151
|
Mendelsohn AR, Larrick JW. Epigenetic Drift Is a Determinant of Mammalian Lifespan. Rejuvenation Res 2018; 20:430-436. [PMID: 28942711 DOI: 10.1089/rej.2017.2024] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The epigenome, which controls cell identity and function, is not maintained with 100% fidelity in somatic animal cells. Errors in the maintenance of the epigenome lead to epigenetic drift, an important hallmark of aging. Numerous studies have described DNA methylation clocks that correlate epigenetic drift with increasing age. The question of how significant a role epigenetic drift plays in creating the phenotypes associated with aging remains open. A recent study describes a new DNA methylation clock that can be slowed by caloric restriction (CR) in a way that correlates with the degree of lifespan and healthspan extension conferred by CR, suggesting that epigenetic drift itself is a determinant of mammalian lifespan. Genetic transplantation using genomic editing of DNA methylation homeostatic genes from long-lived to short-lived species is one way to potentially demonstrate a causative role for DNA methylation. Whether the DNA methylation clock be reset to youthful state, eliminating the effects of epigenetic drift without requiring a pluripotent cell intermediate is a critical question with profound implications for the development of aging therapeutics. Methods that transiently erase the DNA methylation pattern of somatic cells may be developed that reset this aging hallmark with potentially profound effects on lifespan, if DNA methylation-based epigenetic drift really plays a primary role in aging.
Collapse
Affiliation(s)
- Andrew R Mendelsohn
- 1 Regenerative Sciences Institute , Sunnyvale, California.,2 Panorama Research Institute , Sunnyvale, California
| | | |
Collapse
|
152
|
Puca AA, Spinelli C, Accardi G, Villa F, Caruso C. Centenarians as a model to discover genetic and epigenetic signatures of healthy ageing. Mech Ageing Dev 2018; 174:95-102. [DOI: 10.1016/j.mad.2017.10.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/26/2017] [Accepted: 10/28/2017] [Indexed: 01/07/2023]
|
153
|
Singh KP, Miaskowski C, Dhruva AA, Flowers E, Kober KM. Mechanisms and Measurement of Changes in Gene Expression. Biol Res Nurs 2018; 20:369-382. [PMID: 29706088 PMCID: PMC6346310 DOI: 10.1177/1099800418772161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Research on gene expression (GE) provides insights into the physiology of a cell or group of cells at a given point in time. Studies of changes in GE can be used to identify patients at higher risk for various medical conditions, a higher symptom burden, and/or the adverse consequences associated with various treatments. The aims of this article are as follows: (1) to describe the different types of RNA transcripts, (2) to describe the processes involved in GE (i.e., RNA transcription, epigenetics, and posttranscriptional modifications), (3) to describe common sources of variation in GE, (4) to describe the most common methods used to measure GE, and (5) to discuss factors to consider when choosing tissue for a GE study. This article begins with an overview of the mechanisms involved in GE. Then, the factors that can influence the findings from GE experiments (e.g., tissue specificity, host age, host gender, and time of sample collection) are described and potential solutions are presented. This article concludes with a discussion of how the types of tissue used in GE studies can affect study findings. Given that the costs associated with the measurement of changes in GE are decreasing and the methods to analyze GE data are becoming easier to use, nurse scientists need to understand the basic principles that underlie any GE study.
Collapse
Affiliation(s)
- Komal P. Singh
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA, USA
| | - Christine Miaskowski
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA, USA
| | - Anand A. Dhruva
- School of Medicine, University of California, San Francisco, CA, USA
| | - Elena Flowers
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA, USA
| | - Kord M. Kober
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA, USA
| |
Collapse
|
154
|
Cheung P, Vallania F, Warsinske HC, Donato M, Schaffert S, Chang SE, Dvorak M, Dekker CL, Davis MM, Utz PJ, Khatri P, Kuo AJ. Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging. Cell 2018; 173:1385-1397.e14. [PMID: 29706550 PMCID: PMC5984186 DOI: 10.1016/j.cell.2018.03.079] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/27/2018] [Accepted: 03/28/2018] [Indexed: 12/17/2022]
Abstract
Post-translational modifications of histone proteins and exchanges of histone variants of chromatin are central to the regulation of nearly all DNA-templated biological processes. However, the degree and variability of chromatin modifications in specific human immune cells remain largely unknown. Here, we employ a highly multiplexed mass cytometry analysis to profile the global levels of a broad array of chromatin modifications in primary human immune cells at the single-cell level. Our data reveal markedly different cell-type- and hematopoietic-lineage-specific chromatin modification patterns. Differential analysis between younger and older adults shows that aging is associated with increased heterogeneity between individuals and elevated cell-to-cell variability in chromatin modifications. Analysis of a twin cohort unveils heritability of chromatin modifications and demonstrates that aging-related chromatin alterations are predominantly driven by non-heritable influences. Together, we present a powerful platform for chromatin and immunology research. Our discoveries highlight the profound impacts of aging on chromatin modifications.
Collapse
Affiliation(s)
- Peggie Cheung
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Francesco Vallania
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hayley C Warsinske
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Schaffert
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Alex J Kuo
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
155
|
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.
Collapse
Affiliation(s)
- Stephen Frenk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
| | | |
Collapse
|
156
|
Han R, Huang G, Wang Y, Xu Y, Hu Y, Jiang W, Wang T, Xiao T, Zheng D. Increased gene expression noise in human cancers is correlated with low p53 and immune activities as well as late stage cancer. Oncotarget 2018; 7:72011-72020. [PMID: 27713130 PMCID: PMC5342140 DOI: 10.18632/oncotarget.12457] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 01/19/2023] Open
Abstract
Gene expression in metazoans is delicately organized. As genetic information transmits from DNA to RNA and protein, expression noise is inevitably generated. Recent studies begin to unveil the mechanisms of gene expression noise control, but the changes of gene expression precision in pathologic conditions like cancers are unknown. Here we analyzed the transcriptomic data of human breast, liver, lung and colon cancers, and found that the expression noise of more than 74.9% genes was increased in cancer tissues as compared to adjacent normal tissues. This suggested that gene expression precision controlling collapsed during cancer development. A set of 269 genes with noise increased more than 2-fold were identified across different cancer types. These genes were involved in cell adhesion, catalytic and metabolic functions, implying the vulnerability of deregulation of these processes in cancers. We also observed a tendency of increased expression noise in patients with low p53 and immune activity in breast, liver and lung caners but not in colon cancers, which indicated the contributions of p53 signaling and host immune surveillance to gene expression noise in cancers. Moreover, more than 53.7% genes had increased noise in patients with late stage than early stage cancers, suggesting that gene expression precision was associated with cancer outcome. Together, these results provided genomic scale explorations of gene expression noise control in human cancers.
Collapse
Affiliation(s)
- Rongfei Han
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| | - Guanqun Huang
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| | - Yejun Wang
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| | - Yafei Xu
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| | - Yueming Hu
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| | - Wenqi Jiang
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| | - Tianfu Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| | - Tian Xiao
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| | - Duo Zheng
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, 518060, P.R.China
| |
Collapse
|
157
|
Viñuela A, Brown AA, Buil A, Tsai PC, Davies MN, Bell JT, Dermitzakis ET, Spector TD, Small KS. Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort. Hum Mol Genet 2018; 27:732-741. [PMID: 29228364 PMCID: PMC5886097 DOI: 10.1093/hmg/ddx424] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/10/2017] [Accepted: 11/29/2017] [Indexed: 12/13/2022] Open
Abstract
Changes in the mean and variance of gene expression with age have consequences for healthy aging and disease development. Age-dependent changes in phenotypic variance have been associated with a decline in regulatory functions leading to increase in disease risk. Here, we investigate age-related mean and variance changes in gene expression measured by RNA-seq of fat, skin, whole blood and derived lymphoblastoid cell lines (LCLs) expression from 855 adult female twins. We see evidence of up to 60% of age effects on transcription levels shared across tissues, and 47% of those on splicing. Using gene expression variance and discordance between genetically identical MZ twin pairs, we identify 137 genes with age-related changes in variance and 42 genes with age-related discordance between co-twins; implying the latter are driven by environmental effects. We identify four eQTLs whose effect on expression is age-dependent (FDR 5%). Combined, these results show a complicated mix of environmental and genetically driven changes in expression with age. Using the twin structure in our data, we show that additive genetic effects explain considerably more of the variance in gene expression than aging, but less that other environmental factors, potentially explaining why reliable expression-derived biomarkers for healthy-aging have proved elusive compared with those derived from methylation.
