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Li J, Zhang Y, You Y, Huang Z, Wu L, Liang C, Weng B, Pan L, Huang Y, Huang Y, Yang M, Lu M, Li R, Yan X, Liu Q, Deng S. Unraveling the mechanisms of NK cell dysfunction in aging and Alzheimer's disease: insights from GWAS and single-cell transcriptomics. Front Immunol 2024; 15:1360687. [PMID: 38464521 PMCID: PMC10920339 DOI: 10.3389/fimmu.2024.1360687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/06/2024] [Indexed: 03/12/2024] Open
Abstract
Background Aging is an important factor in the development of Alzheimer's disease (AD). The senescent cells can be recognized and removed by NK cells. However, NK cell function is gradually inactivated with age. Therefore, this study used senescence as an entry point to investigate how NK cells affect AD. Methods The study validated the correlation between cognition and aging through a prospective cohort of the National Health and Nutrition Examination Survey database. A cellular trajectory analysis of the aging population was performed using single-cell nuclear transcriptome sequencing data from patients with AD and different ages. The genome-wide association study (GWAS) cohort of AD patients was used as the outcome event, and the expression quantitative trait locus was used as an instrumental variable. Causal associations between genes and AD were analyzed by bidirectional Mendelian randomization (MR) and co-localization. Finally, clinical cohorts were constructed to validate the expression of key genes. Results A correlation between cognition and aging was demonstrated using 2,171 older adults over 60 years of age. Gene regulation analysis revealed that most of the highly active transcription factors were concentrated in the NK cell subpopulation of AD. NK cell trajectories were constructed for different age populations. MR and co-localization analyses revealed that CHD6 may be one of the factors influencing AD. Conclusion We explored different levels of AD and aging from population cohorts, single-cell data, and GWAS cohorts and found that there may be some correlations of NK cells between aging and AD. It also provides some basis for potential causation.
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Affiliation(s)
- Jinwei Li
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, China
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yang Zhang
- Department of Vascular Surgery, Fuwai Yunnan Cardiovascular Hospital, Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yanwei You
- Division of Sports Science and Physical Education, Tsinghua University, Beijing, China
| | - Zhiwei Huang
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, China
| | - Liya Wu
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Cong Liang
- Department of Pharmacy, Liuzhou Workers Hospital, Liuzhou, China
| | - Baohui Weng
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Liya Pan
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Yan Huang
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Yushen Huang
- Department of Pharmacy, Liuzhou Workers Hospital, Liuzhou, China
| | - Mengqi Yang
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
| | - Mengting Lu
- Department of Dermatology, Liuzhou Workers Hospital, Liuzhou, China
| | - Rui Li
- Department of Medical Imaging, Liuzhou Workers Hospital, Liuzhou, China
| | - Xianlei Yan
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, China
| | - Quan Liu
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, China
| | - Shan Deng
- Department of Neurology, Liuzhou Workers Hospital, Liuzhou, China
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2
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Nehar-Belaid D, Sokolowski M, Ravichandran S, Banchereau J, Chaussabel D, Ucar D. Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS. Semin Immunol 2023; 70:101842. [PMID: 37717525 DOI: 10.1016/j.smim.2023.101842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In fact, while some recipients mount a robust response to vaccination that protects them from the disease, others fail to respond. Multiple clinical and epidemiological factors contribute to this heterogeneity in responsiveness. Systems immunology studies fueled by advances in single-cell biology have been instrumental in uncovering pre-vaccination immune cell types and genomic features (i.e., the baseline immune state, BIS) that have been associated with vaccine responsiveness. Here, we review clinical factors that shape the BIS, and the characteristics of the BIS associated with responsiveness to frequently studied vaccines (i.e., influenza, COVID-19, bacterial pneumonia, malaria). Finally, we discuss potential strategies to enhance vaccine responsiveness in high-risk groups, focusing specifically on older adults.
