both oenocytes and liver during aging. Thus, our translatome analysis provide important genomic resource for future dissection of oenocyte function and its role in lipid metabolism, stress response and aging regulation.
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Affiliation(s)
- Kerui Huang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Wenhao Chen
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Fang Zhu
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
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García-López S, Albo-Castellanos C, Urdinguio RG, Cañón S, Sánchez-Cabo F, Martínez-Serrano A, Fraga MF, Bernad A. Deregulation of the imprinted DLK1-DIO3 locus ncRNAs is associated with replicative senescence of human adipose-derived stem cells. PLoS One 2018; 13:e0206534. [PMID: 30395586 PMCID: PMC6218046 DOI: 10.1371/journal.pone.0206534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/15/2018] [Indexed: 12/24/2022] Open
Abstract
Background Human adult adipose-derived stem cells (hADSCs) have become the most promising cell source for regenerative medicine. However the prolonged ex vivo expansion periods required to obtain the necessary therapeutic dose promotes progressive senescence, with the concomitant reduction of their therapeutic potential. Aim and scope A better understanding of the determinants of hADSC senescence is needed to improve biosafety while preserving therapeutic efficiency. Here, we investigated the association between deregulation of the imprinted DLK1-DIO3 region and replicative senescence in hADSC cultures. Methods We compared hADSC cultures at short (PS) and prolonged (PL) passages, both in standard and low [O2] (21 and 3%, respectively), in relation to replicative senescence. hADSCs were evaluated for expression alterations in the DLK1-DIO3 region on chromosome 14q32, and particularly in its main miRNA cluster. Results Comparison of hADSCs cultured at PL or PS surprisingly showed a quite significant fraction (69%) of upregulated miRNAs in PL cultures mapping to the imprinted 14q32 locus, the largest miRNA cluster described in the genome. In agreement, expression of the lncRNA MEG3 (Maternally Expressed 3; Meg3/Gtl2), cultured at 21 and 3% [O2], was also significantly higher in PL than in PS passages. During hADSC replicative senescence the AcK16H4 activating mark was found to be significantly associated with the deregulation of the entire DLK1-DIO3 locus, with a secondary regulatory role for the methylation of DMR regions. Conclusion A direct relationship between DLK1-DIO3 deregulation and replicative senescence of hADSCs is reported, involving upregulation of a very significant fraction of its largest miRNA cluster (14q32.31), paralleled by the progressive overexpression of the lncRNA MEG3, which plays a central role in the regulation of Dlk1/Dio3 activation status in mice.
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Affiliation(s)
- Silvia García-López
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Carmen Albo-Castellanos
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Rocio G. Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Hospital Universitaria Central de Asturias (HUCA) and Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo (UO), Asturias, Spain
| | - Susana Cañón
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Alberto Martínez-Serrano
- Molecular Biology Department (UAM) and Molecular Neuropathology Department, Center of Molecular Biology Severo Ochoa-CSIC, Universidad Autónoma de Madrid, Campus Cantoblanco, Madrid, Spain
| | - Mario F. Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Hospital Universitaria Central de Asturias (HUCA) and Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo (UO), Asturias, Spain
| | - Antonio Bernad
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
- * E-mail:
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Characterization of Critical Functions of Long Non-Coding RNAs and mRNAs in Rhabdomyosarcoma Cells and Mouse Skeletal Muscle Infected by Enterovirus 71 Using RNA-Seq. Viruses 2018; 10:v10100556. [PMID: 30314355 PMCID: PMC6213062 DOI: 10.3390/v10100556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 12/11/2022] Open
Abstract
Enterovirus 71 (EV71) is the main pathogen of severe hand-foot-mouth disease (HFMD). Long non-coding RNAs (lncRNAs) are recognized as pivotal factors during the pathogenesis of viral infection. However, the critical functions of lncRNAs in EV71–host interactions have not been characterized. Here, for the first time, we performed global transcriptome analysis of lncRNA and mRNA expression profiles in EV71-infected human rhabdomyosarcoma (RD) cells and skeletal muscle of mice using second-generation sequencing. In our study, a total of 3801 novel lncRNAs were identified. In addition, 23 lncRNAs and 372 mRNAs exhibited remarkable differences in expression levels between infected and uninfected RD cells, while 104 lncRNAs and 2647 mRNAs were differentially expressed in infected skeletal muscle from neonatal mice. Comprehensive bioinformatics analysis included target gene prediction, lncRNA-mRNA co-expression network construction, as well as gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis mainly focused on differentially-expressed genes (DEGs). Our results suggest that lncRNAs may participate in EV71 infection-induced pathogenesis through regulating immune responses, protein binding, cellular component biogenesis and metabolism. The present study provides novel insights into the functions of lncRNAs and the possible pathogenic mechanism following EV71 infection.