Collapse
Affiliation(s)
- Ana Viñuela
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, SE1 7EH London, UK
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Andrew A Brown
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK
- Division of Mental Health and Addiction, NORMENT, KG Jebsen Centre for Psychosis Research, Oslo University Hospital, Oslo 0450, Norway
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, SE1 7EH London, UK
| | - Matthew N Davies
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, SE1 7EH London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, SE1 7EH London, UK
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, SE1 7EH London, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, SE1 7EH London, UK
| |
Collapse
|
158
|
Yang E, Wang G, Yang J, Zhou B, Tian Y, Cai JJ. Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Hum Mol Genet 2018; 25:4911-4919. [PMID: 28171656 DOI: 10.1093/hmg/ddw314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/19/2016] [Accepted: 09/12/2016] [Indexed: 11/14/2022] Open
Abstract
Increasing evidence shows that phenotypic variance is genetically determined, but the underlying mechanisms of genetic control over the variance remain obscure. Here, we conducted variance-association mapping analyses to identify expression variability QTLs (evQTLs), i.e. genomic loci associated with gene expression variance, in humans. We discovered that common genetic variants may contribute to increasing gene expression variance via two distinct modes of action—epistasis and destabilization. Specifically, epistasis explains a quarter of the identified evQTLs, of which the formation is attributed to the presence of ‘third-party’ eQTLs that influence the gene expression mean in a fraction, rather than the entire set, of sampled individuals. On the other hand, the destabilization model explains the other three-quarters of evQTLs, caused by mutations that disrupt the stability of the transcription process of genes. To show the destabilizing effect, we measured discordant gene expression between monozygotic twins, and estimated the stability of gene expression in single samples using repetitive qRT-PCR assays. The mutations that cause destabilizing evQTLs were found to be associated with more pronounced expression discordance between twin pairs and less stable gene expression in single samples. Together, our results suggest that common genetic variants work either interactively or independently to shape the variability of gene expression in humans. Our findings contribute to the understanding of the mechanisms of genetic control over phenotypic variance and may have implications for the development of variance-centred analytic methods for quantitative trait mapping.
Collapse
Affiliation(s)
- Ence Yang
- Department of Veterinary Integrative Biosciences.,Institute for Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Gang Wang
- Department of Veterinary Integrative Biosciences
| | - Jizhou Yang
- Department of Veterinary Integrative Biosciences
| | - Beiyan Zhou
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA.,Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Yanan Tian
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences.,Interdisciplinary Program of Genetics, Texas A&M University, College Station, TX, USA
| |
Collapse
|
159
|
Kudryavtseva A, Krasnov G, Lipatova A, Alekseev B, Maganova F, Shaposhnikov M, Fedorova M, Snezhkina A, Moskalev A. Effects of Abies sibirica terpenes on cancer- and aging-associated pathways in human cells. Oncotarget 2018; 7:83744-83754. [PMID: 27888805 PMCID: PMC5347801 DOI: 10.18632/oncotarget.13467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/19/2016] [Indexed: 12/31/2022] Open
Abstract
A large number of terpenoids exhibit potential geroprotector and anti-cancer properties. Here, we studied whole transcriptomic effects of Abisil, the extract of fir (Abies sibirica) terpenes, on normal and cancer cell lines. We used early passaged and senescent none-immortalized fibroblasts as cellular aging models. It was revealed that in normal fibroblasts, terpenes induced genes of stress response, apoptosis regulation and tissue regeneration. The restoration of the expression level of some prolongevity genes after fir extract treatment was shown in old cells. In Caco-2 and AsPC-1 cancer cell lines, Abisil induced expression of both onco-suppressors (members of GADD45, DUSP, and DDIT gene families), and proto-oncogenes (c-Myc, c-Jun, EGR and others). Thus, the study demonstrates the potential anti-aging and anti-cancer effects of Abisil on senescent and cancer cell lines.
Collapse
Affiliation(s)
- Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasiya Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Boris Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284, Russia
| | | | - Mikhail Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russia
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasiya Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| |
Collapse
|
160
|
Inukai S, Pincus Z, de Lencastre A, Slack FJ. A microRNA feedback loop regulates global microRNA abundance during aging. RNA (NEW YORK, N.Y.) 2018; 24:159-172. [PMID: 29114017 PMCID: PMC5769744 DOI: 10.1261/rna.062190.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/29/2017] [Indexed: 06/07/2023]
Abstract
Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa. However, little is known about the mechanisms or the biological relevance for this change. We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging. We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs. In particular, miR-71, known to influence life span and itself up-regulated during aging, represses alg-1/Argonaute expression post-transcriptionally during aging. Increased ALG-1 abundance in mir-71 loss-of-function mutants led to globally increased miRNA expression. Interestingly, these mutants demonstrated widespread mRNA expression dysregulation and diminished levels of variability both in gene expression and in overall life span. Thus, the progressive molecular decline often thought to be the result of accumulated damage over an organism's life may be partially explained by a miRNA-directed mechanism of age-associated decline.
Collapse
Affiliation(s)
- Sachi Inukai
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Zachary Pincus
- Department of Developmental Biology
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Alexandre de Lencastre
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| |
Collapse
|
161
|
Söllradl T, Banville FA, Fröhlich U, Canva M, Charette PG, Grandbois M. Label-free visualization and quantification of single cell signaling activity using metal-clad waveguide (MCWG)-based microscopy. Biosens Bioelectron 2018; 100:429-436. [DOI: 10.1016/j.bios.2017.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/01/2017] [Accepted: 09/01/2017] [Indexed: 01/01/2023]
|
162
|
Abstract
Metabolic changes are hallmarks of aging and genetic and pharmacologic alterations of relevant pathways can extend life span. In this review, we will outline how cellular biochemistry and energy homeostasis change during aging. We will highlight protein quality control, mitochondria, epigenetics, nutrient-sensing pathways, as well as the interplay between these systems with respect to their impact on cellular health.
Collapse
Affiliation(s)
- Andre Catic
- Huffington Center on Aging, Stem Cells and Regenerative Medicine Center, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States.
| |
Collapse
|
163
|
Smith S, Grima R. Single-cell variability in multicellular organisms. Nat Commun 2018; 9:345. [PMID: 29367605 PMCID: PMC5783944 DOI: 10.1038/s41467-017-02710-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 12/20/2017] [Indexed: 02/04/2023] Open
Abstract
Noisy gene expression is of fundamental importance to single cells, and is therefore widely studied in single-celled organisms. Extending these studies to multicellular organisms is challenging since their cells are generally not isolated, but individuals in a tissue. Cell–cell coupling via signalling, active transport or pure diffusion, ensures that tissue-bound cells are neither fully independent of each other, nor an entirely homogeneous population. In this article, we show that increasing the strength of coupling between cells can either increase or decrease the single-cell variability (and, therefore, the heterogeneity of the tissue), depending on the statistical properties of the underlying genetic network. We confirm these predictions using spatial stochastic simulations of simple genetic networks, and experimental data from animal and plant tissues. The results suggest that cell–cell coupling may be one of several noise-control strategies employed by multicellular organisms, and highlight the need for a deeper understanding of multicellular behaviour. While gene expression noise in single-celled organisms is well understood, it is less so in the context of tissues. Here the authors show that coupling between cells in tissues can increase or decrease cell-to-cell variability depending on the level of noise intrinsic to the regulatory networks.
Collapse
Affiliation(s)
- Stephen Smith
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JR, Scotland, UK
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JR, Scotland, UK.
| |
Collapse
|
164
|
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.