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Affiliation(s)
| | - Mark Sokolowski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | | | - Damien Chaussabel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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3
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Kübler R, Ormel PR, Sommer IEC, Kahn RS, de Witte LD. Gene expression profiling of monocytes in recent-onset schizophrenia. Brain Behav Immun 2023; 111:334-342. [PMID: 37149105 DOI: 10.1016/j.bbi.2023.04.019] [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: 08/04/2022] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023] Open
Abstract
Immune-related mechanisms have been suggested to be involved in schizophrenia. Various studies have shown changes in monocytes isolated from the blood of schizophrenia patients, including changes in monocyte numbers, as well as altered protein and transcript levels of important markers. However, validation of these findings and understanding how these results are related to immune-related changes in the brain and schizophrenia genetic risk factors, is limited. The goal of this study was to better understand changes observed in monocytes of patients with early-onset schizophrenia. Using RNA sequencing, we analyzed gene expression profiles of monocytes isolated from twenty patients with early-onset schizophrenia and seventeen healthy controls. We validated expression changes of 7 out of 29 genes that were differentially expressed in previous studies including TNFAIP3, DUSP2, and IL6. At a transcriptome-wide level, we found 99 differentially expressed genes. Effect sizes of differentially expressed genes were moderately correlated with differential expression in brain tissue (Pearson's r = 0.49). Upregulated genes were enriched for genes in NF-κB and LPS signaling pathways. Downregulated genes were enriched for glucocorticoid response pathways. These pathways have been implicated in schizophrenia before and play a role in regulating the activation of myeloid cells. Interestingly, they are also involved in several non-inflammatory processes in the central nervous system, such as neurogenesis and neurotransmission. Future studies are needed to better understand how dysregulation of the NF-κB and glucocorticoid pathways affects inflammatory and non-inflammatory processes in schizophrenia. The fact that dysregulation of these pathways is also seen in brain tissue, provides potential possibilities for biomarker development.
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Affiliation(s)
- Raphael Kübler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul R Ormel
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Iris E C Sommer
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; Department of Neuroscience, University Medical Center Groningen, Groningen, the Netherlands
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands.
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4
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Ding J, Lohman K, Molina A, Delbono O, Bertoni A, Shea S, Post W, Guo X, Barr RG, Manichaikul AW, Pankow JS, Rotter JI, Hoeschele I, Kritchevsky SB, Liu Y. The association between aging-related monocyte transcriptional networks and comorbidity burden: the Multi-Ethnic Study of Atherosclerosis (MESA). GeroScience 2023; 45:197-207. [PMID: 35737188 PMCID: PMC9886705 DOI: 10.1007/s11357-022-00608-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/16/2022] [Indexed: 02/03/2023] Open
Abstract
Translating our knowledge of the biological aging from animal models to humans may give rise to novel approaches of targeting multiple aging-related diseases simultaneously and increasing health span. Here, for the first time, we use transcriptomic signatures of monocytes to identify biological aging pathways underlying multiple aging-related diseases in humans. The ordinal logistic regression was used to cross-sectionally investigate transcriptomics of the comorbidity index in 1264 community-based Multi-Ethnic Study of Atherosclerosis (MESA) adults, 47% Caucasian, 32% Hispanic, 21% African American, and 51% female, aged 55-94 years. The comorbidity index was defined as the number of prevalent aging-related diseases including cardiovascular disease, type-2 diabetes, hypertension, cancer, dementia, chronic kidney disease, chronic obstructive pulmonary disease, and hip fracture. We identified 708 gene transcripts associated with the comorbidity index (FDR < 0.05) after adjusting for age, sex, ethnicity, and study site. In a weighted gene co-expression network analysis, as postulated, aging-related declines in apoptosis/autophagy (OR = 1.21 per SD increment, p = 0.0006) and ribosome/mitochondrion (OR = 0.90 per SD increment, p = 0.05) were positively associated with the comorbidity index. After adjusting for multiple comparisons, we identified 10 comorbidity-associated modules (FDR < 0.05), including the module of apoptosis/autophagy. There were three inter-correlated modules of these 10 involved in the complement subcomponent C1q, Fc gamma receptor I, and Fc gamma receptor III of the immune system, respectively. Aging-related upregulation of these three modules was positively associated with the comorbidity index. The odds of comorbidity increased with more of these modules acting together in a dose-response fashion. In conclusion, transcriptomic analysis of human immune cells may identify biomarker panels indicative of comprehensive biological mechanisms, especially immune signaling pathways, contributing to health aging.