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63
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McKinzie PB, McKim KL, Pearce MG, Bishop ME, Parsons BL. Lifespan Kras mutation levels in lung and liver of B6C3F 1 mice. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:715-721. [PMID: 30255594 DOI: 10.1002/em.22198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/21/2018] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Somatic mutations accumulate in the human genome and are correlated with increased cancer incidence as humans age. The standard model for studying the carcinogenic effects of exposures for human risk assessment is the rodent 2-year carcinogenicity assay. However, there is little information regarding the effect of age on cancer-driver gene mutations in these models. The mutant fraction (MF) of Kras codon 12 GGT to GAT and GGT to GTT mutations, oncogenic mutations orthologous between humans and rodents, was quantified over the lifespan of B6C3F1 mice. MFs were measured in lung and liver tissue, organs that frequently develop tumors following carcinogenic exposures. The MFs were evaluated at 4, 6, 8, 12, 21, and 85 weeks, with the 12-week and 21-week time points being coincident with the conclusion of 28-day and 90-day exposure durations used in short-term toxicity testing. The highly sensitive and quantitative Allele-specific Competitive Blocker PCR (ACB-PCR) assay was used to quantify the number of mutant Kras codon 12 alleles. The mouse lung showed a slight, but significant trend increase in the Kras codon 12 GAT mutation over the 85-week period. The trend with age can be equally well-fit by several non-linear functions, but not by a linear function. In contrast, the liver GAT mutation did not increase, and the GTT mutation did not increase for either organ. Even with the slight increase in the lung GAT MFs, our results indicate that the future use of Kras mutation as a biomarker of carcinogenic effect will not be confounded by animal age. Environ. Mol. Mutagen. 59:715-721, 2018. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Page B McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
| | - Karen L McKim
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
| | - Mason G Pearce
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
| | - Michelle E Bishop
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
| | - Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
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64
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He J, Tu C, Liu Y. Role of lncRNAs in aging and age-related diseases. Aging Med (Milton) 2018; 1:158-175. [PMID: 31942494 PMCID: PMC6880696 DOI: 10.1002/agm2.12030] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 01/10/2023] Open
Abstract
Aging is progressive physiological degeneration and consequently declined function, which is linked to senescence on both cellular and organ levels. Accumulating studies indicate that long noncoding RNAs (lncRNAs) play important roles in cellular senescence at all levels-transcriptional, post-transcriptional, translational, and post-translational. Understanding the molecular mechanism of lncRNAs underlying senescence could facilitate interpretation and intervention of aging and age-related diseases. In this review, we describe categories of known and novel lncRNAs that have been involved in the progression of senescence. We also identify the lncRNAs implicated in diseases arising from age-driven degeneration or dysfunction in some representative organs and systems (brains, liver, muscle, cardiovascular system, bone pancreatic islets, and immune system). Improved comprehension of lncRNAs in the aging process on all levels, from cell to organismal, may provide new insights into the amelioration of age-related pathologies and prolonged healthspan.
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Affiliation(s)
- Jieyu He
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Chao Tu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Youshuo Liu
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
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65
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Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging. BMC Biol 2018; 16:82. [PMID: 30068331 PMCID: PMC6090990 DOI: 10.1186/s12915-018-0547-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/28/2018] [Indexed: 12/04/2022] Open
Abstract
Background Mammals display a wide range of variation in their lifespan. Investigating the molecular networks that distinguish long- from short-lived species has proven useful to identify determinants of longevity. Here, we compared the livers of young and old long-lived naked mole-rats (NMRs) and the phylogenetically closely related, shorter-lived, guinea pigs using an integrated omics approach. Results We found that NMR livers display a unique expression pattern of mitochondrial proteins that results in distinct metabolic features of their mitochondria. For instance, we observed a generally reduced respiration rate associated with lower protein levels of respiratory chain components, particularly complex I, and increased capacity to utilize fatty acids. Interestingly, we show that the same molecular networks are affected during aging in both NMRs and humans, supporting a direct link to the extraordinary longevity of both species. Finally, we identified a novel detoxification pathway linked to longevity and validated it experimentally in the nematode Caenorhabditis elegans. Conclusions Our work demonstrates the benefits of integrating proteomic and transcriptomic data to perform cross-species comparisons of longevity-associated networks. Using a multispecies approach, we show at the molecular level that livers of NMRs display progressive age-dependent changes that recapitulate typical signatures of aging despite the negligible senescence and extraordinary longevity of these rodents. Electronic supplementary material The online version of this article (10.1186/s12915-018-0547-y) contains supplementary material, which is available to authorized users.