Collapse
|
165
|
Barteneva NS, Vorobjev IA. Heterogeneity of Metazoan Cells and Beyond: To Integrative Analysis of Cellular Populations at Single-Cell Level. Methods Mol Biol 2018; 1745:3-23. [PMID: 29476460 DOI: 10.1007/978-1-4939-7680-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this paper, we review some of the recent advances in cellular heterogeneity and single-cell analysis methods. In modern research of cellular heterogeneity, there are four major approaches: analysis of pooled samples, single-cell analysis, high-throughput single-cell analysis, and lately integrated analysis of cellular population at a single-cell level. Recently developed high-throughput single-cell genetic analysis methods such as RNA-Seq require purification step and destruction of an analyzed cell often are providing a snapshot of the investigated cell without spatiotemporal context. Correlative analysis of multiparameter morphological, functional, and molecular information is important for differentiation of more uniform groups in the spectrum of different cell types. Simplified distributions (histograms and 2D plots) can underrepresent biologically significant subpopulations. Future directions may include the development of nondestructive methods for dissecting molecular events in intact cells, simultaneous correlative cellular analysis of phenotypic and molecular features by hybrid technologies such as imaging flow cytometry, and further progress in supervised and non-supervised statistical analysis algorithms.
Collapse
Affiliation(s)
- Natasha S Barteneva
- PCMM-Harvard Medical School, Boston Children's Hospital, Boston, MA, USA.
- Department of Biology, School of Sciences and Technology, Nazarbayev University, Astana, Kazakhstan.
| | - Ivan A Vorobjev
- Department of Biology, School of Sciences and Technology, Nazarbayev University, Astana, Kazakhstan
| |
Collapse
|
166
|
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.
Collapse
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:
| |
Collapse
|
167
|
Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges. Proc Natl Acad Sci U S A 2017; 115:E488-E497. [PMID: 29282317 PMCID: PMC5776984 DOI: 10.1073/pnas.1714765115] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Identifying the drivers of the interindividual diversity of the human immune system is crucial to understand their consequences on immune-mediated diseases. By examining the transcriptional responses of 1,000 individuals to various microbial challenges, we show that age and sex influence the expression of many immune-related genes, but their effects are overall moderate, whereas genetic factors affect a smaller gene set but with a stronger effect. We identify numerous genetic variants that affect transcriptional variation on infection, many of which are associated with autoimmune or inflammatory disorders. These results enable additional exploration of the role of regulatory variants in the pathogenesis of immune-related diseases and improve our understanding of the respective effects of age, sex, and genetics on immune response variation. The contribution of host genetic and nongenetic factors to immunological differences in humans remains largely undefined. Here, we generated bacterial-, fungal-, and viral-induced immune transcriptional profiles in an age- and sex-balanced cohort of 1,000 healthy individuals and searched for the determinants of immune response variation. We found that age and sex affected the transcriptional response of most immune-related genes, with age effects being more stimulus-specific relative to sex effects, which were largely shared across conditions. Although specific cell populations mediated the effects of age and sex on gene expression, including CD8+ T cells for age and CD4+ T cells and monocytes for sex, we detected a direct effect of these intrinsic factors for the majority of immune genes. The mapping of expression quantitative trait loci (eQTLs) revealed that genetic factors had a stronger effect on immune gene regulation than age and sex, yet they affected a smaller number of genes. Importantly, we identified numerous genetic variants that manifested their regulatory effects exclusively on immune stimulation, including a Candida albicans-specific master regulator at the CR1 locus. These response eQTLs were enriched in disease-associated variants, particularly for autoimmune and inflammatory disorders, indicating that differences in disease risk may result from regulatory variants exerting their effects only in the presence of immune stress. Together, this study quantifies the respective effects of age, sex, genetics, and cellular heterogeneity on the interindividual variability of immune responses and constitutes a valuable resource for further exploration in the context of different infection risks or disease outcomes.
Collapse
|
168
|
Huang R, Kumar S, Li H. Absence of Correlation between Chimeric RNA and Aging. Genes (Basel) 2017; 8:genes8120386. [PMID: 29240691 PMCID: PMC5748704 DOI: 10.3390/genes8120386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/06/2017] [Accepted: 12/07/2017] [Indexed: 11/16/2022] Open
Abstract
Chimeric RNAs have been recognized as a phenomenon not unique to cancer cells. They also exist in normal physiology. Aging is often characterized by deregulation of molecular and cellular mechanisms, including loss of heterochromatin, increased transcriptional noise, less tight control on alternative splicing, and more stress-induced changes. It is thus assumed that chimeric RNAs are more abundant in older people. In this study, we conducted a preliminary investigation to identify any chimeric RNAs with age-based trends in their expression levels in blood samples. A chimeric RNA candidate list generated by bioinformatic analysis indicated the possibility of both negative and positive trends in the expression of chimeric RNAs. Out of this candidate list, five novel chimeric RNAs were successfully amplified in multiple blood samples and then sequenced. Although primary smaller sample sizes displayed some weak trends with respect to age, analysis of quantitative PCR data from larger sample sizes showed essentially no relationship between expression levels and age. Altogether, these results indicate that, contradictory to the common assumption, chimeric RNAs as a group are not all higher in older individuals and that placing chimeric RNAs in the context of aging will be a much more complex task than initially anticipated.
Collapse
Affiliation(s)
- Reyna Huang
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
| | - Shailesh Kumar
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
| |
Collapse
|
169
|
Popadin K, Peischl S, Garieri M, Sailani MR, Letourneau A, Santoni F, Lukowski SW, Bazykin GA, Nikolaev S, Meyer D, Excoffier L, Reymond A, Antonarakis SE. Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Genome Res 2017; 28:1-10. [PMID: 29237728 PMCID: PMC5749173 DOI: 10.1101/gr.228411.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022]
Abstract
The majority of aneuploid fetuses are spontaneously miscarried. Nevertheless, some aneuploid individuals survive despite the strong genetic insult. Here, we investigate if the survival probability of aneuploid fetuses is affected by the genome-wide burden of slightly deleterious variants. We analyzed two cohorts of live-born Down syndrome individuals (388 genotyped samples and 16 fibroblast transcriptomes) and observed a deficit of slightly deleterious variants on Chromosome 21 and decreased transcriptome-wide variation in the expression level of highly constrained genes. We interpret these results as signatures of embryonic selection, and propose a genetic handicap model whereby an individual bearing an extremely severe deleterious variant (such as aneuploidy) could escape embryonic lethality if the genome-wide burden of slightly deleterious variants is sufficiently low. This approach can be used to study the composition and effect of the numerous slightly deleterious variants in humans and model organisms.
Collapse
Affiliation(s)
- Konstantin Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland.,Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.,Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russia.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Stephan Peischl
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Interfaculty Bioinformatics Unit, University of Bern, 3012 Bern, Switzerland
| | - Marco Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - M Reza Sailani
- Stanford School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, 127051, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, 143026, Russia
| | - Sergey Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of Sao Paulo, 05508-090, Sao Paulo, Brazil
| | - Laurent Excoffier
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Institute for Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| |
Collapse
|
170
|
Mendenhall A, Crane MM, Tedesco PM, Johnson TE, Brent R. Caenorhabditis elegans Genes Affecting Interindividual Variation in Life-span Biomarker Gene Expression. J Gerontol A Biol Sci Med Sci 2017; 72:1305-1310. [PMID: 28158434 DOI: 10.1093/gerona/glw349] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/30/2016] [Indexed: 01/12/2023] Open
Abstract
Genetically identical organisms grown in homogenous environments differ in quantitative phenotypes. Differences in one such trait, expression of a single biomarker gene, can identify isogenic cells or organisms that later manifest different fates. For example, in isogenic populations of young adult Caenorhabditis elegans, differences in Green Fluorescent Protein (GFP) expressed from the hsp-16.2 promoter predict differences in life span. Thus, it is of interest to determine how interindividual differences in biomarker gene expression arise. Prior reports showed that the thermosensory neurons and insulin signaling systems controlled the magnitude of the heat shock response, including absolute expression of hsp-16.2. Here, we tested whether these regulatory signals might also influence variation in hsp-16.2 reporter expression. Genetic experiments showed that the action of AFD thermosensory neurons increases interindividual variation in biomarker expression. Further genetic experimentation showed the insulin signaling system acts to decrease interindividual variation in life-span biomarker expression; in other words, insulin signaling canalizes expression of the hsp-16.2-driven life-span biomarker. Our results show that specific signaling systems regulate not only expression level, but also the amount of interindividual expression variation for a life-span biomarker gene. They raise the possibility that manipulation of these systems might offer means to reduce heterogeneity in the aging process.
