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Hansson C, Hadžibajramović E, Svensson PA, Jonsdottir IH. Increased plasma levels of neuro-related proteins in patients with stress-related exhaustion: A longitudinal study. Psychoneuroendocrinology 2024; 167:107091. [PMID: 38964018 DOI: 10.1016/j.psyneuen.2024.107091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 07/06/2024]
Abstract
Exhaustion disorder (ED) is a stress-related disorder characterized by physical and mental symptoms of exhaustion. Recent data suggest that pathophysiological processes in the central nervous system are involved in the biological mechanisms underlying ED. The aims of this study were to investigate if plasma levels of neuro-related proteins differ between patients with ED and healthy controls, and, if so, to investigate if these differences persist over time. Using the Olink Neuro Exploratory panel, we quantified the plasma levels of 92 neuro-related proteins in 163 ED patients at the time of diagnosis (baseline), 149 patients at long-term follow-up (7-12 years later, median follow-up time 9 years and 5 months), and 100 healthy controls. We found that the plasma levels of 40 proteins were significantly higher in the ED group at baseline compared with the control group. Out of these, the plasma levels of 36 proteins were significantly lower in the ED group at follow-up compared with the same group at baseline and the plasma levels of four proteins did not significantly differ between the groups. At follow-up, the plasma levels of two proteins were significantly lower in the ED group compared with the control group. These data support the hypothesis that pathophysiological processes in the central nervous system are involved in the biological mechanisms underlying ED.
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Affiliation(s)
- Caroline Hansson
- The Institute of Stress Medicine, Region Västra Götaland, Gothenburg, Sweden; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Emina Hadžibajramović
- The Institute of Stress Medicine, Region Västra Götaland, Gothenburg, Sweden; School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per-Arne Svensson
- Institute of Health and Care Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ingibjörg H Jonsdottir
- The Institute of Stress Medicine, Region Västra Götaland, Gothenburg, Sweden; School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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2
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Shi L, Li G, Hou N, Tu L, Li J, Luo J, Hu S. APOB and CCL17 as mediators in the protective effect of SGLT2 inhibition against myocardial infarction: Insights from proteome-wide mendelian randomization. Eur J Pharmacol 2024; 976:176619. [PMID: 38679119 DOI: 10.1016/j.ejphar.2024.176619] [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: 02/07/2024] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
AIMS Sodium-glucose cotransporter 2 (SGLT2) inhibitors offer a novel therapeutic avenue for myocardial infarction (MI). However, the exact nature of this relationship and the underlying mechanisms are not fully understood. METHODS Utilizing a two-sample Mendelian Randomization (MR) analysis, we elucidated the causal effects stemming from the inhibition of SGLT2 on MI. Then, The pool of 4907 circulating proteins within the plasma proteome were utilized to explore the mediators of SGLT2 inhibitors on MI. Protein-protein network and enrichment analysis were conducted to clarify the potential mechanism. Finally, employing MR analysis and meta-analysis techniques, we systematically assessed the causal associations between SGLT2 inhibition and coronary heart diseases (CHD). RESULTS SGLT2 inhibition (per 1 SD decrement in HbA1c) was associated with reduced risk of MI (odds ratio [OR] = 0.462, [95% CI 0.222, 0.958], P = 0.038). Among 4907 circulating proteins, we identified APOB and CCL17 which were related to both SGLT2 inhibition and MI. Mediation analysis showed evidence of the indirect effect of SGLT2 inhibition on MI through APOB (β = -0.557, 95%CI [-1.098, -0.155]) with a mediated proportion of 72%, and CCL17 (β = -0.176, 95%CI [-0.332, -0.056]) with a mediated proportion of 17%. The meta-analysis result showed that SGLT2 inhibition was associated with a lower risk of CHD. CONCLUSION Based on proteome-wide mendelian randomization, APOB and CCL17 were seen as mediators in the protective effect of SGLT2 inhibition against myocardial infarction.
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Affiliation(s)
- Lili Shi
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, China
| | - Gen Li
- Department of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ningxin Hou
- Department of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ling Tu
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, China
| | - Jun Li
- Department of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jinlan Luo
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, China.
| | - Shuiqing Hu
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, China; Division of Cardiology and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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3
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Shafqat A, Masters MC, Tripathi U, Tchkonia T, Kirkland JL, Hashmi SK. Long COVID as a disease of accelerated biological aging: An opportunity to translate geroscience interventions. Ageing Res Rev 2024; 99:102400. [PMID: 38945306 DOI: 10.1016/j.arr.2024.102400] [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: 04/21/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
It has been four years since long COVID-the protracted consequences that survivors of COVID-19 face-was first described. Yet, this entity continues to devastate the quality of life of an increasing number of COVID-19 survivors without any approved therapy and a paucity of clinical trials addressing its biological root causes. Notably, many of the symptoms of long COVID are typically seen with advancing age. Leveraging this similarity, we posit that Geroscience-which aims to target the biological drivers of aging to prevent age-associated conditions as a group-could offer promising therapeutic avenues for long COVID. Bearing this in mind, this review presents a translational framework for studying long COVID as a state of effectively accelerated biological aging, identifying research gaps and offering recommendations for future preclinical and clinical studies.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Mary Clare Masters
- Division of Infectious Diseases, Northwestern University, Chicago, IL, USA
| | - Utkarsh Tripathi
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Tamara Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA; Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shahrukh K Hashmi
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA; Research and Innovation Center, Department of Health, Abu Dhabi, UAE; College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
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4
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Casanova R, Walker KA, Justice JN, Anderson A, Duggan MR, Cordon J, Barnard RT, Lu L, Hsu FC, Sedaghat S, Prizment A, Kritchevsky SB, Wagenknecht LE, Hughes TM. Associations of plasma proteomics and age-related outcomes with brain age in a diverse cohort. GeroScience 2024; 46:3861-3873. [PMID: 38438772 PMCID: PMC11226584 DOI: 10.1007/s11357-024-01112-4] [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: 12/07/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
Machine learning models are increasingly being used to estimate "brain age" from neuroimaging data. The gap between chronological age and the estimated brain age gap (BAG) is potentially a measure of accelerated and resilient brain aging. Brain age calculated in this fashion has been shown to be associated with mortality, measures of physical function, health, and disease. Here, we estimate the BAG using a voxel-based elastic net regression approach, and then, we investigate its associations with mortality, cognitive status, and measures of health and disease in participants from Atherosclerosis Risk in Communities (ARIC) study who had a brain MRI at visit 5 of the study. Finally, we used the SOMAscan assay containing 4877 proteins to examine the proteomic associations with the MRI-defined BAG. Among N = 1849 participants (age, 76.4 (SD 5.6)), we found that increased values of BAG were strongly associated with increased mortality and increased severity of the cognitive status. Strong associations with mortality persisted when the analyses were performed in cognitively normal participants. In addition, it was strongly associated with BMI, diabetes, measures of physical function, hypertension, prevalent heart disease, and stroke. Finally, we found 33 proteins associated with BAG after a correction for multiple comparisons. The top proteins with positive associations to brain age were growth/differentiation factor 15 (GDF-15), Sushi, von Willebrand factor type A, EGF, and pentraxin domain-containing protein 1 (SEVP 1), matrilysin (MMP7), ADAMTS-like protein 2 (ADAMTS), and heat shock 70 kDa protein 1B (HSPA1B) while EGF-receptor (EGFR), mast/stem-cell-growth-factor-receptor (KIT), coagulation-factor-VII, and cGMP-dependent-protein-kinase-1 (PRKG1) were negatively associated to brain age. Several of these proteins were previously associated with dementia in ARIC. These results suggest that circulating proteins implicated in biological aging, cellular senescence, angiogenesis, and coagulation are associated with a neuroimaging measure of brain aging.
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Affiliation(s)
- Ramon Casanova
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, USA.
| | | | - Jamie N Justice
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Andrea Anderson
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, USA
| | | | | | - Ryan T Barnard
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, USA
| | - Lingyi Lu
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, USA
| | - Fang-Chi Hsu
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, USA
| | - Sanaz Sedaghat
- School of Public Health, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Anna Prizment
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Stephen B Kritchevsky
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Timothy M Hughes
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
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5
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Zheng Z, Li J, Liu T, Fan Y, Zhai QC, Xiong M, Wang QR, Sun X, Zheng QW, Che S, Jiang B, Zheng Q, Wang C, Liu L, Ping J, Wang S, Gao DD, Ye J, Yang K, Zuo Y, Ma S, Yang YG, Qu J, Zhang F, Jia P, Liu GH, Zhang W. DNA methylation clocks for estimating biological age in Chinese cohorts. Protein Cell 2024; 15:575-593. [PMID: 38482631 PMCID: PMC11259550 DOI: 10.1093/procel/pwae011] [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: 11/11/2023] [Accepted: 01/10/2024] [Indexed: 07/21/2024] Open
Abstract
Epigenetic clocks are accurate predictors of human chronological age based on the analysis of DNA methylation (DNAm) at specific CpG sites. However, a systematic comparison between DNA methylation data and other omics datasets has not yet been performed. Moreover, available DNAm age predictors are based on datasets with limited ethnic representation. To address these knowledge gaps, we generated and analyzed DNA methylation datasets from two independent Chinese cohorts, revealing age-related DNAm changes. Additionally, a DNA methylation aging clock (iCAS-DNAmAge) and a group of DNAm-based multi-modal clocks for Chinese individuals were developed, with most of them demonstrating strong predictive capabilities for chronological age. The clocks were further employed to predict factors influencing aging rates. The DNAm aging clock, derived from multi-modal aging features (compositeAge-DNAmAge), exhibited a close association with multi-omics changes, lifestyles, and disease status, underscoring its robust potential for precise biological age assessment. Our findings offer novel insights into the regulatory mechanism of age-related DNAm changes and extend the application of the DNAm clock for measuring biological age and aging pace, providing the basis for evaluating aging intervention strategies.
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Affiliation(s)
- Zikai Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianzi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Qiao-Cheng Zhai
- Division of Orthopaedics, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Muzhao Xiong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiao-Ran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi-Wen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Shanshan Che
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beier Jiang
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Quan Zheng
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Cui Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixiao Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiale Ping
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Dan-Dan Gao
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Jinlin Ye
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Kuan Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuesheng Zuo
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Ma
- Aging Biomarker Consortium, Beijing 100101, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Qu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Aging Biomarker Consortium, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Zhang
- Division of Orthopaedics, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Guang-Hui Liu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Aging Biomarker Consortium, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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6
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Shitara Y, Konno R, Yoshihara M, Kashima K, Ito A, Mukai T, Kimoto G, Kakiuchi S, Ishikawa M, Kakihara T, Nagamatsu T, Takahashi N, Fujishiro J, Kawakami E, Ohara O, Kawashima Y, Watanabe E. Host-derived protein profiles of human neonatal meconium across gestational ages. Nat Commun 2024; 15:5543. [PMID: 39019879 PMCID: PMC11255260 DOI: 10.1038/s41467-024-49805-w] [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: 12/06/2023] [Accepted: 06/19/2024] [Indexed: 07/19/2024] Open
Abstract
Meconium, a non-invasive biomaterial reflecting prenatal substance accumulation, could provide valuable insights into neonatal health. However, the comprehensive protein profile of meconium across gestational ages remains unclear. Here, we conducted an extensive proteomic analysis of first meconium from 259 newborns across varied gestational ages to delineate protein composition and elucidate its relevance to neonatal diseases. The first meconium samples were collected, with the majority obtained before feeding, and the mean time for the first meconium passage from the anus was 11.9 ± 9.47 h. Our analysis revealed 5370 host-derived meconium proteins, which varied depending on sex and gestational age. Specifically, meconium from preterm infants exhibited elevated concentrations of proteins associated with the extracellular matrix. Additionally, the protein profiles of meconium also exhibited unique variations depending on both specific diseases, including gastrointestinal diseases, congenital heart diseases, and maternal conditions. Furthermore, we developed a machine learning model to predict gestational ages using meconium proteins. Our model suggests that newborns with gastrointestinal diseases and congenital heart diseases may have immature gastrointestinal systems. These findings highlight the intricate relationship between clinical parameters and meconium protein composition, offering potential for a novel approach to assess neonatal gastrointestinal health.
