1
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Borrego-Ruiz A, Borrego JJ. Influence of human gut microbiome on the healthy and the neurodegenerative aging. Exp Gerontol 2024; 194:112497. [PMID: 38909763 DOI: 10.1016/j.exger.2024.112497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
The gut microbiome plays a crucial role in host health throughout the lifespan by influencing brain function during aging. The microbial diversity of the human gut microbiome decreases during the aging process and, as a consequence, several mechanisms increase, such as oxidative stress, mitochondrial dysfunction, inflammatory response, and microbial gut dysbiosis. Moreover, evidence indicates that aging and neurodegeneration are closely related; consequently, the gut microbiome may serve as a novel marker of lifespan in the elderly. In this narrative study, we investigated how the changes in the composition of the gut microbiome that occur in aging influence to various neuropathological disorders, such as mild cognitive impairment (MCI), dementia, Alzheimer's disease (AD), and Parkinson's disease (PD); and which are the possible mechanisms that govern the relationship between the gut microbiome and cognitive impairment. In addition, several studies suggest that the gut microbiome may be a potential novel target to improve hallmarks of brain aging and to promote healthy cognition; therefore, current and future therapeutic interventions have been also reviewed.
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Affiliation(s)
- Alejandro Borrego-Ruiz
- Departamento de Psicología Social y de las Organizaciones, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Juan J Borrego
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA, Plataforma BIONAND, Málaga, Spain.
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2
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Zheng X. An Introductory Guide to Using Bloomington Drosophila Stock Center and FlyBase for Aging Research. Cells 2024; 13:1192. [PMID: 39056774 PMCID: PMC11275189 DOI: 10.3390/cells13141192] [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: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Studies on numerous species have demonstrated strikingly conserved mechanisms that determine the aging process, from yeasts to worms, flies, zebrafish, mice, and humans. The fruit fly Drosophila melanogaster is an excellent model organism for studying the biological basis of normal aging and etiology of age-related diseases. Since its inception in 1967, the Bloomington Drosophila Stock Center (BDSC) has grown into the largest collection of documented D. melanogaster strains (currently > 91,000). This paper aims to briefly review conserved mechanisms of aging and provides a guide to help users understand the organization of stock listings on the BDSC website and familiarize themselves with the search functions on BDSC and FlyBase, with an emphasis on using genes in conserved pathways as examples to find stocks for aging studies.
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Affiliation(s)
- Xiangzhong Zheng
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
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3
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Bonnefous H, Teulière J, Lapointe FJ, Lopez P, Bapteste E. Most genetic roots of fungal and animal aging are hundreds of millions of years old according to phylostratigraphy analyses of aging networks. GeroScience 2024:10.1007/s11357-024-01234-9. [PMID: 38862758 DOI: 10.1007/s11357-024-01234-9] [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: 11/16/2023] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Few studies have systematically analyzed how old aging is. Gaining a more accurate knowledge about the natural history of aging could however have several payoffs. This knowledge could unveil lineages with dated genetic hardware, possibly maladapted to current environmental challenges, and also uncover "phylogenetic modules of aging," i.e., naturally evolved pathways associated with aging or longevity from a single ancestry, with translational interest for anti-aging therapies. Here, we approximated the natural history of the genetic hardware of aging for five model fungal and animal species. We propose a lower-bound estimate of the phylogenetic age of origination for their protein-encoding gene families and protein-protein interactions. Most aging-associated gene families are hundreds of million years old, older than the other gene families from these genomes. Moreover, we observed a form of punctuated evolution of the aging hardware in all species, as aging-associated families born at specific phylogenetic times accumulate preferentially in genomes. Most protein-protein interactions between aging genes are also old, and old aging-associated proteins showed a reduced potential to contribute to novel interactions associated with aging, suggesting that aging networks are at risk of losing in evolvability over long evolutionary periods. Finally, due to reshuffling events, aging networks presented a very limited phylogenetic structure that challenges the detection of "maladaptive" or "adaptative" phylogenetic modules of aging in present-day genomes.
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Affiliation(s)
- Hugo Bonnefous
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - François-Joseph Lapointe
- Département de Sciences Biologiques, Complexe Des Sciences, Université de Montréal, Montréal, QC, Canada
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France.