Collapse
Affiliation(s)
| | | | | | - Thomas E Johnson
- Institute for Behavioral Genetics.,Department of Integrative Physiology.,Biofrontiers Institute, University of Colorado, Boulder
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| |
Collapse
|
171
|
Wiley CD, Flynn JM, Morrissey C, Lebofsky R, Shuga J, Dong X, Unger MA, Vijg J, Melov S, Campisi J. Analysis of individual cells identifies cell-to-cell variability following induction of cellular senescence. Aging Cell 2017; 16:1043-1050. [PMID: 28699239 PMCID: PMC5595671 DOI: 10.1111/acel.12632] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2017] [Indexed: 01/04/2023] Open
Abstract
Senescent cells play important roles in both physiological and pathological processes, including cancer and aging. In all cases, however, senescent cells comprise only a small fraction of tissues. Senescent phenotypes have been studied largely in relatively homogeneous populations of cultured cells. In vivo, senescent cells are generally identified by a small number of markers, but whether and how these markers vary among individual cells is unknown. We therefore utilized a combination of single‐cell isolation and a nanofluidic PCR platform to determine the contributions of individual cells to the overall gene expression profile of senescent human fibroblast populations. Individual senescent cells were surprisingly heterogeneous in their gene expression signatures. This cell‐to‐cell variability resulted in a loss of correlation among the expression of several senescence‐associated genes. Many genes encoding senescence‐associated secretory phenotype (SASP) factors, a major contributor to the effects of senescent cells in vivo, showed marked variability with a subset of highly induced genes accounting for the increases observed at the population level. Inflammatory genes in clustered genomic loci showed a greater correlation with senescence compared to nonclustered loci, suggesting that these genes are coregulated by genomic location. Together, these data offer new insights into how genes are regulated in senescent cells and suggest that single markers are inadequate to identify senescent cells in vivo.
Collapse
Affiliation(s)
| | - James M. Flynn
- Buck Institute for Research on Aging; Novato CA 94945 USA
| | | | | | - Joe Shuga
- Fluidigm Corporation; South San Francisco CA 94080 USA
| | - Xiao Dong
- Department of Genetics; Albert Einstein College of Medicine; Bronx NY 10461 USA
| | - Marc A. Unger
- Fluidigm Corporation; South San Francisco CA 94080 USA
| | - Jan Vijg
- Department of Genetics; Albert Einstein College of Medicine; Bronx NY 10461 USA
| | - Simon Melov
- Buck Institute for Research on Aging; Novato CA 94945 USA
| | - Judith Campisi
- Buck Institute for Research on Aging; Novato CA 94945 USA
- Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
| |
Collapse
|
172
|
Aunan JR, Cho WC, Søreide K. The Biology of Aging and Cancer: A Brief Overview of Shared and Divergent Molecular Hallmarks. Aging Dis 2017; 8:628-642. [PMID: 28966806 PMCID: PMC5614326 DOI: 10.14336/ad.2017.0103] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/03/2017] [Indexed: 12/17/2022] Open
Abstract
Aging is the inevitable time-dependent decline in physiological organ function and is a major risk factor for cancer development. Due to advances in health care, hygiene control and food availability, life expectancy is increasing and the population in most developed countries is shifting to an increasing proportion of people at a cancer susceptible age. Mechanisms of aging are also found to occur in carcinogenesis, albeit with shared or divergent end-results. It is now clear that aging and cancer development either share or diverge in several disease mechanisms. Such mechanisms include the role of genomic instability, telomere attrition, epigenetic changes, loss of proteostasis, decreased nutrient sensing and altered metabolism, but also cellular senescence and stem cell function. Cancer cells and aged cells are also fundamentally opposite, as cancer cells can be thought of as hyperactive cells with advantageous mutations, rapid cell division and increased energy consumption, while aged cells are hypoactive with accumulated disadvantageous mutations, cell division inability and a decreased ability for energy production and consumption. Nonetheless, aging and cancer are tightly interconnected and many of the same strategies and drugs may be used to target both, while in other cases antagonistic pleiotrophy come into effect and inhibition of one can be the activation of the other. Cancer can be considered an aging disease, though the shared mechanisms underpinning the two processes remain unclear. Better understanding of the shared and divergent pathways of aging and cancer is needed.
Collapse
Affiliation(s)
- Jan R Aunan
- 1Gastrointestinal Translational Research Unit, Molecular Lab, Stavanger University Hospital, Stavanger, Norway.,2Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
| | - William C Cho
- 3Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Kjetil Søreide
- 1Gastrointestinal Translational Research Unit, Molecular Lab, Stavanger University Hospital, Stavanger, Norway.,2Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway.,4Department of Clinical Medicine, University of Bergen, Bergen, Norway
| |
Collapse
|
173
|
Enge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, Quake SR. Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. Cell 2017; 171:321-330.e14. [PMID: 28965763 DOI: 10.1016/j.cell.2017.09.004] [Citation(s) in RCA: 348] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/02/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022]
Abstract
As organisms age, cells accumulate genetic and epigenetic errors that eventually lead to impaired organ function or catastrophic transformation such as cancer. Because aging reflects a stochastic process of increasing disorder, cells in an organ will be individually affected in different ways, thus rendering bulk analyses of postmitotic adult cells difficult to interpret. Here, we directly measure the effects of aging in human tissue by performing single-cell transcriptome analysis of 2,544 human pancreas cells from eight donors spanning six decades of life. We find that islet endocrine cells from older donors display increased levels of transcriptional noise and potential fate drift. By determining the mutational history of individual cells, we uncover a novel mutational signature in healthy aging endocrine cells. Our results demonstrate the feasibility of using single-cell RNA sequencing (RNA-seq) data from primary cells to derive insights into genetic and transcriptional processes that operate on aging human tissue.
Collapse
Affiliation(s)
- Martin Enge
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - H Efsun Arda
- Department of Developmental Biology, Stanford University School of Medicine, CA 94305, USA
| | - Marco Mignardi
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Information Technology, Uppsala University, Sweden and SciLifeLab, Uppsala, Sweden SE-751 05
| | - John Beausang
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Rita Bottino
- Institute of Cellular Therapeutics, Allegheny Health Network, 320 East North Avenue, Pittsburgh, PA 15212, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, CA 94305, USA
| | - Stephen R Quake
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Institute of Cellular Therapeutics, Allegheny Health Network, 320 East North Avenue, Pittsburgh, PA 15212, USA.
| |
Collapse
|
174
|
Noise reduction as an emergent property of single-cell aging. Nat Commun 2017; 8:680. [PMID: 28947742 PMCID: PMC5613028 DOI: 10.1038/s41467-017-00752-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/25/2017] [Indexed: 11/08/2022] Open
Abstract
Noise-induced heterogeneity in gene expression is an inherent reality for cells. However, it is not well understood how noise strength changes for a single gene while the host cell is aging. Using a state-of-the-art microfluidic platform, we measure noise dynamics in aging yeast cells by tracking the generation-specific activity of the canonical GAL1 promoter. We observe noise reduction during normal aging of a cell, followed by a short catastrophe phase in which noise increased. We hypothesize that aging-associated increases in chromatin state transitions are behind the observed noise reduction and a stochastic model provides quantitative support to the proposed mechanism. Noise trends measured from strains with altered GAL1 promoter dynamics (constitutively active, synthetic with nucleosome-disfavoring sequences, and in the absence of RPD3, a global remodeling regulator) lend further support to our hypothesis. Observing similar noise dynamics from a different promoter (HHF2) provides support to the generality of our findings. Gene expression is a noisy process, but it is not known how noise in gene expression changes during the aging of single cells. Here the authors show that noise decreases during normal aging, and provide support for aging-associated increases in chromatin state transitions governing noise reduction.
