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Bergmans S, Noel NCL, Masin L, Harding EG, Krzywańska AM, De Schutter JD, Ayana R, Hu C, Arckens L, Ruzycki PA, MacDonald RB, Clark BS, Moons L. Age-related dysregulation of the retinal transcriptome in African turquoise killifish. Aging Cell 2024; 23:e14192. [PMID: 38742929 PMCID: PMC11320354 DOI: 10.1111/acel.14192] [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: 03/06/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Age-related vision loss caused by retinal neurodegenerative pathologies is becoming more prevalent in our ageing society. To understand the physiological and molecular impact of ageing on retinal homeostasis, we used the short-lived African turquoise killifish, a model known to naturally develop central nervous system (CNS) ageing hallmarks and vision loss. Bulk and single-cell RNA-sequencing (scRNAseq) of three age groups (6-, 12-, and 18-week-old) identified transcriptional ageing fingerprints in the killifish retina, unveiling pathways also identified in the aged brain, including oxidative stress, gliosis, and inflammageing. These findings were comparable to observations in the ageing mouse retina. Additionally, transcriptional changes in genes related to retinal diseases, such as glaucoma and age-related macular degeneration, were observed. The cellular heterogeneity in the killifish retina was characterized, confirming the presence of all typical vertebrate retinal cell types. Data integration from age-matched samples between the bulk and scRNAseq experiments revealed a loss of cellular specificity in gene expression upon ageing, suggesting potential disruption in transcriptional homeostasis. Differential expression analysis within the identified cell types highlighted the role of glial/immune cells as important stress regulators during ageing. Our work emphasizes the value of the fast-ageing killifish in elucidating molecular signatures in age-associated retinal disease and vision decline. This study contributes to the understanding of how age-related changes in molecular pathways may impact CNS health, providing insights that may inform future therapeutic strategies for age-related pathologies.
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Affiliation(s)
- Steven Bergmans
- Department of Biology, Animal Physiology and Neurobiology Division, Neural Circuit Development & Regeneration Research GroupKU Leuven, Leuven Brain InstituteLeuvenBelgium
| | | | - Luca Masin
- Department of Biology, Animal Physiology and Neurobiology Division, Neural Circuit Development & Regeneration Research GroupKU Leuven, Leuven Brain InstituteLeuvenBelgium
| | - Ellen G. Harding
- John F Hardesty, MD Department of Ophthalmology and Visual SciencesWashington University School of MedicineSaint LouisMissouriUSA
| | | | - Julie D. De Schutter
- Department of Biology, Animal Physiology and Neurobiology Division, Neural Circuit Development & Regeneration Research GroupKU Leuven, Leuven Brain InstituteLeuvenBelgium
| | - Rajagopal Ayana
- Department of Biology, Animal Physiology and Neurobiology Section, Laboratory of Neuroplasticity and NeuroproteomicsKU Leuven, Leuven Brain InstituteLeuvenBelgium
| | - Chi‐Kuo Hu
- Department of Biochemistry and Cell BiologyStony Brook UniversityStony BrookUSA
| | - Lut Arckens
- Department of Biology, Animal Physiology and Neurobiology Section, Laboratory of Neuroplasticity and NeuroproteomicsKU Leuven, Leuven Brain InstituteLeuvenBelgium
| | - Philip A. Ruzycki
- John F Hardesty, MD Department of Ophthalmology and Visual SciencesWashington University School of MedicineSaint LouisMissouriUSA
- Department of GeneticsWashington University School of MedicineSaint LouisMissouriUSA
| | | | - Brian S. Clark
- John F Hardesty, MD Department of Ophthalmology and Visual SciencesWashington University School of MedicineSaint LouisMissouriUSA
- Department of Developmental BiologyWashington University School of MedicineSaint LouisMissouriUSA
- Center of Regenerative MedicineCenter of Regenerative Medicine, Washington University School of MedicineSaint LouisMissouriUSA
| | - Lieve Moons
- Department of Biology, Animal Physiology and Neurobiology Division, Neural Circuit Development & Regeneration Research GroupKU Leuven, Leuven Brain InstituteLeuvenBelgium
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2
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Moses E, Atlan T, Sun X, Franěk R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. NATURE AGING 2024; 4:791-813. [PMID: 38750187 DOI: 10.1038/s43587-024-00632-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. In this study, we used the turquoise killifish (Nothobranchius furzeri) to genetically arrest germline development at discrete stages and examine how different modes of infertility impact life history. We first constructed a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. We show here that germline depletion-but not arresting germline differentiation-enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted Caenorhabditis elegans. Our results, therefore, demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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Affiliation(s)
- Eitan Moses
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Tehila Atlan
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Xue Sun
- Department of Biochemistry, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Roman Franěk
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Atif Siddiqui
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | | | - Sagiv Shifman
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - David M Zucker
- Department of Statistics and Data Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Oron-Gottesman
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | - Oren Ram
- Department of Biochemistry, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Itamar Harel
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel.
