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Liu Y, Park J, Lim S, Duan R, Lee DY, Choi D, Choi DK, Rhie B, Cho SY, Ryu H, Ahn SH. Tho2-mediated escort of Nrd1 regulates the expression of aging-related genes. Aging Cell 2024; 23:e14203. [PMID: 38769776 PMCID: PMC11320360 DOI: 10.1111/acel.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The relationship between aging and RNA biogenesis and trafficking is attracting growing interest, yet the precise mechanisms are unknown. The THO complex is crucial for mRNA cotranscriptional maturation and export. Herein, we report that the THO complex is closely linked to the regulation of lifespan. Deficiencies in Hpr1 and Tho2, components of the THO complex, reduced replicative lifespan (RLS) and are linked to a novel Sir2-independent RLS control pathway. Although transcript sequestration in hpr1Δ or tho2Δ mutants was countered by exosome component Rrp6, loss of this failed to mitigate RLS defects in hpr1Δ. However, RLS impairment in hpr1Δ or tho2Δ was counteracted by the additional expression of Nrd1-specific mutants that interacted with Rrp6. This effect relied on the interaction of Nrd1, a transcriptional regulator of aging-related genes, including ribosome biogenesis or RNA metabolism genes, with RNA polymerase II. Nrd1 overexpression reduced RLS in a Tho2-dependent pathway. Intriguingly, Tho2 deletion mirrored Nrd1 overexpression effects by inducing arbitrary Nrd1 chromatin binding. Furthermore, our genome-wide ChIP-seq analysis revealed an increase in the recruitment of Nrd1 to translation-associated genes, known to be related to aging, upon Tho2 loss. Taken together, these findings underscore the importance of Tho2-mediated Nrd1 escorting in the regulation of lifespan pathway through transcriptional regulation of aging-related genes.
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Affiliation(s)
- Yan Liu
- Department of Molecular and Life Science, College of Science and Convergence TechnologyHanyang UniversityAnsanRepublic of Korea
| | - Jeong‐Min Park
- KNU LAMP Research Center, KNU Institute of Basic Sciences, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural SciencesKyungpook National UniversityDaeguRepublic of Korea
| | - Suji Lim
- Department of Molecular and Life Science, College of Science and Convergence TechnologyHanyang UniversityAnsanRepublic of Korea
| | - Ruxin Duan
- Department of Molecular and Life Science, College of Science and Convergence TechnologyHanyang UniversityAnsanRepublic of Korea
| | - Do Yoon Lee
- KNU LAMP Research Center, KNU Institute of Basic Sciences, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural SciencesKyungpook National UniversityDaeguRepublic of Korea
| | - Dahee Choi
- KNU LAMP Research Center, KNU Institute of Basic Sciences, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural SciencesKyungpook National UniversityDaeguRepublic of Korea
| | - Dong Kyu Choi
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural SciencesKyungpook National UniversityDaeguRepublic of Korea
| | - Byung‐Ho Rhie
- Department of Molecular and Life Science, College of Science and Convergence TechnologyHanyang UniversityAnsanRepublic of Korea
| | - Soo Young Cho
- Department of Molecular and Life Science, College of Science and Convergence TechnologyHanyang UniversityAnsanRepublic of Korea
| | - Hong‐Yeoul Ryu
- KNU LAMP Research Center, KNU Institute of Basic Sciences, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural SciencesKyungpook National UniversityDaeguRepublic of Korea
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence TechnologyHanyang UniversityAnsanRepublic of Korea
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2
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Bravo JI, Mizrahi CR, Kim S, Zhang L, Suh Y, Benayoun BA. An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells. PLoS Genet 2024; 20:e1011311. [PMID: 38848448 PMCID: PMC11189215 DOI: 10.1371/journal.pgen.1011311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 06/20/2024] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
Long interspersed element 1 (LINE-1; L1) are a family of transposons that occupy ~17% of the human genome. Though a small number of L1 copies remain capable of autonomous transposition, the overwhelming majority of copies are degenerate and immobile. Nevertheless, both mobile and immobile L1s can exert pleiotropic effects (promoting genome instability, inflammation, or cellular senescence) on their hosts, and L1's contributions to aging and aging diseases is an area of active research. However, because of the cell type-specific nature of transposon control, the catalogue of L1 regulators remains incomplete. Here, we employ an eQTL approach leveraging transcriptomic and genomic data from the GEUVADIS and 1000Genomes projects to computationally identify new candidate regulators of L1 RNA levels in lymphoblastoid cell lines. To cement the role of candidate genes in L1 regulation, we experimentally modulate the levels of top candidates in vitro, including IL16, STARD5, HSD17B12, and RNF5, and assess changes in TE family expression by Gene Set Enrichment Analysis (GSEA). Remarkably, we observe subtle but widespread upregulation of TE family expression following IL16 and STARD5 overexpression. Moreover, a short-term 24-hour exposure to recombinant human IL16 was sufficient to transiently induce subtle, but widespread, upregulation of L1 subfamilies. Finally, we find that many L1 expression-associated genetic variants are co-associated with aging traits across genome-wide association study databases. Our results expand the catalogue of genes implicated in L1 RNA control and further suggest that L1-derived RNA contributes to aging processes. Given the ever-increasing availability of paired genomic and transcriptomic data, we anticipate this new approach to be a starting point for more comprehensive computational scans for regulators of transposon RNA levels.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, California, United States of America
| | - Chanelle R. Mizrahi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- USC Gerontology Enriching MSTEM to Enhance Diversity in Aging Program, University of Southern California, Los Angeles, California, United States of America
| | - Seungsoo Kim
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, United States of America
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, United States of America
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California, United States of America
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California, United States of America
- USC Stem Cell Initiative, Los Angeles, California, United States of America
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3
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Kumar SJ, Shukla S, Kumar S, Mishra P. Immunosenescence and Inflamm-Aging: Clinical Interventions and the Potential for Reversal of Aging. Cureus 2024; 16:e53297. [PMID: 38435871 PMCID: PMC10906346 DOI: 10.7759/cureus.53297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
Inflammation is often associated with the impairment of the ability to sustain the consequences of the physical, chemical, nutritional, and antigenic triggers of inflammation. The process of immunosenescence may only partially be explained by the senescence of cells, tissues, or the organism, and, hence, the hallmarks of immunosenescence may be markedly and differentially affected by the history of an individual's pathogenic encounter. Inflammation is a key component of immunosenescence, which itself is a direct consequence of aging. This review article highlights the therapeutic interventions for slowing the processes of inflamm-aging and immunosenescence and the possible reversal of aging and includes domains of immunomodulatory interventions, vaccination strategies, nutritional interventions, stem cell therapies, personalized medicine, microbiome interventions, and the positive effects of physical activity and exercise.