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4
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Harinath G, Zalzala S, Nyquist A, Wouters M, Isman A, Moel M, Verdin E, Kaeberlein M, Kennedy B, Bischof E. The role of quality of life data as an endpoint for collecting real-world evidence within geroscience clinical trials. Ageing Res Rev 2024; 97:102293. [PMID: 38574864 DOI: 10.1016/j.arr.2024.102293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
With geroscience research evolving at a fast pace, the need arises for human randomized controlled trials to assess the efficacy of geroprotective interventions to prevent age-related adverse outcomes, disease, and mortality in normative aging cohorts. However, to confirm efficacy requires a long-term and costly approach as time to the event of morbidity and mortality can be decades. While this could be circumvented using sensitive biomarkers of aging, current molecular, physiological, and digital endpoints require further validation. In this review, we discuss how collecting real-world evidence (RWE) by obtaining health data that is amenable for collection from large heterogeneous populations in a real-world setting can help speed up validation of geroprotective interventions. Further, we propose inclusion of quality of life (QoL) data as a biomarker of aging and candidate endpoint for geroscience clinical trials to aid in distinguishing healthy from unhealthy aging. We highlight how QoL assays can aid in accelerating data collection in studies gathering RWE on the geroprotective effects of repurposed drugs to support utilization within healthy longevity medicine. Finally, we summarize key metrics to consider when implementing QoL assays in studies, and present the short-form 36 (SF-36) as the most well-suited candidate endpoint.
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Affiliation(s)
| | | | | | | | | | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA
| | | | - Brian Kennedy
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Centre for Healthy Longevity, National University Health System, Singapore
| | - Evelyne Bischof
- Department of Medical Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai University of Medicine and Health Sciences, Shanghai, China; Sheba Longevity Center, Sheba Medical Center, Tel Aviv, Israel.
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5
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Zane F, MacMurray C, Guillermain C, Cansell C, Todd N, Rera M. Ageing as a two-phase process: theoretical framework. FRONTIERS IN AGING 2024; 5:1378351. [PMID: 38651031 PMCID: PMC11034523 DOI: 10.3389/fragi.2024.1378351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/26/2024] [Indexed: 04/25/2024]
Abstract
Human ageing, along with the ageing of conventional model organisms, is depicted as a continuous and progressive decline of biological capabilities accompanied by an exponentially increasing mortality risk. However, not all organisms experience ageing identically and our understanding of the phenomenon is coloured by human-centric views. Ageing is multifaceted and influences a diverse range of species in varying ways. Some undergo swift declines post-reproduction, while others exhibit insubstantial changes throughout their existence. This vast array renders defining universally applicable "ageing attributes" a daunting task. It is nonetheless essential to recognize that not all ageing features are organism-specific. These common attributes have paved the way for identifying "hallmarks of ageing," processes that are intertwined with age, amplified during accelerated ageing, and manipulations of which can potentially modulate or even reverse the ageing process. Yet, a glaring observation is that individuals within a single population age at varying rates. To address this, demographers have coined the term 'frailty'. Concurrently, scientific advancements have ushered in the era of molecular clocks. These innovations enable a distinction between an individual's chronological age (time since birth) and biological age (physiological status and mortality risk). In 2011, the "Smurf" phenotype was unveiled in Drosophila, delineating an age-linked escalation in intestinal permeability that presages imminent mortality. It not only acts as a predictor of natural death but identifies individuals exhibiting traits normally described as age-related. Subsequent studies have revealed the phenotype in organisms like nematodes, zebrafish, and mice, invariably acting as a death predictor. Collectively, these findings have steered our conception of ageing towards a framework where ageing is not linear and continuous but marked by two distinct, necessary phases, discernible in vivo, courtesy of the Smurf phenotype. This framework includes a mathematical enunciation of longevity trends based on three experimentally measurable parameters. It facilitates a fresh perspective on the evolution of ageing as a function. In this article, we aim to delineate and explore the foundational principles of this innovative framework, emphasising its potential to reshape our understanding of ageing, challenge its conventional definitions, and recalibrate our comprehension of its evolutionary trajectory.