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66
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Cho BA, Yoo SK, Seo JS. Signatures of photo-aging and intrinsic aging in skin were revealed by transcriptome network analysis. Aging (Albany NY) 2018; 10:1609-1626. [PMID: 30021930 PMCID: PMC6075446 DOI: 10.18632/aging.101496] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022]
Abstract
There are various factors that alter physiological characteristics in skin. Elucidating the underlying mechanism of transcriptional alterations by intrinsic and extrinsic factors may lead us to understand the aging process of skin. To identify the transcriptomic changes of the aging skin, we analyzed publicly available RNA sequencing data from Genotype-Tissue Expression (GTEx) project. GTEx provided RNA sequencing data of suprapubic (n=228) and lower leg (n=349) skins, which are photo-protected and photo-damaged. Using differentially expressed gene analysis and weighted gene co-expression network analysis, we characterized transcriptomic changes due to UV exposure and aging. Genes involved in skin development such as epidermal differentiation complex component (SPRR and LCE families), vasculature development (TGFBR1, TGFBR2, TGFBR3, KDR, FGF2, and VEGFC), and matrix metalloproteinase (MMP2, MMP3, MMP8, MMP10, and MMP13) were up-regulated by UV exposure. Also, down-regulated lipid metabolism and mitochondrial biogenesis were observed in photo-damaged skin. Moreover, wound healing process was universally down-regulated in suprapubic and lower leg with aging and further down-regulation of lipid metabolism and up-regulation of vasculature development were found as photo-aging signatures. In this study, dynamic transcriptomic alterations were observed in aged skin. Hence, our findings may help to discover a potential therapeutic target for skin rejuvenation.
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Affiliation(s)
- Byuri Angela Cho
- Gong Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- These authors contributed equally to this work
| | - Seong-Keun Yoo
- Genomic Institute, Macrogen Inc., Seoul, Republic of Korea
- These authors contributed equally to this work
| | - Jeong-Sun Seo
- Gong Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Genomic Institute, Macrogen Inc., Seoul, Republic of Korea
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67
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Müller C, Zidek LM, Ackermann T, de Jong T, Liu P, Kliche V, Zaini MA, Kortman G, Harkema L, Verbeek DS, Tuckermann JP, von Maltzahn J, de Bruin A, Guryev V, Wang ZQ, Calkhoven CF. Reduced expression of C/EBPβ-LIP extends health and lifespan in mice. eLife 2018; 7:34985. [PMID: 29708496 PMCID: PMC5986274 DOI: 10.7554/elife.34985] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023] Open
Abstract
Ageing is associated with physical decline and the development of age-related diseases such as metabolic disorders and cancer. Few conditions are known that attenuate the adverse effects of ageing, including calorie restriction (CR) and reduced signalling through the mechanistic target of rapamycin complex 1 (mTORC1) pathway. Synthesis of the metabolic transcription factor C/EBPβ-LIP is stimulated by mTORC1, which critically depends on a short upstream open reading frame (uORF) in the Cebpb-mRNA. Here, we describe that reduced C/EBPβ-LIP expression due to genetic ablation of the uORF delays the development of age-associated phenotypes in mice. Moreover, female C/EBPβΔuORF mice display an extended lifespan. Since LIP levels increase upon aging in wild type mice, our data reveal an important role for C/EBPβ in the aging process and suggest that restriction of LIP expression sustains health and fitness. Thus, therapeutic strategies targeting C/EBPβ-LIP may offer new possibilities to treat age-related diseases and to prolong healthspan. The risks of major diseases including type II diabetes, cancer and Alzheimer’s are linked to the biological process of ageing. By finding ways to slow ageing, we can help more people to live longer healthier lives while avoiding these illnesses. Placing some animals on a diet that contains only two-thirds as many calories as they would normally eat can improve their fitness during old age and delay the onset of many age-related problems. It is unrealistic to expect people to control their diet to this extent, yet there may be other ways to bring about the same effects. Calorie restriction affects the activity of many different genes; for example, it causes a gene that produces a protein known as Liver-enriched Inhibitory Protein (LIP for short) to shut down. LIP controls the activity of many genes involved in metabolism, so it could be a key target for drugs to control ageing. Müller, Zidek et al. used mice that are unable to produce LIP to study this protein’s effect on ageing. The life expectancy of female mice lacking LIP increased by up to 20%. These mice were leaner, fitter, more resistant to cancer, had stronger immune systems and controlled their blood sugar levels better than normal mice. Male mice that lacked LIP did not live longer but did experience some ageing-related benefits. Genetic analysis also showed that gene activity particularly of metabolic genes is more robust in old female LIP-deficient mice and thus more similar to young control mice than old control mice. The results presented by Müller, Zidek et al. suggest that targeting the activity of the LIP gene could help to slow the ageing process. It is not yet clear whether shutting off LIP has similar beneficial effects in humans. Further research is also needed to investigate why female mice gain more benefits from a lack of LIP than males do.