Collapse
|
175
|
Picollet-D'hahan N, Dolega ME, Freida D, Martin DK, Gidrol X. Deciphering Cell Intrinsic Properties: A Key Issue for Robust Organoid Production. Trends Biotechnol 2017; 35:1035-1048. [PMID: 28927991 DOI: 10.1016/j.tibtech.2017.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 07/18/2017] [Accepted: 08/08/2017] [Indexed: 02/07/2023]
Abstract
We highlight the disposition of various cell types to self-organize into complex organ-like structures without necessarily the support of any stromal cells, provided they are placed into permissive 3D culture conditions. The goal of generating organoids reproducibly and efficiently has been hampered by poor understanding of the exact nature of the intrinsic cell properties at the origin of organoid generation, and of the signaling pathways governing their differentiation. Using microtechnologies like microfluidics to engineer organoids would create opportunities for single-cell genomics and high-throughput functional genomics to exhaustively characterize cell intrinsic properties. A more complete understanding of the development of organoids would enhance their relevance as models to study organ morphology, function, and disease and would open new avenues in drug development and regenerative medicine.
Collapse
Affiliation(s)
| | - Monika E Dolega
- Université Grenoble Alpes, INSERM, CEA, BIG, F-38000 Grenoble, France
| | - Delphine Freida
- Université Grenoble Alpes, INSERM, CEA, BIG, F-38000 Grenoble, France
| | - Donald K Martin
- Université Grenoble Alpes, F-38000 Grenoble, France; TIMC-IMAG/CNRS UMR 5525, F-38041 Grenoble, France
| | - Xavier Gidrol
- Université Grenoble Alpes, INSERM, CEA, BIG, F-38000 Grenoble, France.
| |
Collapse
|
176
|
Lu Y, Biancotto A, Cheung F, Remmers E, Shah N, McCoy JP, Tsang JS. Systematic Analysis of Cell-to-Cell Expression Variation of T Lymphocytes in a Human Cohort Identifies Aging and Genetic Associations. Immunity 2017; 45:1162-1175. [PMID: 27851916 DOI: 10.1016/j.immuni.2016.10.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/21/2016] [Accepted: 10/04/2016] [Indexed: 12/21/2022]
Abstract
Cell-to-cell expression variation (CEV) is a prevalent feature of even well-defined cell populations, but its functions, particularly at the organismal level, are not well understood. Using single-cell data obtained via high-dimensional flow cytometry of T cells as a model, we introduce an analysis framework for quantifying CEV in primary cell populations and studying its functional associations in human cohorts. Analyses of 840 CEV phenotypes spanning multiple baseline measurements of 14 proteins in 28 T cell subpopulations suggest that the quantitative extent of CEV can exhibit substantial subject-to-subject differences and yet remain stable within healthy individuals over months. We linked CEV to age and disease-associated genetic polymorphisms, thus implicating CEV as a biomarker of aging and disease susceptibility and suggesting that it might play an important role in health and disease. Our dataset, interactive figures, and software for computing CEV with flow cytometry data provide a resource for exploring CEV functions.
Collapse
Affiliation(s)
- Yong Lu
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Angelique Biancotto
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA
| | - Foo Cheung
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA
| | - Elaine Remmers
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Naisha Shah
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - J Philip McCoy
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA; Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
177
|
Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses. Sci Immunol 2017; 2:2/14/eaal4656. [PMID: 28842433 DOI: 10.1126/sciimmunol.aal4656] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/24/2017] [Indexed: 12/13/2022]
Abstract
Annual influenza vaccinations are currently recommended for all individuals 6 months and older. Antibodies induced by vaccination are an important mechanism of protection against infection. Despite the overall public health success of influenza vaccination, many individuals fail to induce a substantial antibody response. Systems-level immune profiling studies have discerned associations between transcriptional and cell subset signatures with the success of antibody responses. However, existing signatures have relied on small cohorts and have not been validated in large independent studies. We leveraged multiple influenza vaccination cohorts spanning distinct geographical locations and seasons from the Human Immunology Project Consortium (HIPC) and the Center for Human Immunology (CHI) to identify baseline (i.e., before vaccination) predictive transcriptional signatures of influenza vaccination responses. Our multicohort analysis of HIPC data identified nine genes (RAB24, GRB2, DPP3, ACTB, MVP, DPP7, ARPC4, PLEKHB2, and ARRB1) and three gene modules that were significantly associated with the magnitude of the antibody response, and these associations were validated in the independent CHI cohort. These signatures were specific to young individuals, suggesting that distinct mechanisms underlie the lower vaccine response in older individuals. We found an inverse correlation between the effect size of signatures in young and older individuals. Although the presence of an inflammatory gene signature, for example, was associated with better antibody responses in young individuals, it was associated with worse responses in older individuals. These results point to the prospect of predicting antibody responses before vaccination and provide insights into the biological mechanisms underlying successful vaccination responses.
Collapse
|
178
|
Ashapkin VV, Kutueva LI, Vanyushin BF. Aging as an Epigenetic Phenomenon. Curr Genomics 2017; 18:385-407. [PMID: 29081695 PMCID: PMC5635645 DOI: 10.2174/1389202918666170412112130] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 01/17/2016] [Accepted: 02/09/2016] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Hypermethylation of genes associated with promoter CpG islands, and hypomethylation of CpG poor genes, repeat sequences, transposable elements and intergenic genome sections occur during aging in mammals. Methylation levels of certain CpG sites display strict correlation to age and could be used as "epigenetic clock" to predict biological age. Multi-substrate deacetylases SIRT1 and SIRT6 affect aging via locus-specific modulations of chromatin structure and activity of multiple regulatory proteins involved in aging. Random errors in DNA methylation and other epigenetic marks during aging increase the transcriptional noise, and thus lead to enhanced phenotypic variation between cells of the same tissue. Such variation could cause progressive organ dysfunction observed in aged individuals. Multiple experimental data show that induction of NF-κB regulated gene sets occurs in various tissues of aged mammals. Upregulation of multiple miRNAs occurs at mid age leading to downregulation of enzymes and regulatory proteins involved in basic cellular functions, such as DNA repair, oxidative phosphorylation, intermediate metabolism, and others. CONCLUSION Strong evidence shows that all epigenetic systems contribute to the lifespan control in various organisms. Similar to other cell systems, epigenome is prone to gradual degradation due to the genome damage, stressful agents, and other aging factors. But unlike mutations and other kinds of the genome damage, age-related epigenetic changes could be fully or partially reversed to a "young" state.
Collapse
Affiliation(s)
- Vasily V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Lyudmila I Kutueva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
179
|
Khan SS, Singer BD, Vaughan DE. Molecular and physiological manifestations and measurement of aging in humans. Aging Cell 2017; 16:624-633. [PMID: 28544158 PMCID: PMC5506433 DOI: 10.1111/acel.12601] [Citation(s) in RCA: 271] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2017] [Indexed: 12/11/2022] Open
Abstract
Biological aging is associated with a reduction in the reparative and regenerative potential in tissues and organs. This reduction manifests as a decreased physiological reserve in response to stress (termed homeostenosis) and a time-dependent failure of complex molecular mechanisms that cumulatively create disorder. Aging inevitably occurs with time in all organisms and emerges on a molecular, cellular, organ, and organismal level with genetic, epigenetic, and environmental modulators. Individuals with the same chronological age exhibit differential trajectories of age-related decline, and it follows that we should assess biological age distinctly from chronological age. In this review, we outline mechanisms of aging with attention to well-described molecular and cellular hallmarks and discuss physiological changes of aging at the organ-system level. We suggest methods to measure aging with attention to both molecular biology (e.g., telomere length and epigenetic marks) and physiological function (e.g., lung function and echocardiographic measurements). Finally, we propose a framework to integrate these molecular and physiological data into a composite score that measures biological aging in humans. Understanding the molecular and physiological phenomena that drive the complex and multifactorial processes underlying the variable pace of biological aging in humans will inform how researchers assess and investigate health and disease over the life course. This composite biological age score could be of use to researchers seeking to characterize normal, accelerated, and exceptionally successful aging as well as to assess the effect of interventions aimed at modulating human aging.