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Affiliation(s)
- Samayak J Kumar
- Pathology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Samarth Shukla
- Pathology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sunil Kumar
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Preeti Mishra
- Pathology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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4
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Bravo JI, Mizrahi CR, Kim S, Zhang L, Suh Y, Benayoun BA. An eQTL-based Approach Reveals Candidate Regulators of LINE-1 RNA Levels in Lymphoblastoid Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553416. [PMID: 37645920 PMCID: PMC10461994 DOI: 10.1101/2023.08.15.553416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Long interspersed element 1 (L1) are a family of autonomous, actively mobile transposons that occupy ~17% of the human genome. A number of pleiotropic effects induced by L1 (promoting genome instability, inflammation, or cellular senescence) have been observed, and L1's contributions to aging and aging diseases is an area of active research. However, because of the cell type-specific nature of transposon control, the catalogue of L1 regulators remains incomplete. Here, we employ an eQTL approach leveraging transcriptomic and genomic data from the GEUVADIS and 1000Genomes projects to computationally identify new candidate regulators of L1 RNA levels in lymphoblastoid cell lines. To cement the role of candidate genes in L1 regulation, we experimentally modulate the levels of top candidates in vitro, including IL16, STARD5, HSDB17B12, and RNF5, and assess changes in TE family expression by Gene Set Enrichment Analysis (GSEA). Remarkably, we observe subtle but widespread upregulation of TE family expression following IL16 and STARD5 overexpression. Moreover, a short-term 24-hour exposure to recombinant human IL16 was sufficient to transiently induce subtle, but widespread, upregulation of L1 subfamilies. Finally, we find that many L1 expression-associated genetic variants are co-associated with aging traits across genome-wide association study databases. Our results expand the catalogue of genes implicated in L1 RNA control and further suggest that L1-derived RNA contributes to aging processes. Given the ever-increasing availability of paired genomic and transcriptomic data, we anticipate this new approach to be a starting point for more comprehensive computational scans for transposon transcriptional regulators.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Chanelle R. Mizrahi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Gerontology Enriching MSTEM to Enhance Diversity in Aging Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Seungsoo Kim
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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5
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Nikopoulou C, Kleinenkuhnen N, Parekh S, Sandoval T, Ziegenhain C, Schneider F, Giavalisco P, Donahue KF, Vesting AJ, Kirchner M, Bozukova M, Vossen C, Altmüller J, Wunderlich T, Sandberg R, Kondylis V, Tresch A, Tessarz P. Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver. NATURE AGING 2023; 3:1430-1445. [PMID: 37946043 PMCID: PMC10645594 DOI: 10.1038/s43587-023-00513-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023]
Abstract
Tissues within an organism and even cell types within a tissue can age with different velocities. However, it is unclear whether cells of one type experience different aging trajectories within a tissue depending on their spatial location. Here, we used spatial transcriptomics in combination with single-cell ATAC-seq and RNA-seq, lipidomics and functional assays to address how cells in the male murine liver are affected by age-related changes in the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. The epigenome changed in a zonation-dependent manner and functionally, periportal hepatocytes were characterized by decreased mitochondrial fitness, whereas pericentral hepatocytes accumulated large lipid droplets. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.
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Affiliation(s)
- Chrysa Nikopoulou
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
| | - Niklas Kleinenkuhnen
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Swati Parekh
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma, Biberach, Germany
| | - Tonantzi Sandoval
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Farina Schneider
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - Patrick Giavalisco
- Metabolic Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Kat-Folz Donahue
- FACS and Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Marcel Kirchner
- FACS and Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Mihaela Bozukova
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany; Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thomas Wunderlich
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vangelis Kondylis
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty at Heinrich-Heine-University, Duesseldorf, Germany
| | - Achim Tresch
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany.
| | - Peter Tessarz
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
- Department of Human Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
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6
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Mei X, Blanchard J, Luellen C, Conboy MJ, Conboy IM. Fail-tests of DNA methylation clocks, and development of a noise barometer for measuring epigenetic pressure of aging and disease. Aging (Albany NY) 2023; 15:8552-8575. [PMID: 37702598 PMCID: PMC10522373 DOI: 10.18632/aging.205046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/20/2023] [Indexed: 09/14/2023]
Abstract
This study shows that Elastic Net (EN) DNA methylation (DNAme) clocks have low accuracy of predictions for individuals of the same age and a low resolution between healthy and disease cohorts; caveats inherent in applying linear model to non-linear processes. We found that change in methylation of cytosines with age is, interestingly, not the determinant for their selection into the clocks. Moreover, an EN clock's selected cytosines change when non-clock cytosines are removed from the training data; as expected from optimization in a machine learning (ML) context, but inconsistently with the identification of health markers in a biological context. To address these limitations, we moved from predictions to measurement of biological age, focusing on the cytosines that on average remain invariable in their methylation through lifespan, postulated to be homeostatically vital. We established that dysregulation of such cytosines, measured as the sums of standard deviations of their methylation values, quantifies biological noise, which in our hypothesis is a biomarker of aging and disease. We term this approach a "noise barometer" - the pressure of aging and disease on an organism. These noise-detecting cytosines are particularly important as sums of SD on the entire 450K DNAme array data yield a random pattern through chronology. Testing how many cytosines of the 450K arrays become noisier with age, we found that the paradigm of DNAme noise as a biomarker of aging and disease remarkably manifests in ~1/4 of the total. In that large set even the cytosines that have on average constant methylation through age show increased SDs and can be used as noise detectors of the barometer.