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Affiliation(s)
- Flaminia Zane
- Université Paris Cité, INSERM UMR U1284, Paris, France
| | | | | | - Céline Cansell
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, Palaiseau, France
| | - Nicolas Todd
- Eco-Anthropologie (EA), Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Musée de l’Homme, Paris, France
| | - Michael Rera
- Université Paris Cité, Institut Jacques Monod, CNRS UMR 7592, Paris, France
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6
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Rafikova E, Nemirovich-Danchenko N, Ogmen A, Parfenenkova A, Velikanova A, Tikhonov S, Peshkin L, Rafikov K, Spiridonova O, Belova Y, Glinin T, Egorova A, Batin M. Open Genes-a new comprehensive database of human genes associated with aging and longevity. Nucleic Acids Res 2024; 52:D950-D962. [PMID: 37665017 PMCID: PMC10768108 DOI: 10.1093/nar/gkad712] [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: 06/29/2023] [Revised: 07/31/2023] [Accepted: 08/19/2023] [Indexed: 09/05/2023] Open
Abstract
The Open Genes database was created to enhance and simplify the search for potential aging therapy targets. We collected data on 2402 genes associated with aging and developed convenient tools for searching and comparing gene features. A comprehensive description of genes has been provided, including lifespan-extending interventions, age-related changes, longevity associations, gene evolution, associations with diseases and hallmarks of aging, and functions of gene products. For each experiment, we presented the necessary structured data for evaluating the experiment's quality and interpreting the study's findings. Our goal was to stay objective and precise while connecting a particular gene to human aging. We distinguished six types of studies and 12 criteria for adding genes to our database. Genes were classified according to the confidence level of the link between the gene and aging. All the data collected in a database are provided both by an API and a user interface. The database is publicly available on a website at https://open-genes.org/.
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Affiliation(s)
- Ekaterina Rafikova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Nikolay Nemirovich-Danchenko
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
- Faculty of Cytology and Genetics, National Research Tomsk State University, Tomsk 634050, Russia
| | - Anna Ogmen
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Anna Parfenenkova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | | | - Stanislav Tikhonov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119991, Russia
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantin Rafikov
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Olga Spiridonova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Yulia Belova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Timofey Glinin
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
- Endocrine Neoplasia Laboratory, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Genetics & Biotechnology, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Anastasia Egorova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Mikhail Batin
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
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7
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Zane F, Bouzid H, Sosa Marmol S, Brazane M, Besse S, Molina JL, Cansell C, Aprahamian F, Durand S, Ayache J, Antoniewski C, Todd N, Carré C, Rera M. Smurfness-based two-phase model of ageing helps deconvolve the ageing transcriptional signature. Aging Cell 2023; 22:e13946. [PMID: 37822253 PMCID: PMC10652310 DOI: 10.1111/acel.13946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 10/13/2023] Open
Abstract
Ageing is characterised at the molecular level by six transcriptional 'hallmarks of ageing', that are commonly described as progressively affected as time passes. By contrast, the 'Smurf' assay separates high-and-constant-mortality risk individuals from healthy, zero-mortality risk individuals, based on increased intestinal permeability. Performing whole body total RNA sequencing, we found that Smurfness distinguishes transcriptional changes associated with chronological age from those associated with biological age. We show that transcriptional heterogeneity increases with chronological age in non-Smurf individuals preceding the other five hallmarks of ageing that are specifically associated with the Smurf state. Using this approach, we also devise targeted pro-longevity genetic interventions delaying entry in the Smurf state. We anticipate that increased attention to the evolutionary conserved Smurf phenotype will bring about significant advances in our understanding of the mechanisms of ageing.