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Affiliation(s)
- Jingzhong Ding
- Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, USA.
| | - Kurt Lohman
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27701, USA
| | - Anthony Molina
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Osvaldo Delbono
- Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, USA
| | - Alain Bertoni
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Steven Shea
- Departments of Medicine and Epidemiology, Columbia University, New York, NY, 10032, USA
| | - Wendy Post
- Departments of Pathology and Cardiology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - R Graham Barr
- Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - James S Pankow
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Ina Hoeschele
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Stephen B Kritchevsky
- Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27701, USA
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5
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Teo YV, Hinthorn SJ, Webb AE, Neretti N. Single-cell transcriptomics of peripheral blood in the aging mouse. Aging (Albany NY) 2023; 15:6-20. [PMID: 36622281 PMCID: PMC9876630 DOI: 10.18632/aging.204471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023]
Abstract
Compositional and transcriptional changes in the hematopoietic system have been used as biomarkers of immunosenescence and aging. Here, we use single-cell RNA-sequencing to study the aging peripheral blood in mice and characterize the changes in cell-type composition and transcriptional profiles associated with age. We identified 17 clusters from a total of 14,588 single cells. We detected a general upregulation of antigen processing and presentation and chemokine signaling pathways and a downregulation of genes involved in ribosome pathways with age. In old peripheral blood, we also observed an increased percentage of cells expressing senescence markers (Cdkn1a, and Cdkn2a). In addition, we detected a cluster of activated T cells exclusively found in old blood, with lower expression of Cd28 and higher expression of Bcl2 and Cdkn2a, suggesting that the cells are senescent and resistant to apoptosis.
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Affiliation(s)
- Yee Voan Teo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Samuel J. Hinthorn
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Ashley E. Webb
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
- Center on the Biology of Aging, Brown University, Providence, RI 02903, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Center on the Biology of Aging, Brown University, Providence, RI 02903, USA
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6
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Singh B, Kumar Rai A. Loss of immune regulation in aged T-cells: A metabolic review to show lack of ability to control responses within the self. Hum Immunol 2022; 83:808-817. [DOI: 10.1016/j.humimm.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/19/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
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7
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Parker DC, Wan M, Lohman K, Hou L, Nguyen AT, Ding J, Bertoni A, Shea S, Burke GL, Jacobs DR, Post W, Corcoran D, Hoeschele I, Parks JS, Liu Y. Monocyte miRNAs Are Associated With Type 2 Diabetes. Diabetes 2022; 71:853-861. [PMID: 35073575 PMCID: PMC8965663 DOI: 10.2337/db21-0704] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022]
Abstract
miRNAs are small noncoding RNAs that may contribute to common diseases through epigenetic regulation of gene expression. Little is known regarding the role of miRNAs in type 2 diabetes (T2D). We performed miRNA sequencing and transcriptomic profiling of peripheral monocytes from the longitudinal Multi-Ethnic Study of Atherosclerosis (MESA) (N = 1,154). We examined associations between miRNAs and prevalent impaired fasting glucose and T2D and evaluated the T2D-associated miRNA effect on incident T2D. Of 774 detected miRNAs, 6 (miR-22-3p, miR-33a-5p, miR-181c-5p, miR-92b-3p, miR-222-3p, and miR-944) were associated with prevalent T2D. For five of the six miRNAs (all but miR-222-3p), our findings suggest a dose-response relationship with impaired fasting glucose and T2D. Two of the six miRNAs were associated with incident T2D (miR-92b-3p: hazard ratio [HR] 1.64, P = 1.30E-03; miR-222-3p: HR 1.97, P = 9.10E-03) in the highest versus lowest tertile of expression. Most of the T2D-associated miRNAs were also associated with HDL cholesterol concentrations. The genes targeted by these miRNAs belong to key nodes of a cholesterol metabolism transcriptomic network. Higher levels of miRNA expression expected to increase intracellular cholesterol accumulation in monocytes are linked to an increase in T2D risk.