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Affiliation(s)
- Xiaoyue Mei
- Department of Bioengineering and QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joshua Blanchard
- Department of Bioengineering and QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Connor Luellen
- Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael J. Conboy
- Department of Bioengineering and QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Irina M. Conboy
- Department of Bioengineering and QB3, University of California, Berkeley, Berkeley, CA 94720, USA
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7
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Culberson JW, Kopel J, Sehar U, Reddy PH. Urgent needs of caregiving in ageing populations with Alzheimer's disease and other chronic conditions: Support our loved ones. Ageing Res Rev 2023; 90:102001. [PMID: 37414157 PMCID: PMC10756323 DOI: 10.1016/j.arr.2023.102001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
The ageing process begins at birth. It is a life-long process, and its exact origins are still unknown. Several hypotheses attempt to describe the normal ageing process, including hormonal imbalance, formation of reactive oxygen species, DNA methylation & DNA damage accumulation, loss of proteostasis, epigenetic alterations, mitochondrial dysfunction, senescence, inflammation, and stem cell depletion. With increased lifespan in elderly individuals, the prevalence of age-related diseases including, cancer, diabetes, obesity, hypertension, Alzheimer's, Alzheimer's disease and related dementias, Parkinson's, and other mental illnesses are increased. These increased age-related illnesses, put tremendous pressure & burden on caregivers, family members, and friends who are living with patients with age-related diseases. As medical needs evolve, the caregiver is expected to experience an increase in duties and challenges, which may result in stress on themselves, and impact their own family life. In the current article, we assess the biological mechanisms of ageing and its effect on body systems, exploring lifestyle and ageing, with a specific focus on age-related disorders. We also discussed the history of caregiving and specific challenges faced by caregivers in the presence of multiple comorbidities. We also assessed innovative approaches to funding caregiving, and efforts to improve the medical system to better organize chronic care efforts, while improving the skill and efficiency of both informal and formal caregivers. We also discussed the role of caregiving in end-of-life care. Our critical analysis strongly suggests that there is an urgent need for caregiving in aged populations and support from local, state, and federal agencies.
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Affiliation(s)
- John W Culberson
- Department of Family and Community Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jonathan Kopel
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ujala Sehar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA; Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
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8
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Cheng Z, Ferris C, Crowe MA, Ingvartsen KL, Grelet C, Vanlierde A, Foldager L, Becker F, Wathes DC. Hepatic Global Transcriptomic Profiles of Holstein Cows According to Parity Reveal Age-Related Changes in Early Lactation. Int J Mol Sci 2023; 24:9906. [PMID: 37373054 DOI: 10.3390/ijms24129906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Cows can live for over 20 years, but their productive lifespan averages only around 3 years after first calving. Liver dysfunction can reduce lifespan by increasing the risk of metabolic and infectious disease. This study investigated the changes in hepatic global transcriptomic profiles in early lactation Holstein cows in different lactations. Cows from five herds were grouped as primiparous (lactation number 1, PP, 534.7 ± 6.9 kg, n = 41), or multiparous with lactation numbers 2-3 (MP2-3, 634.5 ± 7.5 kg, n = 87) or 4-7 (MP4-7, 686.6 ± 11.4 kg, n = 40). Liver biopsies were collected at around 14 days after calving for RNA sequencing. Blood metabolites and milk yields were measured, and energy balance was calculated. There were extensive differences in hepatic gene expression between MP and PP cows, with 568 differentially expressed genes (DEGs) between MP2-3 and PP cows, and 719 DEGs between MP4-7 and PP cows, with downregulated DEGs predominating in MP cows. The differences between the two age groups of MP cows were moderate (82 DEGs). The gene expression differences suggested that MP cows had reduced immune functions compared with the PP cows. MP cows had increased gluconeogenesis but also evidence of impaired liver functionality. The MP cows had dysregulated protein synthesis and glycerophospholipid metabolism, and impaired genome and RNA stability and nutrient transport (22 differentially expressed solute carrier transporters). The genes associated with cell cycle arrest, apoptosis, and the production of antimicrobial peptides were upregulated. More surprisingly, evidence of hepatic inflammation leading to fibrosis was present in the primiparous cows as they started their first lactation. This study has therefore shown that the ageing process in the livers of dairy cows is accelerated by successive lactations and increasing milk yields. This was associated with evidence of metabolic and immune disorders together with hepatic dysfunction. These problems are likely to increase involuntary culling, thus reducing the average longevity in dairy herds.
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Affiliation(s)
- Zhangrui Cheng
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Herts AL9 7TA, UK
| | - Conrad Ferris
- Agri-Food and Biosciences Institute, Newforge Lane, Upper Malone Road, Belfast BT9 5PX, UK
| | - Mark A Crowe
- School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Klaus L Ingvartsen
- Department of Animal and Veterinary Sciences, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark
| | - Clément Grelet
- Valorisation of Agricultural Products Department, Walloon Agricultural Research Centre, 5030 Gembloux, Belgium
| | - Amélie Vanlierde
- Valorisation of Agricultural Products Department, Walloon Agricultural Research Centre, 5030 Gembloux, Belgium
| | - Leslie Foldager
- Department of Animal and Veterinary Sciences, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark
- Bioinformatics Research Centre, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
| | - Frank Becker
- Research Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - D Claire Wathes
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Herts AL9 7TA, UK
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9
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Zhu P, Liu W, Zhang X, Li M, Liu G, Yu Y, Li Z, Li X, Du J, Wang X, Grueter CC, Li M, Zhou X. Correlated evolution of social organization and lifespan in mammals. Nat Commun 2023; 14:372. [PMID: 36720880 PMCID: PMC9889386 DOI: 10.1038/s41467-023-35869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/05/2023] [Indexed: 02/02/2023] Open
Abstract
Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
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Affiliation(s)
- Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Yang Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,International Center of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, 671003, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.
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10
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Lim S, Liu Y, Rhie BH, Kim C, Ryu HY, Ahn SH. Sus1 maintains a normal lifespan through regulation of TREX-2 complex-mediated mRNA export. Aging (Albany NY) 2022; 14:4990-5012. [PMID: 35771153 PMCID: PMC9271307 DOI: 10.18632/aging.204146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
Eukaryotic gene expression requires multiple cellular events, including transcription and RNA processing and transport. Sus1, a common subunit in both the Spt-Ada-Gcn5 acetyltransferase (SAGA) and transcription and export complex-2 (TREX-2) complexes, is a key factor in coupling transcription activation to mRNA nuclear export. Here, we report that the SAGA DUB module and TREX-2 distinctly regulate yeast replicative lifespan in a Sir2-dependent and -independent manner, respectively. The growth and lifespan impaired by SUS1 loss depend on TREX-2 but not on the SAGA DUB module. Notably, an increased dose of the mRNA export factors Mex67 and Dbp5 rescues the growth defect, shortened lifespan, and nuclear accumulation of poly(A)+ RNA in sus1Δ cells, suggesting that boosting the mRNA export process restores the mRNA transport defect and the growth and lifespan damage in sus1Δ cells. Moreover, Sus1 is required for the proper association of Mex67 and Dbp5 with the nuclear rim. Together, these data indicate that Sus1 links transcription and mRNA nuclear export to the lifespan control pathway, suggesting that prevention of an abnormal accumulation of nuclear RNA is necessary for maintenance of a normal lifespan.