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Affiliation(s)
- Yoshihiko Shitara
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Masahito Yoshihara
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba, Japan
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, Japan
| | - Kohei Kashima
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsushi Ito
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeo Mukai
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Goh Kimoto
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satsuki Kakiuchi
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Tomo Kakihara
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Nagamatsu
- Department of Obstetrics and Gynecology, Faculty of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Naoto Takahashi
- Department of Pediatrics, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Fujishiro
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eiryo Kawakami
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba, Japan
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Kanagawa, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan.
| | - Eiichiro Watanabe
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
- Department of Surgery, Gunma Children's Medical Center, Gunma, Japan.
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7
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Han KS, Sander IB, Kumer J, Resnick E, Booth C, Cheng G, Im Y, Starich B, Kiemen AL, Phillip JM, Reddy S, Joshu CE, Sunshine JC, Walston JD, Wirtz D, Wu PH. qMAP enabled microanatomical mapping of human skin aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.588011. [PMID: 39005293 PMCID: PMC11244916 DOI: 10.1101/2024.04.03.588011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Aging is a major driver of diseases in humans. Identifying features associated with aging is essential for designing robust intervention strategies and discovering novel biomarkers of aging. Extensive studies at both the molecular and organ/whole-body physiological scales have helped determined features associated with aging. However, the lack of meso-scale studies, particularly at the tissue level, limits the ability to translate findings made at molecular scale to impaired tissue functions associated with aging. In this work, we established a tissue image analysis workflow - quantitative micro-anatomical phenotyping (qMAP) - that leverages deep learning and machine vision to fully label tissue and cellular compartments in tissue sections. The fully mapped tissue images address the challenges of finding an interpretable feature set to quantitatively profile age-related microanatomic changes. We optimized qMAP for skin tissues and applied it to a cohort of 99 donors aged 14 to 92. We extracted 914 microanatomic features and found that a broad spectrum of these features, represented by 10 cores processes, are strongly associated with aging. Our analysis shows that microanatomical features of the skin can predict aging with a mean absolute error (MAE) of 7.7 years, comparable to state-of-the-art epigenetic clocks. Our study demonstrates that tissue-level architectural changes are strongly associated with aging and represent a novel category of aging biomarkers that complement molecular markers. Our results highlight the complex and underexplored multi-scale relationship between molecular and tissue microanatomic scales.
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Affiliation(s)
- Kyu Sang Han
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- The Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD
| | - Inbal B Sander
- Department of Dermatology, Johns Hopkins University, Baltimore, MD
| | - Jacqueline Kumer
- Department of Illustration Practice, Maryland Institute College of Art, Baltimore, MD
| | - Eric Resnick
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Clare Booth
- Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Guoqing Cheng
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- The Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD
| | - Yebin Im
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- The Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD
| | - Bartholomew Starich
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- The Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD
| | - Ashley L Kiemen
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Jude M Phillip
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- The Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Sashank Reddy
- The Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD
- Department of Plastic and Reconstructive Surgery, Johns Hopkins School of Medicine, Baltimore, MD
| | - Corrine E Joshu
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD
| | - Joel C Sunshine
- Department of Dermatology, Johns Hopkins University, Baltimore, MD
| | - Jeremy D Walston
- Department of Medicine, Division of Geriatrics and Gerontology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Denis Wirtz
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- The Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Pei-Hsun Wu
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- The Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD
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8
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Neto S, Reis A, Pinheiro M, Ferreira M, Neves V, Castanho TC, Santos N, Rodrigues AJ, Sousa N, Santos MAS, Moura GR. Unveiling the molecular landscape of cognitive aging: insights from polygenic risk scores, DNA methylation, and gene expression. Hum Genomics 2024; 18:75. [PMID: 38956648 PMCID: PMC11221141 DOI: 10.1186/s40246-024-00640-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Aging represents a significant risk factor for the occurrence of cerebral small vessel disease, associated with white matter (WM) lesions, and to age-related cognitive alterations, though the precise mechanisms remain largely unknown. This study aimed to investigate the impact of polygenic risk scores (PRS) for WM integrity, together with age-related DNA methylation, and gene expression alterations, on cognitive aging in a cross-sectional healthy aging cohort. The PRSs were calculated using genome-wide association study (GWAS) summary statistics for magnetic resonance imaging (MRI) markers of WM integrity, including WM hyperintensities, fractional anisotropy (FA), and mean diffusivity (MD). These scores were utilized to predict age-related cognitive changes and evaluate their correlation with structural brain changes, which distinguish individuals with higher and lower cognitive scores. To reduce the dimensionality of the data and identify age-related DNA methylation and transcriptomic alterations, Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) was used. Subsequently, a canonical correlation algorithm was used to integrate the three types of omics data (PRS, DNA methylation, and gene expression data) and identify an individual "omics" signature that distinguishes subjects with varying cognitive profiles. RESULTS We found a positive association between MD-PRS and long-term memory, as well as a correlation between MD-PRS and structural brain changes, effectively discriminating between individuals with lower and higher memory scores. Furthermore, we observed an enrichment of polygenic signals in genes related to both vascular and non-vascular factors. Age-related alterations in DNA methylation and gene expression indicated dysregulation of critical molecular features and signaling pathways involved in aging and lifespan regulation. The integration of multi-omics data underscored the involvement of synaptic dysfunction, axonal degeneration, microtubule organization, and glycosylation in the process of cognitive aging. CONCLUSIONS These findings provide valuable insights into the biological mechanisms underlying the association between WM coherence and cognitive aging. Additionally, they highlight how age-associated DNA methylation and gene expression changes contribute to cognitive aging.
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Affiliation(s)
- Sonya Neto
- Institute for Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Andreia Reis
- Institute for Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Miguel Pinheiro
- Institute for Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Margarida Ferreira
- Institute for Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Vasco Neves
- Institute for Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Teresa Costa Castanho
- ICVS - School of Medicine, Campus Gualtar, University of Minho, 4710-057, Braga, Portugal
- Clinical Academic Center - Braga (2CA-B), Braga, Portugal
| | - Nadine Santos
- ICVS - School of Medicine, Campus Gualtar, University of Minho, 4710-057, Braga, Portugal
- Clinical Academic Center - Braga (2CA-B), Braga, Portugal
| | - Ana João Rodrigues
- ICVS - School of Medicine, Campus Gualtar, University of Minho, 4710-057, Braga, Portugal
- Clinical Academic Center - Braga (2CA-B), Braga, Portugal
| | - Nuno Sousa
- ICVS - School of Medicine, Campus Gualtar, University of Minho, 4710-057, Braga, Portugal
- Clinical Academic Center - Braga (2CA-B), Braga, Portugal
- P5 Medical Center, Braga, Portugal
| | - Manuel A S Santos
- Institute for Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
- Multidisciplinary Institute of Aging, MIA-Portugal, Faculty of Medicine, University of Coimbra, Rua Largo 2, 3º, 3000-370, Coimbra, Portugal
| | - Gabriela R Moura
- Institute for Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal.
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9
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Ammar OF, Massarotti C, Mincheva M, Sharma K, Liperis G, Herraiz S, Rodríguez-Nuevo A, Zambelli F, Mihalas BP, Fraire-Zamora JJ. Oxidative stress and ovarian aging: from cellular mechanisms to diagnostics and treatment. Hum Reprod 2024; 39:1582-1586. [PMID: 38670545 DOI: 10.1093/humrep/deae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/08/2024] [Indexed: 04/28/2024] Open
Affiliation(s)
- Omar F Ammar
- IVF Department, Ar-Razzi Hospital, Ramadi, Iraq
- Department of Obstetrics and Gynaecology, College of Medicine, University of Anbar, Ramadi, Iraq
| | - Claudia Massarotti
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- DINOGMI Department, University of Genova, Genova, Italy
| | | | - Kashish Sharma
- HealthPlus Fertility Center, HealthPlus Network of Specialty Centers, Abu Dhabi, United Arab Emirates
| | - George Liperis
- Westmead Fertility Centre, Institute of Reproductive Medicine, University of Sydney, Westmead, NSW, Australia
- Embryorigin Fertility Centre, Larnaca, Cyprus
| | - Sonia Herraiz
- IVIRMA Global Research Alliance, IVI Foundation-IIS la Fe, Valencia, Spain
| | - Aida Rodríguez-Nuevo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Bettina P Mihalas
- The Oocyte Biology Research Unit, Discipline of Women's Health, School of Clinical Medicine, Faculty of Medicine and Health, The University of NSW Sydney, Randwick, NSW, Australia
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10
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Wang T, Beyene HB, Yi C, Cinel M, Mellett NA, Olshansky G, Meikle TG, Wu J, Dakic A, Watts GF, Hung J, Hui J, Beilby J, Blangero J, Kaddurah-Daouk R, Salim A, Moses EK, Shaw JE, Magliano DJ, Huynh K, Giles C, Meikle PJ. A lipidomic based metabolic age score captures cardiometabolic risk independent of chronological age. EBioMedicine 2024; 105:105199. [PMID: 38905750 PMCID: PMC11246009 DOI: 10.1016/j.ebiom.2024.105199] [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: 01/02/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/23/2024] Open
Abstract
BACKGROUND Metabolic ageing biomarkers may capture the age-related shifts in metabolism, offering a precise representation of an individual's overall metabolic health. METHODS Utilising comprehensive lipidomic datasets from two large independent population cohorts in Australia (n = 14,833, including 6630 males, 8203 females), we employed different machine learning models, to predict age, and calculated metabolic age scores (mAge). Furthermore, we defined the difference between mAge and age, termed mAgeΔ, which allow us to identify individuals sharing similar age but differing in their metabolic health status. FINDINGS Upon stratification of the population into quintiles by mAgeΔ, we observed that participants in the top quintile group (Q5) were more likely to have cardiovascular disease (OR = 2.13, 95% CI = 1.62-2.83), had a 2.01-fold increased risk of 12-year incident cardiovascular events (HR = 2.01, 95% CI = 1.45-2.57), and a 1.56-fold increased risk of 17-year all-cause mortality (HR = 1.56, 95% CI = 1.34-1.79), relative to the individuals in the bottom quintile group (Q1). Survival analysis further revealed that men in the Q5 group faced the challenge of reaching a median survival rate due to cardiovascular events more than six years earlier and reaching a median survival rate due to all-cause mortality more than four years earlier than men in the Q1 group. INTERPRETATION Our findings demonstrate that the mAge score captures age-related metabolic changes, predicts health outcomes, and has the potential to identify individuals at increased risk of metabolic diseases. FUNDING The specific funding of this article is provided in the acknowledgements section.
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Affiliation(s)
- Tingting Wang
- Baker Heart and Diabetes Institute, Melbourne, Australia; Baker Department of Cardiometabolic Health, Melbourne University, Melbourne, Australia
| | - Habtamu B Beyene
- Baker Heart and Diabetes Institute, Melbourne, Australia; Baker Department of Cardiometabolic Health, Melbourne University, Melbourne, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Australia
| | - Changyu Yi
- Baker Heart and Diabetes Institute, Melbourne, Australia; Baker Department of Cardiometabolic Health, Melbourne University, Melbourne, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Australia
| | - Michelle Cinel
- Baker Heart and Diabetes Institute, Melbourne, Australia
| | | | | | - Thomas G Meikle
- Baker Heart and Diabetes Institute, Melbourne, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Australia
| | - Jingqin Wu
- Baker Heart and Diabetes Institute, Melbourne, Australia; Baker Department of Cardiometabolic Health, Melbourne University, Melbourne, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Australia
| | | | - Gerald F Watts
- School of Medicine, University of Western Australia, Perth, Australia; Lipid Disorders Clinic, Department of Cardiology, Royal Perth Hospital, Perth, Australia
| | - Joseph Hung
- School of Medicine, University of Western Australia, Perth, Australia
| | - Jennie Hui
- PathWest Laboratory Medicine of Western Australia, Nedlands, Western Australia, Australia; School of Population and Global Health, University of Western Australia, Crawley, Western Australia, Australia; School of Biomedical Sciences, University of Western Australia, Australia
| | - John Beilby
- PathWest Laboratory Medicine of Western Australia, Nedlands, Western Australia, Australia; School of Biomedical Sciences, University of Western Australia, Australia
| | - John Blangero
- South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioural Sciences, Duke University, Durham, NC, USA; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University, Durham, NC, USA
| | - Agus Salim
- Baker Heart and Diabetes Institute, Melbourne, Australia; Melbourne School of Population and Global Health School of Mathematics and Statistics, The University of Melbourne, Australia
| | - Eric K Moses
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | | | - Kevin Huynh
- Baker Heart and Diabetes Institute, Melbourne, Australia; Baker Department of Cardiometabolic Health, Melbourne University, Melbourne, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Australia
| | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Australia; Baker Department of Cardiometabolic Health, Melbourne University, Melbourne, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Australia; Baker Department of Cardiometabolic Health, Melbourne University, Melbourne, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Australia.