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Affiliation(s)
- Daniel C. Parker
- Division of Geriatrics, Department of Medicine, Duke University School of Medicine, Durham, NC
- Duke University Center for the Study of Aging and Human Development, Durham, NC
| | - Ma Wan
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
| | - Kurt Lohman
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
| | - Li Hou
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
| | - Anh Tram Nguyen
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
| | - Jingzhong Ding
- Wake Forest University School of Medicine, Winston-Salem, NC
| | - Alain Bertoni
- Wake Forest University School of Medicine, Winston-Salem, NC
| | - Steve Shea
- Columbia University School of Medicine, New York, NY
| | | | - David R. Jacobs
- University of Minnesota School of Public Health, Minneapolis, MN
| | - Wendy Post
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - David Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC
| | - Ina Hoeschele
- Department of Statistics and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA
| | - John S. Parks
- Wake Forest University School of Medicine, Winston-Salem, NC
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC
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8
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Luo OJ, Lei W, Zhu G, Ren Z, Xu Y, Xiao C, Zhang H, Cai J, Luo Z, Gao L, Su J, Tang L, Guo W, Su H, Zhang ZJ, Fang EF, Ruan Y, Leng SX, Ju Z, Lou H, Gao J, Peng N, Chen J, Bao Z, Liu F, Chen G. Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty. NATURE AGING 2022; 2:348-364. [PMID: 37117750 DOI: 10.1038/s43587-022-00198-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 02/25/2022] [Indexed: 12/15/2022]
Abstract
Frailty is an intermediate status of the human aging process, associated with decompensated homeostasis and death. The immune phenotype of frailty and its underlying cellular and molecular processes remain poorly understood. We profiled 114,467 immune cells from cord blood, young adults and healthy and frail old adults using single-cell RNA and TCR sequencing. Here we show an age-dependent accumulation of transcriptome heterogeneity and variability in immune cells. Characteristic transcription factors were identified in given cell types of specific age groups. Trajectory analysis revealed cells from non-frail and frail old adults often fall into distinct paths. Numerous TCR clonotypes were shared among T-cell subtypes in old adults, indicating differential pluripotency and resilience capabilities of aged T cells. A frailty-specific monocyte subset was identified with exclusively high expression of long noncoding RNAs NEAT1 and MALAT1. Our study discovers human frailty-specific immune cell characteristics based on the comprehensive dimensions in the immune landscape of aging and frailty.
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Abstract
Ageing leads to profound alterations in the immune system and increases susceptibility to some chronic, infectious and autoimmune diseases. In recent years, widespread application of single-cell techniques has enabled substantial progress in our understanding of the ageing immune system. These comprehensive approaches have expanded and detailed the current views of ageing and immunity. Here we review a body of recent studies that explored how the immune system ages using unbiased profiling techniques at single-cell resolution. Specifically, we discuss an emergent understanding of age-related alterations in innate and adaptive immune cell populations, antigen receptor repertoires and immune cell-supporting microenvironments of the peripheral tissues. Focusing on the results obtained in mice and humans, we describe the multidimensional data that align with established concepts of immune ageing as well as novel insights emerging from these studies. We further discuss outstanding questions in the field and highlight techniques that will advance our understanding of immune ageing in the future.