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Affiliation(s)
- Suji Lim
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Yan Liu
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Byung-Ho Rhie
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Chun Kim
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Hong-Yeoul Ryu
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
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11
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Mallik S, Grodstein F, Bennett DA, Vavvas DG, Lemos B. Novel Epigenetic Clock Biomarkers of Age-Related Macular Degeneration. Front Med (Lausanne) 2022; 9:856853. [PMID: 35783640 PMCID: PMC9244395 DOI: 10.3389/fmed.2022.856853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/19/2022] [Indexed: 01/05/2023] Open
Abstract
Age-Related Macular Degeneration (AMD) is a bilateral ocular condition resulting in irreversible vision impairment caused by the progressive loss of photoreceptors in the macula, a region at the center of the retina. The progressive loss of photoreceptor is a key feature of dry AMD but not always wet AMD, though both forms of AMD can lead to loss of vision. Regression-based biological age clocks are one of the most promising biomarkers of aging but have not yet been used in AMD. Here we conducted analyses to identify regression-based biological age clocks for the retina and explored their use in AMD using transcriptomic data consisting of a total of 453 retina samples including 105 Minnesota Grading System (MGS) level 1 samples, 175 MGS level 2, 112 MGS level 3 and 61 MGS level 4 samples, as well as 167 fibroblast samples. The clocks yielded good separation among AMD samples with increasing severity score viz., MGS1-4, regardless of whether clocks were trained in retina tissue, dermal fibroblasts, or in combined datasets. Clock application to cultured fibroblasts, embryonic stem cells, and induced Pluripotent Stem Cells (iPSCs) were consistent with age reprograming in iPSCs. Moreover, clock application to in vitro neuronal differentiation suggests broader applications. Interesting, many of the age clock genes identified include known targets mechanistically linked to AMD and aging, such as GDF11, C16ORF72, and FBN2. This study provides new observations for retina age clocks and suggests new applications for monitoring in vitro neuronal differentiation. These clocks could provide useful markers for AMD monitoring and possible intervention, as well as potential targets for in vitro screens.
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Affiliation(s)
- Saurav Mallik
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Fran Grodstein
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
| | - Demetrios G. Vavvas
- Ines and Frederick Yeatts Retina Research Laboratory, Retina Service, Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
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12
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Nuclear mRNA Export and Aging. Int J Mol Sci 2022; 23:ijms23105451. [PMID: 35628261 PMCID: PMC9142925 DOI: 10.3390/ijms23105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, although the nuclear events after transcription are coupled closely with the transcription pathway because the essential factors required for mRNA transport, namely TREX, TREX-2, and nuclear pore complex (NPC), physically and functionally interact with various transcription factors, including the activator/repressor and pre-mRNA processing factors. Dysregulation of the mediating factors for mRNA export from the nucleus generally leads to the aberrant accumulation of nuclear mRNA and further impairment in the vegetative growth and normal lifespan and the pathogenesis of neurodegenerative diseases. The optimal stoichiometry and density of NPC are destroyed during the process of cellular aging, and their damage triggers a defect of function in the nuclear permeability barrier. This review describes recent findings regarding the role of the nuclear mRNA export in cellular aging and age-related neurodegenerative disorders.
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13
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Identification and functional characterization of CD133+GFAP+CD117+Sca1+ neural stem cells. Mol Cell Biochem 2022; 477:897-914. [DOI: 10.1007/s11010-021-04339-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 12/15/2021] [Indexed: 02/03/2023]
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14
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McCauley BS, Sun L, Yu R, Lee M, Liu H, Leeman DS, Huang Y, Webb AE, Dang W. Altered Chromatin States Drive Cryptic Transcription in Aging Mammalian Stem Cells. ACTA ACUST UNITED AC 2021; 1:684-697. [PMID: 34746802 DOI: 10.1038/s43587-021-00091-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A repressive chromatin state featuring trimethylated lysine 36 on histone H3 (H3K36me3) and DNA methylation suppresses cryptic transcription in embryonic stem cells. Cryptic transcription is elevated with age in yeast and nematodes, and reducing it extends yeast lifespan, though whether this occurs in mammals is unknown. We show that cryptic transcription is elevated in aged mammalian stem cells, including murine hematopoietic stem cells (mHSCs) and neural stem cells (NSCs) and human mesenchymal stem cells (hMSCs). Precise mapping allowed quantification of age-associated cryptic transcription in hMSCs aged in vitro. Regions with significant age-associated cryptic transcription have a unique chromatin signature: decreased H3K36me3 and increased H3K4me1, H3K4me3, and H3K27ac with age. Genomic regions undergoing such changes resemble known promoter sequences and are bound by TBP even in young cells. Hence, the more permissive chromatin state at intragenic cryptic promoters likely underlies increased cryptic transcription in aged mammalian stem cells.
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Affiliation(s)
- Brenna S McCauley
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luyang Sun
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruofan Yu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Minjung Lee
- Center for Epigenetics & Disease Prevention, Institute of Bioscience and Technology, Texas A&M University, Houston, TX 77030, USA.,Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Haiying Liu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dena S Leeman
- Department of Genetics, Stanford University, Stanford, CA, 94305 USA.,Department of Discovery Immunology, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Bioscience and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Ashley E Webb
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
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15
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Abstract
Aging has provided fruitful challenges for evolutionary theory, and evolutionary theory has deepened our understanding of aging. A great deal of genetic and molecular data now exists concerning mortality regulation and there is a growing body of knowledge concerning the life histories of diverse species. Assimilating all relevant data into a framework for the evolution of aging promises to significantly advance the field. We propose extensions of some key concepts to provide greater precision when applying these concepts to age-structured contexts. Secondary or byproduct effects of mutations are proposed as an important factor affecting survival patterns, including effects that may operate in small populations subject to genetic drift, widening the possibilities for mutation accumulation and pleiotropy. Molecular and genetic studies have indicated a diverse array of mechanisms that can modify aging and mortality rates, while transcriptome data indicate a high level of tissue and species specificity for genes affected by aging. The diversity of mechanisms and gene effects that can contribute to the pattern of aging in different organisms may mirror the complex evolutionary processes behind aging.