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11
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Krzistetzko J, Géraud C, Dormann C, Riedel A, Leibing T. Phenotypical and biochemical characterization of murine psoriasiform and fibrotic skin disease models in Stabilin-deficient mice. FEBS Open Bio 2024. [PMID: 38946049 DOI: 10.1002/2211-5463.13857] [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: 03/09/2024] [Revised: 05/21/2024] [Accepted: 06/20/2024] [Indexed: 07/02/2024] Open
Abstract
Stabilin-1 (Stab1) and Stabilin-2 (Stab2) are scavenger receptors expressed by liver sinusoidal endothelial cells (LSECs). The Stabilin-mediated scavenging function is responsible for regulating the molecular composition of circulating blood in mammals. Stab1 and Stab2 have been shown to influence fibrosis in liver and kidneys and to modulate inflammation in atherosclerosis. In this context, circulating and localized TGFBi and POSTN are differentially controlled by the Stabilins as their receptors. To assess Stab1 and Stab2 functions in inflammatory and fibrotic skin disease, topical Imiquimod (IMQ) was used to induce psoriasis-like skin lesions in mice and Bleomycin (BLM) was applied subcutaneously to induce scleroderma-like effects in the skin. The topical treatment with IMQ, as expected, led to psoriasis-like changes in the skin of mice, including increased epidermal thickness and significant weight loss. Clinical severity was reduced in Stab2-deficient compared to Stab1-deficient mice. We did not observe differential effects in the skin of Stabilin-deficient mice after bleomycin injection. Interestingly, treatment with IMQ led to a significant increase of Stabilin ligand TGFBi plasma levels in Stab2-/- mice, treatment with BLM resulted in a significant decrease in TGFBi levels in Stab1-/- mice. Overall, Stab1 and Stab2 deficiency resulted in minor alterations of the disease phenotypes accompanied by alterations of circulating ligands in the blood in response to the disease models. Stabilin-mediated clearance of TGFBi was altered in these disease processes. Taken together our results suggest that Stabilin deficiency-associated plasma alterations may interfere with preclinical disease severity and treatment responses in patients.
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Affiliation(s)
- Jessica Krzistetzko
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Section of Clinical and Molecular Dermatology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Cyrill Géraud
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Section of Clinical and Molecular Dermatology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christof Dormann
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Section of Clinical and Molecular Dermatology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anna Riedel
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Section of Clinical and Molecular Dermatology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Leibing
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Section of Clinical and Molecular Dermatology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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12
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Kuo CL, Liu P, Chen Z, Pilling LC, Atkins JL, Fortinsky RH, Kuchel GA, Diniz BS. A proteomic signature of healthspan. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.26.24309530. [PMID: 38978645 PMCID: PMC11230312 DOI: 10.1101/2024.06.26.24309530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The focus of aging research has shifted from increasing lifespan to enhancing healthspan to reduce the time spent living with disability. Despite significant efforts to develop biomarkers of aging, few studies have focused on biomarkers of healthspan. We developed a proteomics-based signature of healthspan (healthspan proteomic score (HPS)) using data from the UK Biobank Pharma Proteomics Project (53,018 individuals and 2920 proteins). A lower HPS was associated with higher mortality risk and several age-related conditions, such as COPD, diabetes, heart failure, cancer, myocardial infarction, dementia, and stroke. HPS showed superior predictive accuracy for these outcomes compared to chronological age and biological age measures. Proteins associated with HPS were enriched in hallmark pathways such as immune response, inflammation, cellular signaling, and metabolic regulation. Our findings demonstrate the validity of HPS, making it a valuable tool for assessing healthspan and as a potential surrogate marker in geroscience-guided studies.
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Affiliation(s)
- Chia-Ling Kuo
- Department of Public Health Sciences, University of Connecticut Health Center, Farmington Connecticut, USA
- The Cato T. Laurencin Institute for Regenerative Engineering, University of Connecticut Health Center, Farmington, Connecticut, USA
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - Peiran Liu
- The Cato T. Laurencin Institute for Regenerative Engineering, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Zhiduo Chen
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - Luke C Pilling
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Janice L Atkins
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Richard H Fortinsky
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - George A Kuchel
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
| | - Breno S Diniz
- Department of Public Health Sciences, University of Connecticut Health Center, Farmington Connecticut, USA
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, USA
- Department of Psychiatry, University of Connecticut Health Center, Farmington Connecticut, USA
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13
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Wang Y, Ye M, Ji Q, Liu Q, Xu X, Zhan Y. The longitudinal trajectory of CSF sTREM2: the alzheimer's disease neuroimaging initiative. Alzheimers Res Ther 2024; 16:138. [PMID: 38926894 PMCID: PMC11202383 DOI: 10.1186/s13195-024-01506-8] [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: 01/03/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND The soluble triggering receptor expressed on myeloid cells 2 (sTREM2) in cerebrospinal fluid (CSF) is considered a biomarker of microglia activity. The objective of this study was to investigate the trajectory of CSF sTREM2 levels over time and examine its association with sex. METHODS A total of 1,017 participants from the Alzheimer's Disease Neuroimaging Initiative Study (ADNI) with at least one CSF sTREM2 record were included. The trajectory of CSF sTREM2 was analyzed using a growth curve model. The association between CSF sTREM2 levels and sex was assessed using linear mixed-effect models. RESULTS CSF sTREM2 levels were increased with age over time (P < 0.0001). No significant sex difference was observed in sTREM2 levels across the entire sample; however, among the APOE ε4 allele carriers, women exhibited significantly higher sTREM2 levels than men (β = 0.146, P = 0.002). CONCLUSION Our findings highlight the association between CSF sTREM2 levels and age-related increments, underscoring the potential influence of aging on sTREM2 dynamics. Furthermore, our observations indicate a noteworthy association between sex and CSF sTREM2 levels, particularly in individuals carrying the APOE ε4 allele.
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Affiliation(s)
- Yu Wang
- Department of Epidemiology, School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, China
| | - Meijie Ye
- Department of Epidemiology, School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, China
| | - Qianqian Ji
- Department of Epidemiology, School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, China
| | - Qi Liu
- Department of Epidemiology, School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, China
| | - Xiaowei Xu
- Department of Neurology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China.
| | - Yiqiang Zhan
- Department of Epidemiology, School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, China.
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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14
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Song Z, Bian W, Lin J, Guo Y, Shi W, Meng H, Chen Y, Zhang M, Liu Z, Lin Z, Ma K, Li L. Heart proteomic profiling discovers MYH6 and COX5B as biomarkers for sudden unexplained death. Forensic Sci Int 2024; 361:112121. [PMID: 38971138 DOI: 10.1016/j.forsciint.2024.112121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/03/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Sudden unexplained death (SUD) is not uncommon in forensic pathology. Yet, diagnosis of SUD remains challenging due to lack of specific biomarkers. This study aimed to screen differentially expressed proteins (DEPs) and validate their usefulness as diagnostic biomarkers for SUD cases. We designed a three-phase investigation, where in the discovery phase, formalin-fixed paraffin-embedded (FFPE) heart specimens were screened through label-free proteomic analysis of cases dying from SUD, mechanical injury and carbon monoxide (CO) intoxication. A total of 26 proteins were identified to be DEPs for the SUD cases after rigorous criterion. Bioinformatics and Adaboost-recursive feature elimination (RFE) analysis further revealed that three of the 26 proteins (MYH6, COX5B and TNNT2) were potential discriminative biomarkers. In the training phase, MYH6 and COX5B were verified to be true DEPs in cardiac tissues from 29 independent SUD cases as compared with a serial of control cases (n = 42). Receiver operating characteristic (ROC) analysis illustrated that combination of MYH6 and COX5B achieved optimal diagnostic sensitivity (89.7 %) and specificity (84.4 %), with area under the curve (AUC) being 0.91. A diagnostic software based on the logistic regression formula derived from the training phase was then constructed. In the validation phase, the diagnostic software was applied to eight authentic SUD cases, seven (87.5 %) of which were accurately recognized. Our study provides a valid strategy towards practical diagnosis of SUD by integrating cardiac MYH6 and COX5B as dual diagnostic biomarkers.
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Affiliation(s)
- Ziyan Song
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Wensi Bian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Junyi Lin
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Yadong Guo
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, PR China.
| | - Weibo Shi
- Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, Hebei 050017, PR China.
| | - Hang Meng
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
| | - Yuanyuan Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, Jiangxi 341000, PR China.
| | - Molin Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Zheng Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Zijie Lin
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Kaijun Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
| | - Liliang Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China; Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, Hebei 050017, PR China; Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
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15
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Liu Y, Lu S, Yang J, Yang Y, Jiao L, Hu J, Li Y, Yang F, Pang Y, Zhao Y, Gao Y, Liu W, Shu P, Ge W, He Z, Peng X. Analysis of the aging-related biomarker in a nonhuman primate model using multilayer omics. BMC Genomics 2024; 25:639. [PMID: 38926642 PMCID: PMC11209966 DOI: 10.1186/s12864-024-10556-z] [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: 02/09/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Aging is a prominent risk factor for diverse diseases; therefore, an in-depth understanding of its physiological mechanisms is required. Nonhuman primates, which share the closest genetic relationship with humans, serve as an ideal model for exploring the complex aging process. However, the potential of the nonhuman primate animal model in the screening of human aging markers is still not fully exploited. Multiomics analysis of nonhuman primate peripheral blood offers a promising approach to evaluate new therapies and biomarkers. This study explores aging-related biomarker through multilayer omics, including transcriptomics (mRNA, lncRNA, and circRNA) and proteomics (serum and serum-derived exosomes) in rhesus monkeys (Macaca mulatta). RESULTS Our findings reveal that, unlike mRNAs and circRNAs, highly expressed lncRNAs are abundant during the key aging period and are associated with cancer pathways. Comparative analysis highlighted exosomal proteins contain more types of proteins than serum proteins, indicating that serum-derived exosomes primarily regulate aging through metabolic pathways. Finally, eight candidate aging biomarkers were identified, which may serve as blood-based indicators for detecting age-related brain changes. CONCLUSIONS Our results provide a comprehensive understanding of nonhuman primate blood transcriptomes and proteomes, offering novel insights into the aging mechanisms for preventing or treating age-related diseases.
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Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, CAMS & PUMC, Beijing, 100021, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Jing Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yun Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Li Jiao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Jingwen Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yanyan Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Fengmei Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yunli Pang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yuan Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yanpan Gao
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Wei Liu
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Pengcheng Shu
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Wei Ge
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China.
| | - Xiaozhong Peng
- State Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, CAMS & PUMC, Beijing, 100021, China.
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China.
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China.
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16
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Premeaux TA, Bowler S, Friday CM, Moser CB, Hoenigl M, Lederman MM, Landay AL, Gianella S, Ndhlovu LC. Machine learning models based on fluid immunoproteins that predict non-AIDS adverse events in people with HIV. iScience 2024; 27:109945. [PMID: 38812553 PMCID: PMC11134891 DOI: 10.1016/j.isci.2024.109945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/12/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
Despite the success of antiretroviral therapy (ART), individuals with HIV remain at risk for experiencing non-AIDS adverse events (NAEs), including cardiovascular complications and malignancy. Several surrogate immune biomarkers in blood have shown predictive value in predicting NAEs; however, composite panels generated using machine learning may provide a more accurate advancement for monitoring and discriminating NAEs. In a nested case-control study, we aimed to develop machine learning models to discriminate cases (experienced an event) and matched controls using demographic and clinical characteristics alongside 49 plasma immunoproteins measured prior to and post-ART initiation. We generated support vector machine (SVM) classifier models for high-accuracy discrimination of individuals aged 30-50 years who experienced non-fatal NAEs at pre-ART and one-year post-ART. Extreme gradient boosting generated a high-accuracy model at pre-ART, while K-nearest neighbors performed poorly all around. SVM modeling may offer guidance to improve disease monitoring and elucidate potential therapeutic interventions.
