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Rispo F, De Negri Atanasio G, Demori I, Costa G, Marchese E, Perera-Del-Rosario S, Serrano-Candelas E, Palomino-Schätzlein M, Perata E, Robino F, Ferrari PF, Ferrando S, Letasiova S, Markus J, Zanotti-Russo M, Grasselli E. An extensive review on phenolic compounds and their potential estrogenic properties on skin physiology. Front Cell Dev Biol 2024; 11:1305835. [PMID: 38250328 PMCID: PMC10798251 DOI: 10.3389/fcell.2023.1305835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024] Open
Abstract
Polyphenolic compounds constitute a diverse group of natural components commonly occurring in various plant species, known for their potential to exert both beneficial and detrimental effects. Additionally, these polyphenols have also been implicated as endocrine-disrupting (ED) chemicals, raising concerns about their widespread use in the cosmetics industry. In this comprehensive review, we focus on the body of literature pertaining to the estrogenic properties of ED chemicals, with a particular emphasis on the interaction of isoflavones with estrogen receptors. Within this review, we aim to elucidate the multifaceted roles and effects of polyphenols on the skin, exploring their potential benefits as well as their capacity to act as ED agents. By delving into this intricate subject matter, we intend to provoke thoughtful consideration, effectively opening a Pandora's box of questions for the reader to ponder. Ultimately, we invite the reader to contemplate whether polyphenols should be regarded as friends or foes in the realm of skincare and endocrine disruption.
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Affiliation(s)
- Francesca Rispo
- Department of Earth, Environment and Life Science, University of Genoa, Genova, Italy
| | | | - Ilaria Demori
- Department of Pharmacy, University of Genoa, Genova, Italy
| | - Giosuè Costa
- Department of Health Sciences, University "Magna Graecia", Catanzaro, Italy
| | - Emanuela Marchese
- Department of Health Sciences, University "Magna Graecia", Catanzaro, Italy
| | - Simón Perera-Del-Rosario
- ProtoQSAR SL, Centro Europeo de Empresas Innovadoras (CEEI), Parque Tecnológico de Valencia, Valencia, Spain
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Eva Serrano-Candelas
- ProtoQSAR SL, Centro Europeo de Empresas Innovadoras (CEEI), Parque Tecnológico de Valencia, Valencia, Spain
| | | | | | | | - Pier Francesco Ferrari
- Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genova, Italy
| | - Sara Ferrando
- Department of Earth, Environment and Life Science, University of Genoa, Genova, Italy
| | | | - Jan Markus
- MatTek In Vitro Life Science Laboratories, Bratislava, Slovakia
| | | | - Elena Grasselli
- Department of Earth, Environment and Life Science, University of Genoa, Genova, Italy
- Interuniversity Center for the Promotion of 3R Principles in Teaching and Research (Centro 3R), Pisa, Italy
- National Center for the Development of New Technologies in Agriculture (Agritech), Napoli, Italy
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2
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Baralle M, Romano M. Age-Related Alternative Splicing: Driver or Passenger in the Aging Process? Cells 2023; 12:2819. [PMID: 38132139 PMCID: PMC10742131 DOI: 10.3390/cells12242819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy;
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
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3
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Winsky-Sommerer R, King HA, Iadevaia V, Möller-Levet C, Gerber AP. A post-transcriptional regulatory landscape of aging in the female mouse hippocampus. Front Aging Neurosci 2023; 15:1119873. [PMID: 37122377 PMCID: PMC10135431 DOI: 10.3389/fnagi.2023.1119873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2023] Open
Abstract
Aging is associated with substantial physiological changes and constitutes a major risk factor for neurological disorders including dementia. Alterations in gene expression upon aging have been extensively studied; however, an in-depth characterization of post-transcriptional regulatory events remains elusive. Here, we profiled the age-related changes of the transcriptome and translatome in the female mouse hippocampus by RNA sequencing of total RNA and polysome preparations at four ages (3-, 6-, 12-, 20-month-old); and we implemented a variety of bioinformatics approaches to unravel alterations in transcript abundance, alternative splicing, and polyadenylation site selection. We observed mostly well-coordinated transcriptome and translatome expression signatures across age including upregulation of transcripts related to immune system processes and neuroinflammation, though transcripts encoding ribonucleoproteins or associated with mitochondrial functions, calcium signaling and the cell-cycle displayed substantial discordant profiles, suggesting translational control associated with age-related deficits in hippocampal-dependent behavior. By contrast, alternative splicing was less preserved, increased with age and was associated with distinct functionally-related transcripts encoding proteins acting at synapses/dendrites, RNA-binding proteins; thereby predicting regulatory roles for RBM3 and CIRBP. Only minor changes in polyadenylation site selection were identified, indicating pivotal 3'-end selection in young adults compared to older groups. Overall, our study provides a comprehensive resource of age-associated post-transcriptional regulatory events in the mouse hippocampus, enabling further examination of the molecular features underlying age-associated neurological diseases.