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Affiliation(s)
- Flaminia Zane
- Université Paris Cité, INSERM UMR U1284ParisFrance
- Institut de Biologie Paris Seine, Sorbonne UniversitéParisFrance
| | - Hayet Bouzid
- Université Paris Cité, INSERM UMR U1284ParisFrance
- Institut de Biologie Paris Seine, Sorbonne UniversitéParisFrance
| | | | - Mira Brazane
- Institut de Biologie Paris Seine, Sorbonne UniversitéParisFrance
| | | | | | - Céline Cansell
- Université Paris‐Saclay, AgroParisTech, INRAE, UMR PNCAPalaiseauFrance
| | - Fanny Aprahamian
- Metabolomics and Cell Biology Platforms, UMS AMMICaInstitut Gustave RoussyVillejuifFrance
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le CancerUniversité de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de FranceParisFrance
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, UMS AMMICaInstitut Gustave RoussyVillejuifFrance
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le CancerUniversité de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de FranceParisFrance
| | - Jessica Ayache
- Institut Jacques Monod, CNRS UMR 7592, Université Paris CitéParisFrance
| | | | - Nicolas Todd
- Eco‐Anthropologie (EA), Muséum National d'Histoire Naturelle, CNRSUniversité de Paris, Musée de l'HommeParisFrance
| | - Clément Carré
- Institut de Biologie Paris Seine, Sorbonne UniversitéParisFrance
| | - Michael Rera
- Université Paris Cité, INSERM UMR U1284ParisFrance
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8
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Nunn AVW, Guy GW, Bell JD. Informing the Cannabis Conjecture: From Life's Beginnings to Mitochondria, Membranes and the Electrome-A Review. Int J Mol Sci 2023; 24:13070. [PMID: 37685877 PMCID: PMC10488084 DOI: 10.3390/ijms241713070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Before the late 1980s, ideas around how the lipophilic phytocannabinoids might be working involved membranes and bioenergetics as these disciplines were "in vogue". However, as interest in genetics and pharmacology grew, interest in mitochondria (and membranes) waned. The discovery of the cognate receptor for tetrahydrocannabinol (THC) led to the classification of the endocannabinoid system (ECS) and the conjecture that phytocannabinoids might be "working" through this system. However, the how and the "why" they might be beneficial, especially for compounds like CBD, remains unclear. Given the centrality of membranes and mitochondria in complex organisms, and their evolutionary heritage from the beginnings of life, revisiting phytocannabinoid action in this light could be enlightening. For example, life can be described as a self-organising and replicating far from equilibrium dissipating system, which is defined by the movement of charge across a membrane. Hence the building evidence, at least in animals, that THC and CBD modulate mitochondrial function could be highly informative. In this paper, we offer a unique perspective to the question, why and how do compounds like CBD potentially work as medicines in so many different conditions? The answer, we suggest, is that they can modulate membrane fluidity in a number of ways and thus dissipation and engender homeostasis, particularly under stress. To understand this, we need to embrace origins of life theories, the role of mitochondria in plants and explanations of disease and ageing from an adaptive thermodynamic perspective, as well as quantum mechanics.
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Affiliation(s)
- Alistair V. W. Nunn
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London W1W 6UW, UK; (G.W.G.); (J.D.B.)
- The Guy Foundation, Beaminster DT8 3HY, UK
| | - Geoffrey W. Guy
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London W1W 6UW, UK; (G.W.G.); (J.D.B.)
- The Guy Foundation, Beaminster DT8 3HY, UK
| | - Jimmy D. Bell
- Research Centre for Optimal Health, Department of Life Sciences, University of Westminster, London W1W 6UW, UK; (G.W.G.); (J.D.B.)
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9
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Salazar J, Durán P, Díaz MP, Chacín M, Santeliz R, Mengual E, Gutiérrez E, León X, Díaz A, Bernal M, Escalona D, Hernández LAP, Bermúdez V. Exploring the Relationship between the Gut Microbiota and Ageing: A Possible Age Modulator. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20105845. [PMID: 37239571 DOI: 10.3390/ijerph20105845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/20/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023]
Abstract
The gut microbiota (GM) has been the subject of intense research in recent years. Therefore, numerous factors affecting its composition have been thoroughly examined, and with them, their function and role in the individual's systems. The gut microbiota's taxonomical composition dramatically impacts older adults' health status. In this regard, it could either extend their life expectancy via the modulation of metabolic processes and the immune system or, in the case of dysbiosis, predispose them to age-related diseases, including bowel inflammatory and musculoskeletal diseases and metabolic and neurological disorders. In general, the microbiome of the elderly tends to present taxonomic and functional changes, which can function as a target to modulate the microbiota and improve the health of this population. The GM of centenarians is unique, with the faculty-promoting metabolic pathways capable of preventing and counteracting the different processes associated with age-related diseases. The molecular mechanisms by which the microbiota can exhibit anti-ageing properties are mainly based on anti-inflammatory and antioxidant actions. This review focuses on analysing the current knowledge of gut microbiota characteristics and modifiers, its relationship with ageing, and the GM-modulating approaches to increase life expectancy.