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Affiliation(s)
- Thomas A. Premeaux
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott Bowler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Courtney M. Friday
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Carlee B. Moser
- Center for Biostatistics in AIDS Research in the Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA, USA
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Michael M. Lederman
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Alan L. Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sara Gianella
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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17
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Yusri K, Kumar S, Fong S, Gruber J, Sorrentino V. Towards Healthy Longevity: Comprehensive Insights from Molecular Targets and Biomarkers to Biological Clocks. Int J Mol Sci 2024; 25:6793. [PMID: 38928497 PMCID: PMC11203944 DOI: 10.3390/ijms25126793] [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: 05/23/2024] [Revised: 06/16/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Aging is a complex and time-dependent decline in physiological function that affects most organisms, leading to increased risk of age-related diseases. Investigating the molecular underpinnings of aging is crucial to identify geroprotectors, precisely quantify biological age, and propose healthy longevity approaches. This review explores pathways that are currently being investigated as intervention targets and aging biomarkers spanning molecular, cellular, and systemic dimensions. Interventions that target these hallmarks may ameliorate the aging process, with some progressing to clinical trials. Biomarkers of these hallmarks are used to estimate biological aging and risk of aging-associated disease. Utilizing aging biomarkers, biological aging clocks can be constructed that predict a state of abnormal aging, age-related diseases, and increased mortality. Biological age estimation can therefore provide the basis for a fine-grained risk stratification by predicting all-cause mortality well ahead of the onset of specific diseases, thus offering a window for intervention. Yet, despite technological advancements, challenges persist due to individual variability and the dynamic nature of these biomarkers. Addressing this requires longitudinal studies for robust biomarker identification. Overall, utilizing the hallmarks of aging to discover new drug targets and develop new biomarkers opens new frontiers in medicine. Prospects involve multi-omics integration, machine learning, and personalized approaches for targeted interventions, promising a healthier aging population.
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Affiliation(s)
- Khalishah Yusri
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Sanjay Kumar
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Sheng Fong
- Department of Geriatric Medicine, Singapore General Hospital, Singapore 169608, Singapore
- Clinical and Translational Sciences PhD Program, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jan Gruber
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Science Division, Yale-NUS College, Singapore 138527, Singapore
| | - Vincenzo Sorrentino
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Gastroenterology Endocrinology Metabolism and Amsterdam Neuroscience Cellular & Molecular Mechanisms, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
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18
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Seo D, Lee CM, Apio C, Heo G, Timsina J, Kohlfeld P, Boada M, Orellana A, Fernandez MV, Ruiz A, Morris JC, Schindler SE, Park T, Cruchaga C, Sung YJ. Sex and aging signatures of proteomics in human cerebrospinal fluid identify distinct clusters linked to neurodegeneration. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.18.24309102. [PMID: 38947020 PMCID: PMC11213043 DOI: 10.1101/2024.06.18.24309102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Sex and age are major risk factors for chronic diseases. Recent studies examining age-related molecular changes in plasma provided insights into age-related disease biology. Cerebrospinal fluid (CSF) proteomics can provide additional insights into brain aging and neurodegeneration. By comprehensively examining 7,006 aptamers targeting 6,139 proteins in CSF obtained from 660 healthy individuals aged from 43 to 91 years old, we subsequently identified significant sex and aging effects on 5,097 aptamers in CSF. Many of these effects on CSF proteins had different magnitude or even opposite direction as those on plasma proteins, indicating distinctive CSF-specific signatures. Network analysis of these CSF proteins revealed not only modules associated with healthy aging but also modules showing sex differences. Through subsequent analyses, several modules were highlighted for their proteins implicated in specific diseases. Module 2 and 6 were enriched for many aging diseases including those in the circulatory systems, immune mechanisms, and neurodegeneration. Together, our findings fill a gap of current aging research and provide mechanistic understanding of proteomic changes in CSF during a healthy lifespan and insights for brain aging and diseases.
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19
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Chan LJG, Olsson N, Preciado López M, Hake K, Tomono H, Veras MA, McAllister FE. Plasma and Kidney Proteome Profiling Combined with Laser Capture Microdissection Reveal Large Increases in Immunoglobulins with Age. Proteomes 2024; 12:16. [PMID: 38921822 PMCID: PMC11207650 DOI: 10.3390/proteomes12020016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024] Open
Abstract
One of the main hallmarks of aging is aging-associated inflammation, also known as inflammaging. In this study, by comparing plasma and kidney proteome profiling of young and old mice using LC-MS profiling, we discovered that immunoglobulins are the proteins that exhibit the highest increase with age. This observation seems to have been disregarded because conventional proteome profiling experiments typically overlook the expression of high-abundance proteins or employ depletion methods to remove them before LC-MS analysis. We show that proteome profiling of immunoglobulins will likely be a useful biomarker of aging. Spatial profiling using immunofluorescence staining of kidney sections indicates that the main increases in immunoglobulins with age are localized in the glomeruli of the kidney. Using laser capture microdissection coupled with LC-MS, we show an increase in multiple immune-related proteins in glomeruli from aged mice. Increased deposition of immunoglobulins, immune complexes, and complement proteins in the kidney glomeruli may be a factor leading to reduced filtering capacity of the kidney with age. Therapeutic strategies to reduce the deposition of immunoglobulins in the kidney may be an attractive strategy for healthy aging.
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Affiliation(s)
| | | | | | | | | | | | - Fiona E. McAllister
- Calico Life Sciences LLC, 1130 Veterans Blvd, South San Francisco, CA 94080, USA
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20
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Shokhirev MN, Torosin NS, Kramer DJ, Johnson AA, Cuellar TL. CheekAge: a next-generation buccal epigenetic aging clock associated with lifestyle and health. GeroScience 2024; 46:3429-3443. [PMID: 38441802 PMCID: PMC11009193 DOI: 10.1007/s11357-024-01094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/05/2024] [Indexed: 04/13/2024] Open
Abstract
Epigenetic aging clocks are computational models that predict age using DNA methylation information. Initially, first-generation clocks were developed to make predictions using CpGs that change with age. Over time, next-generation clocks were created using CpGs that relate to both age and health. Since existing next-generation clocks were constructed in blood, we sought to develop a next-generation clock optimized for prediction in cheek swabs, which are non-invasive and easy to collect. To do this, we collected MethylationEPIC data as well as lifestyle and health information from 8045 diverse adults. Using a novel simulated annealing approach that allowed us to incorporate lifestyle and health factors into training as well as a combination of CpG filtering, CpG clustering, and clock ensembling, we constructed CheekAge, an epigenetic aging clock that has a strong correlation with age, displays high test-retest reproducibility across replicates, and significantly associates with a plethora of lifestyle and health factors, such as BMI, smoking status, and alcohol intake. We validated CheekAge in an internal dataset and multiple publicly available datasets, including samples from patients with progeria or meningioma. In addition to exploring the underlying biology of the data and clock, we provide a free online tool that allows users to mine our methylomic data and predict epigenetic age.
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21
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Dormann D, Lemke EA. Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 2024; 26:851-858. [PMID: 38783141 DOI: 10.1038/s41556-024-01423-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.
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Affiliation(s)
- Dorothee Dormann
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
| | - Edward Anton Lemke
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg University, Mainz, Germany.
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22
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Cardim-Pires TR, de Rus Jacquet A, Cicchetti F. Healthy blood, healthy brain: a window into understanding and treating neurodegenerative diseases. J Neurol 2024; 271:3682-3689. [PMID: 38607433 DOI: 10.1007/s00415-024-12337-w] [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: 01/26/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
Our limited understanding of complex neurodegenerative disorders has held us back on the development of efficient therapies. While several approaches are currently being considered, it is still unclear what will be most successful. Among the latest and more novel ideas, the concept of blood or plasma transfusion from young healthy donors to diseased patients is gaining momentum and attracting attention beyond the scientific arena. While young or healthy blood is enriched with protective and restorative components, blood from older subjects may accumulate neurotoxic agents or be impoverished of beneficial factors. In this commentary, we present an overview of the compelling evidence collected in various animal models of brain diseases (e.g., Alzheimer, Parkinson, Huntington) to the actual clinical trials that have been conducted to test the validity of blood-related treatments in neurodegenerative diseases and argue in favor of such approach.
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Affiliation(s)
- Thyago R Cardim-Pires
- Centre de Recherche du CHU de Québec, Université Laval, Axe Neurosciences, T2-07, 2705, Boulevard Laurier, Québec, QC, G1V 4G2, Canada
| | - Aurélie de Rus Jacquet
- Centre de Recherche du CHU de Québec, Université Laval, Axe Neurosciences, T2-07, 2705, Boulevard Laurier, Québec, QC, G1V 4G2, Canada
- Département de Psychiatrie & Neurosciences, Université Laval, Québec, QC, G1K 0A6, Canada
| | - Francesca Cicchetti
- Centre de Recherche du CHU de Québec, Université Laval, Axe Neurosciences, T2-07, 2705, Boulevard Laurier, Québec, QC, G1V 4G2, Canada.
- Département de Psychiatrie & Neurosciences, Université Laval, Québec, QC, G1K 0A6, Canada.
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23
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Sandalova E, Maier AB. Targeting the epigenetically older individuals for geroprotective trials: the use of DNA methylation clocks. Biogerontology 2024; 25:423-431. [PMID: 37968337 DOI: 10.1007/s10522-023-10077-4] [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: 09/08/2023] [Accepted: 10/15/2023] [Indexed: 11/17/2023]
Abstract
Chronological age is the most important risk factor for the incidence of age-related diseases. The pace of ageing determines the magnitude of that risk and can be expressed as biological age. Targeting fundamental pathways of human aging with geroprotectors has the potential to lower the biological age and therewith prolong the healthspan, the period of life one spends in good health. Target populations for geroprotective interventions should be chosen based on the ageing mechanisms being addressed and the expected effect of the geroprotector on the primary outcome. Biomarkers of ageing, such as DNA methylation age, can be used to select populations for geroprotective interventions and as a surrogate outcome. Here, the use of DNA methylation clocks for selecting target populations for geroprotective intervention is explored.
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Affiliation(s)
- Elena Sandalova
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore.
| | - Andrea B Maier
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore.
- Department of Human Movement Sciences, @AgeAmsterdam, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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24
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Agca S, Kir S. EDA2R-NIK signaling in cancer cachexia. Curr Opin Support Palliat Care 2024:01263393-990000000-00079. [PMID: 38801457 DOI: 10.1097/spc.0000000000000705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
PURPOSE OF REVIEW Cachexia is a debilitating condition causing weight loss and skeletal muscle wasting that negatively influences treatment and survival of cancer patients. The objective of this review is to describe recent discoveries on the role of a novel signaling pathway involving ectodysplasin A2 receptor (EDA2R) and nuclear factor κB (NFκB)-inducing kinase (NIK) in muscle atrophy. RECENT FINDINGS Studies identified tumor-induced upregulation of EDA2R expression in muscle tissues in pre-clinical cachexia models and patients with various cancers. Activation of EDA2R by its ligand promoted atrophy in cultured myotubes and muscle tissue, which depended on NIK activity. The non-canonical NFκB pathway via NIK also stimulated muscle atrophy. Mice lacking EDA2R or NIK were protected from muscle loss due to tumors. Tumor-induced cytokine oncostatin M (OSM) upregulated EDA2R expression in muscles whereas OSM receptor-deficient mice were resistant to muscle wasting. SUMMARY Recent discoveries revealed a mechanism involving EDA2R-NIK signaling and OSM that drives cancer-associated muscle loss, opening up new directions for designing anti-cachexia treatments. The therapeutic potential of targeting this mechanism to prevent muscle loss should be further investigated. Future research should also explore broader implications of the EDA2R-NIK pathway in other muscle wasting diseases and overall muscle health.