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4
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Pabis K, Chiari Y, Sala C, Straka E, Giacconi R, Provinciali M, Li X, Brown-Borg H, Nowikovsky K, Valencak TG, Gundacker C, Garagnani P, Malavolta M. Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging. GeroScience 2021; 43:1975-1993. [PMID: 34117600 DOI: 10.1007/s11357-021-00393-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/24/2021] [Indexed: 11/29/2022] Open
Abstract
Cadmium (Cd) accumulates with aging and is elevated in long-lived species. Metallothioneins (MTs), small cysteine-rich proteins involved in metal homeostasis and Cd detoxification, are known to be related to longevity. However, the relationship between Cd accumulation, the role of MTs, and aging is currently unclear. Specifically, we do not know if long-lived species evolved an efficient metal stress response by upregulating their MT levels to reduce the toxic effects of environmental pollutants, such as Cd, that accumulate over their longer life span. It is also unknown if the number of MT genes, their expression, or both protect the organisms from potentially damaging effects during aging. To address these questions, we reanalyzed several cross-species studies and obtained data on MT expression and Cd accumulation in long-lived mouse models. We confirmed a relationship between species maximum life span in captive mammals and their Cd content in liver and kidney. We found that although the number of MT genes does not affect longevity, gene expression and protein amount of specific MT paralogs are strongly related to life span in mammals. MT expression rather than gene number may influence the high Cd levels and longevity of some species. In support of this, we found that overexpression of MT-1 accelerated Cd accumulation in mice and that tissue Cd was higher in long-lived mouse strains with high MT expression. We conclude that long-lived species have evolved a more efficient stress response by upregulating the expression of MT genes in presence of Cd, which contributes to elevated tissue Cd levels.
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Affiliation(s)
- Kamil Pabis
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, 40126, Bologna, Italy
| | - Elisabeth Straka
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy
| | - Xinna Li
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Holly Brown-Borg
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58203, USA
| | - Karin Nowikovsky
- Department of Internal Medicine I and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Teresa G Valencak
- Department of Animal Science and Technology, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Claudia Gundacker
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), and Interdepartmental Centre "L. Galvani" (CIG), University of Bologna, Bologna, Italy.,Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy.
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5
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Shafir A, Azouri D, Goldberg EE, Mayrose I. Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates. Evolution 2020; 74:1620-1639. [PMID: 32510165 DOI: 10.1111/evo.14036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/17/2020] [Indexed: 12/01/2022]
Abstract
As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study, we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Dana Azouri
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel.,School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | | | - Itay Mayrose
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
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6
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Turan ZG, Parvizi P, Dönertaş HM, Tung J, Khaitovich P, Somel M. Molecular footprint of Medawar's mutation accumulation process in mammalian aging. Aging Cell 2019; 18:e12965. [PMID: 31062469 PMCID: PMC6612638 DOI: 10.1111/acel.12965] [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: 09/03/2018] [Revised: 02/14/2019] [Accepted: 03/28/2019] [Indexed: 12/20/2022] Open
Abstract
Medawar's mutation accumulation hypothesis explains aging by the declining force of natural selection with age: Slightly deleterious germline mutations expressed in old age can drift to fixation and thereby lead to aging‐related phenotypes. Although widely cited, empirical evidence for this hypothesis has remained limited. Here, we test one of its predictions that genes relatively highly expressed in old adults should be under weaker purifying selection than genes relatively highly expressed in young adults. Combining 66 transcriptome datasets (including 16 tissues from five mammalian species) with sequence conservation estimates across mammals, here we report that the overall conservation level of expressed genes is lower at old age compared to young adulthood. This age‐related decrease in transcriptome conservation (ADICT) is systematically observed in diverse mammalian tissues, including the brain, liver, lung, and artery, but not in others, most notably in the muscle and heart. Where observed, ADICT is driven partly by poorly conserved genes being up‐regulated during aging. In general, the more often a gene is found up‐regulated with age among tissues and species, the lower its evolutionary conservation. Poorly conserved and up‐regulated genes have overlapping functional properties that include responses to age‐associated tissue damage, such as apoptosis and inflammation. Meanwhile, these genes do not appear to be under positive selection. Hence, genes contributing to old age phenotypes are found to harbor an excess of slightly deleterious alleles, at least in certain tissues. This supports the notion that genetic drift shapes aging in multicellular organisms, consistent with Medawar's mutation accumulation hypothesis.
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Affiliation(s)
- Zeliha Gözde Turan
- Department of Biological Sciences Middle East Technical University Ankara Turkey
| | - Poorya Parvizi
- Department of Biological Sciences Middle East Technical University Ankara Turkey
- Usher Institute of Population Health Sciences and Informatics University of Edinburgh Edinburgh UK
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL‐EBI Wellcome Trust Genome Campus Cambridge UK
| | - Jenny Tung
- Department of Evolutionary Anthropology Duke University Durham North Carolina
- Department of Biology Duke University Durham North Carolina
- Duke Population Research Institute Duke University Durham North Carolina
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration Skolkovo Institute of Science and Technology Moscow Russia
- CAS Key Laboratory of Computational Biology, CAS‐MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
| | - Mehmet Somel
- Department of Biological Sciences Middle East Technical University Ankara Turkey
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7
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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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8
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Alfego D, Rodeck U, Kriete A. Global mapping of transcription factor motifs in human aging. PLoS One 2018; 13:e0190457. [PMID: 29293662 PMCID: PMC5749797 DOI: 10.1371/journal.pone.0190457] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/14/2017] [Indexed: 12/12/2022] Open
Abstract
Biological aging is a complex process dependent on the interplay of cell autonomous and tissue contextual changes which occur in response to cumulative molecular stress and manifest through adaptive transcriptional reprogramming. Here we describe a transcription factor (TF) meta-analysis of gene expression datasets accrued from 18 tissue sites collected at different biological ages and from 7 different in-vitro aging models. In-vitro aging platforms included replicative senescence and an energy restriction model in quiescence (ERiQ), in which ATP was transiently reduced. TF motifs in promoter regions of trimmed sets of target genes were scanned using JASPAR and TRANSFAC. TF signatures established a global mapping of agglomerating motifs with distinct clusters when ranked hierarchically. Remarkably, the ERiQ profile was shared with the majority of in-vivo aged tissues. Fitting motifs in a minimalistic protein-protein network allowed to probe for connectivity to distinct stress sensors. The DNA damage sensors ATM and ATR linked to the subnetwork associated with senescence. By contrast, the energy sensors PTEN and AMPK connected to the nodes in the ERiQ subnetwork. These data suggest that metabolic dysfunction may be linked to transcriptional patterns characteristic of many aged tissues and distinct from cumulative DNA damage associated with senescence.