Collapse
Affiliation(s)
- Sadiya S. Khan
- Department of MedicineNorthwestern University Feinberg School of MedicineChicagoIL60611USA
| | - Benjamin D. Singer
- Department of MedicineNorthwestern University Feinberg School of MedicineChicagoIL60611USA
| | - Douglas E. Vaughan
- Department of MedicineNorthwestern University Feinberg School of MedicineChicagoIL60611USA
| |
Collapse
|
180
|
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: 122] [Impact Index Per Article: 17.4] [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.
Collapse
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.
| |
Collapse
|
181
|
Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M. Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity. Sci Rep 2017; 7:5894. [PMID: 28724976 PMCID: PMC5517654 DOI: 10.1038/s41598-017-05927-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 06/06/2017] [Indexed: 01/21/2023] Open
Abstract
It was previously reported that mRNA expression levels in the prefrontal cortex at old age start to resemble pre-adult levels. Such expression reversals could imply loss of cellular identity in the aging brain, and provide a link between aging-related molecular changes and functional decline. Here we analyzed 19 brain transcriptome age-series datasets, comprising 17 diverse brain regions, to investigate the ubiquity and functional properties of expression reversal in the human brain. Across all 19 datasets, 25 genes were consistently up-regulated during postnatal development and down-regulated in aging, displaying an "up-down" pattern that was significant as determined by random permutations. In addition, 113 biological processes, including neuronal and synaptic functions, were consistently associated with genes showing an up-down tendency among all datasets. Genes up-regulated during in vitro neuronal differentiation also displayed a tendency for up-down reversal, although at levels comparable to other genes. We argue that reversals may not represent aging-related neuronal loss. Instead, expression reversals may be associated with aging-related accumulation of stochastic effects that lead to loss of functional and structural identity in neurons.
Collapse
Affiliation(s)
- Handan Melike Dönertaş
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
| | - Hamit İzgi
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Altuğ Kamacıoğlu
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Zhisong He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Philipp Khaitovich
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey.
| |
Collapse
|
182
|
Genome instability: a conserved mechanism of ageing? Essays Biochem 2017; 61:305-315. [PMID: 28550046 DOI: 10.1042/ebc20160082] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/18/2017] [Accepted: 05/02/2017] [Indexed: 01/09/2023]
Abstract
DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals. More recently, next-generation sequencing-based methods have been developed to accurately determine the complete landscape of base substitution mutations in single cells. The first results show that the somatic mutation rate is much higher than the germline mutation rate and that base substitution loads in somatic cells are high enough to potentially affect cellular function.
Collapse
|
183
|
Phillip JM, Wu PH, Gilkes DM, Williams W, McGovern S, Daya J, Chen J, Aifuwa I, Lee JSH, Fan R, Walston J, Wirtz D. Biophysical and biomolecular determination of cellular age in humans. Nat Biomed Eng 2017; 1. [PMID: 31372309 DOI: 10.1038/s41551-017-0093] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ageing research has focused either on assessing organ- and tissue-based changes, such as lung capacity and cardiac function, or on changes at the molecular scale such as gene expression, epigenetic modifications and metabolism. Here, by using a cohort of 32 samples of primary dermal fibroblasts collected from individuals between 2 and 96 years of age, we show that the degradation of functional cellular biophysical features-including cell mechanics, traction strength, morphology and migratory potential-and associated descriptors of cellular heterogeneity predict cellular age with higher accuracy than conventional biomolecular markers. We also demonstrate the use of high-throughput single-cell technologies, together with a deterministic model based on cellular features, to compute the cellular age of apparently healthy males and females, and to explore these relationships in cells from individuals with Werner syndrome and Hutchinson-Gilford progeria syndrome, two rare genetic conditions that result in phenotypes that show aspects of premature ageing. Our findings suggest that the quantification of cellular age may be used to stratify individuals on the basis of cellular phenotypes and serve as a biological proxy of healthspan.
Collapse
Affiliation(s)
- Jude M Phillip
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Pei-Hsun Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Daniele M Gilkes
- Johns Hopkins Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Wadsworth Williams
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Shaun McGovern
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Jena Daya
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Jonathan Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
| | - Ivie Aifuwa
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Jerry S H Lee
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Center for Strategic Scientific Initiatives, Office of the Director, National Cancer Institute, National Institute of Health, Bethesda, Maryland 20892, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
| | - Jeremy Walston
- Department of Medicine, Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA
| | - Denis Wirtz
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| |
Collapse
|
184
|
Stegeman R, Weake VM. Transcriptional Signatures of Aging. J Mol Biol 2017; 429:2427-2437. [PMID: 28684248 DOI: 10.1016/j.jmb.2017.06.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/02/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022]
Abstract
Genome-wide studies of aging have identified subsets of genes that show age-related changes in expression. Although the types of genes that are age regulated vary among different tissues and organisms, some patterns emerge from these large data sets. First, aging is associated with a broad induction of stress response pathways, although the specific genes and pathways involved differ depending on cell type and species. In contrast, a wide variety of functional classes of genes are downregulated with age, often including tissue-specific genes. Although the upregulation of age-regulated genes is likely to be governed by stress-responsive transcription factors, questions remain as to why particular genes are susceptible to age-related transcriptional decline. Here, we discuss recent findings showing that splicing is misregulated with age. While defects in splicing could lead to changes in protein isoform levels, they could also impact gene expression through nonsense-mediated decay of intron-retained transcripts. The discovery that splicing is misregulated with age suggests that other aspects of gene expression, such as transcription elongation, termination, and polyadenylation, must also be considered as potential mechanisms for age-related changes in transcript levels. Moreover, the considerable variation between genome-wide aging expression studies indicates that there is a critical need to analyze the transcriptional signatures of aging in single-cell types rather than whole tissues. Since age-associated decreases in gene expression could contribute to a progressive decline in cellular function, understanding the mechanisms that determine the aging transcriptome provides a potential target to extend healthy cellular lifespan.
Collapse
Affiliation(s)
- R Stegeman
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - V M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN 47907, USA.
| |
Collapse
|
185
|
Latorre E, Harries LW. Splicing regulatory factors, ageing and age-related disease. Ageing Res Rev 2017; 36:165-170. [PMID: 28456680 DOI: 10.1016/j.arr.2017.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 12/12/2022]
Abstract
Alternative splicing is a co-transcriptional process, which allows for the production of multiple transcripts from a single gene and is emerging as an important control point for gene expression. Alternatively expressed isoforms often have antagonistic function and differential temporal or spatial expression patterns, yielding enormous plasticity and adaptability to cells and increasing their ability to respond to environmental challenge. The regulation of alternative splicing is critical for numerous cellular functions in both pathological and physiological conditions, and deregulated alternative splicing is a key feature of common chronic diseases. Isoform choice is controlled by a battery of splicing regulatory proteins, which include the serine arginine rich (SRSF) proteins and the heterogeneous ribonucleoprotein (hnRNP) classes of genes. These important splicing regulators have been implicated in age-related disease, and in the ageing process itself. This review will outline the important contribution of splicing regulator proteins to ageing and age-related disease.