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Affiliation(s)
- Samet Agca
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
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25
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Sun BB, Suhre K, Gibson BW. Promises and Challenges of populational Proteomics in Health and Disease. Mol Cell Proteomics 2024; 23:100786. [PMID: 38761890 PMCID: PMC11193116 DOI: 10.1016/j.mcpro.2024.100786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Advances in proteomic assay technologies have significantly increased coverage and throughput, enabling recent increases in the number of large-scale population-based proteomic studies of human plasma and serum. Improvements in multiplexed protein assays have facilitated the quantification of thousands of proteins over a large dynamic range, a key requirement for detecting the lowest-ranging, and potentially the most disease-relevant, blood-circulating proteins. In this perspective, we examine how populational proteomic datasets in conjunction with other concurrent omic measures can be leveraged to better understand the genomic and non-genomic correlates of the soluble proteome, constructing biomarker panels for disease prediction, among others. Mass spectrometry workflows are discussed as they are becoming increasingly competitive with affinity-based array platforms in terms of speed, cost, and proteome coverage due to advances in both instrumentation and workflows. Despite much success, there remain considerable challenges such as orthogonal validation and absolute quantification. We also highlight emergent challenges associated with study design, analytical considerations, and data integration as population-scale studies are run in batches and may involve longitudinal samples collated over many years. Lastly, we take a look at the future of what the nascent next-generation proteomic technologies might provide to the analysis of large sets of blood samples, as well as the difficulties in designing large-scale studies that will likely require participation from multiple and complex funding sources and where data sharing, study designs, and financing must be solved.
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Affiliation(s)
- Benjamin B Sun
- Human Genetics, Informatics and Predictive Sciences, Bristol-Myers Squibb, Cambridge, Massachusetts, USA.
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Bradford W Gibson
- Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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26
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Lu H, Jing Y, Zhang C, Ma S, Zhang W, Huang D, Zhang B, Zuo Y, Qin Y, Liu GH, Yu Y, Qu J, Wang S. Aging hallmarks of the primate ovary revealed by spatiotemporal transcriptomics. Protein Cell 2024; 15:364-384. [PMID: 38126810 DOI: 10.1093/procel/pwad063] [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: 10/04/2023] [Accepted: 10/29/2023] [Indexed: 12/23/2023] Open
Abstract
The ovary is indispensable for female reproduction, and its age-dependent functional decline is the primary cause of infertility. However, the molecular basis of ovarian aging in higher vertebrates remains poorly understood. Herein, we apply spatiotemporal transcriptomics to benchmark architecture organization as well as cellular and molecular determinants in young primate ovaries and compare these to aged primate ovaries. From a global view, somatic cells within the non-follicle region undergo more pronounced transcriptional fluctuation relative to those in the follicle region, likely constituting a hostile microenvironment that facilitates ovarian aging. Further, we uncovered that inflammation, the senescent-associated secretory phenotype, senescence, and fibrosis are the likely primary contributors to ovarian aging (PCOA). Of note, we identified spatial co-localization between a PCOA-featured spot and an unappreciated MT2 (Metallothionein 2) highly expressing spot (MT2high) characterized by high levels of inflammation, potentially serving as an aging hotspot in the primate ovary. Moreover, with advanced age, a subpopulation of MT2high accumulates, likely disseminating and amplifying the senescent signal outward. Our study establishes the first primate spatiotemporal transcriptomic atlas, advancing our understanding of mechanistic determinants underpinning primate ovarian aging and unraveling potential biomarkers and therapeutic targets for aging and age-associated human ovarian disorders.
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Affiliation(s)
- Huifen Lu
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Ying Jing
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Chen Zhang
- The Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
- Sino-Danish Center for Education and Research, Beijing 101408, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Daoyuan Huang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Bin Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuesheng Zuo
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Yingying Qin
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan 250012, China
| | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Yang Yu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University, Third Hospital, Beijing 100191, China
- Clinical Stem Cell Research Center, Peking University, Third Hospital, Beijing 100191, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- The Fifth People's Hospital of Chongqing, Chongqing 400062, China
- Aging Biomarker Consortium, Beijing 100101, China
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27
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Wang X, Tazearslan C, Kim S, Guo Q, Contreras D, Yang J, Hudgins AD, Suh Y. In vitro heterochronic parabiosis identifies pigment epithelium-derived factor as a systemic mediator of rejuvenation by young blood. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592258. [PMID: 38746475 PMCID: PMC11092633 DOI: 10.1101/2024.05.02.592258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Several decades of heterochronic parabiosis (HCPB) studies have demonstrated the restorative impact of young blood, and deleterious influence of aged blood, on physiological function and homeostasis across tissues, although few of the factors responsible for these observations have been identified. Here we develop an in vitro HCPB system to identify these circulating factors, using replicative lifespan (RLS) of primary human fibroblasts as an endpoint of cellular health. We find that RLS is inversely correlated with serum donor age and sensitive to the presence or absence of specific serum components. Through in vitro HCPB, we identify the secreted protein pigment epithelium-derived factor (PEDF) as a circulating factor that extends RLS of primary human fibroblasts and declines with age in mammals. Systemic administration of PEDF to aged mice reverses age-related functional decline and pathology across several tissues, improving cognitive function and reducing hepatic fibrosis and renal lipid accumulation. Together, our data supports PEDF as a systemic mediator of the effect of young blood on organismal health and homeostasis and establishes our in vitro HCPB system as a valuable screening platform for the identification of candidate circulating factors involved in aging and rejuvenation.
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Affiliation(s)
- Xizhe Wang
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY
- These authors contributed equally
| | - Cagdas Tazearslan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
- These authors contributed equally
| | - Seungsoo Kim
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY
| | - Qinghua Guo
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY
| | - Daniela Contreras
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY
| | - Jiping Yang
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY
| | - Adam D. Hudgins
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY
- Department of Genetics and Development, Columbia University Medical Center, New York, NY
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Jiang Z, Huang C, Guo E, Zhu X, Li N, Huang Y, Wang P, Shan H, Yin Y, Wang H, Huang L, Han Z, Ouyang K, Sun L. Platelet-Rich Plasma in Young and Elderly Humans Exhibits a Different Proteomic Profile. J Proteome Res 2024; 23:1788-1800. [PMID: 38619924 DOI: 10.1021/acs.jproteome.4c00030] [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] [Indexed: 04/17/2024]
Abstract
As people age, their ability to resist injury and repair damage decreases significantly. Platelet-rich plasma (PRP) has demonstrated diverse therapeutic effects on tissue repair. However, the inconsistency of patient outcomes poses a challenge to the practical application of PRP in clinical practice. Furthermore, a comprehensive understanding of the specific impact of aging on PRP requires a systematic investigation. We derived PRP from 6 young volunteers and 6 elderly volunteers, respectively. Subsequently, 95% of high-abundance proteins were removed, followed by mass spectrometry analysis. Data are available via ProteomeXchange with the identifier PXD050061. We detected a total of 739 proteins and selected 311 proteins that showed significant differences, including 76 upregulated proteins in the young group and 235 upregulated proteins in the elderly group. Functional annotation and enrichment analysis unveiled upregulation of proteins associated with cell apoptosis, angiogenesis, and complement and coagulation cascades in the elderly. Conversely, IGF1 was found to be upregulated in the young group, potentially serving as the central source of enhanced cell proliferation ability. Our investigation not only provides insights into standardizing PRP preparation but also offers novel strategies for augmenting the functionality of aging cells or tissues.
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Affiliation(s)
- Zhitong Jiang
- Department of Cardiovascular Surgery, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Can Huang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Erliang Guo
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Xiangbin Zhu
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Na Li
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yu Huang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Peihe Wang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Hui Shan
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yuxin Yin
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Hong Wang
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Lei Huang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Zhen Han
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Lu Sun
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
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29
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Qu R, Zhang Z, Fu W. Potential of Serum Glycoproteome Profiling in Prediction of Advanced Adenomas and Colorectal Carcinoma: Individual Heterogeneity Should Be Taken Into Account. Gastroenterology 2024; 166:946. [PMID: 38147931 DOI: 10.1053/j.gastro.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/28/2023]
Affiliation(s)
- Ruize Qu
- Department of General Surgery; Cancer Center, Peking University Third Hospital, Beijing, China
| | - Zhipeng Zhang
- Department of General Surgery; Cancer Center, Peking University Third Hospital, Beijing, China
| | - Wei Fu
- Department of General Surgery; Cancer Center, Peking University Third Hospital, Beijing, China
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30
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Özen SD, Kir S. Ectodysplasin A2 receptor signaling in skeletal muscle pathophysiology. Trends Mol Med 2024; 30:471-483. [PMID: 38443222 DOI: 10.1016/j.molmed.2024.02.002] [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: 11/30/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024]
Abstract
Skeletal muscle is essential in generating mechanical force and regulating energy metabolism and body temperature. Pathologies associated with muscle tissue often lead to impaired physical activity and imbalanced metabolism. Recently, ectodysplasin A2 receptor (EDA2R) signaling has been shown to promote muscle loss and glucose intolerance. Upregulated EDA2R expression in muscle tissue was associated with aging, denervation, cancer cachexia, and muscular dystrophies. Here, we describe the roles of EDA2R signaling in muscle pathophysiology, including muscle atrophy, insulin resistance, and aging-related sarcopenia. We also discuss the EDA2R pathway, which involves EDA-A2 as the ligand and nuclear factor (NF)κB-inducing kinase (NIK) as a downstream mediator, and the therapeutic potential of targeting these proteins in the treatment of muscle wasting and metabolic dysfunction.
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Affiliation(s)
- Sevgi Döndü Özen
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Serkan Kir
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
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31
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Pena-Leon V, Perez-Lois R, Villalon M, Folgueira C, Barja-Fernández S, Prida E, Baltar J, Santos F, Fernø J, García-Caballero T, Nogueiras R, Quiñones M, Al-Massadi O, Seoane LM. Gastric GDF15 levels are regulated by age, sex, and nutritional status in rodents and humans. J Endocrinol Invest 2024; 47:1139-1154. [PMID: 37955834 DOI: 10.1007/s40618-023-02232-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/21/2023] [Indexed: 11/14/2023]
Abstract
AIM Growth differentiation factor 15 (GDF15) is a stress response cytokine that has been proposed as a relevant metabolic hormone. Descriptive studies have shown that plasma GDF15 levels are regulated by short term changes in nutritional status, such as fasting, or in obesity. However, few data exist regarding how GDF15 levels are regulated in peripheral tissues. The aim of the present work was to study the variations on gastric levels of GDF15 and its precursor under different physiological conditions, such as short-term changes in nutritional status or overfeeding achieved by HFD. Moreover, we also address the sex- and age-dependent alterations in GDF15 physiology. METHODS The levels of gastric and plasma GDF15 and its precursor were measured in lean and obese mice, rats and humans by western blot, RT-PCR, ELISA, immunohistochemistry and by an in vitro organ culture system. RESULTS Our results show a robust regulation of gastric GDF15 production by fasting in rodents. In obesity an increase in GDF15 secretion from the stomach is reflected with an increase in circulating levels of GDF15 in rats and humans. Moreover, gastric GDF15 levels increase with age in both rats and humans. Finally, gastric GDF15 levels display sexual dimorphism, which could explain the difference in circulating GFD15 levels between males and females, observed in both humans and rodents. CONCLUSIONS Our results provide clear evidence that gastric GDF15 is a critical contributor of circulating GDF15 levels and can explain some of the metabolic effects induced by GDF15.
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Affiliation(s)
- V Pena-Leon
- Grupo Fisiopatología Endocrina, Área de Endocrinología, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - R Perez-Lois
- Grupo Fisiopatología Endocrina, Área de Endocrinología, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - M Villalon
- Grupo Fisiopatología Endocrina, Área de Endocrinología, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - C Folgueira
- Grupo Fisiopatología Endocrina, Área de Endocrinología, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - S Barja-Fernández
- Grupo Fisiopatología Endocrina, Área de Endocrinología, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - E Prida
- Translational Endocrinology Group, Endocrinology Section, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (IDIS/CHUS), Santiago de Compostela, Spain
| | - J Baltar
- Servicio de Cirugía General y del Aparato Digestivo, CHUS7SERGAS Santiago de Compostela, Rua R Baltar s/n, 15706, Santiago de Compostela, Spain
| | - F Santos
- Servicio de Cirugía General y del Aparato Digestivo, CHUS7SERGAS Santiago de Compostela, Rua R Baltar s/n, 15706, Santiago de Compostela, Spain
| | - J Fernø
- Hormone Laboratory, Department of Biochemistry and Pharmacology, Haukeland University Hospital, 5201, Bergen, Norway
| | - T García-Caballero
- Departamento de Ciencias Morfologicas, Facultad de Medicina, USC, Complejo Hospitalario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - R Nogueiras
- Departamento de Fisiología, Instituto de Investigación Sanitaria de Santiago de Compostela, CIMUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
- CIBER de Fisiopatología de la Obesidad y la Nutrición, Instituto de Salud Carlos III, Spain, Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - M Quiñones
- Grupo Fisiopatología Endocrina, Área de Endocrinología, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
- CIBER de Fisiopatología de la Obesidad y la Nutrición, Instituto de Salud Carlos III, Spain, Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - O Al-Massadi
- Translational Endocrinology Group, Endocrinology Section, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (IDIS/CHUS), Santiago de Compostela, Spain.