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Affiliation(s)
- Christine Müller
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands.,Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Laura M Zidek
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Tobias Ackermann
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Tristan de Jong
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Peng Liu
- Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Verena Kliche
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Mohamad Amr Zaini
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Gertrud Kortman
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Liesbeth Harkema
- Dutch Molecular Pathology Centre, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jan P Tuckermann
- Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | | | - Alain de Bruin
- Dutch Molecular Pathology Centre, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Cornelis F Calkhoven
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands.,Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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68
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Min KW, Zealy RW, Davila S, Fomin M, Cummings JC, Makowsky D, Mcdowell CH, Thigpen H, Hafner M, Kwon SH, Georgescu C, Wren JD, Yoon JH. Profiling of m6A RNA modifications identified an age-associated regulation of AGO2 mRNA stability. Aging Cell 2018; 17:e12753. [PMID: 29573145 PMCID: PMC5946072 DOI: 10.1111/acel.12753] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2018] [Indexed: 11/30/2022] Open
Abstract
Gene expression is dynamically regulated in a variety of mammalian physiologies. During mammalian aging, there are changes that occur in protein expression that are highly controlled by the regulatory steps in transcription, post-transcription, and post-translation. Although there are global profiles of human transcripts during the aging processes available, the mechanism(s) by which transcripts are differentially expressed between young and old cohorts remains unclear. Here, we report on N6-methyladenosine (m6A) RNA modification profiles of human peripheral blood mononuclear cells (PBMCs) from young and old cohorts. An m6A RNA profile identified a decrease in overall RNA methylation during the aging process as well as the predominant modification on proteincoding mRNAs. The m6A-modified transcripts tend to be more highly expressed than nonmodified ones. Among the many methylated mRNAs, those of DROSHA and AGO2 were heavily methylated in young PBMCs which coincided with a decreased steady-state level of AGO2 mRNA in the old PBMC cohort. Similarly, downregulation of AGO2 in proliferating human diploid fibroblasts (HDFs) also correlated with a decrease in AGO2 mRNA modifications and steady-state levels. In addition, the overexpression of RNA methyltransferases stabilized AGO2 mRNA but not DROSHA and DICER1 mRNA in HDFs. Moreover, the abundance of miRNAs also changed in the young and old PBMCs which are possibly due to a correlation with AGO2 expression as observed in AGO2-depleted HDFs. Taken together, we uncovered the role of mRNA methylation on the abundance of AGO2 mRNA resulting in the repression of miRNA expression during the process of human aging.
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Affiliation(s)
- Kyung-Won Min
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
| | - Richard W. Zealy
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
| | - Sylvia Davila
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
| | - Mikhail Fomin
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
| | - James C. Cummings
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
| | - Daniel Makowsky
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
| | - Catherine H. Mcdowell
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
| | - Haley Thigpen
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation; National Institute of Arthritis and Musculoskeletal and Skin Diseases; Bethesda MD USA
| | - Sang-Ho Kwon
- Department of Medicine; Division of Nephrology; Medical University of South Carolina; Charleston SC USA
| | - Constantin Georgescu
- Arthritis and Clinical Immunology Research Program; Division of Genomics and Data Sciences; Oklahoma Medical Research Foundation; Oklahoma City OK USA
| | - Jonathan D. Wren
- Arthritis and Clinical Immunology Research Program; Division of Genomics and Data Sciences; Oklahoma Medical Research Foundation; Oklahoma City OK USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology; Medical University of South Carolina; Charleston SC USA
- Laboratory of Genetics; National Institute on Aging-Intramural Research Program, NIH; Baltimore MD USA
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69
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miR-494-3p is a novel tumor driver of lung carcinogenesis. Oncotarget 2018; 8:7231-7247. [PMID: 27980227 PMCID: PMC5352317 DOI: 10.18632/oncotarget.13933] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/07/2016] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the leading cause of tumor-related death worldwide and more efforts are needed to elucidate lung carcinogenesis. Here we investigated the expression of 641 miRNAs in lung tumorigenesis in a K-Ras(+/LSLG12Vgeo);RERTn(ert/ert) mouse model and 113 human tumors. The conserved miRNA cluster on chromosome 12qF1 was significantly and progressively upregulated during murine lung carcinogenesis. In particular, miR-494-3p expression was correlated with lung cancer progression in mice and with worse survival in lung cancer patients. Mechanistically, ectopic expression of miR-494-3p in A549 lung cancer cells boosted the tumor-initiating population, enhanced cancer cell motility, and increased the expression of stem cell-related genes. Importantly, miR-494-3p improved the ability of A549 cells to grow and metastasize in vivo, modulating NOTCH1 and PTEN/PI3K/AKT signaling.Overall, these data identify miR-494-3p as a key factor in lung cancer onset and progression and possible therapeutic target.
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70
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Abstract
Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing. These encompass widely reported features of ageing such as increased senescence and inflammation, reduced electron transport chain activity and reduced ribosome synthesis, but also reveal a surprising lack of gene expression responses to known age-linked cellular stresses. We discuss how the existence of conserved transcriptomic hallmarks relates to genome-wide epigenetic differences underlying ageing clocks, and how the changing transcriptome results in proteomic alterations where data is available and to variations in cell physiology characteristic of ageing. Identification of gene expression events that occur during ageing across distant organisms should be informative as to conserved underlying mechanisms of ageing, and provide additional biomarkers to assess the effects of diet and other environmental factors on the rate of ageing.