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Moses E, Atlan T, Sun X, Franek R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572041. [PMID: 38187630 PMCID: PMC10769255 DOI: 10.1101/2023.12.18.572041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Classical evolutionary theories propose tradeoffs between reproduction, damage repair, and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. Here, we use the turquoise killifish ( N. furzeri ) to genetically arrest germline development at discrete stages, and examine how different modes of infertility impact life-history. We first construct a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. Next, we show that germline depletion - but not arresting germline differentiation - enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted C. elegans . Our results therefore demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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4
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Bergmans S, Noel NCL, Masin L, Harding EG, Krzywańska AM, De Schutter JD, Ayana R, Hu CK, Arckens L, Ruzycki PA, MacDonald RB, Clark BS, Moons L. Age-related dysregulation of the retinal transcriptome in African turquoise killifish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581372. [PMID: 38559206 PMCID: PMC10979842 DOI: 10.1101/2024.02.21.581372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Age-related vision loss caused by retinal neurodegenerative pathologies is becoming more prevalent in our ageing society. To understand the physiological and molecular impact of ageing on retinal homeostasis, we used the short-lived African turquoise killifish, a model known to naturally develop central nervous system (CNS) ageing hallmarks and vision loss. Bulk and single-cell RNA-sequencing (scRNA-seq) of three age groups (6-, 12-, and 18-week-old) identified transcriptional ageing fingerprints in the killifish retina, unveiling pathways also identified in the aged brain, including oxidative stress, gliosis, and inflammageing. These findings were comparable to observations in ageing mouse retina. Additionally, transcriptional changes in genes related to retinal diseases, such as glaucoma and age-related macular degeneration, were observed. The cellular heterogeneity in the killifish retina was characterised, confirming the presence of all typical vertebrate retinal cell types. Data integration from age-matched samples between the bulk and scRNA-seq experiments revealed a loss of cellular specificity in gene expression upon ageing, suggesting potential disruption in transcriptional homeostasis. Differential expression analysis within the identified cell types highlighted the role of glial/immune cells as important stress regulators during ageing. Our work emphasises the value of the fast-ageing killifish in elucidating molecular signatures in age-associated retinal disease and vision decline. This study contributes to the understanding of how age-related changes in molecular pathways may impact CNS health, providing insights that may inform future therapeutic strategies for age-related pathologies.