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Affiliation(s)
- Stewart Frankel
- Biology Department, University of Hartford, West Hartford, CT, United States
| | - Blanka Rogina
- Genetics and Genome Sciences, Institute for Systems Genomics, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
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16
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Comparison of the transcriptome in circulating leukocytes in early lactation between primiparous and multiparous cows provides evidence for age-related changes. BMC Genomics 2021; 22:693. [PMID: 34563126 PMCID: PMC8466696 DOI: 10.1186/s12864-021-07977-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 09/06/2021] [Indexed: 12/18/2022] Open
Abstract
Background Previous studies have identified many immune pathways which are consistently altered in humans and model organisms as they age. Dairy cows are often culled at quite young ages due to an inability to cope adequately with metabolic and infectious diseases, resulting in reduced milk production and infertility. Improved longevity is therefore a desirable trait which would benefit both farmers and their cows. This study analysed the transcriptome derived from RNA-seq data of leukocytes obtained from Holstein cows in early lactation with respect to lactation number. Results Samples were divided into three lactation groups for analysis: i) primiparous (PP, n = 53), ii) multiparous in lactations 2–3 (MP 2–3, n = 121), and iii) MP in lactations 4–7 (MP > 3, n = 55). Leukocyte expression was compared between PP vs MP > 3 cows with MP 2–3 as background using DESeq2 followed by weighted gene co-expression network analysis (WGCNA). Seven modules were significantly correlated (r ≥ 0.25) to the trait lactation number. Genes from the modules which were more highly expressed in either the PP or MP > 3 cows were pooled, and the gene lists subjected to David functional annotation cluster analysis. The top three clusters from modules more highly expressed in the PP cows all involved regulation of gene transcription, particularly zinc fingers. Another cluster included genes encoding enzymes in the mitochondrial beta-oxidation pathway. Top clusters up-regulated in MP > 3 cows included the terms Glycolysis/Gluconeogenesis, C-type lectin, and Immunity. Differentially expressed candidate genes for ageing previously identified in the human blood transcriptome up-regulated in PP cows were mainly associated with T-cell function (CCR7, CD27, IL7R, CAMK4, CD28), mitochondrial ribosomal proteins (MRPS27, MRPS9, MRPS31), and DNA replication and repair (WRN). Those up-regulated in MP > 3 cows encoded immune defence proteins (LYZ, CTSZ, SREBF1, GRN, ANXA5, ADARB1). Conclusions Genes and pathways associated with lactation number in cows were identified for the first time to date, and we found that many were comparable to those known to be associated with ageing in humans and model organisms. We also detected changes in energy utilization and immune responses in leukocytes from older cows. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07977-5.
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17
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Samokhina LM, Lomako VV. Activity of Chymase, Tonin, and Calpains in Tissues of Male and Female Rats of Different Ages. ADVANCES IN GERONTOLOGY 2021. [DOI: 10.1134/s2079057021030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Lu RJ, Taylor S, Contrepois K, Kim M, Bravo JI, Ellenberger M, Sampathkumar NK, Benayoun BA. Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex and age-related functional regulation. NATURE AGING 2021; 1:715-733. [PMID: 34514433 PMCID: PMC8425468 DOI: 10.1038/s43587-021-00086-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 06/10/2021] [Indexed: 12/18/2022]
Abstract
Neutrophils are the most abundant human white blood cell and constitute a first line of defense in the innate immune response. Neutrophils are short-lived cells, and thus the impact of organismal aging on neutrophil biology, especially as a function of biological sex, remains poorly understood. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male mice, at the transcriptomic, metabolomic and lipidomic levels. We identify widespread regulation of neutrophil 'omics' landscapes with organismal aging and biological sex. In addition, we leverage our resource to predict functional differences, including changes in neutrophil responses to activation signals. To date, this dataset represents the largest multi-omics resource for neutrophils across sex and ages. This resource identifies neutrophil characteristics which could be targeted to improve immune responses as a function of sex and/or age.
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Affiliation(s)
- Ryan J. Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Shalina Taylor
- Departments of Pediatrics and of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Nirmal K. Sampathkumar
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Present Address: UK-Dementia Research Institute, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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19
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Yusifov A, Chhatre VE, Koplin EK, Wilson CE, Schmitt EE, Woulfe KC, Bruns DR. Transcriptomic analysis of cardiac gene expression across the life course in male and female mice. Physiol Rep 2021; 9:e14940. [PMID: 34245129 PMCID: PMC8271347 DOI: 10.14814/phy2.14940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/22/2021] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Risk for heart disease increases with advanced age and differs between sexes, with females generally protected from heart disease until menopause. Despite these epidemiological observations, the molecular mechanisms that underlie sex‐specific differences in cardiac function have not been fully described. We used high throughput transcriptomics in juvenile (5 weeks), adult (4–6 months), and aged (18 months) male and female mice to understand how cardiac gene expression changes across the life course and by sex. While male gene expression profiles differed between juvenile‐adult and juvenile‐aged (254 and 518 genes, respectively), we found no significant differences in adult‐aged gene expression. Females had distinct gene expression changes across the life course with 1835 genes in juvenile‐adult and 1328 in adult‐aged. Analysis of differentially expressed genes (DEGs) suggests that juvenile to adulthood genes were clustered in cell cycle and development‐related pathways in contrast to adulthood‐aged which were characterized by immune‐and inflammation‐related pathways. Analysis of sex differences within each age suggests that juvenile and aged cardiac transcriptomes are different between males and females, with significantly fewer DEGs identified in adult males and females. Interestingly, the male–female differences in early age were distinct from those in advanced age. These findings are in contrast to expected sex differences historically attributed to estrogen and could not be explained by estrogen‐direct mechanisms alone as evidenced by juvenile sexual immaturity and reproductive incompetence in the aged mice. Together, distinct trajectories in cardiac transcriptomic profiles highlight fundamental sex differences across the life course and demonstrate the need for the consideration of age and sex as biological variables in heart disease.