- CIBER de Fisiopatología de la Obesidad y la Nutrición, Instituto de Salud Carlos III, Spain, Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain.
| | - L M Seoane
- Grupo Fisiopatología Endocrina, Área de Endocrinología, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain.
- CIBER de Fisiopatología de la Obesidad y la Nutrición, Instituto de Salud Carlos III, Spain, Compostela, Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain.
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32
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Duggan MR, Walker KA. Organ-specific aging in the plasma proteome predicts disease. Trends Mol Med 2024; 30:423-424. [PMID: 38302317 PMCID: PMC11081809 DOI: 10.1016/j.molmed.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
In their recent Nature paper, Oh et al. use 4979 plasma proteins collected across multiple cohorts, publicly available gene expression data, and machine learning models to identify 11 organ-specific aging scores that are linked to organ-specific disease and mortality risk, including heart failure, cognitive decline, and Alzheimer's disease.
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Affiliation(s)
- Michael R Duggan
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Keenan A Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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33
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Sathyan S, Milman S, Ayers E, Gao T, Verghese J, Barzilai N. Plasma proteomic profile of abdominal obesity in older adults. Obesity (Silver Spring) 2024; 32:938-948. [PMID: 38439214 PMCID: PMC11039368 DOI: 10.1002/oby.24000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/30/2023] [Accepted: 01/07/2024] [Indexed: 03/06/2024]
Abstract
OBJECTIVE This study examines the plasma proteomic profile of abdominal obesity in older adults. METHODS The association of abdominal obesity (waist circumference [WC]) with 4265 plasma proteins identified using the SomaScan Assay was examined in 969 Ashkenazi Jewish participants (LonGenity cohort), aged 65 years and older (mean [SD] age 75.7 [6.7] years, 55.4% women), using regression models. Pathway analysis, as well as weighted correlation network analysis, was performed. WC was determined from the proteome using elastic net regression. RESULTS A total of 480 out of 4265 proteins were associated with WC in the linear regression model. Leptin (β [SE] = 12.363 [0.490]), inhibin β C chain (INHBC; β [SE] = 24.324 [1.448]), insulin-like growth factor-binding protein 2 (IGFBP-2; β [SE] = -12.782 [0.841]), heparan-sulfate 6-O-sulfotransferase 3 (H6ST3; β [SE] = -39.995 [2.729]), and matrix-remodeling-associated protein 8 (MXRA8; β [SE] = -27.101 [1.850]) were the top proteins associated with WC. Cell adhesion, extracellular matrix remodeling, and IGF transport pathways were the top enriched pathways associated with WC. WC signature determined from plasma proteins was highly correlated with measured WC (r = 0.80) and was associated with various metabolic and physical traits. CONCLUSIONS The study unveiled a multifaceted plasma proteomic profile of abdominal obesity in older adults, offering insights into its wide-ranging impact on the proteome. It also elucidated novel proteins, clusters of correlated proteins, and pathways that are intricately associated with abdominal obesity.
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Affiliation(s)
- Sanish Sathyan
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sofiya Milman
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Emmeline Ayers
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tina Gao
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joe Verghese
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nir Barzilai
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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34
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Nyárády BB, Kiss LZ, Bagyura Z, Merkely B, Dósa E, Láng O, Kőhidai L, Pállinger É. Growth and differentiation factor-15: A link between inflammaging and cardiovascular disease. Biomed Pharmacother 2024; 174:116475. [PMID: 38522236 DOI: 10.1016/j.biopha.2024.116475] [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: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
Age-related disorders are closely linked to the accumulation of senescent cells. The senescence-associated secretory phenotype (SASP) sustains and progresses chronic inflammation, which is involved in cellular and tissue dysfunction. SASP-related growth and differentiation factor-15 (GDF-15) is an immunoregulatory cytokine that is coupled to aging and thus may have a regulatory role in the development and maintenance of atherosclerosis, a major cause of cardiovascular disease (CVD). Although the effects of GDF-15 are tissue-specific and dependent on microenvironmental changes such as inflammation, available data suggest that GDF-15 has a significant role in CVD. Thus, GDF-15 is a promising biomarker and potential therapeutic target for atherosclerotic CVD.
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Affiliation(s)
- Balázs Bence Nyárády
- Heart and Vascular Center, Semmelweis University, Városmajor utca 68, Budapest H-1122, Hungary.
| | - Loretta Zsuzsa Kiss
- Heart and Vascular Center, Semmelweis University, Városmajor utca 68, Budapest H-1122, Hungary.
| | - Zsolt Bagyura
- Heart and Vascular Center, Semmelweis University, Városmajor utca 68, Budapest H-1122, Hungary.
| | - Béla Merkely
- Heart and Vascular Center, Semmelweis University, Városmajor utca 68, Budapest H-1122, Hungary.
| | - Edit Dósa
- Heart and Vascular Center, Semmelweis University, Városmajor utca 68, Budapest H-1122, Hungary.
| | - Orsolya Láng
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad tér 4, Budapest H-1089, Hungary.
| | - László Kőhidai
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad tér 4, Budapest H-1089, Hungary.
| | - Éva Pállinger
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad tér 4, Budapest H-1089, Hungary.
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35
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Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [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: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
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Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
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36
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Bi S, Jiang X, Ji Q, Wang Z, Ren J, Wang S, Yu Y, Wang R, Liu Z, Liu J, Hu J, Sun G, Wu Z, Diao Z, Li J, Sun L, Izpisua Belmonte JC, Zhang W, Liu GH, Qu J. The sirtuin-associated human senescence program converges on the activation of placenta-specific gene PAPPA. Dev Cell 2024; 59:991-1009.e12. [PMID: 38484732 DOI: 10.1016/j.devcel.2024.02.008] [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: 03/12/2023] [Revised: 09/15/2023] [Accepted: 02/20/2024] [Indexed: 04/25/2024]
Abstract
Sirtuins are pro-longevity genes with chromatin modulation potential, but how these properties are connected is not well understood. Here, we generated a panel of isogeneic human stem cell lines with SIRT1-SIRT7 knockouts and found that any sirtuin deficiency leads to accelerated cellular senescence. Through large-scale epigenomic analyses, we show how sirtuin deficiency alters genome organization and that genomic regions sensitive to sirtuin deficiency are preferentially enriched in active enhancers, thereby promoting interactions within topologically associated domains and the formation of de novo enhancer-promoter loops. In all sirtuin-deficient human stem cell lines, we found that chromatin contacts are rewired to promote aberrant activation of the placenta-specific gene PAPPA, which controls the pro-senescence effects associated with sirtuin deficiency and serves as a potential aging biomarker. Based on our survey of the 3D chromatin architecture, we established connections between sirtuins and potential target genes, thereby informing the development of strategies for aging interventions.
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Affiliation(s)
- Shijia Bi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zehua Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Science and Engineering, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Yang Yu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Ruoqi Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junhang Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianli Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zhiqing Diao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyi Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Liang Sun
- NHC Beijing Institute of Geriatrics, NHC Key Laboratory of Geriatrics, Institute of Geriatric Medicine of Chinese Academy of Medical Sciences, National Center of Gerontology/Beijing Hospital, Beijing 100730, China; Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | | | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Aging Biomarker Consortium, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Aging Biomarker Consortium, Beijing 100101, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Biomarker Consortium, Beijing 100101, China.
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37
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Reed ER, Chandler KB, Lopez P, Costello CE, Andersen SL, Perls TT, Li M, Bae H, Soerensen M, Monti S, Sebastiani P. Cross-platform proteomics signatures of extreme old age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588876. [PMID: 38645061 PMCID: PMC11030369 DOI: 10.1101/2024.04.10.588876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
In previous work we used a Somalogic platform targeting approximately 5000 proteins to generate a serum protein signature of centenarians that we validated in independent studies that used the same technology. We set here to validate and possibly expand the results by profiling the serum proteome of a subset of individuals included in the original study using liquid chromatography tandem mass spectrometry (LC-MS/MS). Following pre-processing, the LC-MS/MS data provided quantification of 398 proteins, with only 266 proteins shared by both platforms. At 1% FDR statistical significance threshold, the analysis of LC-MS/MS data detected 44 proteins associated with extreme old age, including 23 of the original analysis. To identify proteins for which associations between expression and extreme-old age were conserved across platforms, we performed inter-study conservation testing of the 266 proteins quantified by both platforms using a method that accounts for the correlation between the results. From these tests, a total of 80 proteins reached 5% FDR statistical significance, and 26 of these proteins had concordant pattern of gene expression in whole blood. This signature of 80 proteins points to blood coagulation, IGF signaling, extracellular matrix (ECM) organization, and complement cascade as important pathways whose protein level changes provide evidence for age-related adjustments that distinguish centenarians from younger individuals.
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Affiliation(s)
- Eric R Reed
- Data Intensive Study Center, Tufts University, Boston, MA, USA
| | - Kevin B Chandler
- Center for Biomedical Mass Spectrometry, Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Cellular and Molecular Medicine, Florida International University, Miami, FL, USA
| | - Prisma Lopez
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Stacy L Andersen
- Geriatric Section, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Thomas T Perls
- Geriatric Section, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Mengze Li
- Division of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Harold Bae
- Biostatistics Program, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Mette Soerensen
- Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Stefano Monti
- Division of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Paola Sebastiani
- Data Intensive Study Center, Tufts University, Boston, MA, USA
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA
- Department of Medicine, School of Medicine, Tufts University, Boston, MA, USA
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38
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Olecka M, van Bömmel A, Best L, Haase M, Foerste S, Riege K, Dost T, Flor S, Witte OW, Franzenburg S, Groth M, von Eyss B, Kaleta C, Frahm C, Hoffmann S. Nonlinear DNA methylation trajectories in aging male mice. Nat Commun 2024; 15:3074. [PMID: 38594255 PMCID: PMC11004021 DOI: 10.1038/s41467-024-47316-2] [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: 07/10/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024] Open
Abstract
Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigate the methylation trajectories of male mouse colon at five different time points of aging. Our study indicates the existence of sudden hypermethylation events at specific stages of life. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 months) and mid-to-late-life (15-24 months) transitions, separating the rodents' life into three stages. These nonlinear methylation dynamics predominantly affect genes associated with the nervous system and enrich in bivalently marked chromatin regions. Based on groups of nonlinearly modified loci, we construct a clock-like classifier STageR (STage of aging estimatoR) that accurately predicts murine epigenetic stage. We demonstrate the universality of our clock in an independent mouse cohort and with publicly available datasets.