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Affiliation(s)
- Stephen Frenk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
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71
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Unnikrishnan A, Hadad N, Masser DR, Jackson J, Freeman WM, Richardson A. Revisiting the genomic hypomethylation hypothesis of aging. Ann N Y Acad Sci 2018; 1418:69-79. [PMID: 29363785 DOI: 10.1111/nyas.13533] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/19/2017] [Accepted: 09/26/2017] [Indexed: 12/26/2022]
Abstract
The genomic hypomethylation hypothesis of aging proposes that an overall decrease in global DNA methylation occurs with age, and it has been argued that the decrease in global DNA methylation could be an important factor in aging, resulting in the relaxation of gene expression regulation and abnormal gene expression. Since it was initially observed that DNA methylation decreased with age in 1974, 16 articles have been published describing the effect of age on global DNA methylation in various tissues from rodents and humans. We critically reviewed the publications on the effect of age on DNA methylation and the expression of the enzymes involved in DNA methylation to evaluate the validity of the hypomethylation hypothesis of aging. On the basis of the current scientific literature, we conclude that a decrease in the global methylation of the genome occurs in most if not all tissues/cells as an animal ages. However, age-related changes in DNA methylation in specific regions or at specific sites in the genome occur even though the global DNA methylation does not change.
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Affiliation(s)
- Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Dustin R Masser
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Jordan Jackson
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Willard M Freeman
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Arlan Richardson
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Oklahoma City VA Medical Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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72
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Swindell WR, Xing X, Fritz Y, Diaconu D, Simon DI, Ward NL, Gudjonsson JE. Deficiency of myeloid-related proteins 8 and 14 (Mrp8/Mrp14) does not block inflammaging but prevents steatosis. Oncotarget 2018; 7:35535-35551. [PMID: 27224926 PMCID: PMC5094943 DOI: 10.18632/oncotarget.9550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 05/13/2016] [Indexed: 12/24/2022] Open
Abstract
The Mrp8 and Mrp14 proteins (calprotectin) accumulate within tissues during aging and may contribute to chronic inflammation. To address this possibility, we evaluated female calprotectin-deficient Mrp14-KO and wild-type (WT) mice at 5 and 24 months of age. However, there was no evidence that age-related inflammation is blunted in KO mice. Inflammation markers were in fact elevated in livers from old KO mice, and microarray analysis revealed more consistent elevation of genes specifically expressed by B-cells and T-cells. Adipose-specific genes, however, were less consistently elevated in aged KO mice, suggesting an anti-steatosis effect of Mrp8/14 deficiency. Consistent with this, genes decreased by the anti-steatosis agent SRT1720 were decreased in old KO compared to old WT mice. Expression of lipid metabolism genes was altered in KO mice at 5 months of age, along with genes associated with development, biosynthesis and immunity. These early-age effects of Mrp8/14 deficiency, in the absence of any external stressor, were unexpected. Taken together, our findings demonstrate a pro-steatosis rather than pro-inflammatory role of calprotectin within the aging liver. This appears to reflect a developmental-metabolic phenotype of Mrp14-KO mice that is manifest at a young age in the absence of pro-inflammatory stimuli.
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Affiliation(s)
- William R Swindell
- Ohio University Heritage College of Osteopathic Medicine, Athens, OH, USA.,Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Fritz
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Doina Diaconu
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Daniel I Simon
- Harrington Heart and Vascular Institute, University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nicole L Ward
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA.,The Murdough Family Center for Psoriasis, Case Western Reserve University, Cleveland, OH, USA
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73
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Abstract
As the popular adage goes, all diseases run into old age and almost all physiological changes are associated with alterations in gene expression, irrespective of whether they are causal or consequential. Therefore, the quest for mechanisms that delay ageing and decrease age-associated diseases has propelled researchers to unravel regulatory factors that lead to changes in chromatin structure and function, which ultimately results in deregulated gene expression. It is therefore essential to bring together literature, which until recently has investigated gene expression and chromatin independently. With advances in biomedical research and the emergence of epigenetic regulators as potential therapeutic targets, enhancing our understanding of mechanisms that 'derail' transcription and identification of causal genes/pathways during ageing will have a significant impact. In this context, this chapter aims to not only summarize the key features of age-associated changes in epigenetics and transcription, but also identifies gaps in the field and proposes aspects that need to be investigated in the future.
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74
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Comprehensive transcriptional landscape of porcine cardiac and skeletal muscles reveals differences of aging. Oncotarget 2017; 9:1524-1541. [PMID: 29416711 PMCID: PMC5788579 DOI: 10.18632/oncotarget.23290] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 12/08/2017] [Indexed: 12/11/2022] Open
Abstract
Aging significantly affects the cardiac muscle (CM) and skeletal muscles (SM). Since the aging process of CM and SM may be different, high throughput RNA sequencing was performed using CM and SM in different age conditions to evaluate the expression profiles of messenger RNA (mRNA), long non-coding RNA (lncRNA), micro RNA (miRNA), and circular (circRNA). Several mRNAs, lncRNAs, and miRNAs were highly expressed and consistently appeared in both ages in one of the two muscle tissues. Gene ontology (GO) annotation described that these genes were required for maintaining normal biological functions of CM and SM tissues. Furthermore, 26 mRNAs, 4 lncRNAs, 22 miRNAs, and 26 circRNAs were differentially expressed during cardiac muscle aging. Moreover, 81 mRNAs, 5 lncRNAs, 79 miRNAs, and 62 circRNAs were differentially expressed during aging of skeletal muscle. When comparing the expression profiles of CM and SM during aging, the senescence process in CM and SM was found to be fundamentally different. In addition, we assessed multi-group cooperative control relationships and constructed circRNA-miRNA-mRNA co-expression networks in muscular aging. In conclusion, our findings will contribute to the understanding of muscular aging and provide a foundation for future studies on the molecular mechanisms underlying muscular aging.