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Affiliation(s)
- David Alfego
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Ulrich Rodeck
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Andres Kriete
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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9
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Wong KC. MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences. Bioinformatics 2017. [DOI: 10.1093/bioinformatics/btx381] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong
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10
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Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing. PLoS One 2016; 11:e0165913. [PMID: 27829007 PMCID: PMC5102383 DOI: 10.1371/journal.pone.0165913] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/19/2016] [Indexed: 01/23/2023] Open
Abstract
While much is known about genes that promote aging, little is known about genes that protect against or prevent aging, particularly in human skin. The main objective of this study was to perform an unbiased, whole transcriptome search for genes that associate with intrinsic skin youthfulness. To accomplish this, healthy women (n = 122) of European descent, ages 18–89 years with Fitzpatrick skin type I/II were examined for facial skin aging parameters and clinical covariates, including smoking and ultraviolet exposure. Skin youthfulness was defined as the top 10% of individuals whose assessed skin aging features were most discrepant with their chronological ages. Skin biopsies from sun-protected inner arm were subjected to 3’-end sequencing for expression quantification, with results verified by quantitative reverse transcriptase-polymerase chain reaction. Unbiased clustering revealed gene expression signatures characteristic of older women with skin youthfulness (n = 12) compared to older women without skin youthfulness (n = 33), after accounting for gene expression changes associated with chronological age alone. Gene set analysis was performed using Genomica open-access software. This study identified a novel set of candidate skin youthfulness genes demonstrating differences between SY and non-SY group, including pleckstrin homology like domain family A member 1 (PHLDA1) (p = 2.4x10-5), a follicle stem cell marker, and hyaluronan synthase 2-anti-sense 1 (HAS2-AS1) (p = 0.00105), a non-coding RNA that is part of the hyaluronan synthesis pathway. We show that immunologic gene sets are the most significantly altered in skin youthfulness (with the most significant gene set p = 2.4x10-5), suggesting the immune system plays an important role in skin youthfulness, a finding that has not previously been recognized. These results are a valuable resource from which multiple future studies may be undertaken to better understand the mechanisms that promote skin youthfulness in humans.
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11
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Major differences between human atopic dermatitis and murine models, as determined by using global transcriptomic profiling. J Allergy Clin Immunol 2016; 139:562-571. [PMID: 27702671 DOI: 10.1016/j.jaci.2016.08.029] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/04/2016] [Accepted: 08/08/2016] [Indexed: 01/04/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) is caused by a complex interplay between immune and barrier abnormalities. Murine models of AD are essential for preclinical assessments of new treatments. Although many models have been used to simulate AD, their transcriptomic profiles are not fully understood, and a comparison of these models with the human AD transcriptomic fingerprint is lacking. OBJECTIVE We sought to evaluate the transcriptomic profiles of 6 common murine models and determine how they relate to human AD skin. METHODS Transcriptomic profiling was performed by using microarrays and quantitative RT-PCR on biopsy specimens from NC/Nga, flaky tail, Flg-mutated, ovalbumin-challenged, oxazolone-challenged, and IL-23-injected mice. Gene expression data of patients with AD, psoriasis, and contact dermatitis were obtained from previous patient cohorts. Criteria of a fold change of 2 or greater and a false discovery rate of 0.05 or less were used for gene arrays. RESULTS IL-23-injected, NC/Nga, and oxazolone-challenged mice show the largest homology with our human meta-analysis-derived AD transcriptome (37%, 18%, 17%, respectively). Similar to human AD, robust TH1, TH2, and also TH17 activation are seen in IL-23-injected and NC/Nga mice, with similar but weaker inflammation in ovalbumin-challenged mice. Oxazolone-challenged mice show a TH1-centered reaction, and flaky tail mice demonstrate a strong TH17 polarization. Flg-mutated mice display filaggrin downregulation without significant inflammation. CONCLUSION No single murine model fully captures all aspects of the AD profile; instead, each model reflects different immune or barrier disease aspects. Overall, among the 6 murine models, IL-23-injected mice best simulate human AD; still, the translational focus of the investigation should determine which model is most applicable.
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12
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Lucas ER, Privman E, Keller L. Higher expression of somatic repair genes in long-lived ant queens than workers. Aging (Albany NY) 2016; 8:1940-1951. [PMID: 27617474 PMCID: PMC5076446 DOI: 10.18632/aging.101027] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/19/2016] [Indexed: 12/20/2022]
Abstract
Understanding why organisms senesce is a fundamental question in biology. One common explanation is that senescence results from an increase in macromolecular damage with age. The tremendous variation in lifespan between genetically identical queen and worker ants, ranging over an order of magnitude, provides a unique system to study how investment into processes of somatic maintenance and macromolecular repair influence lifespan. Here we use RNAseq to compare patterns of expression of genes involved in DNA and protein repair of age-matched queens and workers. There was no difference between queens and workers in 1-day-old individuals, but the level of expression of these genes increased with age and this up-regulation was greater in queens than in workers, resulting in significantly queen-biased expression in 2-month-old individuals in both legs and brains. Overall, these differences are consistent with the hypothesis that higher longevity is associated with increased investment into somatic repair.