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Affiliation(s)
- Juan Salazar
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Pablo Durán
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - María P Díaz
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Maricarmen Chacín
- Centro de Investigaciones en Ciencias de la Vida, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Sociedad Internacional de Rejuvenecimiento Facial No Quirúrgico (SIRF), Barranquilla 080002, Colombia
| | - Raquel Santeliz
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Edgardo Mengual
- Biological Research Institute "Doctors Orlando Castejon and Haydee V Castejon", Faculty of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Emma Gutiérrez
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Xavier León
- Instituto Ecuatoriano de Seguridad Social, Cuenca 010101, Ecuador
| | - Andrea Díaz
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | - Marycarlota Bernal
- Facultad de Ingenierias, Universidad Simón Bolívar, Cúcuta 540001, Colombia
| | - Daniel Escalona
- Endocrine and Metabolic Diseases Research Center, School of Medicine, University of Zulia, Maracaibo 4001, Venezuela
| | | | - Valmore Bermúdez
- Centro de Investigaciones en Ciencias de la Vida, Universidad Simón Bolívar, Barranquilla 080002, Colombia
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10
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Martínez-Magaña JJ, Krystal JH, Girgenti MJ, Núnez-Ríos DL, Nagamatsu ST, Andrade-Brito DE, Montalvo-Ortiz JL. Decoding the role of transcriptomic clocks in the human prefrontal cortex. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.19.23288765. [PMID: 37163025 PMCID: PMC10168432 DOI: 10.1101/2023.04.19.23288765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Aging is a complex process with interindividual variability, which can be measured by aging biological clocks. Aging clocks are machine-learning algorithms guided by biological information and associated with mortality risk and a wide range of health outcomes. One of these aging clocks are transcriptomic clocks, which uses gene expression data to predict biological age; however, their functional role is unknown. Here, we profiled two transcriptomic clocks (RNAAgeCalc and knowledge-based deep neural network clock) in a large dataset of human postmortem prefrontal cortex (PFC) samples. We identified that deep-learning transcriptomic clock outperforms RNAAgeCalc to predict transcriptomic age in the human PFC. We identified associations of transcriptomic clocks with psychiatric-related traits. Further, we applied system biology algorithms to identify common gene networks among both clocks and performed pathways enrichment analyses to assess its functionality and prioritize genes involved in the aging processes. Identified gene networks showed enrichment for diseases of signal transduction by growth factor receptors and second messenger pathways. We also observed enrichment of genome-wide signals of mental and physical health outcomes and identified genes previously associated with human brain aging. Our findings suggest a link between transcriptomic aging and health disorders, including psychiatric traits. Further, it reveals functional genes within the human PFC that may play an important role in aging and health risk.
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Affiliation(s)
- José J. Martínez-Magaña
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven
- National Center for PTSD, US Department of Veterans Affairs, West Haven, CT, USA
| | - John H. Krystal
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven
- National Center for PTSD, US Department of Veterans Affairs, West Haven, CT, USA
- Psychiatry Service, VA Connecticut Health Care System, West Haven, CT, USA
| | - Matthew J. Girgenti
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven
- National Center for PTSD, US Department of Veterans Affairs, West Haven, CT, USA
| | - Diana L. Núnez-Ríos
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven
- National Center for PTSD, US Department of Veterans Affairs, West Haven, CT, USA
| | - Sheila T. Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven
- National Center for PTSD, US Department of Veterans Affairs, West Haven, CT, USA
| | - Diego E. Andrade-Brito
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven
- National Center for PTSD, US Department of Veterans Affairs, West Haven, CT, USA
| | | | - Janitza L. Montalvo-Ortiz
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven
- National Center for PTSD, US Department of Veterans Affairs, West Haven, CT, USA
- Psychiatry Service, VA Connecticut Health Care System, West Haven, CT, USA
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11
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Valencia CI, Saunders D, Daw J, Vasquez A. DNA methylation accelerated age as captured by epigenetic clocks influences breast cancer risk. Front Oncol 2023; 13:1150731. [PMID: 37007096 PMCID: PMC10050548 DOI: 10.3389/fonc.2023.1150731] [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: 01/24/2023] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Introduction Breast cancer continues to be the leading form of cancer among women in the United States. Additionally, disparities across the breast cancer continuum continue to increase for women of historically marginalized populations. The mechanism driving these trends are unclear, however, accelerated biological age may provide key insights into better understanding these disease patterns. Accelerated age measured by DNA methylation using epigenetic clocks is to date the most robust method for estimating accelerated age. Here we synthesize the existing evidence on epigenetic clocks measurement of DNA methylation based accelerated age and breast cancer outcomes. Methods Our database searches were conducted from January 2022 to April 2022 and yielded a total of 2,908 articles for consideration. We implemented methods derived from guidance of the PROSPERO Scoping Review Protocol to assess articles in the PubMed database on epigenetic clocks and breast cancer risk. Results Five articles were deemed appropriate for inclusion in this review. Ten epigenetic clocks were used across the five articles demonstrating statistically significant results for breast cancer risk. DNA methylation accelerated age varied by sample type. The studies did not consider social factors or epidemiological risk factors. The studies lacked representation of ancestrally diverse populations. Discussion DNA methylation based accelerated age as captured by epigenetic clocks has a statistically significant associative relationship with breast cancer risk, however, important social factors that contribute to patterns of methylation were not comprehensively considered in the available literature. More research is needed on DNA methylation based accelerated age across the lifespan including during menopausal transition and in diverse populations. This review demonstrates that DNA methylation accelerated age may provide key insights for tackling increasing rates of U.S. breast cancer incidence and overall disease disparities experienced by women from minoritized backgrounds.