Collapse
|
186
|
Ageing: Biomarkers get physical. Nat Biomed Eng 2017. [DOI: 10.1038/s41551-017-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
187
|
Elitas M, Sadeghi S, Karamahmutoglu H, Gozuacik D, Serdar Turhal N. Microfabricated platforms to quantitatively investigate cellular behavior under the influence of chemical gradients. Biomed Phys Eng Express 2017. [DOI: 10.1088/2057-1976/aa7400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
188
|
Ishii S, Torii M, Son AI, Rajendraprasad M, Morozov YM, Kawasawa YI, Salzberg AC, Fujimoto M, Brennand K, Nakai A, Mezger V, Gage FH, Rakic P, Hashimoto-Torii K. Variations in brain defects result from cellular mosaicism in the activation of heat shock signalling. Nat Commun 2017; 8:15157. [PMID: 28462912 PMCID: PMC5418582 DOI: 10.1038/ncomms15157] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 03/03/2017] [Indexed: 11/18/2022] Open
Abstract
Repetitive prenatal exposure to identical or similar doses of harmful agents results in highly variable and unpredictable negative effects on fetal brain development ranging in severity from high to little or none. However, the molecular and cellular basis of this variability is not well understood. This study reports that exposure of mouse and human embryonic brain tissues to equal doses of harmful chemicals, such as ethanol, activates the primary stress response transcription factor heat shock factor 1 (Hsf1) in a highly variable and stochastic manner. While Hsf1 is essential for protecting the embryonic brain from environmental stress, excessive activation impairs critical developmental events such as neuronal migration. Our results suggest that mosaic activation of Hsf1 within the embryonic brain in response to prenatal environmental stress exposure may contribute to the resulting generation of phenotypic variations observed in complex congenital brain disorders. Prenatal exposure to environmental stressors is known to impair cortical development. Here the authors show that upon exposure to stressors, the activation of Hsf1-Hsp signalling is highly variable among cells in the embryonic cortex of mice, and either too much or too little activation can result in defects in cortical development.
Collapse
Affiliation(s)
- Seiji Ishii
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA
| | - Masaaki Torii
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA.,Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Pediatrics, Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia 20052, USA
| | - Alexander I Son
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA
| | - Meenu Rajendraprasad
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA.,Department of Biomedical Engineering, School of Engineering and Applied Science, George Washington University, Washington, District of Columbia 20052, USA
| | - Yury M Morozov
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, Pennsylvania State University College of Medicine, 500 University Dr., Hershey, Pennsylvania 17033, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, 500 University Dr., Hershey, Pennsylvania 17033, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Dr., Hershey, Pennsylvania 17033, USA
| | - Anna C Salzberg
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Dr., Hershey, Pennsylvania 17033, USA
| | - Mitsuaki Fujimoto
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube 755-8505, Japan
| | - Kristen Brennand
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York 10029, USA.,Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, California 92037, USA
| | - Akira Nakai
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube 755-8505, Japan
| | - Valerie Mezger
- CNRS, UMR7216 Epigenetics and Cell Fate, Paris 75205, France.,University Paris Diderot, 75205 Paris, France.,Département Hospitalo-Universitaire DHU PROTECT, Paris 75019, France
| | - Fred H Gage
- Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, California 92037, USA
| | - Pasko Rakic
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Kazue Hashimoto-Torii
- Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA.,Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA.,Department of Pediatrics, Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia 20052, USA
| |
Collapse
|
189
|
Variation in gene expression within clones of the earthworm Dendrobaena octaedra. PLoS One 2017; 12:e0174960. [PMID: 28384196 PMCID: PMC5383104 DOI: 10.1371/journal.pone.0174960] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 03/19/2017] [Indexed: 12/23/2022] Open
Abstract
Gene expression is highly plastic, which can help organisms to both acclimate and adapt to changing environments. Possible variation in gene expression among individuals with the same genotype (among clones) is not widely considered, even though it could impact the results of studies that focus on gene expression phenotypes, for example studies using clonal lines. We examined the extent of within and between clone variation in gene expression in the earthworm Dendrobaena octaedra, which reproduces through apomictic parthenogenesis. Five microsatellite markers were developed and used to confirm that offspring are genetic clones of their parent. After that, expression of 12 genes was measured from five individuals each from six clonal lines after exposure to copper contaminated soil. Variation in gene expression was higher over all genotypes than within genotypes, as initially assumed. A subset of the genes was also examined in the offspring of exposed individuals in two of the clonal lines. In this case, variation in gene expression within genotypes was as high as that observed over all genotypes. One gene in particular (chymotrypsin inhibitor) also showed significant differences in the expression levels among genetically identical individuals. Gene expression can vary considerably, and the extent of variation may depend on the genotypes and genes studied. Ensuring a large sample, with many different genotypes, is critical in studies comparing gene expression phenotypes. Researchers should be especially cautious inferring gene expression phenotypes when using only a single clonal or inbred line, since the results might be specific to only certain genotypes.
Collapse
|
190
|
Veitia RA, Govindaraju DR, Bottani S, Birchler JA. Aging: Somatic Mutations, Epigenetic Drift and Gene Dosage Imbalance. Trends Cell Biol 2017; 27:299-310. [DOI: 10.1016/j.tcb.2016.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
|
191
|
Brunet A, Rando TA. Interaction between epigenetic and metabolism in aging stem cells. Curr Opin Cell Biol 2017; 45:1-7. [PMID: 28129586 PMCID: PMC5482778 DOI: 10.1016/j.ceb.2016.12.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/31/2016] [Indexed: 01/03/2023]
Abstract
Aging is accompanied by a decline in tissue function, regeneration, and repair. A large part of this decline is caused by the deterioration of tissue stem cell function. Understanding the mechanisms that drive stem cell aging and how to counteract them is a critical step for enhancing tissue repair and maintenance during aging. Emerging evidence indicates that epigenetic modifiers and metabolism regulators interact to impact lifespan, suggesting that this mechanism may also affect stem cell function with age. This review focuses on the interaction between chromatin and metabolism in the regulation of tissue stem cells during aging. We also discuss how these mechanisms integrate environmental stimuli such as nutrient stress to regulate stem cell function. Finally, this review examines new perspectives for regeneration, rejuvenation, and treatment of age-related decline of stem cell function.
Collapse
Affiliation(s)
- Anne Brunet
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Glenn Center for the Biology of Aging, Stanford University, USA.
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Glenn Center for the Biology of Aging, Stanford University, USA; Center for Tissue Regeneration, Repair and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| |
Collapse
|
192
|
Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT. Aging increases cell-to-cell transcriptional variability upon immune stimulation. Science 2017; 355:1433-1436. [PMID: 28360329 PMCID: PMC5405862 DOI: 10.1126/science.aah4115] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/07/2016] [Accepted: 02/23/2017] [Indexed: 12/24/2022]
Abstract
Aging is characterized by progressive loss of physiological and cellular functions, but the molecular basis of this decline remains unclear. We explored how aging affects transcriptional dynamics using single-cell RNA sequencing of unstimulated and stimulated naïve and effector memory CD4+ T cells from young and old mice from two divergent species. In young animals, immunological activation drives a conserved transcriptomic switch, resulting in tightly controlled gene expression characterized by a strong up-regulation of a core activation program, coupled with a decrease in cell-to-cell variability. Aging perturbed the activation of this core program and increased expression heterogeneity across populations of cells in both species. These discoveries suggest that increased cell-to-cell transcriptional variability will be a hallmark feature of aging across most, if not all, mammalian tissues.
Collapse
Affiliation(s)
- Celia Pilar Martinez-Jimenez
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nils Eling
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hung-Chang Chen
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Catalina A Vallejos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Aleksandra A Kolodziejczyk
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Frances Connor
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Lovorka Stojic
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Timothy F Rayner
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Michael J T Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maike de la Roche
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - John C Marioni
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| |
Collapse
|
193
|
Shilovsky GA, Putyatina TS, Lysenkov SN, Ashapkin VV, Luchkina OS, Markov AV, Skulachev VP. Is It Possible to Prove the Existence of an Aging Program by Quantitative Analysis of Mortality Dynamics? BIOCHEMISTRY (MOSCOW) 2017; 81:1461-1476. [PMID: 28259123 DOI: 10.1134/s0006297916120075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Accumulation of various types of lesions in the course of aging increases an organism's vulnerability and results in a monotonous elevation of mortality rate, irrespective of the position of a species on the evolutionary tree. Stroustrup et al. (Nature, 530, 103-107) [1] showed in 2016 that in the nematode Caenorhabditis elegans, longevity-altering factors (e.g. oxidative stress, temperature, or diet) do not change the shape of the survival curve, but either stretch or shrink it along the time axis, which the authors attributed to the existence of an "aging program". Modification of the accelerated failure time model by Stroustrup et al. uses temporal scaling as a basic approach for distinguishing between quantitative and qualitative changes in aging dynamics. Thus we analyzed data on the effects of various longevity-increasing genetic manipulations in flies, worms, and mice and used several models to choose a theory that would best fit the experimental results. The possibility to identify the moment of switch from a mortality-governing pathway to some other pathways might be useful for testing geroprotective drugs. In this work, we discuss this and other aspects of temporal scaling.