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Affiliation(s)
- Eric R. Lucas
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, 31905 Haifa, Israel
| | - Laurent Keller
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
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13
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Stout MB, Swindell WR, Zhi X, Rohde K, List EO, Berryman DE, Kopchick JJ, Gesing A, Fang Y, Masternak MM. Transcriptome profiling reveals divergent expression shifts in brown and white adipose tissue from long-lived GHRKO mice. Oncotarget 2016; 6:26702-15. [PMID: 26436954 PMCID: PMC4694946 DOI: 10.18632/oncotarget.5760] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 08/29/2015] [Indexed: 12/24/2022] Open
Abstract
Mice lacking the growth hormone receptor (GHRKO) exhibit improved lifespan and healthspan due to loss of growth hormone signaling. Both the distribution and activity of brown and white adipose tissue (BAT and WAT) are altered in GHRKO mice, but the contribution of each tissue to age-related phenotypes has remained unclear. We therefore used whole-genome microarrays to evaluate transcriptional differences in BAT and WAT depots between GHRKO and normal littermates at six months of age. Our findings reveal a unique BAT transcriptome as well as distinctive responses of BAT to Ghr ablation. BAT from GHRKO mice exhibited elevated expression of genes associated with mitochondria and metabolism, along with reduced expression of genes expressed by monocyte-derived cells (dendritic cells [DC] and macrophages). Largely the opposite was observed in WAT, with increased expression of DC-expressed genes and reduced expression of genes associated with metabolism, cellular respiration and the mitochondrial inner envelope. These findings demonstrate divergent response patterns of BAT and WAT to loss of GH signaling in GHRKO mice. These patterns suggest both BAT and WAT contribute in different ways to phenotypes in GHRKO mice, with Ghr ablation blunting inflammation in BAT as well as cellular metabolism and mitochondrial biogenesis in WAT.
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Affiliation(s)
- Michael B Stout
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | | | - Xu Zhi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Kyle Rohde
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Edward O List
- Edison Biotechnology Institute and Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Darlene E Berryman
- Edison Biotechnology Institute and Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - John J Kopchick
- Edison Biotechnology Institute and Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Adam Gesing
- Department of Oncological Endocrinology, Medical University of Lodz, Lodz, Poland
| | - Yimin Fang
- Geriatrics Research Laboratory, Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Michal M Masternak
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA.,Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan, Poland
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14
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Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, Schadt EE, Zhu J, Tu Z. Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. Sci Rep 2015; 5:15145. [PMID: 26477495 PMCID: PMC4609956 DOI: 10.1038/srep15145] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 09/21/2015] [Indexed: 01/06/2023] Open
Abstract
Aging is one of the most important biological processes and is a known risk factor for many age-related diseases in human. Studying age-related transcriptomic changes in tissues across the whole body can provide valuable information for a holistic understanding of this fundamental process. In this work, we catalogue age-related gene expression changes in nine tissues from nearly two hundred individuals collected by the Genotype-Tissue Expression (GTEx) project. In general, we find the aging gene expression signatures are very tissue specific. However, enrichment for some well-known aging components such as mitochondria biology is observed in many tissues. Different levels of cross-tissue synchronization of age-related gene expression changes are observed, and some essential tissues (e.g., heart and lung) show much stronger "co-aging" than other tissues based on a principal component analysis. The aging gene signatures and complex disease genes show a complex overlapping pattern and only in some cases, we see that they are significantly overlapped in the tissues affected by the corresponding diseases. In summary, our analyses provide novel insights to the co-regulation of age-related gene expression in multiple tissues; it also presents a tissue-specific view of the link between aging and age-related diseases.
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Affiliation(s)
- Jialiang Yang
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Tao Huang
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Francesca Petralia
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Quan Long
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Bin Zhang
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Carmen Argmann
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Yong Zhao
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Charles V. Mobbs
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Medicine, Endocrinology, Diabetes and Bone Disease, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Eric E. Schadt
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Jun Zhu
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Zhidong Tu
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
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15
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Jung M, Jin SG, Zhang X, Xiong W, Gogoshin G, Rodin AS, Pfeifer GP. Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging. Nucleic Acids Res 2015; 43:e100. [PMID: 25977295 PMCID: PMC4551908 DOI: 10.1093/nar/gkv473] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/29/2015] [Indexed: 12/28/2022] Open
Abstract
Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.
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Affiliation(s)
- Marc Jung
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Seung-Gi Jin
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiaoying Zhang
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Wenying Xiong
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Grigoriy Gogoshin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Andrei S Rodin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gerd P Pfeifer
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
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16
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Stauffer BL, Dockstader K, Russell G, Hijmans J, Walker L, Cecil M, Demos-Davies K, Medway A, McKinsey TA, Sucharov CC. Transgenic over-expression of YY1 induces pathologic cardiac hypertrophy in a sex-specific manner. Biochem Biophys Res Commun 2015; 462:131-7. [PMID: 25935483 DOI: 10.1016/j.bbrc.2015.04.106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/11/2015] [Indexed: 02/08/2023]
Abstract
YY1 can activate or repress transcription of various genes. In cardiac myocytes in culture YY1 has been shown to regulate expression of several genes involved in myocyte pathology. YY1 can also acutely protect the heart against detrimental changes in gene expression. In this study we show that cardiac over-expression of YY1 induces pathologic cardiac hypertrophy in male mice, measured by changes in gene expression and lower ejection fraction/fractional shortening. In contrast, female animals are protected against pathologic gene expression changes and cardiac dysfunction. Furthermore, we show that YY1 regulates, in a sex-specific manner, the expression of mammalian enable (Mena), a factor that regulates cytoskeletal actin dynamics and whose expression is increased in several models of cardiac pathology, and that Mena expression in humans with heart failure is sex-dependent. Finally, we show that sex differences in YY1 expression are also observed in human heart failure. In summary, this is the first work to show that YY1 has a sex-specific effect in the regulation of cardiac pathology.
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Affiliation(s)
- Brian L Stauffer
- Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA; Division of Cardiology, Denver Health and Hospital Authority, Denver, CO, USA
| | - Karen Dockstader
- Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gloria Russell
- Pontificia Universidad Católica Madre y Maestra, Departamento de Medicina, Santiago, Dominican Republic
| | - Jamie Hijmans
- Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA
| | | | | | | | - Allen Medway
- Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Timothy A McKinsey
- Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Carmen C Sucharov
- Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA.