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Affiliation(s)
- Aykhan Yusifov
- Kinesiology and Health, University of Wyoming, Laramie, WY, USA
| | | | - Eva K Koplin
- Kinesiology and Health, University of Wyoming, Laramie, WY, USA
| | - Cortney E Wilson
- Division of Cardiology, University of Colorado-Denver, Aurora, CO, USA
| | - Emily E Schmitt
- Kinesiology and Health, University of Wyoming, Laramie, WY, USA
| | - Kathleen C Woulfe
- Division of Cardiology, University of Colorado-Denver, Aurora, CO, USA.,Division of Geriatric Medicine, University of Colorado-Denver, Aurora, CO, USA
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20
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Ni X, Wang Z, Gao D, Yuan H, Sun L, Zhu X, Zhou Q, Yang Z. A description of the relationship in healthy longevity and aging-related disease: from gene to protein. Immun Ageing 2021; 18:30. [PMID: 34172062 PMCID: PMC8229348 DOI: 10.1186/s12979-021-00241-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/14/2021] [Indexed: 11/22/2022]
Abstract
Human longevity is a complex phenotype influenced by both genetic and environmental factors. It is also known to be associated with various types of age-related diseases, such as Alzheimer's disease (AD) and cardiovascular disease (CVD). The central dogma of molecular biology demonstrates the conversion of DNA to RNA to the encoded protein. These proteins interact to form complex cell signaling pathways, which perform various biological functions. With prolonged exposure to the environment, the in vivo homeostasis adapts to the changes, and finally, humans adopt the phenotype of longevity or aging-related diseases. In this review, we focus on two different states: longevity and aging-related diseases, including CVD and AD, to discuss the relationship between genetic characteristics, including gene variation, the level of gene expression, regulation of gene expression, the level of protein expression, both genetic and environmental influences and homeostasis based on these phenotypes shown in organisms.
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Affiliation(s)
- Xiaolin Ni
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R. China
| | - Zhaoping Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Danni Gao
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China
| | - Huiping Yuan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Liang Sun
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Xiaoquan Zhu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Qi Zhou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Ze Yang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China.
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R. China.
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21
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Lu RJ, Wang EK, Benayoun BA. Functional genomics of inflamm-aging and immunosenescence. Brief Funct Genomics 2021; 21:43-55. [PMID: 33690792 DOI: 10.1093/bfgp/elab009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
The aging population is at a higher risk for age-related diseases and infections. This observation could be due to immunosenescence: the decline in immune efficacy of both the innate and the adaptive immune systems. Age-related immune decline also links to the concept of 'inflamm-aging,' whereby aging is accompanied by sterile chronic inflammation. Along with a decline in immune function, aging is accompanied by a widespread of 'omics' remodeling. Transcriptional landscape changes linked to key pathways of immune function have been identified across studies, such as macrophages having decreased expression of genes associated to phagocytosis, a major function of macrophages. Therefore, a key mechanism underlying innate immune cell dysfunction during aging may stem from dysregulation of youthful genomic networks. In this review, we discuss both molecular and cellular phenotypes of innate immune cells that contribute to age-related inflammation.
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Affiliation(s)
- Ryan J Lu
- Leonard Davis School of Gerontology at the University of Southern California
| | - Emily K Wang
- Leonard Davis School of Gerontology at the University of Southern California
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology at the University of Southern California
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22
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Meyer DH, Schumacher B. BiT age: A transcriptome-based aging clock near the theoretical limit of accuracy. Aging Cell 2021; 20:e13320. [PMID: 33656257 PMCID: PMC7963339 DOI: 10.1111/acel.13320] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/22/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Aging clocks dissociate biological from chronological age. The estimation of biological age is important for identifying gerontogenes and assessing environmental, nutritional, or therapeutic impacts on the aging process. Recently, methylation markers were shown to allow estimation of biological age based on age‐dependent somatic epigenetic alterations. However, DNA methylation is absent in some species such as Caenorhabditis elegans and it remains unclear whether and how the epigenetic clocks affect gene expression. Aging clocks based on transcriptomes have suffered from considerable variation in the data and relatively low accuracy. Here, we devised an approach that uses temporal scaling and binarization of C. elegans transcriptomes to define a gene set that predicts biological age with an accuracy that is close to the theoretical limit. Our model accurately predicts the longevity effects of diverse strains, treatments, and conditions. The involved genes support a role of specific transcription factors as well as innate immunity and neuronal signaling in the regulation of the aging process. We show that this binarized transcriptomic aging (BiT age) clock can also be applied to human age prediction with high accuracy. The BiT age clock could therefore find wide application in genetic, nutritional, environmental, and therapeutic interventions in the aging process.
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Affiliation(s)
- David H. Meyer
- Institute for Genome Stability in Ageing and Disease Medical Faculty University of Cologne Cologne Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing‐Associated Diseases (CECAD) Center for Molecular Medicine Cologne (CMMC) University of Cologne Cologne Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease Medical Faculty University of Cologne Cologne Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing‐Associated Diseases (CECAD) Center for Molecular Medicine Cologne (CMMC) University of Cologne Cologne Germany
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23
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Proshkina E, Yushkova E, Koval L, Zemskaya N, Shchegoleva E, Solovev I, Yakovleva D, Pakshina N, Ulyasheva N, Shaposhnikov M, Moskalev A. Tissue-Specific Knockdown of Genes of the Argonaute Family Modulates Lifespan and Radioresistance in Drosophila Melanogaster. Int J Mol Sci 2021; 22:2396. [PMID: 33673647 PMCID: PMC7957547 DOI: 10.3390/ijms22052396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Small RNAs are essential to coordinate many cellular processes, including the regulation of gene expression patterns, the prevention of genomic instability, and the suppression of the mutagenic transposon activity. These processes determine the aging, longevity, and sensitivity of cells and an organism to stress factors (particularly, ionizing radiation). The biogenesis and activity of small RNAs are provided by proteins of the Argonaute family. These proteins participate in the processing of small RNA precursors and the formation of an RNA-induced silencing complex. However, the role of Argonaute proteins in regulating lifespan and radioresistance remains poorly explored. We studied the effect of knockdown of Argonaute genes (AGO1, AGO2, AGO3, piwi) in various tissues on the Drosophila melanogaster lifespan and survival after the γ-irradiation at a dose of 700 Gy. In most cases, these parameters are reduced or did not change significantly in flies with tissue-specific RNA interference. Surprisingly, piwi knockdown in both the fat body and the nervous system causes a lifespan increase. But changes in radioresistance depend on the tissue in which the gene was knocked out. In addition, analysis of changes in retrotransposon levels and expression of stress response genes allow us to determine associated molecular mechanisms.
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Affiliation(s)
- Ekaterina Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Liubov Koval
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Nadezhda Zemskaya
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Evgeniya Shchegoleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Ilya Solovev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Daria Yakovleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Natalya Pakshina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Natalia Ulyasheva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Mikhail Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Laboratory of Post-Genomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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25
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Principles of the Molecular and Cellular Mechanisms of Aging. J Invest Dermatol 2021; 141:951-960. [PMID: 33518357 DOI: 10.1016/j.jid.2020.11.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]
Abstract
Aging can be defined as a state of progressive functional decline accompanied by an increase in mortality. Time-dependent accumulation of cellular damage, namely lesions and mutations in the DNA and misfolded proteins, impair organellar and cellular function. Ensuing cell fate alterations lead to the accumulation of dysfunctional cells and hamper homeostatic processes, thus limiting regenerative potential; trigger low-grade inflammation; and alter intercellular and intertissue communication. The accumulation of molecular damage together with modifications in the epigenetic landscape, dysregulation of gene expression, and altered endocrine communication, drive the aging process and establish age as the main risk factor for age-associated diseases and multimorbidity.