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Affiliation(s)
- Maja Olecka
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Alena van Bömmel
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Madlen Haase
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Silke Foerste
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Konstantin Riege
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Stefano Flor
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Otto W Witte
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Marco Groth
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Björn von Eyss
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Christiane Frahm
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Steve Hoffmann
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
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39
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Neagu AN, Bruno P, Johnson KR, Ballestas G, Darie CC. Biological Basis of Breast Cancer-Related Disparities in Precision Oncology Era. Int J Mol Sci 2024; 25:4113. [PMID: 38612922 PMCID: PMC11012526 DOI: 10.3390/ijms25074113] [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: 03/03/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Precision oncology is based on deep knowledge of the molecular profile of tumors, allowing for more accurate and personalized therapy for specific groups of patients who are different in disease susceptibility as well as treatment response. Thus, onco-breastomics is able to discover novel biomarkers that have been found to have racial and ethnic differences, among other types of disparities such as chronological or biological age-, sex/gender- or environmental-related ones. Usually, evidence suggests that breast cancer (BC) disparities are due to ethnicity, aging rate, socioeconomic position, environmental or chemical exposures, psycho-social stressors, comorbidities, Western lifestyle, poverty and rurality, or organizational and health care system factors or access. The aim of this review was to deepen the understanding of BC-related disparities, mainly from a biomedical perspective, which includes genomic-based differences, disparities in breast tumor biology and developmental biology, differences in breast tumors' immune and metabolic landscapes, ecological factors involved in these disparities as well as microbiomics- and metagenomics-based disparities in BC. We can conclude that onco-breastomics, in principle, based on genomics, proteomics, epigenomics, hormonomics, metabolomics and exposomics data, is able to characterize the multiple biological processes and molecular pathways involved in BC disparities, clarifying the differences in incidence, mortality and treatment response for different groups of BC patients.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iași, Carol I bvd. 20A, 700505 Iasi, Romania
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Kaya R Johnson
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Gabriella Ballestas
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY 13699-5810, USA
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40
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Prattichizzo F, Frigé C, Pellegrini V, Scisciola L, Santoro A, Monti D, Rippo MR, Ivanchenko M, Olivieri F, Franceschi C. Organ-specific biological clocks: Ageotyping for personalized anti-aging medicine. Ageing Res Rev 2024; 96:102253. [PMID: 38447609 DOI: 10.1016/j.arr.2024.102253] [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: 12/12/2023] [Revised: 02/11/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Aging is a complex multidimensional, progressive remodeling process affecting multiple organ systems. While many studies have focused on studying aging across multiple organs, assessment of the contribution of individual organs to overall aging processes is a cutting-edge issue. An organ's biological age might influence the aging of other organs, revealing a multiorgan aging network. Recent data demonstrated a similar yet asynchronous inter-organs and inter-individuals progression of aging, thereby providing a foundation to track sources of declining health in old age. The integration of multiple omics with common clinical parameters through artificial intelligence has allowed the building of organ-specific aging clocks, which can predict the development of specific age-related diseases at high resolution. The peculiar individual aging-trajectory, referred to as ageotype, might provide a novel tool for a personalized anti-aging, preventive medicine. Here, we review data relative to biological aging clocks and omics-based data, suggesting different organ-specific aging rates. Additional research on longitudinal data, including young subjects and analyzing sex-related differences, should be encouraged to apply ageotyping analysis for preventive purposes in clinical practice.
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Affiliation(s)
| | | | | | - Lucia Scisciola
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Aurelia Santoro
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Daniela Monti
- Department of Experimental and Clinical, Biomedical Sciences "Mario Serio" University of Florence, Florence, Italy
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, and Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy; Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy.
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, and Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia
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41
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Schmidt S. Speeding Up Time: New Urinary Peptide Clock Associates Greater Air Pollution Exposures with Faster Biological Aging. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:44001. [PMID: 38568857 PMCID: PMC10990112 DOI: 10.1289/ehp14528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/26/2024] [Indexed: 04/05/2024]
Abstract
A study in Belgium supports earlier findings on associations between higher air pollution exposures and markers of faster biological aging, this time by using urinary peptide levels instead of DNA-based markers.
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42
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Morandini F, Rechsteiner C, Perez K, Praz V, Lopez Garcia G, Hinte LC, von Meyenn F, Ocampo A. ATAC-clock: An aging clock based on chromatin accessibility. GeroScience 2024; 46:1789-1806. [PMID: 37924441 PMCID: PMC10828344 DOI: 10.1007/s11357-023-00986-0] [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: 07/15/2023] [Accepted: 10/14/2023] [Indexed: 11/06/2023] Open
Abstract
The establishment of aging clocks highlighted the strong link between changes in DNA methylation and aging. Yet, it is not known if other epigenetic features could be used to predict age accurately. Furthermore, previous studies have observed a lack of effect of age-related changes in DNA methylation on gene expression, putting the interpretability of DNA methylation-based aging clocks into question. In this study, we explore the use of chromatin accessibility to construct aging clocks. We collected blood from 159 human donors and generated chromatin accessibility, transcriptomic, and cell composition data. We investigated how chromatin accessibility changes during aging and constructed a novel aging clock with a median absolute error of 5.27 years. The changes in chromatin accessibility used by the clock were strongly related to transcriptomic alterations, aiding clock interpretation. We additionally show that our chromatin accessibility clock performs significantly better than a transcriptomic clock trained on matched samples. In conclusion, we demonstrate that the clock relies on cell-intrinsic chromatin accessibility alterations rather than changes in cell composition. Further, we present a new approach to construct epigenetic aging clocks based on chromatin accessibility, which bear a direct link to age-related transcriptional alterations, but which allow for more accurate age predictions than transcriptomic clocks.
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Affiliation(s)
- Francesco Morandini
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Cheyenne Rechsteiner
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Kevin Perez
- EPITERNA SA, Route de la Corniche 5, Epalinges, Switzerland
| | - Viviane Praz
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Guillermo Lopez Garcia
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
- Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga, Málaga, Spain
| | - Laura C Hinte
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | | | - Alejandro Ocampo
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland.
- EPITERNA SA, Route de la Corniche 5, Epalinges, Switzerland.
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43
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Dohm-Hansen S, English JA, Lavelle A, Fitzsimons CP, Lucassen PJ, Nolan YM. The 'middle-aging' brain. Trends Neurosci 2024; 47:259-272. [PMID: 38508906 DOI: 10.1016/j.tins.2024.02.001] [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: 10/16/2023] [Revised: 01/09/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024]
Abstract
Middle age has historically been an understudied period of life compared to older age, when cognitive and brain health decline are most pronounced, but the scope for intervention may be limited. However, recent research suggests that middle age could mark a shift in brain aging. We review emerging evidence on multiple levels of analysis indicating that midlife is a period defined by unique central and peripheral processes that shape future cognitive trajectories and brain health. Informed by recent developments in aging research and lifespan studies in humans and animal models, we highlight the utility of modeling non-linear changes in study samples with wide subject age ranges to distinguish life stage-specific processes from those acting linearly throughout the lifespan.
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Affiliation(s)
- Sebastian Dohm-Hansen
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; INFANT Research Centre, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jane A English
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; INFANT Research Centre, University College Cork, Cork, Ireland
| | - Aonghus Lavelle
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Carlos P Fitzsimons
- Swammerdam Institute for Life Sciences, Brain Plasticity Group, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul J Lucassen
- Swammerdam Institute for Life Sciences, Brain Plasticity Group, University of Amsterdam, Amsterdam, The Netherlands
| | - Yvonne M Nolan
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
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44
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Meng D, Zhang S, Huang Y, Mao K, Han JDJ. Application of AI in biological age prediction. Curr Opin Struct Biol 2024; 85:102777. [PMID: 38310737 DOI: 10.1016/j.sbi.2024.102777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/12/2023] [Accepted: 01/15/2024] [Indexed: 02/06/2024]
Abstract
The development of anti-aging interventions requires quantitative measurement of biological age. Machine learning models, known as "aging clocks," are built by leveraging diverse aging biomarkers that vary across lifespan to predict biological age. In addition to traditional aging clocks harnessing epigenetic signatures derived from bulk samples, emerging technologies allow the biological age estimating at single-cell level to dissect cellular diversity in aging tissues. Moreover, imaging-based aging clocks are increasingly employed with the advantage of non-invasive measurement, making it suitable for large-scale human cohort studies. To fully capture the features in the ever-growing multi-modal and high-dimensional aging-related data and uncover disease associations, deep-learning based approaches, which are effective to learn complex and non-linear relationships without relying on pre-defined features, are increasingly applied. The use of big data and AI-based aging clocks has achieved high accuracy, interpretability and generalizability, guiding clinical applications to delay age-related diseases and extend healthy lifespans.
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Affiliation(s)
- Dawei Meng
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Yuanfang Huang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Kehang Mao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China.
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45
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Sarver DC, Saqib M, Chen F, Wong GW. Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586781. [PMID: 38586038 PMCID: PMC10996676 DOI: 10.1101/2024.03.26.586781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Organ function declines with age, and large-scale transcriptomic analyses have highlighted differential aging trajectories across tissues. The mechanisms underlying shared and organ-selective functional changes across the lifespan, however, still remains poorly understood. Given the central role of mitochondria in powering cellular processes needed to maintain tissue health, we therefore undertook a systematic assessment of respiratory activity across 33 different tissues in young (2.5 months) and old (20 months) mice of both sexes. Our high-resolution mitochondrial respiration atlas reveals: 1) within any group of mice, mitochondrial activity varies widely across tissues, with the highest values consistently seen in heart, brown fat, and kidney; 2) biological sex is a significant but minor contributor to mitochondrial respiration, and its contributions are tissue-specific, with major differences seen in the pancreas, stomach, and white adipose tissue; 3) age is a dominant factor affecting mitochondrial activity, especially across different fat depots and skeletal muscle groups, and most brain regions; 4) age-effects can be sex- and tissue-specific, with some of the largest effects seen in pancreas, heart, adipose tissue, and skeletal muscle; and 5) while aging alters the functional trajectories of mitochondria in a majority of tissues, some are remarkably resilient to age-induced changes. Altogether, our data provide the most comprehensive compendium of mitochondrial respiration and illuminate functional signatures of aging across diverse tissues and organ systems.
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Affiliation(s)
- Dylan C. Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore
| | - Muzna Saqib
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore
| | - Fangluo Chen
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore
| | - G. William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore
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46
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Wang Y, Chen X, Song C, Wu Y, Liu L, Yang L, Hao X. A qualitative internet-based study of parental experiences of adolescents suffering from affective disorders with non-suicidal self-injury during the COVID-19 pandemic. Front Psychiatry 2024; 15:1361144. [PMID: 38596632 PMCID: PMC11002897 DOI: 10.3389/fpsyt.2024.1361144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
Objective Non-suicidal self-injury (NSSI) behaviors of adolescents with affective disorders can directly deteriorate parents' internal experiences, and negative parental experiences can exacerbate or even worsen NSSI behaviors. This study investigates the impact of NSSI behaviors exhibited by adolescents with affective disorders on the internal experiences of parents. Specifically, our research focuses on the inner experiences of parents when their children engage in NSSI behaviors during social isolation of the COVID-19, offering insights for addressing parental mental health issues related to NSSI and developing positive parental behavioral models to optimize adolescent behavior during major public health events. Methods Semi-structured interviews were conducted with 21 parents of adolescents with affective disorders displaying NSSI behaviors during the COVID-19 pandemic. The Colaizzi 7-step analysis was employed to refine and categorize emerging themes. Results Our study revealed that parents of adolescents facing NSSI during the COVID-19 pandemic underwent different internal experiences, which could be classified into four themes: negative experience, high caregiving burden, lack of caregiving capacity, and resilience. Conclusion This Internet-based research is the first to explore the internal experiences of parents of adolescents with affective disorders experiencing NSSI during the COVID-19 pandemic. It sheds light on how parents, in response to their children's NSSI behaviors, undergo resilience following negative experiences, explore more open and supportive family model. Despite these positive outcomes, parents express a need for increased knowledge about NSSI illness care and a desire for professional assistance.