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75
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Lenk L, Pein M, Will O, Gomez B, Viol F, Hauser C, Egberts JH, Gundlach JP, Helm O, Tiwari S, Weiskirchen R, Rose-John S, Röcken C, Mikulits W, Wenzel P, Schneider G, Saur D, Schäfer H, Sebens S. The hepatic microenvironment essentially determines tumor cell dormancy and metastatic outgrowth of pancreatic ductal adenocarcinoma. Oncoimmunology 2017; 7:e1368603. [PMID: 29296518 DOI: 10.1080/2162402x.2017.1368603] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/11/2017] [Accepted: 08/12/2017] [Indexed: 12/30/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed when liver metastases already emerged. This study elucidated the impact of hepatic stromal cells on growth behavior of premalignant and malignant pancreatic ductal epithelial cells (PDECs). Liver sections of tumor-bearing KPC mice comprised micrometastases displaying low proliferation located in an unobtrusive hepatic microenvironment whereas macrometastases containing more proliferating cells were surrounded by hepatic myofibroblasts (HMFs). In an age-related syngeneic PDAC mouse model livers with signs of age-related inflammation exhibited significantly more proliferating disseminated tumor cells (DTCs) and micrometastases despite comparable primary tumor growth and DTC numbers. Hepatic stellate cells (HSC), representing a physiologic liver stroma, promoted an IL-8 mediated quiescence-associated phenotype (QAP) of PDECs in coculture. QAP included flattened cell morphology, Ki67-negativity and reduced proliferation, elevated senescence-associated β galactosidase activity and diminished p-Erk/p-p38-ratio. In contrast, proliferation of PDECs was enhanced by VEGF in the presence of HMF. Switching the micromilieu from HSC to HMF or blocking VEGF reversed QAP in PDECs. This study demonstrates how HSCs induce and maintain a reversible QAP in disseminated PDAC cells, while inflammatory HMFs foster QAP reversal and metastatic outgrowth. Overall, the importance of the hepatic microenvironment in induction and reversal of dormancy during PDAC metastasis is emphasized.
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Affiliation(s)
- Lennart Lenk
- Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel (CAU) and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Maren Pein
- Cell Biology and Tumor Biology Program, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Olga Will
- Molecular Imaging North Competence Center, Clinic of Radiology and Neuroradiology, CAU and UKSH Campus Kiel, Kiel, Germany
| | - Beatriz Gomez
- Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel (CAU) and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Fabrice Viol
- Department of Medicine I, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Charlotte Hauser
- Department of General, Visceral-, Thoracic-, Transplantation- and Pediatric Surgery, UKSH Campus Kiel, Kiel, Germany
| | - Jan-Hendrik Egberts
- Department of General, Visceral-, Thoracic-, Transplantation- and Pediatric Surgery, UKSH Campus Kiel, Kiel, Germany
| | - Jan-Paul Gundlach
- Department of General, Visceral-, Thoracic-, Transplantation- and Pediatric Surgery, UKSH Campus Kiel, Kiel, Germany
| | - Ole Helm
- Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel (CAU) and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Sanjay Tiwari
- Molecular Imaging North Competence Center, Clinic of Radiology and Neuroradiology, CAU and UKSH Campus Kiel, Kiel, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH Aachen University, Aachen, Germany
| | | | | | - Wolfgang Mikulits
- Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Patrick Wenzel
- II. Medizinische Klinik und Poliklinik, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Günter Schneider
- II. Medizinische Klinik und Poliklinik, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Dieter Saur
- II. Medizinische Klinik und Poliklinik, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Heiner Schäfer
- Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel (CAU) and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Susanne Sebens
- Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel (CAU) and University Medical Center Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
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76
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Xing W, Gao W, Mao G, Zhang J, Lv X, Wang G, Yan J. Long non-coding RNAs in aging organs and tissues. Clin Exp Pharmacol Physiol 2017; 44 Suppl 1:30-37. [PMID: 28602041 DOI: 10.1111/1440-1681.12795] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/27/2017] [Accepted: 05/07/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Wenmin Xing
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Wenyan Gao
- Institute of Materia Medica; Zhejiang Academy of Medical Sciences; Hangzhou China
| | - Genxiang Mao
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Jing Zhang
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Xiaoling Lv
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Guofu Wang
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
| | - Jing Yan
- Geriatrics Institute of Zhejiang Province & Zhejiang Provincial Key Lab of Geriatrics; Zhejiang Hospital; Hangzhou China
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77
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Saied-Santiago K, Townley RA, Attonito JD, da Cunha DS, Díaz-Balzac CA, Tecle E, Bülow HE. Coordination of Heparan Sulfate Proteoglycans with Wnt Signaling To Control Cellular Migrations and Positioning in Caenorhabditis elegans. Genetics 2017; 206:1951-1967. [PMID: 28576860 PMCID: PMC5560800 DOI: 10.1534/genetics.116.198739] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/20/2017] [Indexed: 11/18/2022] Open
Abstract