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Affiliation(s)
- Steven Bergmans
- KU Leuven, Leuven Brain Institute, Department of Biology, Animal Physiology and Neurobiology division, Neural circuit development & regeneration research group, 3000 Leuven, Belgium
| | - Nicole C L Noel
- University College London, Institute of Ophthalmology, London, UK, EC1V 9EL
| | - Luca Masin
- KU Leuven, Leuven Brain Institute, Department of Biology, Animal Physiology and Neurobiology division, Neural circuit development & regeneration research group, 3000 Leuven, Belgium
| | - Ellen G Harding
- Washington University School of Medicine, John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Saint Louis, Missouri, 63110 United States of America
| | | | - Julie D De Schutter
- KU Leuven, Leuven Brain Institute, Department of Biology, Animal Physiology and Neurobiology division, Neural circuit development & regeneration research group, 3000 Leuven, Belgium
| | - Rajagopal Ayana
- KU Leuven, Leuven Brain Institute, Department of Biology, Animal Physiology and Neurobiology section, Laboratory of Neuroplasticity and Neuroproteomics, 3000 Leuven, Belgium
| | - Chi-Kuo Hu
- Stony Brook University, Department of Biochemistry and Cell Biology, 11790 Stony Brook, United States of America
| | - Lut Arckens
- KU Leuven, Leuven Brain Institute, Department of Biology, Animal Physiology and Neurobiology section, Laboratory of Neuroplasticity and Neuroproteomics, 3000 Leuven, Belgium
| | - Philip A Ruzycki
- Washington University School of Medicine, John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Saint Louis, Missouri, 63110 United States of America
- Washington University School of Medicine, Department of Genetics, Saint Louis, Missouri, 63110 United States of America
| | - Ryan B MacDonald
- University College London, Institute of Ophthalmology, London, UK, EC1V 9EL
| | - Brian S Clark
- Washington University School of Medicine, John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Saint Louis, Missouri, 63110 United States of America
- Washington University School of Medicine, Department of Developmental Biology, Saint Louis, Missouri, 63110 United States of America
- Washington University School of Medicine, Center of Regenerative Medicine, Saint Louis, Missouri, 63110 United States of America
| | - Lieve Moons
- KU Leuven, Leuven Brain Institute, Department of Biology, Animal Physiology and Neurobiology division, Neural circuit development & regeneration research group, 3000 Leuven, Belgium
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Moses E, Franek R, Harel I. A scalable and tunable platform for functional interrogation of peptide hormones in fish. eLife 2023; 12:e85960. [PMID: 37872843 PMCID: PMC10597582 DOI: 10.7554/elife.85960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/16/2023] [Indexed: 10/25/2023] Open
Abstract
Pituitary hormones play a central role in shaping vertebrate life history events, including growth, reproduction, metabolism, and aging. The regulation of these traits often requires precise control of hormone levels across diverse timescales. However, fine tuning circulating hormones in-vivo has traditionally been experimentally challenging. Here, using the naturally short-lived turquoise killifish (N. furzeri), we describe a high-throughput platform that combines loss- and gain-of-function of peptide hormones. Mutation of three primary pituitary hormones, growth hormone (gh1), follicle stimulating hormone (fshb), and thyroid stimulating hormone (tshb), alters somatic growth and reproduction. Thus, suggesting that while the killifish undergoes extremely rapid growth and maturity, it still relies on vertebrate-conserved genetic networks. As the next stage, we developed a gain-of-function vector system in which a hormone is tagged using a self-cleavable fluorescent reporter, and ectopically expressed in-vivo through intramuscular electroporation. Following a single electroporation, phenotypes, such as reproduction, are stably rescued for several months. Notably, we demonstrate the versatility of this approach by using multiplexing, dose-dependent, and doxycycline-inducible systems to achieve tunable and reversible expression. In summary, this method is relatively high-throughput, and facilitates large-scale interrogation of life-history strategies in fish. Ultimately, this approach could be adapted for modifying aquaculture species and exploring pro-longevity interventions.
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Affiliation(s)
- Eitan Moses
- Department of Genetics, the Silberman Institute, The Hebrew University of JerusalemJerusalemIsrael
| | - Roman Franek
- Department of Genetics, the Silberman Institute, The Hebrew University of JerusalemJerusalemIsrael
- University of South Bohemia in Ceske Budejovice, South Bohemian Research Center of Aquaculture and Biodiversity of HydrocenosesVodnanyCzech Republic
| | - Itamar Harel
- Department of Genetics, the Silberman Institute, The Hebrew University of JerusalemJerusalemIsrael
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