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Affiliation(s)
- Celina I. Valencia
- Department of Family and Community Medicine, College of Medicine—Tucson, University of Arizona, Tucson, AZ, United States
| | - Devin Saunders
- Department of Nutritional Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, United States
| | - Jennifer Daw
- Cancer Biology Program, College of Medicine, University of Arizona, Tucson, AZ, United States
| | - Adria Vasquez
- Department of Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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12
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Decoupling of mRNA and Protein Expression in Aging Brains Reveals the Age-Dependent Adaptation of Specific Gene Subsets. Cells 2023; 12:cells12040615. [PMID: 36831282 PMCID: PMC9954025 DOI: 10.3390/cells12040615] [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: 01/26/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023] Open
Abstract
During aging, changes in gene expression are associated with a decline in physical and cognitive abilities. Here, we investigate the connection between changes in mRNA and protein expression in the brain by comparing the transcriptome and proteome of the mouse cortex during aging. Our transcriptomic analysis revealed that aging mainly triggers gene activation in the cortex. We showed that an increase in mRNA expression correlates with protein expression, specifically in the anterior cingulate cortex, where we also observed an increase in cortical thickness during aging. Genes exhibiting an aging-dependent increase of mRNA and protein levels are involved in sensory perception and immune functions. Our proteomic analysis also identified changes in protein abundance in the aging cortex and highlighted a subset of proteins that were differentially enriched but exhibited stable mRNA levels during aging, implying the contribution of aging-related post- transcriptional and post-translational mechanisms. These specific genes were associated with general biological processes such as translation, ribosome assembly and protein degradation, and also important brain functions related to neuroplasticity. By decoupling mRNA and protein expression, we have thus characterized distinct subsets of genes that differentially adjust to cellular aging in the cerebral cortex.
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13
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de Vries C, Erten EY, Kokko H. Does symmetry preclude the evolution of senescence? A comment on Pen and Flatt 2021. Proc Biol Sci 2023; 290:20221101. [PMID: 36695035 PMCID: PMC9874263 DOI: 10.1098/rspb.2022.1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Charlotte de Vries
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - E. Yagmur Erten
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland,Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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14
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Targeting the "hallmarks of aging" to slow aging and treat age-related disease: fact or fiction? Mol Psychiatry 2023; 28:242-255. [PMID: 35840801 PMCID: PMC9812785 DOI: 10.1038/s41380-022-01680-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 01/09/2023]
Abstract
Aging is a major risk factor for a number of chronic diseases, including neurodegenerative and cerebrovascular disorders. Aging processes have therefore been discussed as potential targets for the development of novel and broadly effective preventatives or therapeutics for age-related diseases, including those affecting the brain. Mechanisms thought to contribute to aging have been summarized under the term the "hallmarks of aging" and include a loss of proteostasis, mitochondrial dysfunction, altered nutrient sensing, telomere attrition, genomic instability, cellular senescence, stem cell exhaustion, epigenetic alterations and altered intercellular communication. We here examine key claims about the "hallmarks of aging". Our analysis reveals important weaknesses that preclude strong and definitive conclusions concerning a possible role of these processes in shaping organismal aging rate. Significant ambiguity arises from the overreliance on lifespan as a proxy marker for aging, the use of models with unclear relevance for organismal aging, and the use of study designs that do not allow to properly estimate intervention effects on aging rate. We also discuss future research directions that should be taken to clarify if and to what extent putative aging regulators do in fact interact with aging. These include multidimensional analytical frameworks as well as designs that facilitate the proper assessment of intervention effects on aging rate.