Heparan sulfates (HS) are linear polysaccharides with complex modification patterns, which are covalently bound via conserved attachment sites to core proteins to form heparan sulfate proteoglycans (HSPGs). HSPGs regulate many aspects of the development and function of the nervous system, including cell migration, morphology, and network connectivity. HSPGs function as cofactors for multiple signaling pathways, including the Wnt-signaling molecules and their Frizzled receptors. To investigate the functional interactions among the HSPG and Wnt networks, we conducted genetic analyses of each, and also between these networks using five cellular migrations in the nematode Caenorhabditis elegans We find that HSPG core proteins act genetically in a combinatorial fashion dependent on the cellular contexts. Double mutant analyses reveal distinct redundancies among HSPGs for different migration events, and different cellular migrations require distinct heparan sulfate modification patterns. Our studies reveal that the transmembrane HSPG SDN-1/Syndecan functions within the migrating cell to promote cellular migrations, while the GPI-linked LON-2/Glypican functions cell nonautonomously to establish the final cellular position. Genetic analyses with the Wnt-signaling system show that (1) a given HSPG can act with different Wnts and Frizzled receptors, and that (2) a given Wnt/Frizzled pair acts with different HSPGs in a context-dependent manner. Lastly, we find that distinct HSPG and Wnt/Frizzled combinations serve separate functions to promote cellular migration and establish position of specific neurons. Our studies suggest that HSPGs use structurally diverse glycans in coordination with Wnt-signaling pathways to control multiple cellular behaviors, including cellular and axonal migrations and, cellular positioning.
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Affiliation(s)
| | - Robert A Townley
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - John D Attonito
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Dayse S da Cunha
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Carlos A Díaz-Balzac
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Eillen Tecle
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461
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78
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Mangold CA, Wronowski B, Du M, Masser DR, Hadad N, Bixler GV, Brucklacher RM, Ford MM, Sonntag WE, Freeman WM. Sexually divergent induction of microglial-associated neuroinflammation with hippocampal aging. J Neuroinflammation 2017; 14:141. [PMID: 28732515 PMCID: PMC5521082 DOI: 10.1186/s12974-017-0920-8] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 07/13/2017] [Indexed: 01/11/2023] Open
Abstract
Background The necessity of including both males and females in molecular neuroscience research is now well understood. However, there is relatively limited basic biological data on brain sex differences across the lifespan despite the differences in age-related neurological dysfunction and disease between males and females. Methods Whole genome gene expression of young (3 months), adult (12 months), and old (24 months) male and female C57BL6 mice hippocampus was analyzed. Subsequent bioinformatic analyses and confirmations of age-related changes and sex differences in hippocampal gene and protein expression were performed. Results Males and females demonstrate both common expression changes with aging and marked sex differences in the nature and magnitude of the aging responses. Age-related hippocampal induction of neuroinflammatory gene expression was sexually divergent and enriched for microglia-specific genes such as complement pathway components. Sexually divergent C1q protein expression was confirmed by immunoblotting and immunohistochemistry. Similar patterns of cortical sexually divergent gene expression were also evident. Additionally, inter-animal gene expression variability increased with aging in males, but not females. Conclusions These findings demonstrate sexually divergent neuroinflammation with aging that may contribute to sex differences in age-related neurological diseases such as stroke and Alzheimer’s, specifically in the complement system. The increased expression variability in males suggests a loss of fidelity in gene expression regulation with aging. These findings reveal a central role of sex in the transcriptomic response of the hippocampus to aging that warrants further, in depth, investigations. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0920-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colleen A Mangold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA, USA
| | - Benjamin Wronowski
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Mei Du
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Dustin R Masser
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Reynolds Oklahoma Center on Aging & Nathan Shock Center of Excellence in the Biology of Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging & Nathan Shock Center of Excellence in the Biology of Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Georgina V Bixler
- Genome Sciences Facility, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Robert M Brucklacher
- Genome Sciences Facility, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Matthew M Ford
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon, USA
| | - William E Sonntag
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Reynolds Oklahoma Center on Aging & Nathan Shock Center of Excellence in the Biology of Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Reynolds Oklahoma Center on Aging & Nathan Shock Center of Excellence in the Biology of Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, USA. .,, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.
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79
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Rawle RA, Hamerly T, Tripet BP, Giannone RJ, Wurch L, Hettich RL, Podar M, Copié V, Bothner B. Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association. Biochim Biophys Acta Gen Subj 2017; 1861:2218-2227. [PMID: 28591626 DOI: 10.1016/j.bbagen.2017.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 05/13/2017] [Accepted: 06/02/2017] [Indexed: 12/27/2022]
Abstract
BACKGROUND Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted 'omics' analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. METHODS We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. RESULTS Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis-N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. CONCLUSIONS This multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis-N. equitans association. GENERAL SIGNIFICANCE Our study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies.
