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Costa EK, Chen J, Guldner IH, Mboning L, Schmahl N, Tsenter A, Wu MR, Moran-Losada P, Bouchard LS, Wang S, Singh PP, Pellegrini M, Brunet A, Wyss-Coray T. Multi-tissue transcriptomic aging atlas reveals predictive aging biomarkers in the killifish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.28.635350. [PMID: 39975269 PMCID: PMC11838286 DOI: 10.1101/2025.01.28.635350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Aging is associated with progressive tissue dysfunction, leading to frailty and mortality. Characterizing aging features, such as changes in gene expression and dynamics, shared across tissues or specific to each tissue, is crucial for understanding systemic and local factors contributing to the aging process. We performed RNA-sequencing on 13 tissues at 6 different ages in the African turquoise killifish, the shortest-lived vertebrate that can be raised in captivity. This comprehensive, sex-balanced 'atlas' dataset reveals the varying strength of sex-age interactions across killifish tissues and identifies age-altered biological pathways that are evolutionarily conserved. Demonstrating the utility of this resource, we discovered that the killifish head kidney exhibits a myeloid bias during aging, a phenomenon more pronounced in females than in males. In addition, we developed tissue-specific 'transcriptomic clocks' and identified biomarkers predictive of chronological age. We show the importance of sex-specific clocks for selected tissues and use the tissue clocks to evaluate a dietary intervention in the killifish. Our work provides a comprehensive resource for studying aging dynamics across tissues in the killifish, a powerful vertebrate aging model.
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Affiliation(s)
- Emma K Costa
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Neurosciences Interdepartmental Program, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Jingxun Chen
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Ian H Guldner
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Lajoyce Mboning
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Natalie Schmahl
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Aleksandra Tsenter
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Man-Ru Wu
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA, USA
| | - Patricia Moran-Losada
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, CA, USA
| | - Louis S Bouchard
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Sui Wang
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA, USA
- Present address: Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Present address: Bakar Aging Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Glenn Laboratories for the Biology of Aging, Stanford University, CA, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Glenn Laboratories for the Biology of Aging, Stanford University, CA, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, CA, USA
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2
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Xu Y, Wang Z, Li S, Su J, Gao L, Ou J, Lin Z, Luo OJ, Xiao C, Chen G. An in-depth understanding of the role and mechanisms of T cells in immune organ aging and age-related diseases. SCIENCE CHINA. LIFE SCIENCES 2025; 68:328-353. [PMID: 39231902 DOI: 10.1007/s11427-024-2695-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/28/2024] [Indexed: 09/06/2024]
Abstract
T cells play a critical and irreplaceable role in maintaining overall health. However, their functions undergo alterations as individuals age. It is of utmost importance to comprehend the specific characteristics of T-cell aging, as this knowledge is crucial for gaining deeper insights into the pathogenesis of aging-related diseases and developing effective therapeutic strategies. In this review, we have thoroughly examined the existing studies on the characteristics of immune organ aging. Furthermore, we elucidated the changes and potential mechanisms that occur in T cells during the aging process. Additionally, we have discussed the latest research advancements pertaining to T-cell aging-related diseases. These findings provide a fresh perspective for the study of T cells in the context of aging.
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Affiliation(s)
- Yudai Xu
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Zijian Wang
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Shumin Li
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Jun Su
- First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Lijuan Gao
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Junwen Ou
- Anti Aging Medical Center, Clifford Hospital, Guangzhou, 511495, China
| | - Zhanyi Lin
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Chanchan Xiao
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China.
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, 523000, China.
- Zhuhai Institute of Jinan University, Jinan University, Zhuhai, 519070, China.
| | - Guobing Chen
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China.
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, 523000, China.
- Zhuhai Institute of Jinan University, Jinan University, Zhuhai, 519070, China.
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Calubag MF, Ademi I, Grunow I, Breuer L, Babygirija R, Lialios P, Le S, Minton D, Sonsalla MM, Illiano J, Knopf BA, Xiao F, Konopka AR, Harris DA, Lamming DW. Tissue-specific effects of dietary protein on cellular senescence are mediated by branched-chain amino acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.13.632607. [PMID: 39868338 PMCID: PMC11761368 DOI: 10.1101/2025.01.13.632607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Dietary protein is a key regulator of healthy aging in both mice and humans. In mice, reducing dietary levels of the branched-chain amino acids (BCAAs) recapitulates many of the benefits of a low protein diet; BCAA-restricted diets extend lifespan, reduce frailty, and improve metabolic health, while BCAA supplementation shortens lifespan, promotes obesity, and impairs glycemic control. Recently, high protein diets have been shown to promote cellular senescence, a hallmark of aging implicated in many age-related diseases, in the liver of mice. Here, we test the hypothesis that the effects of high protein diets on metabolic health and on cell senescence are mediated by BCAAs. We find that reducing dietary levels of BCAAs protects male and female mice from the negative metabolic consequences of both normal and high protein diets. Further, we identify tissue-specific effects of BCAAs on cellular senescence, with restriction of all three BCAAs - but not individual BCAAs - protecting from hepatic cellular senescence while potentiating cell senescence in white adipose tissue. We find that the effects of BCAAs on hepatic cellular senescence are cell-autonomous, with lower levels of BCAAs protecting cultured cells from antimycin-A induced senescence. Our results demonstrate a direct effect of a specific dietary component on a hallmark of aging and suggest that cellular senescence may be highly susceptible to dietary interventions.