Collapse
Affiliation(s)
- G A Shilovsky
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119991, Russia.
| | | | | | | | | | | | | |
Collapse
|
194
|
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.
Collapse
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.
| |
Collapse
|
195
|
Cannon L, Zambon AC, Cammarato A, Zhang Z, Vogler G, Munoz M, Taylor E, Cartry J, Bernstein SI, Melov S, Bodmer R. Expression patterns of cardiac aging in Drosophila. Aging Cell 2017; 16:82-92. [PMID: 28090760 PMCID: PMC5242310 DOI: 10.1111/acel.12559] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2016] [Indexed: 11/27/2022] Open
Abstract
Aging causes cardiac dysfunction, often leading to heart failure and death. The molecular basis of age-associated changes in cardiac structure and function is largely unknown. The fruit fly, Drosophila melanogaster, is well-suited to investigate the genetics of cardiac aging. Flies age rapidly over the course of weeks, benefit from many tools to easily manipulate their genome, and their heart has significant genetic and phenotypic similarities to the human heart. Here, we performed a cardiac-specific gene expression study on aging Drosophila and carried out a comparative meta-analysis with published rodent data. Pathway level transcriptome comparisons suggest that age-related, extra-cellular matrix remodeling and alterations in mitochondrial metabolism, protein handling, and contractile functions are conserved between Drosophila and rodent hearts. However, expression of only a few individual genes similarly changed over time between and even within species. We also examined gene expression in single fly hearts and found significant variability as has been reported in rodents. We propose that individuals may arrive at similar cardiac aging phenotypes via dissimilar transcriptional changes, including those in transcription factors and micro-RNAs. Finally, our data suggest the transcription factor Odd-skipped, which is essential for normal heart development, is also a crucial regulator of cardiac aging.
Collapse
Affiliation(s)
- Leah Cannon
- Development, Aging and Regeneration Program; Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla CA USA
| | - Alexander C. Zambon
- Development, Aging and Regeneration Program; Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla CA USA
- Department of Biopharmaceutical Sciences; Keck Graduate Institute; Claremont CA USA
| | - Anthony Cammarato
- Division of Cardiology; Department of Medicine; Johns Hopkins University; Baltimore MD USA
| | - Zhi Zhang
- Development, Aging and Regeneration Program; Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla CA USA
| | - Georg Vogler
- Development, Aging and Regeneration Program; Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla CA USA
| | - Matthew Munoz
- Department of Biopharmaceutical Sciences; Keck Graduate Institute; Claremont CA USA
| | - Erika Taylor
- Development, Aging and Regeneration Program; Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla CA USA
| | - Jérôme Cartry
- Development, Aging and Regeneration Program; Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla CA USA
| | - Sanford I. Bernstein
- Department of Biology, Molecular Biology Institute, and The Heart Institute; San Diego State University; San Diego CA USA
| | - Simon Melov
- Buck Institute for Research on Aging; Novato CA USA
| | - Rolf Bodmer
- Development, Aging and Regeneration Program; Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla CA USA
| |
Collapse
|
196
|
Mashaghi A, Hong J, Chauhan SK, Dana R. Ageing and ocular surface immunity. Br J Ophthalmol 2017; 101:1-5. [PMID: 27378485 PMCID: PMC5583682 DOI: 10.1136/bjophthalmol-2015-307848] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 04/26/2016] [Accepted: 06/19/2016] [Indexed: 12/22/2022]
Abstract
The prevalence of ocular surface immunopathologies is enhanced in the elderly. This increased prevalence has been attributed to age-related dysregulation of innate and adaptive immune system responses. Age-related changes in ocular surface immunity have similar and distinct characteristics to those changes seen in other mucosal tissues. This mini review provides a brief outline of key findings in the field of ocular ageing, draws comparisons with other mucosal tissues and, finally, discusses age-related changes in the context of immunopathogenesis of infectious keratitis and dry eye disease, two of the most common inflammatory disorders of the ocular surface.
Collapse
Affiliation(s)
- Alireza Mashaghi
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Jiaxu Hong
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Sunil K Chauhan
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Reza Dana
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
197
|
Romanowicz H, Strapagiel D, Słomka M, Sobalska-Kwapis M, Kępka E, Siewierska-Górska A, Zadrożny M, Bieńkiewicz J, Smolarz B. New single nucleotide polymorphisms (SNPs) in homologous recombination repair genes detected by microarray analysis in Polish breast cancer patients. Clin Exp Med 2016; 17:541-546. [DOI: 10.1007/s10238-016-0441-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/14/2016] [Indexed: 11/29/2022]
|
198
|
Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion. PLoS Comput Biol 2016; 12:e1005122. [PMID: 27893768 PMCID: PMC5125560 DOI: 10.1371/journal.pcbi.1005122] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/26/2016] [Indexed: 01/24/2023] Open
Abstract
We seek to elucidate the role of macromolecular crowding in transcription and translation. It is well known that stochasticity in gene expression can lead to differential gene expression and heterogeneity in a cell population. Recent experimental observations by Tan et al. have improved our understanding of the functional role of macromolecular crowding. It can be inferred from their observations that macromolecular crowding can lead to robustness in gene expression, resulting in a more homogeneous cell population. We introduce a spatial stochastic model to provide insight into this process. Our results show that macromolecular crowding reduces noise (as measured by the kurtosis of the mRNA distribution) in a cell population by limiting the diffusion of transcription factors (i.e. removing the unstable intermediate states), and that crowding by large molecules reduces noise more efficiently than crowding by small molecules. Finally, our simulation results provide evidence that the local variation in chromatin density as well as the total volume exclusion of the chromatin in the nucleus can induce a homogenous cell population. The cellular nucleus is packed with macromolecules such as DNAs and proteins, which leaves limited space for other molecules to move around. Recent experimental results by C. Tan et al. have shown that macromolecular crowding can regulate gene expression, resulting in a more homogenous cell population. We introduce a computational model to uncover the mechanism by which macromolecular crowding functions. Our results suggest that macromolecular crowding limits the diffusion of the transcription factors and attenuates the transcriptional bursting, which leads to a more homogenous cell population. Regulation of gene expression noise by macromolecules depends on the size of the crowders, i.e. larger macromolecules can reduce the noise more effectively than smaller macromolecules. We also demonstrate that local variation of chromatin density can affect the noise of gene expression. This shows the importance of the chromatin structure in gene expression regulation.
Collapse
|
199
|
Abstract
Why do cells age? Recent advances show that the cytoplasm is organized into many membrane‐less compartments via a process known as phase separation, which ensures spatiotemporal control over diffusion‐limited biochemical reactions. Although phase separation is a powerful mechanism to organize biochemical reactions, it comes with the trade‐off that it is extremely sensitive to changes in physical‐chemical parameters, such as protein concentration, pH, or cellular energy levels. Here, we highlight recent findings showing that age‐related neurodegenerative diseases are linked to aberrant phase transitions in neurons. We discuss how these aberrant phase transitions could be tied to a failure to maintain physiological physical‐chemical conditions. We generalize this idea to suggest that the process of cellular aging involves a progressive loss of the organization of phase‐separated compartments in the cytoplasm.
Collapse
Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
200
|
Abstract
Aging is an inevitable outcome of life, characterized by progressive decline in tissue and organ function and increased risk of mortality. Accumulating evidence links aging to genetic and epigenetic alterations. Given the reversible nature of epigenetic mechanisms, these pathways provide promising avenues for therapeutics against age-related decline and disease. In this review, we provide a comprehensive overview of epigenetic studies from invertebrate organisms, vertebrate models, tissues, and in vitro systems. We establish links between common operative aging pathways and hallmark chromatin signatures that can be used to identify "druggable" targets to counter human aging and age-related disease.
Collapse
Affiliation(s)
- Payel Sen
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Parisha P Shah
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Raffaella Nativio
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Shelley L Berger
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA.
| |
Collapse
|