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Affiliation(s)
- Yongna Wang
- Beijing Hui-Long-Guan Hospital, Peking University, Beijing, China
| | - Xueqiu Chen
- Beijing Hui-Long-Guan Hospital, Peking University, Beijing, China
| | - Chun Song
- Xinjiang Key Laboratory of Neurological Disorder Research, The Second Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yan Wu
- Beijing Hui-Long-Guan Hospital, Peking University, Beijing, China
| | - Lihua Liu
- Beijing Hui-Long-Guan Hospital, Peking University, Beijing, China
| | - Lili Yang
- Beijing Hui-Long-Guan Hospital, Peking University, Beijing, China
| | - Xuege Hao
- Beijing Hui-Long-Guan Hospital, Peking University, Beijing, China
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47
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Ryu HE, Jung DH, Heo SJ, Park B, Lee YJ. METS-IR and all-cause mortality in Korean over 60 years old: Korean genome and epidemiology study-health examinees (KoGES-HEXA) cohorts. Front Endocrinol (Lausanne) 2024; 15:1346158. [PMID: 38572476 PMCID: PMC10987815 DOI: 10.3389/fendo.2024.1346158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/19/2024] [Indexed: 04/05/2024] Open
Abstract
Background The metabolic score for insulin resistance index (METS-IR) is a novel non insulin-based marker that indicates the risk for metabolic syndrome and type 2 diabetes mellitus (T2DM). However, METS-IR has not been investigated in relation to all-cause mortality. We investigated the longitudinal effect of METS-IR on all-cause mortality in a significantly large cohort of Korean adults over 60 years old. Methods Data were assessed from 30,164 Korean participants over 60 years of age from the Korean Genome and Epidemiology Study-Health Examinees (KoGES-HEXA) cohort data, linked with the death certificate database of the National Statistical Office. The participants were grouped into three according to METS-IR tertiles. We used multivariate Cox proportional-hazard regression models to prospectively assess hazard ratios (HRs) for all-cause mortality with 95% confidence intervals (CIs) over an 11-year postbaseline period. Results During the mean 11.7 years of follow-up, 2,821 individuals expired. The HRs of mortality for METS-IR tertiles were 1.16 (95% CI, 1.01-1.34) in T3 after adjustment for metabolic parameters, but the T2 did not show statistical significance towards increases for incident mortality respectively. In subgroup analysis depending on the cause of mortality, higher METS-IR was associated with cancer mortality (HR, 1.23, 95% CI, 1.01-1.51) but not with cardiovascular mortality (HR, 1.14, 95% CI, 0.83-1.57) after adjustment for the same confounding variables. Conclusion The METS-IR may be a useful predictive marker for all-cause mortality and cancer mortality, but not for cardiovascular mortality in subjects over 60 years of age. This implies that early detection and intervention strategies for metabolic syndrome could potentially benefit this identified group.
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Affiliation(s)
- Ha Eun Ryu
- Department of Family Medicine, Yongin Severance Hospital, Yongin-si, Republic of Korea
- Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dong Hyuk Jung
- Department of Family Medicine, Yongin Severance Hospital, Yongin-si, Republic of Korea
- Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seok-Jae Heo
- Division of Biostatistics, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Byoungjin Park
- Department of Family Medicine, Yongin Severance Hospital, Yongin-si, Republic of Korea
- Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yong Jae Lee
- Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Family Medicine, Gangnam Severance Hospital, Seoul, Republic of Korea
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48
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Kjerulff B, Dowsett J, Jacobsen RL, Gladov J, Larsen MH, Lundgaard AT, Banasik K, Westergaard D, Mikkelsen S, Dinh KM, Hindhede L, Kaspersen KA, Schwinn M, Juul A, Poulsen B, Lindegaard B, Pedersen CB, Sabel CE, Bundgaard H, Nielsen HS, Møller JA, Boldsen JK, Burgdorf KS, Kessing LV, Handgaard LJ, Thørner LW, Didriksen M, Nyegaard M, Grarup N, Ødum N, Johansson PI, Jennum P, Frikke-Schmidt R, Berger SS, Brunak S, Jacobsen S, Hansen TF, Lundquist TK, Hansen T, Sørensen TL, Sigsgaard T, Nielsen KR, Bruun MT, Hjalgrim H, Ullum H, Rostgaard K, Sørensen E, Pedersen OB, Ostrowski SR, Erikstrup C. Lifestyle and demographic associations with 47 inflammatory and vascular stress biomarkers in 9876 blood donors. COMMUNICATIONS MEDICINE 2024; 4:50. [PMID: 38493237 PMCID: PMC10944541 DOI: 10.1038/s43856-024-00474-2] [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: 03/31/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The emerging use of biomarkers in research and tailored care introduces a need for information about the association between biomarkers and basic demographics and lifestyle factors revealing expectable concentrations in healthy individuals while considering general demographic differences. METHODS A selection of 47 biomarkers, including markers of inflammation and vascular stress, were measured in plasma samples from 9876 Danish Blood Donor Study participants. Using regression models, we examined the association between biomarkers and sex, age, Body Mass Index (BMI), and smoking. RESULTS Here we show that concentrations of inflammation and vascular stress biomarkers generally increase with higher age, BMI, and smoking. Sex-specific effects are observed for multiple biomarkers. CONCLUSION This study provides comprehensive information on concentrations of 47 plasma biomarkers in healthy individuals. The study emphasizes that knowledge about biomarker concentrations in healthy individuals is critical for improved understanding of disease pathology and for tailored care and decision support tools.
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Affiliation(s)
- Bertram Kjerulff
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- BERTHA Big Data Centre for Environment and Health, Aarhus University, Aarhus, Denmark.
| | - Joseph Dowsett
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Josephine Gladov
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- BERTHA Big Data Centre for Environment and Health, Aarhus University, Aarhus, Denmark
| | - Margit Hørup Larsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Agnete Troen Lundgaard
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karina Banasik
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Westergaard
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Susan Mikkelsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Khoa Manh Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Lotte Hindhede
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Kathrine Agergård Kaspersen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- BERTHA Big Data Centre for Environment and Health, Aarhus University, Aarhus, Denmark
| | - Michael Schwinn
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Anders Juul
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Betina Poulsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Birgitte Lindegaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Pulmonary and Infectious Diseases, Copenhagen University Hospital-North Zealand, Hillerød, Denmark
| | - Carsten Bøcker Pedersen
- BERTHA Big Data Centre for Environment and Health, Aarhus University, Aarhus, Denmark
- National Centre for Register-based Research, Aarhus BSS, Aarhus University, Aarhus, Denmark
| | - Clive Eric Sabel
- BERTHA Big Data Centre for Environment and Health, Aarhus University, Aarhus, Denmark
- Department of Public Health, Aarhus University, DK-8000, Aarhus, Denmark
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Henning Bundgaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Heart Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Recurrent Pregnancy Loss Unit, Capital Region, Copenhagen University Hospitals, Hvidovre and Rigshospitalet, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Janne Amstrup Møller
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Jens Kjærgaard Boldsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- BERTHA Big Data Centre for Environment and Health, Aarhus University, Aarhus, Denmark
| | - Kristoffer Sølvsten Burgdorf
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Vedel Kessing
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Affective Disorder Research Center (CADIC), Psychiatric Center Copenhagen, Copenhagen, Denmark
| | - Linda Jenny Handgaard
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Lise Wegner Thørner
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Ødum
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Pär I Johansson
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Poul Jennum
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Center for Sleep Medicine, Department of Clinical Neurophysiology, Rigshospitalet, Copenhagen, Denmark
| | - Ruth Frikke-Schmidt
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Sanne Schou Berger
- Centre for Diagnostics, DTU Health Technology, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Søren Brunak
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Jacobsen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Lupus and Vasculitis Clinic, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Headache Center and Danish Multiple Sclerosis Center, Copenhagen University Hospital, Rigshospitalet Glostrup, Glostrup, Denmark
| | - Tine Kirkeskov Lundquist
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Lykke Sørensen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical Eye Research Division, Department of Ophthalmology, Zealand University, Hospital, Roskilde, Denmark
| | - Torben Sigsgaard
- BERTHA Big Data Centre for Environment and Health, Aarhus University, Aarhus, Denmark
- Department of Public Health, Aarhus University, DK-8000, Aarhus, Denmark
| | - Kaspar René Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
- Department of Hematology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Klaus Rostgaard
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- BERTHA Big Data Centre for Environment and Health, Aarhus University, Aarhus, Denmark
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49
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Blanc RS, Shah N, Salama NAS, Meng FW, Mousaei A, Yang BA, Aguilar CA, Chakkalakal JV, Onukwufor JO, Murphy PJ, Calvi L, Dirksen R. Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis. RESEARCH SQUARE 2024:rs.3.rs-3937628. [PMID: 38410478 PMCID: PMC10896381 DOI: 10.21203/rs.3.rs-3937628/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Aging is associated with a decline in stem cell functionality and number across the organism. In this study, we aimed to further unravel Muscle Stem Cells (MuSCs) aging by assessing how systemic factors influence MuSC fate decisions through long-term epigenetic landscape remodelling. As aging is intricately linked to a pro-inflammatory shift, we studied the epigenetic effects of inflammatory signals in MuSCs and measured decreased H4K20me1 levels. This loss disrupts MuSC quiescence, largely through epigenetic silencing of Notch target genes. In the setting of inflammatory signals or aging, the lack of Kmt5a and the subsequent absence of de novoH4K20me1 culminate in cell death by ferroptosis. Aged MuSCs manifest abnormal iron metabolism and reduced Gpx4 levels, resulting in the accumulation of intracellular iron, increased reactive oxygen species, genomic instability, and lipid peroxidation. We showed that ferroptosis is the predominant mode of cell death in aged MuSCs, with remarkably high levels of lipid peroxidation; a phenomenon we also observed in aged hematopoietic stem cells. Implementing preventative strategies to inhibit systemic inflammation prevented aged MuSC ferroptosis, preserving their numbers and regenerative capabilities. This intervention significantly enhanced aged muscle regeneration and strength recovery and extended both lifespan and healthspan in mice. This study delineates a previously underappreciated fate trajectory for stem cell aging, and offers meaningful insights into the treatment of age-related disorders.
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50
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Rutledge J, Lehallier B, Zarifkar P, Losada PM, Shahid-Besanti M, Western D, Gorijala P, Ryman S, Yutsis M, Deutsch GK, Mormino E, Trelle A, Wagner AD, Kerchner GA, Tian L, Cruchaga C, Henderson VW, Montine TJ, Borghammer P, Wyss-Coray T, Poston KL. Comprehensive proteomics of CSF, plasma, and urine identify DDC and other biomarkers of early Parkinson's disease. Acta Neuropathol 2024; 147:52. [PMID: 38467937 PMCID: PMC10927779 DOI: 10.1007/s00401-024-02706-0] [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: 01/18/2024] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024]
Abstract
Parkinson's disease (PD) starts at the molecular and cellular level long before motor symptoms appear, yet there are no early-stage molecular biomarkers for diagnosis, prognosis prediction, or monitoring therapeutic response. This lack of biomarkers greatly impedes patient care and translational research-L-DOPA remains the standard of care more than 50 years after its introduction. Here, we performed a large-scale, multi-tissue, and multi-platform proteomics study to identify new biomarkers for early diagnosis and disease monitoring in PD. We analyzed 4877 cerebrospinal fluid, blood plasma, and urine samples from participants across seven cohorts using three orthogonal proteomics methods: Olink proximity extension assay, SomaScan aptamer precipitation assay, and liquid chromatography-mass spectrometry proteomics. We discovered that hundreds of proteins were upregulated in the CSF, blood, or urine of PD patients, prodromal PD patients with DAT deficit and REM sleep behavior disorder or anosmia, and non-manifesting genetic carriers of LRRK2 and GBA mutations. We nominate multiple novel hits across our analyses as promising markers of early PD, including DOPA decarboxylase (DDC), also known as L-aromatic acid decarboxylase (AADC), sulfatase-modifying factor 1 (SUMF1), dipeptidyl peptidase 2/7 (DPP7), glutamyl aminopeptidase (ENPEP), WAP four-disulfide core domain 2 (WFDC2), and others. DDC, which catalyzes the final step in dopamine synthesis, particularly stands out as a novel hit with a compelling mechanistic link to PD pathogenesis. DDC is consistently upregulated in the CSF and urine of treatment-naïve PD, prodromal PD, and GBA or LRRK2 carrier participants by all three proteomics methods. We show that CSF DDC levels correlate with clinical symptom severity in treatment-naïve PD patients and can be used to accurately diagnose PD and prodromal PD. This suggests that urine and CSF DDC could be a promising diagnostic and prognostic marker with utility in both clinical care and translational research.
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Affiliation(s)
- Jarod Rutledge
- Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Pardis Zarifkar
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Clinical Epidemiology, Aarhus University, Aarhus, Denmark
| | - Patricia Moran Losada
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Marian Shahid-Besanti
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Dan Western
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Sephira Ryman
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Translational Neuroscience, Mind Research Network, Albuquerque, NM, USA
| | - Maya Yutsis
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Gayle K Deutsch
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Elizabeth Mormino
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Alexandra Trelle
- Department of Psychology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Anthony D Wagner
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Psychology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Geoffrey A Kerchner
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Roche Medical, Basel, Switzerland
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University School of Humanities and Sciences, Stanford University, Stanford, CA, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Victor W Henderson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Per Borghammer
- Department of Nuclear Medicine and PET, Aarhus University Hospital, Aarhus, Denmark
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA.
- The Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
| | - Kathleen L Poston
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA.
- The Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
- Department of Neurosurgery, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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