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17
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Age-Associated Increase in Skin Fibroblast-Derived Prostaglandin E2 Contributes to Reduced Collagen Levels in Elderly Human Skin. J Invest Dermatol 2015; 135:2181-2188. [PMID: 25905589 PMCID: PMC4537382 DOI: 10.1038/jid.2015.157] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/15/2015] [Accepted: 04/07/2015] [Indexed: 01/16/2023]
Abstract
Production of type I collagen declines during aging, leading to skin thinning and impaired function. Prostaglandin E2 (PGE2) is a pleiotropic lipid mediator that is synthesized from arachidonic acid by the sequential actions of cyclooxygenases (COX) and PGE synthases (PTGES). PGE2 inhibits collagen production by fibroblasts in vitro. We report that PTGES1 and COX2 progressively increase with aging in sun-protected human skin. PTGES1 and COX2 mRNA were increased 3.4-fold and 2.7-fold, respectively, in the dermis of elderly (>80 years) versus young (21-30 years) individuals. Fibroblasts were the major cell source of both enzymes. PGE2 levels were increased 70% in elderly skin. Fibroblasts in aged skin display reduced spreading due to collagen fibril fragmentation. To investigate the relationship between spreading and PGE2 synthesis, fibroblasts were cultured on micropost arrays or hydrogels of varying mechanical compliance. Reduced spreading/mechanical force resulted in increased expression of both PTGES1 and COX2 and elevated levels of PGE2. Inhibition of PGE2 synthesis by diclofenac enhanced collagen production in skin organ cultures. These data suggest that reduced spreading/mechanical force of fibroblasts in aged skin elevates PGE2 production, contributing to reduced collagen production. Inhibition of PGE2 production may be therapeutically beneficial for combating age-associated collagen deficit in human skin.
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18
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Mansergh FC, Carrigan M, Hokamp K, Farrar GJ. Gene expression changes during retinal development and rod specification. Mol Vis 2015; 21:61-87. [PMID: 25678762 PMCID: PMC4301594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/16/2015] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) typically results from individual mutations in any one of >70 genes that cause rod photoreceptor cells to degenerate prematurely, eventually resulting in blindness. Gene therapies targeting individual RP genes have shown efficacy at clinical trial; however, these therapies require the surviving photoreceptor cells to be viable and functional, and may be economically feasible for only the more commonly mutated genes. An alternative potential treatment strategy, particularly for late stage disease, may involve stem cell transplants into the photoreceptor layer of the retina. Rod progenitors from postnatal mouse retinas can be transplanted and can form photoreceptors in recipient adult retinas; optimal numbers of transplantable cells are obtained from postnatal day 3-5 (P3-5) retinas. These cells can also be expanded in culture; however, this results in the loss of photoreceptor potential. Gene expression differences between postnatal retinas, cultured retinal progenitor cells (RPCs), and rod photoreceptor precursors were investigated to identify gene expression patterns involved in the specification of rod photoreceptors. METHODS Microarrays were used to investigate differences in gene expression between cultured RPCs that have lost photoreceptor potential, P1 retinas, and fresh P5 retinas that contain significant numbers of transplantable photoreceptors. Additionally, fluorescence-activated cell sorting (FACS) sorted Rho-eGFP-expressing rod photoreceptor precursors were compared with Rho-eGFP-negative cells from the same P5 retinas. Differential expression was confirmed with quantitative polymerase chain reaction (q-PCR). RESULTS Analysis of the microarray data sets, including the use of t-distributed stochastic neighbor embedding (t-SNE) to identify expression pattern neighbors of key photoreceptor specific genes, resulted in the identification of 636 genes differentially regulated during rod specification. Forty-four of these genes when mutated have previously been found to cause retinal disease. Although gene function in other tissues may be known, the retinal function of approximately 61% of the gene list is as yet undetermined. Many of these genes' promoters contain binding sites for the key photoreceptor transcription factors Crx and Nr2e3; moreover, the genomic clustering of differentially regulated genes appears to be non-random. CONCLUSIONS This study aids in understanding gene expression differences between rod photoreceptor progenitors versus cultured RPCs that have lost photoreceptor potential. The results provide insights into rod photoreceptor development and should expedite the development of cell-based treatments for RP. Furthermore, the data set includes a large number of retinopathy genes; less-well-characterized genes within this data set are a resource for those seeking to identify novel retinopathy genes in patients with RP (GEO accession: GSE59201).
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Affiliation(s)
- Fiona C Mansergh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew Carrigan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - G Jane Farrar
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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19
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Grzegorski SJ, Chiari EF, Robbins A, Kish PE, Kahana A. Natural variability of Kozak sequences correlates with function in a zebrafish model. PLoS One 2014; 9:e108475. [PMID: 25248153 PMCID: PMC4172775 DOI: 10.1371/journal.pone.0108475] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/29/2014] [Indexed: 12/02/2022] Open
Abstract
In eukaryotes, targeting the small ribosomal subunit to the mRNA transcript requires a Kozak sequence at the translation initiation site. Despite the critical importance of the Kozak sequence to regulation of gene expression, there have been no correlation studies between its natural variance and efficiency of translation. Combining bioinformatics analysis with molecular biology techniques, and using zebrafish as a test case, we identify Kozak sequences based on their natural variance and characterize their function invivo. Our data reveal that while the canonical Kozak sequence is efficient, in zebrafish it is neither the most common nor the most efficient translation initiation sequence. Rather, the most frequent natural variation of the Kozak sequence is almost twice as efficient. We conclude that the canonical Kozak sequence is a poor predictor of translation efficiency in different model organisms. Furthermore, our results provide an experimental approach to testing and optimizing an important tool for molecular biology.