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Affiliation(s)
- Mariah F Calubag
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ismail Ademi
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
| | - Isaac Grunow
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
| | - Lucia Breuer
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
| | - Reji Babygirija
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Penelope Lialios
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
| | - Sandra Le
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
| | - Dennis Minton
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Michelle M Sonsalla
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Julia Illiano
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Wisconsin Laboratory for Surgical Metabolism, Department of Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Bailey A Knopf
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Fan Xiao
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Nutrition and Metabolism Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam R Konopka
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Comprehensive Diabetes Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - David A Harris
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Wisconsin Laboratory for Surgical Metabolism, Department of Surgery, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Comprehensive Diabetes Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Dudley W Lamming
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705 USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705 USA
- Cell and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Nutrition and Metabolism Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Comprehensive Diabetes Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
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Dvir-Ginzberg M, Maatuf YH, Mobasheri A. Do we understand sex-related differences governing dimorphic disease mechanisms in preclinical animal models of osteoarthritis? Osteoarthritis Cartilage 2024; 32:1054-1057. [PMID: 38531464 DOI: 10.1016/j.joca.2024.03.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/28/2024]
Abstract
Research conducted using murine preclinical models of osteoarthritis (OA) over the last three decades has brought forth many exciting developments showcasing mechanisms and pathways that drive disease pathogenesis. These models have identified therapeutic targets that can be modulated via innovative biologicals and pharmaceuticals. However, many of these approaches have failed to translate to humans and reach the clinic. This commentary aims to highlight some of the key hurdles in the translation of novel findings using preclinical OA models with a focus on sex-related differences and variations in chondrosenescence in these animal models. Notably, besides chondrosenescence, other signaling mechanisms have been shown to be affected by sexual dimorphism (i.e. TGFβ signaling, EGFR/integrin α1β1 and Trpv4). Preclinical models of OA mainly utilize male mice due to their capacity to manifest fast progressing OA structural phenotype compared to female mice. This experimental trend has overlooked and ignored the sex-related effects of numerous mechanisms affecting joint structure, that influence OA structural progression. Future work should focus on analyzing both sexes and understanding sex-related differences, which will enable us to gain a better understanding of the progression of OA based on sex-related mechanistic discrepancies, and potentially improve translatability.
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Affiliation(s)
- Mona Dvir-Ginzberg
- Laboratory of Cartilage Biology, Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Yonathan H Maatuf
- Laboratory of Cartilage Biology, Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ali Mobasheri
- Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland; Department of Regenerative Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania; Department of Joint Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; World Health Organization Collaborating Center for Public Health Aspects of Musculoskeletal Health and Aging, Université de Liège, Liège, Belgium
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Maatuf YH, Marco M, Unger-Gelman S, Farhat E, Zobrab A, Roy A, Kumar A, Carmon I, Reich E, Dvir-Ginzberg M. Diverse Response to Local Pharmacological Blockade of Sirt1 Cleavage in Age-Induced versus Trauma-Induced Osteoarthritis Female Mice. Biomolecules 2024; 14:81. [PMID: 38254681 PMCID: PMC10813022 DOI: 10.3390/biom14010081] [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: 11/22/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Objective: Previous studies have shown that the cleavage of Sirt1 contributes to the development of osteoarthritis (OA). In fact, OA was effectively abrogated by the intra-articular (IA) administration of two compounds, one blocking Sirt1 cleavage (CA074me) and the other activating Sirt1 (SRT1720), using a post-traumatically induced model (PTOA) in young female mice. In this study, we attempted to understand if this local treatment is effective in preventing age-associated OA (AOA) progression and symptoms. Design: A group of 17-month-old female C57BL/6J mice were IA administered with CA074me and/or SRT1720 or their combination. Joint histopathological analysis and bone histomorphometry were carried out, with an assessment of knee mechanical hyperalgesia. A serum analysis for NT/CT Sirt1 was carried out along with immunohistochemistry for articular cartilage to detect p16INK4A or γH2A.X. Similarly, meniscal cartilage was monitored for Lef1 and Col1a1 deposition. The data were compared for young female mice subjected to post-traumatic OA (PTOA). Results: Similar to PTOA, combination-treated AOA exhibited improved knee hyperalgesia, yet structural improvements were undetected, corresponding to unchanged NT/CT Sirt1 serum levels. Both AOA and PTOA exhibited unchanged staining for nuclear p16INK4A or γH2A.X and lacked a correlation with OA severity. Contrarily to PTOA, the combination treatment with AOA did not exhibit a local reduction in the Lef1 and Col1 targets. Conclusions: When targeting Sirt1 cleavage, the PTOA and AOA models exhibited a similar pain response to the combination treatment; however, they displayed diverse structural outcomes for joint-related damage, related to Lef1-dependent signaling. Interestingly, nuclear p16INK4A was unaffected in both models, regardless of the treatment's effectiveness. Finally, these findings highlight the variations in the responses between two highly researched OA preclinical models, reflecting OA pathophysiology heterogeneity and variations in gender-related drug-response mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mona Dvir-Ginzberg
- Institute of Biomedical and Oral research, Faculty of Dental Medicine, Hebrew University of Jerusalem, P.O. Box 12272, Jerusalem 9112102, Israel; (Y.H.M.); (M.M.); (S.U.-G.); (E.F.); (A.Z.); (A.R.); (A.K.); (I.C.); (E.R.)
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