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15
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Donati Zeppa S, Agostini D, Ferrini F, Gervasi M, Barbieri E, Bartolacci A, Piccoli G, Saltarelli R, Sestili P, Stocchi V. Interventions on Gut Microbiota for Healthy Aging. Cells 2022; 12:cells12010034. [PMID: 36611827 PMCID: PMC9818603 DOI: 10.3390/cells12010034] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
In recent years, the improvement in health and social conditions has led to an increase in the average lifespan. Since aging is the most important risk factor for the majority of chronic human diseases, the development of therapies and intervention to stop, lessen or even reverse various age-related morbidities is an important target to ameliorate the quality of life of the elderly. The gut microbiota, that is, the complex ecosystem of microorganisms living in the gastrointestinal tract, plays an important role, not yet fully understood, in maintaining the host's health and homeostasis, influencing metabolic, oxidative and cognitive status; for this reason, it is also named "the forgotten endocrine organ" or "the second brain". On the other hand, the gut microbiota diversity and richness are affected by unmodifiable factors, such as aging and sex, and modifiable ones, such as diet, pharmacological therapies and lifestyle. In this review, we discuss the changes, mostly disadvantageous, for human health, induced by aging, in microbiota composition and the effects of dietary intervention, of supplementation with probiotics, prebiotics, synbiotics, psychobiotics and antioxidants and of physical exercise. The development of an integrated strategy to implement microbiota health will help in the goal of healthy aging.
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Affiliation(s)
- Sabrina Donati Zeppa
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Deborah Agostini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Fabio Ferrini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
- Correspondence: (F.F.); (M.G.)
| | - Marco Gervasi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
- Correspondence: (F.F.); (M.G.)
| | - Elena Barbieri
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Alessia Bartolacci
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Giovanni Piccoli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Roberta Saltarelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Piero Sestili
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Vilberto Stocchi
- Department of Human Science for Promotion of Quality of Life, Univerity San Raffaele, 00166 Rome, Italy
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16
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Hurvitz N, Elkhateeb N, Sigawi T, Rinsky-Halivni L, Ilan Y. Improving the effectiveness of anti-aging modalities by using the constrained disorder principle-based management algorithms. FRONTIERS IN AGING 2022; 3:1044038. [PMID: 36589143 PMCID: PMC9795077 DOI: 10.3389/fragi.2022.1044038] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
Aging is a complex biological process with multifactorial nature underlined by genetic, environmental, and social factors. In the present paper, we review several mechanisms of aging and the pre-clinically and clinically studied anti-aging therapies. Variability characterizes biological processes from the genome to cellular organelles, biochemical processes, and whole organs' function. Aging is associated with alterations in the degrees of variability and complexity of systems. The constrained disorder principle defines living organisms based on their inherent disorder within arbitrary boundaries and defines aging as having a lower variability or moving outside the boundaries of variability. We focus on associations between variability and hallmarks of aging and discuss the roles of disorder and variability of systems in the pathogenesis of aging. The paper presents the concept of implementing the constrained disease principle-based second-generation artificial intelligence systems for improving anti-aging modalities. The platform uses constrained noise to enhance systems' efficiency and slow the aging process. Described is the potential use of second-generation artificial intelligence systems in patients with chronic disease and its implications for the aged population.
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Affiliation(s)
- Noa Hurvitz
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Narmine Elkhateeb
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Tal Sigawi
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Lilah Rinsky-Halivni
- Braun School of Public Health, Hebrew University of Jerusalem, Jerusalem, Israel,Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Yaron Ilan
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel,*Correspondence: Yaron Ilan,
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17
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Effects of lifespan-extending interventions on cognitive healthspan. Expert Rev Mol Med 2022; 25:e2. [PMID: 36377361 DOI: 10.1017/erm.2022.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ageing is known to be the primary risk factor for most neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease and Huntington's disease. They are currently incurable and worsen over time, which has broad implications in the context of lifespan and healthspan extension. Adding years to life and even to physical health is suboptimal or even insufficient, if cognitive ageing is not adequately improved. In this review, we will examine how interventions that have the potential to extend lifespan in animals affect the brain, and if they would be able to thwart or delay the development of cognitive dysfunction and/or neurodegeneration. These interventions range from lifestyle (caloric restriction, physical exercise and environmental enrichment) through pharmacological (nicotinamide adenine dinucleotide precursors, resveratrol, rapamycin, metformin, spermidine and senolytics) to epigenetic reprogramming. We argue that while many of these interventions have clear potential to improve cognitive health and resilience, large-scale and long-term randomised controlled trials are needed, along with studies utilising washout periods to determine the effects of supplementation cessation, particularly in aged individuals.