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Affiliation(s)
- Steven J. Grzegorski
- Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Estelle F. Chiari
- Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Amy Robbins
- Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Phillip E. Kish
- Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alon Kahana
- Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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20
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Melis JPM, Jonker MJ, Vijg J, Hoeijmakers JHJ, Breit TM, van Steeg H. Aging on a different scale--chronological versus pathology-related aging. Aging (Albany NY) 2014; 5:782-8. [PMID: 24131799 PMCID: PMC3838780 DOI: 10.18632/aging.100606] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the next decades the elderly population will increase dramatically, demanding appropriate solutions in health care and aging research focusing on healthy aging to prevent high burdens and costs in health care. For this, research targeting tissue-specific and individual aging is paramount to make the necessary progression in aging research. In a recently published study we have attempted to make a step interpreting aging data on chronological as well as pathological scale. For this, we sampled five major tissues at regular time intervals during the entire C57BL/6J murine lifespan from a controlled in vivo aging study, measured the whole transcriptome and incorporated temporal as well as physical health aspects into the analyses. In total, we used 18 different age-related pathological parameters and transcriptomic profiles of liver, kidney, spleen, lung and brain and created a database that can now be used for a broad systems biology approach. In our study, we focused on the dynamics of biological processes during chronological aging and the comparison between chronological and pathology-related aging.
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Affiliation(s)
- Joost P M Melis
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, the Netherlands
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21
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Boyette LB, Tuan RS. Adult Stem Cells and Diseases of Aging. J Clin Med 2014; 3:88-134. [PMID: 24757526 PMCID: PMC3992297 DOI: 10.3390/jcm3010088] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/15/2013] [Accepted: 12/17/2013] [Indexed: 02/06/2023] Open
Abstract
Preservation of adult stem cells pools is critical for maintaining tissue homeostasis into old age. Exhaustion of adult stem cell pools as a result of deranged metabolic signaling, premature senescence as a response to oncogenic insults to the somatic genome, and other causes contribute to tissue degeneration with age. Both progeria, an extreme example of early-onset aging, and heritable longevity have provided avenues to study regulation of the aging program and its impact on adult stem cell compartments. In this review, we discuss recent findings concerning the effects of aging on stem cells, contributions of stem cells to age-related pathologies, examples of signaling pathways at work in these processes, and lessons about cellular aging gleaned from the development and refinement of cellular reprogramming technologies. We highlight emerging therapeutic approaches to manipulation of key signaling pathways corrupting or exhausting adult stem cells, as well as other approaches targeted at maintaining robust stem cell pools to extend not only lifespan but healthspan.
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Affiliation(s)
- Lisa B Boyette
- Center for Cellular and Molecular Engineering, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA; ; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Rocky S Tuan
- Center for Cellular and Molecular Engineering, Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA; ; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA ; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
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22
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Sun LY, Spong A, Swindell WR, Fang Y, Hill C, Huber JA, Boehm JD, Westbrook R, Salvatori R, Bartke A. Growth hormone-releasing hormone disruption extends lifespan and regulates response to caloric restriction in mice. eLife 2013; 2:e01098. [PMID: 24175087 PMCID: PMC3810783 DOI: 10.7554/elife.01098] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/25/2013] [Indexed: 12/18/2022] Open
Abstract
We examine the impact of targeted disruption of growth hormone-releasing hormone (GHRH) in mice on longevity and the putative mechanisms of delayed aging. GHRH knockout mice are remarkably long-lived, exhibiting major shifts in the expression of genes related to xenobiotic detoxification, stress resistance, and insulin signaling. These mutant mice also have increased adiponectin levels and alterations in glucose homeostasis consistent with the removal of the counter-insulin effects of growth hormone. While these effects overlap with those of caloric restriction, we show that the effects of caloric restriction (CR) and the GHRH mutation are additive, with lifespan of GHRH-KO mutants further increased by CR. We conclude that GHRH-KO mice feature perturbations in a network of signaling pathways related to stress resistance, metabolic control and inflammation, and therefore provide a new model that can be used to explore links between GHRH repression, downregulation of the somatotropic axis, and extended longevity. DOI:http://dx.doi.org/10.7554/eLife.01098.001 There is increasing evidence that the hormonal systems involved in growth, the metabolism of glucose, and the processes that balance energy intake and expenditure might also be involved in the aging process. In rodents, mutations in genes involved in these hormone-signaling pathways can substantially increase lifespan, as can a diet that is low in calories but which avoids malnutrition. As well as living longer, such mice also show reductions in age-related conditions such as diabetes, memory loss and cancer. Many of these effects appear to involve the actions of growth hormone. Mice with mutations that disrupt the development of the pituitary gland, which produces growth hormone, show increased longevity, as do mice that lack the receptor for growth hormone. However, these animals also show changes in a number of other hormones, making it difficult to be sure that the reduction in growth hormone signaling is responsible for their increased lifespan. Now, Sun et al. have studied mutant mice that lack a gene called GHRH, which promotes the release of growth hormone. These mice, which have normal levels of all other pituitary hormones, lived for up to 50% longer than their wild-type littermates. They were more active than normal mice and had more body fat, and showed greatly increased sensitivity to insulin. Some of the changes in these mutant mice resembled those seen in animals with a restricted calorie intake, suggesting that the same mechanisms may be implicated in both. However, Sun et al. found that caloric restriction further increased the lifespans of their GHRH knockout mice, indicating that at least some of the effects of caloric restriction are independent of disrupted growth hormone signaling. The results of this study are an important step forward for understanding how growth hormone signaling and caloric restriction regulate aging, both individually and in combination. The GHRH knockout mice are likely to become an important model system for studying these processes and for understanding the complex interactions between diet and hormonal pathways. DOI:http://dx.doi.org/10.7554/eLife.01098.002