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Affiliation(s)
- Rachel A Rawle
- Department of Microbiology, Montana State University, Bozeman, MT 59717, United States; Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Timothy Hamerly
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Brian P Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | | | - Louie Wurch
- Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Robert L Hettich
- Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Mircea Podar
- Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Valerie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States; Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States.
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States; Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States.
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80
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Milholland B, Suh Y, Vijg J. Mutation and catastrophe in the aging genome. Exp Gerontol 2017; 94:34-40. [PMID: 28263867 DOI: 10.1016/j.exger.2017.02.073] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 02/06/2023]
Abstract
In the 1960s, Leslie Orgel proposed what is now known as the error catastrophe theory of aging, arguing that errors in protein translation that reduce the fidelity of the protein-translating enzymes would lead to a feedback loop of increasingly inaccurate protein synthesis, terminating in the death of the organism. This mechanism of aging would be consistent with the exponential increase of mortality observed in humans, but the error catastrophe theory of aging has been generally disregarded by researchers due to a lack of evidence for an age-related increase in protein errors. Another theory of aging, proposed at roughly the same time, is Leo Szilard's two-hit model of somatic mutation accumulation, which assumed a linear increase in mutations over time but explained the nonlinear pattern of human mortality through a mechanism of genetic and cellular redundancy which kept mortality low until the redundancy was exhausted, at which point mortality rapidly rose. Here, we synthesize the two theories, along with the latest advances in genomics research. We propose a new catastrophe theory of aging, this time with somatic mutations as the primary agent of the feedback loop. Similar to protein errors affecting translation itself, somatic mutations in genes involved in DNA replication and repair would lead to a feedback loop of exponentially increasing mutation load. The difference from protein errors is that somatic mutations would mainly affect gene regulatory regions rather than the much smaller part of the genome encoding protein-coding information. Although the self-stimulating accumulation of somatic mutations is not mutually exclusive with the Szilard-based loss of redundancy, we present evidence that suggests that the accumulated mutations themselves could be numerous enough to cause mortality. Finally, we acknowledge the limits of our current knowledge and propose a course of research practices that will help to confirm or refute our model and advance the field of aging research as a whole.
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Affiliation(s)
- Brandon Milholland
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States.
| | - Yousin Suh
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States; Department of Ophthalmology & Visual Sciences, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States; Department of Medicine, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States; Department of Ophthalmology & Visual Sciences, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States.
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81
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Abstract
Differences in DNA repair capacity have been hypothesized to underlie the great range of maximum lifespans among mammals. However, measurements of individual DNA repair activities in cells and animals have not substantiated such a relationship because utilization of repair pathways among animals—depending on habitats, anatomical characteristics, and life styles—varies greatly between mammalian species. Recent advances in high-throughput genomics, in combination with increased knowledge of the genetic pathways involved in genome maintenance, now enable a comprehensive comparison of DNA repair transcriptomes in animal species with extreme lifespan differences. Here we compare transcriptomes of liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, with maximum lifespans of ∼120, 30, and 3 years, respectively, with a focus on genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of DNA repair genes, including core genes in several DNA repair pathways. A more systematic approach of signaling pathway analysis indicates statistically significant upregulation of several DNA repair signaling pathways in human and naked mole rat compared with mouse. The results of this present work indicate, for the first time, that DNA repair is upregulated in a major metabolic organ in long-lived humans and naked mole rats compared with short-lived mice. These results strongly suggest that DNA repair can be considered a genuine longevity assurance system.
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82
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Systematic Analysis of Long Noncoding RNAs in the Senescence-accelerated Mouse Prone 8 Brain Using RNA Sequencing. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e343. [PMID: 27483026 PMCID: PMC5023402 DOI: 10.1038/mtna.2016.57] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/14/2016] [Indexed: 02/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) may play an important role in Alzheimer's disease (AD) pathogenesis. However, despite considerable research in this area, the comprehensive and systematic understanding of lncRNAs in AD is still limited. The emergence of RNA sequencing provides a predictor and has incomparable advantage compared with other methods, including microarray. In this study, we identified lncRNAs in a 7-month-old mouse brain through deep RNA sequencing using the senescence-accelerated mouse prone 8 (SAMP8) and senescence-accelerated mouse resistant 1 (SAMR1) models. A total of 599,985,802 clean reads and 23,334 lncRNA transcripts were obtained. Then, we identified 97 significantly upregulated and 114 significantly downregulated lncRNA transcripts from all cases in SAMP8 mice relative to SAMR1 mice. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these significantly dysregulated lncRNAs were involved in regulating the development of AD from various angles, such as nerve growth factor term (GO: 1990089), mitogen-activated protein kinase signaling pathway, and AD pathway. Furthermore, the most probable AD-associated lncRNAs were predicted and listed in detail. Our study provided the systematic dissection of lncRNA profiling in SAMP8 mouse brain and accelerated the development of lncRNA biomarkers in AD. These attracting biomarkers could provide significant insights into AD therapy in the future.
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