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18
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Reprogramming neurons for regeneration: The fountain of youth. Prog Neurobiol 2022; 214:102284. [PMID: 35533809 DOI: 10.1016/j.pneurobio.2022.102284] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/03/2022] [Accepted: 05/02/2022] [Indexed: 01/22/2023]
Abstract
Neurons in the central nervous system (CNS) are terminally differentiated cells that gradually lose their ability to support regeneration during maturation due to changes in transcriptomic and chromatin landscape. Similar transcriptomic changes also occur during development when stem cells differentiate into different types of somatic cells. Importantly, differentiated cells can be reprogrammed back to induced pluripotent stems cells (iPSCs) via global epigenetic remodeling by combined overexpression of pluripotent reprogramming factors, including Oct4, Sox2, Klf4, c-Myc, Nanog, and/or Lin28. Moreover, recent findings showed that many proneural transcription factors were able to convert non-neural somatic cells into neurons bypassing the pluripotent stage via direct reprogramming. Interestingly, many of these factors have recently been identified as key regulators of CNS neural regeneration. Recent studies indicated that these factors could rejuvenate mature CNS neurons back to a younger state through cellular state reprogramming, thus favoring regeneration. Here we will review some recent findings regarding the roles of genetic cellular state reprogramming in regulation of neural regeneration and explore the potential underlying molecular mechanisms. Moreover, by using newly emerging techniques, such as multiomics sequencing with big data analysis and Crispr-based gene editing, we will discuss future research directions focusing on better revealing cellular state reprogramming-induced remodeling of chromatin landscape and potential translational application.
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19
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Ratanapokasatit Y, Laisuan W, Rattananukrom T, Petchlorlian A, Thaipisuttikul I, Sompornrattanaphan M. How Microbiomes Affect Skin Aging: The Updated Evidence and Current Perspectives. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070936. [PMID: 35888025 PMCID: PMC9320090 DOI: 10.3390/life12070936] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/05/2022]
Abstract
The skin has a multifactorial aging process, caused by both intrinsic and extrinsic factors. A major theory of aging involves cellular senescence or apoptosis resulting from oxidative damage as the skin’s antioxidant system tends to weaken with age. The human microbiota is a complex ecosystem that is made up of microorganisms (bacteria, fungi, and viruses). Both gut and skin microbiota have essential roles in the protection against invading pathogens, mediating inflammatory conditions, and the modulation of the immune system which is involved in both innate and adaptive immune responses. However, the human microbiome could be changed during the life stage and affected by various perturbations. An alteration of the intestinal bacteria results in “microbial dysbiosis” which is associated with the influence of various diseases, including aging. The skin interactome is a novel integration of the “genome-microbiome-exposome” that plays a significant role in skin aging and skin health. Mitigating the negative impacts of factors influencing the skin interactome should be the future strategy to protect, prevent, and delay skin aging along with preserving healthy skin conditions. This review summarizes the current evidence on how human microbiomes affect skin aging and demonstrates the possible interventions, relating to human microbiomes, to modulate skin health and aging. Probiotics-based products are currently available mainly for the add-on treatment of many dermatologic conditions. However, at this point, there are limited clinical studies on skin anti-aging purposes and more are required as this evolving concept is on the rise and might provide an insight into future therapeutic options.
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Affiliation(s)
- Yanisa Ratanapokasatit
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (Y.R.); (T.R.)
| | - Wannada Laisuan
- Division of Allergy Immunology and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Teerapong Rattananukrom
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (Y.R.); (T.R.)
| | - Aisawan Petchlorlian
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- Geriatric Excellence Center, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Iyarit Thaipisuttikul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Mongkhon Sompornrattanaphan
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Faculty of Medicine Siriraj Hospital, Center of Research Excellence in Allergy and Immunology, Mahidol University, Bangkok 10700, Thailand
- Correspondence:
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