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Affiliation(s)
- Liou Y Sun
- Department of Internal Medicine , Southern Illinois University School of Medicine , Springfield , United States
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23
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Stephens DN, Klein RH, Salmans ML, Gordon W, Ho H, Andersen B. The Ets transcription factor EHF as a regulator of cornea epithelial cell identity. J Biol Chem 2013; 288:34304-24. [PMID: 24142692 DOI: 10.1074/jbc.m113.504399] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The cornea is the clear, outermost portion of the eye composed of three layers: an epithelium that provides a protective barrier while allowing transmission of light into the eye, a collagen-rich stroma, and an endothelium monolayer. How cornea development and aging is controlled is poorly understood. Here we characterize the mouse cornea transcriptome from early embryogenesis through aging and compare it with transcriptomes of other epithelial tissues, identifying cornea-enriched genes, pathways, and transcriptional regulators. Additionally, we profiled cornea epithelium and stroma, defining genes enriched in these layers. Over 10,000 genes are differentially regulated in the mouse cornea across the time course, showing dynamic expression during development and modest expression changes in fewer genes during aging. A striking transition time point for gene expression between postnatal days 14 and 28 corresponds with completion of cornea development at the transcriptional level. Clustering classifies co-expressed, and potentially co-regulated, genes into biologically informative categories, including groups that exhibit epithelial or stromal enriched expression. Based on these findings, and through loss of function studies and ChIP-seq, we show that the Ets transcription factor EHF promotes cornea epithelial fate through complementary gene activating and repressing activities. Furthermore, we identify potential interactions between EHF, KLF4, and KLF5 in promoting cornea epithelial differentiation. These data provide insights into the mechanisms underlying epithelial development and aging, identifying EHF as a regulator of cornea epithelial identity and pointing to interactions between Ets and KLF factors in promoting epithelial fate. Furthermore, this comprehensive gene expression data set for the cornea is a powerful tool for discovery of novel cornea regulators and pathways.
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24
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Jonker MJ, Melis JPM, Kuiper RV, van der Hoeven TV, Wackers PFK, Robinson J, van der Horst GTJ, Dollé MET, Vijg J, Breit TM, Hoeijmakers JHJ, van Steeg H. Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs. Aging Cell 2013; 12:901-909. [PMID: 23795901 DOI: 10.1111/acel.12118] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2013] [Indexed: 01/10/2023] Open
Abstract
Aging and age-related pathology is a result of a still incompletely understood intricate web of molecular and cellular processes. We present a C57BL/6J female mice in vivo aging study of five organs (liver, kidney, spleen, lung, and brain), in which we compare genome-wide gene expression profiles during chronological aging with pathological changes throughout the entire murine life span (13, 26, 52, 78, 104, and 130 weeks). Relating gene expression changes to chronological aging revealed many differentially expressed genes (DEGs), and altered gene sets (AGSs) were found in most organs, indicative of intraorgan generic aging processes. However, only ≤ 1% of these DEGs are found in all organs. For each organ, at least one of 18 tested pathological parameters showed a good age-predictive value, albeit with much inter- and intraindividual (organ) variation. Relating gene expression changes to pathology-related aging revealed correlated genes and gene sets, which made it possible to characterize the difference between biological and chronological aging. In liver, kidney, and brain, a limited number of overlapping pathology-related AGSs were found. Immune responses appeared to be common, yet the changes were specific in most organs. Furthermore, changes were observed in energy homeostasis, reactive oxygen species, cell cycle, cell motility, and DNA damage. Comparison of chronological and pathology-related AGSs revealed substantial overlap and interesting differences. For example, the presence of immune processes in liver pathology-related AGSs that were not detected in chronological aging. The many cellular processes that are only found employing aging-related pathology could provide important new insights into the progress of aging.
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Affiliation(s)
| | | | | | - Tessa V. van der Hoeven
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU); Swammerdam Institute for Life Sciences (SILS); Faculty of Science (FNWI); University of Amsterdam (UvA); Amsterdam; The Netherlands
| | | | | | | | - Martijn E. T. Dollé
- National Institute for Public Health and the Environment (RIVM); Center for Health Protection; Bilthoven; The Netherlands
| | - Jan Vijg
- Department of Genetics; Albert Einstein College of Medicine; New York; NY; USA
| | | | - Jan H. J. Hoeijmakers
- CGC Department of Genetics; Erasmus University Medical Center; Rotterdam; The Netherlands
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25
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Valdes AM, Glass D, Spector TD. Omics technologies and the study of human ageing. Nat Rev Genet 2013; 14:601-7. [PMID: 23938363 DOI: 10.1038/nrg3553] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Normal ageing is associated with diverse physiological changes in all organ systems but the rate and extent of these changes vary markedly among individuals. One aspect of ageing research focuses on the molecular profiling of the changes that occur with increasing age in humans. Such profiling has implications for disease prevention and treatment. New high-throughput 'omics' technologies (such as genomics, metabolomics, metagenomics and transcriptomics) are enabling detailed studies of these molecular changes and are thus revealing information about the biological pathways that change with age.