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26
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Proshkina EN, Solovev IA, Shaposhnikov MV, Moskalev AA. Key Molecular Mechanisms of Aging, Biomarkers, and Potential Interventions. Mol Biol 2021. [DOI: 10.1134/s0026893320060096] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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27
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Kowal K, Tkaczyk A, Pierzchała M, Bownik A, Ślaska B. Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna. Int J Mol Sci 2020; 21:E8725. [PMID: 33218217 PMCID: PMC7699184 DOI: 10.3390/ijms21228725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/30/2023] Open
Abstract
This is the first study in which the Daphnia magna (D. magna) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in D. magna genome. This study aimed to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome (mtDNA) analyses. Bioinformatic analysis showed 1909 fragments of the mtDNA of D. magna, of which 1630 were located in ten linkage groups (LG) of the nDNA. The best-matched NUMTs covering >90% of the gene sequence have been identified for two mt-tRNA genes, and they may be functional nuclear RNA molecules. Isolating the total DNA in mtDNA studies, co-amplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes. It was observed that TRNA-MET fragments had the highest level of sequence homology, thus they could be evolutionarily the youngest. The lowest homology was found in the D-loop-derived pseudogene. It may probably be the oldest NUMT incorporated into the nDNA; however, further analysis is necessary.
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Affiliation(s)
- Krzysztof Kowal
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
| | - Angelika Tkaczyk
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
| | - Mariusz Pierzchała
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36a Str., 05-552 Jastrzębiec, Poland;
| | - Adam Bownik
- Faculty of Environmental Biology, Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37 Str., 20-262 Lublin, Poland;
| | - Brygida Ślaska
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
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28
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Capp JP, Thomas F. Tissue-disruption-induced cellular stochasticity and epigenetic drift: Common origins of aging and cancer? Bioessays 2020; 43:e2000140. [PMID: 33118188 DOI: 10.1002/bies.202000140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 01/10/2023]
Abstract
Age-related and cancer-related epigenomic modifications have been associated with enhanced cell-to-cell gene expression variability that characterizes increased cellular stochasticity. Since gene expression variability appears to be highly reduced by-and epigenetic and phenotypic stability acquired through-direct or long-range cellular interactions during cell differentiation, we propose a common origin for aging and cancer in the failure to control cellular stochasticity by cell-cell interactions. Tissue-disruption-induced cellular stochasticity associated with epigenetic drift would be at the origin of organ dysfunction because of an increase in phenotypic variation among cells, ultimately leading to cell death and organ failure through a loss of coordination in cellular functions, and eventually to cancerization. We propose mechanistic research perspectives to corroborate this hypothesis and explore its evolutionary consequences, highlighting a positive correlation between the median age of mass loss onset (a proxy for the onset of organ aging) and the median age at cancer diagnosis.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Frédéric Thomas
- CREEC (CREES), UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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29
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Cakouros D, Gronthos S. The changing epigenetic landscape of Mesenchymal Stem/Stromal Cells during aging. Bone 2020; 137:115440. [PMID: 32445894 DOI: 10.1016/j.bone.2020.115440] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/17/2020] [Accepted: 05/17/2020] [Indexed: 12/17/2022]
Abstract
There is mounting evidence in the literature that mesenchymal stromal/stem cell (MSC) like populations derived from different tissues, undergo epigenetic changes during aging, leading to compromised connective tissue integrity and function. This body of work has linked the biological aging of MSC to changes in their epigenetic signatures affecting growth, lifespan, self-renewal and multi-potential, due to deregulation of processes such as cellular senescence, oxidative stress, DNA damage, telomere shortening and DNA damage. This review addresses recent findings examining DNA methylation, histone modifications and miRNA changes in aging MSC populations. Moreover, we explore how epigenetic factors alter cellular pathways and associated biological networks, contributing to the MSC aging phenotype. Finally we discuss the crucial areas requiring a greater understanding of these processes, in order to piece together a global picture of the changing epigenetic landscape in MSC during aging.
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Affiliation(s)
- Dimitrios Cakouros
- Mesenchymal Stem Cell Laboratory, School of Medical Sciences, Faculty of Health Sciences, The University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Stan Gronthos
- Mesenchymal Stem Cell Laboratory, School of Medical Sciences, Faculty of Health Sciences, The University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
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30
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Fonseca Costa SS, Robinson-Rechavi M, Ripperger JA. Single-cell transcriptomics allows novel insights into aging and circadian processes. Brief Funct Genomics 2020; 19:343-349. [PMID: 32633783 PMCID: PMC7716582 DOI: 10.1093/bfgp/elaa014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/14/2022] Open
Abstract
Aging and circadian rhythms are two biological processes that affect an organism, although at different time scales. Nevertheless, due to the overlap of their actions, it was speculated that both interfere or interact with each other. However, to address this question, a much deeper insight into these processes is necessary, especially at the cellular level. New methods such as single-cell RNA-sequencing (scRNA-Seq) have the potential to close this gap in our knowledge. In this review, we analyze applications of scRNA-Seq from the aging and circadian rhythm fields and highlight new findings emerging from the analysis of single cells, especially in humans or rodents. Furthermore, we judge the potential of scRNA-Seq to identify common traits of both processes. Overall, this method offers several advantages over more traditional methods analyzing gene expression and will become an important tool to unravel the link between these biological processes.
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Affiliation(s)
- Sara S Fonseca Costa
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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31
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Abstract
Exonic circular RNAs (circRNAs) have been discovered in all kingdoms of life. In many cases, the details of circRNA function and their involvement in cellular processes and diseases are not yet fully understood. However, the past few years have seen significant developments in bioinformatics and in experimental protocols that advance the ongoing research in this still-emerging field. Sophisticated methods for circRNA generation in vitro and in vivo have been developed, allowing model studies into circRNA function and application. We here review the ongoing circRNA research, giving special attention to recent progress in the field.
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Affiliation(s)
| | - Theodor Schnarr
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
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32
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Bravo JI, Nozownik S, Danthi PS, Benayoun BA. Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation. Development 2020; 147:dev175786. [PMID: 32527937 PMCID: PMC10680986 DOI: 10.1242/dev.175786] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.