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Affiliation(s)
- Ana M Valdes
- 1] Department of Twin Research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK. [2] Academic Rheumatology, University of Nottingham, Nottingham NG5 1PB, UK
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Swindell WR, Johnston A, Voorhees JJ, Elder JT, Gudjonsson JE. Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients. BMC Genomics 2013; 14:527. [PMID: 23915137 PMCID: PMC3751090 DOI: 10.1186/1471-2164-14-527] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 07/31/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Psoriasis lesions are characterized by large-scale shifts in gene expression. Mechanisms that underlie differentially expressed genes (DEGs), however, are not completely understood. We analyzed existing datasets to evaluate genome-wide expression in lesions from 163 psoriasis patients. Our aims were to identify mechanisms that drive differential expression and to characterize heterogeneity among lesions in this large sample. RESULTS We identified 1233 psoriasis-increased DEGs and 977 psoriasis-decreased DEGs. Increased DEGs were attributed to keratinocyte activity (56%) and infiltration of lesions by T-cells (14%) and macrophages (11%). Decreased DEGs, in contrast, were associated with adipose tissue (63%), epidermis (14%) and dermis (4%). KC/epidermis DEGs were enriched for genes induced by IL-1, IL-17A and IL-20 family cytokines, and were also disproportionately associated with AP-1 binding sites. Among all patients, 50% exhibited a heightened inflammatory signature, with increased expression of genes expressed by T-cells, monocytes and dendritic cells. 66% of patients displayed an IFN-γ-strong signature, with increased expression of genes induced by IFN-γ in addition to several other cytokines (e.g., IL-1, IL-17A and TNF). We show that such differences in gene expression can be used to differentiate between etanercept responders and non-responders. CONCLUSIONS Psoriasis DEGs are partly explained by shifts in the cellular composition of psoriasis lesions. Epidermal DEGs, however, may be driven by the activity of AP-1 and cellular responses to IL-1, IL-17A and IL-20 family cytokines. Among patients, we uncovered a range of inflammatory- and cytokine-associated gene expression patterns. Such patterns may provide biomarkers for predicting individual responses to biologic therapy.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA
| | - James T Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA
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Beclin 1 interactome controls the crosstalk between apoptosis, autophagy and inflammasome activation: impact on the aging process. Ageing Res Rev 2013; 12:520-34. [PMID: 23220384 DOI: 10.1016/j.arr.2012.11.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 11/28/2012] [Accepted: 11/28/2012] [Indexed: 01/10/2023]
Abstract
Autophagy and apoptosis are crucial cellular housekeeping and tissue survival mechanisms. There is emerging evidence of important crosstalk between apoptosis and autophagy which can be linked to inflammasome activation. Beclin 1 is a platform protein which assembles an interactome consisting of diverse proteins which control the initiation of autophagocytosis and distinct phases in endocytosis. Recent studies have demonstrated that the anti-apoptotic Bcl-2 family members can interact with Beclin 1 and inhibit autophagy. Consequently, impaired autophagy can trigger inflammasome activation. Interestingly, the hallmarks of the ageing process include a decline in autophagy, increased resistance to apoptosis and a low-grade inflammatory phenotype. Age-related stresses, e.g. genotoxic, metabolic and environmental insults, enhance the expression of NF-κB-driven anti-apoptotic Bcl-2 proteins which repress the Beclin 1-dependent autophagy. Suppression of autophagocytosis provokes inflammation including NF-κB activation which further potentiates anti-apoptotic defence. In a context-dependent manner, this feedback defence mechanism can enhance the aging process or provoke tumorigenesis or cellular senescence. We will review the role of Beclin 1 interactome in the crosstalk between apoptosis, autophagy and inflammasomes emphasizing that disturbances in Beclin 1-dependent autophagy can have a crucial impact on the aging process.
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Swindell WR, Johnston A, Xing X, Little A, Robichaud P, Voorhees JJ, Fisher G, Gudjonsson JE. Robust shifts in S100a9 expression with aging: a novel mechanism for chronic inflammation. Sci Rep 2013; 3:1215. [PMID: 23386971 PMCID: PMC3564041 DOI: 10.1038/srep01215] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 01/16/2013] [Indexed: 02/08/2023] Open
Abstract
The S100a8 and S100a9 genes encode a pro-inflammatory protein (calgranulin) that has been implicated in multiple diseases. However, involvement of S100a8/a9 in the basic mechanisms of intrinsic aging has not been established. In this study, we show that shifts in the abundance of S100a8 and S100a9 mRNA are a robust feature of aging in mammalian tissues, involving a range of cell types including the central nervous system. To identify transcription factors that control S100a9 expression, we performed a large-scale transcriptome analysis of 62 mouse and human cell types. We identified cell type-specific trends, as well as robust associations linking S100a9 coexpression to elevated frequency of ETS family motifs, and in particular, to motifs recognized by the transcription factor SPI/PU.1. Sparse occurrence of SATB1 motifs was also a strong predictor of S100a9 coexpression. These findings offer support for a novel mechanism by which a SPI1/PU.1-S100a9 axis sustains chronic inflammation during aging.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA.
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Context-Dependent Regulation of Autophagy by IKK-NF-κB Signaling: Impact on the Aging Process. Int J Cell Biol 2012; 2012:849541. [PMID: 22899934 PMCID: PMC3412117 DOI: 10.1155/2012/849541] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 06/21/2012] [Indexed: 12/19/2022] Open
Abstract
The NF-κB signaling system and the autophagic degradation pathway are crucial cellular survival mechanisms, both being well conserved during evolution. Emerging studies have indicated that the IKK/NF-κB signaling axis regulates autophagy in a context-dependent manner. IKK complex and NF-κB can enhance the expression of Beclin 1 and other autophagy-related proteins and stimulate autophagy whereas as a feedback response, autophagy can degrade IKK components. Moreover, NF-κB signaling activates the expression of autophagy inhibitors (e.g., A20 and Bcl-2/xL) and represses the activators of autophagy (BNIP3, JNK1, and ROS). Several studies have indicated that NF-κB signaling is enhanced both during aging and cellular senescence, inducing a proinflammatory phenotype. The aging process is also associated with a decline in autophagic degradation. It seems that the activity of Beclin 1 initiation complex could be impaired with aging, since the expression of Beclin 1 decreases as does the activity of type III PI3K. On the other hand, the expression of inhibitory Bcl-2/xL proteins increases with aging. We will review the recent literature on the control mechanisms of autophagy through IKK/NF-κB signaling and emphasize that NF-κB signaling could be a potent repressor of autophagy with ageing.
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