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Affiliation(s)
- Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Séverine Nozownik
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Magistère européen de Génétique, Université Paris Diderot-Paris 7, Paris 75014, France
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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33
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Sampathkumar NK, Bravo JI, Chen Y, Danthi PS, Donahue EK, Lai RW, Lu R, Randall LT, Vinson N, Benayoun BA. Widespread sex dimorphism in aging and age-related diseases. Hum Genet 2020; 139:333-356. [PMID: 31677133 PMCID: PMC7031050 DOI: 10.1007/s00439-019-02082-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/26/2019] [Indexed: 02/07/2023]
Abstract
Although aging is a conserved phenomenon across evolutionary distant species, aspects of the aging process have been found to differ between males and females of the same species. Indeed, observations across mammalian studies have revealed the existence of longevity and health disparities between sexes, including in humans (i.e. with a female or male advantage). However, the underlying mechanisms for these sex differences in health and lifespan remain poorly understood, and it is unclear which aspects of this dimorphism stem from hormonal differences (i.e. predominance of estrogens vs. androgens) or from karyotypic differences (i.e. XX vs. XY sex chromosome complement). In this review, we discuss the state of the knowledge in terms of sex dimorphism in various aspects of aging and in human age-related diseases. Where the interplay between sex differences and age-related differences has not been explored fully, we present the state of the field to highlight important future research directions. We also discuss various dietary, drug or genetic interventions that were shown to improve longevity in a sex-dimorphic fashion. Finally, emerging tools and models that can be leveraged to decipher the mechanisms underlying sex differences in aging are also briefly discussed.
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Affiliation(s)
- Nirmal K Sampathkumar
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yilin Chen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Masters Program in Nutrition, Healthspan, and Longevity, University of Southern California, Los Angeles, CA, 90089, USA
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Erin K Donahue
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rochelle W Lai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Lewis T Randall
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Nika Vinson
- Department of Urology, Pelvic Medicine and Reconstructive Surgery, UCLA David Geffen School of Medicine, Los Angeles, CA, 90024, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, 90089, USA.
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA.
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34
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Aging and Caloric Restriction Modulate the DNA Methylation Profile of the Ribosomal RNA Locus in Human and Rat Liver. Nutrients 2020; 12:nu12020277. [PMID: 31973116 PMCID: PMC7070571 DOI: 10.3390/nu12020277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 12/21/2022] Open
Abstract
A growing amount of evidence suggests that the downregulation of protein synthesis is an adaptive response during physiological aging, which positively contributes to longevity and can be modulated by nutritional interventions like caloric restriction (CR). The expression of ribosomal RNA (rRNA) is one of the main determinants of translational rate, and epigenetic modifications finely contribute to its regulation. Previous reports suggest that hypermethylation of ribosomal DNA (rDNA) locus occurs with aging, although with some species- and tissue- specificity. In the present study, we experimentally measured DNA methylation of three regions (the promoter, the 5′ of the 18S and the 5′ of 28S sequences) in the rDNA locus in liver tissues from rats at two, four, 10, and 18 months. We confirm previous findings, showing age-related hypermethylation, and describe, for the first time, that this gain in methylation also occurs in human hepatocytes. Furthermore, we show that age-related hypermethylation is enhanced in livers of rat upon CR at two and 10 months, and that at two months a trend towards the reduction of rRNA expression occurs. Collectively, our results suggest that CR modulates age-related regulation of methylation at the rDNA locus, thus providing an epigenetic readout of the pro-longevity effects of CR.
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35
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Chen Y, Bravo JI, Son JM, Lee C, Benayoun BA. Remodeling of the H3 nucleosomal landscape during mouse aging. TRANSLATIONAL MEDICINE OF AGING 2020; 4:22-31. [PMID: 32462102 DOI: 10.1016/j.tma.2019.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and deregulation of gene expression correlates with aging. A key layer in the study of gene regulation mechanisms lies at the level of chromatin: cellular chromatin states (i.e. the 'epigenome') can tune transcriptional profiles, and, in line with the prevalence of transcriptional alterations with aging, accumulating evidence suggests that the chromatin landscape is altered with aging across cell types and species. However, although alterations in the chromatin make-up of cells are considered to be a hallmark of aging, little is known of the genomic loci that are specifically affected by age-related chromatin state remodeling and of their biological significance. Here, we report the analysis of genome-wide profiles of core histone H3 occupancy in aging male mouse tissues (i.e. heart, liver, cerebellum and olfactory bulb) and primary cultures of neural stem cells. We find that, although no drastic changes in H3 levels are observed, local changes in H3 occupancy occur with aging across tissues and cells with both regions of increased or decreased occupancy. These changes are compatible with a general increase in chromatin accessibility at pro-inflammatory genes and may thus mechanistically underlie known shift in gene expression programs during aging.
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Affiliation(s)
- Yilin Chen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,Master of Science in Nutrition, Healthspan, and Longevity, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Jyung Mean Son
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA.,Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, Republic of Korea
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA.,USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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36
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Kollbaum PS, Bradley A. Correction of presbyopia: old problems with old (and new) solutions. Clin Exp Optom 2019; 103:21-30. [PMID: 31734940 DOI: 10.1111/cxo.12987] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/05/2019] [Accepted: 09/20/2019] [Indexed: 12/23/2022] Open
Abstract
We live in a three-dimensional world and the human eye can focus images from a wide range of distances by adjusting the power of the eye's lens (accommodation). Progressive senescent changes in the lens ultimately lead to a complete loss of this ability by about age 50, which then requires alternative strategies to generate high-quality retinal images for far and close viewing distances. This review paper highlights the biomimetic properties and underlying optical mechanisms of induced anisometropia, small apertures, dynamic lenses, and multi-optic lenses in ameliorating the visual consequences of presbyopia. Specifically, the advantages and consequences of non-liner neural summation leveraged in monovision treatments are reviewed. Additionally, the value of a small pupil is quantified, and the impact of pinhole pupil location and their effects on neural sensitivity are examined. Different strategies of generating multifocal optics are also examined, and specifically the interaction between ocular and contact or intraocular lens aberrations and their effect on resulting image quality are simulated. Interestingly, most of the novel strategies for aiding presbyopic and pseudophakic eyes (for example, monovision, multifocality, pinhole pupils) have emerged naturally via evolution in a range of species.
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Affiliation(s)
- Pete S Kollbaum
- School of Optometry, Indiana University, Bloomington, Indiana, USA
| | - Arthur Bradley
- School of Optometry, Indiana University, Bloomington, Indiana, USA
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