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Affiliation(s)
- Denis A. Mogilenko
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO USA
| | - Irina Shchukina
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO USA
| | - Maxim N. Artyomov
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO USA
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Evaluation of an RNAseq-Based Immunogenomic Liquid Biopsy Approach in Early-Stage Prostate Cancer. Cells 2021; 10:cells10102567. [PMID: 34685549 PMCID: PMC8533765 DOI: 10.3390/cells10102567] [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: 08/07/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022] Open
Abstract
The primary objective of this study is to detect biomarkers and develop models that enable the identification of clinically significant prostate cancer and to understand the biologic implications of the genes involved. Peripheral blood samples (1018 patients) were split chronologically into independent training (n = 713) and validation (n = 305) sets. Whole transcriptome RNA sequencing was performed on isolated phagocytic CD14+ and non-phagocytic CD2+ cells and their gene expression levels were used to develop predictive models that correlate to adverse pathologic features. The immune-transcriptomic model with the highest performance for predicting adverse pathology, based on a subtraction of the log-transformed expression signals of the two cell types, displayed an area under the curve (AUC) of the receiver operating characteristic of 0.70. The addition of biomarkers in combination with traditional clinical risk factors (age, serum prostate-specific antigen (PSA), PSA density, race, digital rectal examination (DRE), and family history) enhanced the AUC to 0.91 and 0.83 for the training and validation sets, respectively. The markers identified by this approach uncovered specific pathway associations relevant to (prostate) cancer biology. Increased phagocytic activity in conjunction with cancer-associated (mis-)regulation is also represented by these markers. Differential gene expression of circulating immune cells gives insight into the cellular immune response to early tumor development and immune surveillance.
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Alonso M, Zabala C, Mansilla S, De Brun L, Martínez J, Garau M, Rivas G, Acosta C, Lens D, Cerisola A, Graña M, Naya H, Puentes R, Spangenberg L, Raggio V, Lemes A, Castro L, Quijano C. Blood cell respiration rates and mtDNA copy number: A promising tool for the diagnosis of mitochondrial disease. Mitochondrion 2021; 61:31-43. [PMID: 34536563 DOI: 10.1016/j.mito.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 10/20/2022]
Abstract
Human mitochondrial diseases are a group of heterogeneous diseases caused by defects in oxidative phosphorylation, due to mutations in mitochondrial (mtDNA) or nuclear DNA. The diagnosis of mitochondrial disease is challenging since mutations in multiple genes can affect mitochondrial function, there is considerable clinical variability and a poor correlation between genotype and phenotype. Herein we assessed mitochondrial function in peripheral blood mononuclear cells (PBMCs) and platelets from volunteers without known metabolic pathology and patients with mitochondrial disease. Oxygen consumption rates were evaluated and respiratory parameters indicative of mitochondrial function were obtained. A negative correlation between age and respiratory parameters of PBMCs from control individuals was observed. Surprisingly, respiratory parameters of PBMCs normalized by cell number were similar in patients and young controls. Considering possible compensatory mechanisms, mtDNA copy number in PBMCs was quantified and an increase was found in patients with respect to controls. Hence, respiratory parameters normalized by mtDNA copy number were determined, and in these conditions a decrease in maximum respiration rate and spare respiratory capacity was observed in patients relative to control individuals. In platelets no decay was seen in mitochondrial function with age, while a reduction in basal, ATP-independent and ATP-dependent respiration normalized by cell number was detected in patients compared to control subjects. In summary, our results offer promising perspectives regarding the assessment of mitochondrial function in blood cells for the diagnosis of mitochondrial disease, minimizing the need for invasive procedures such as muscle biopsies, and for following disease progression and response to treatments.
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Affiliation(s)
- Martina Alonso
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Uruguay
| | - Cristina Zabala
- Clínica Pediátrica A, Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, Uruguay; Centro de Referencia Nacional en Defectos Congénitos y Enfermedades Raras (CRENADECER) del Banco de Previsión Social (BPS), Uruguay
| | - Santiago Mansilla
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Uruguay; Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Uruguay
| | - Laureana De Brun
- Departamento de Patobiología, Unidad de Microbiología, Facultad de Veterinaria, Universidad de la República, Uruguay
| | - Jennyfer Martínez
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Uruguay
| | - Mariela Garau
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Uruguay
| | - Gabriela Rivas
- Cátedra y Departamento de Hemoterapia y Medicina Transfusional, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Uruguay
| | - Cecilia Acosta
- Cátedra y Departamento de Hemoterapia y Medicina Transfusional, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Uruguay
| | - Daniela Lens
- Departamento Básico de Medicina, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Uruguay
| | - Alfredo Cerisola
- Centro de Referencia Nacional en Defectos Congénitos y Enfermedades Raras (CRENADECER) del Banco de Previsión Social (BPS), Uruguay; Cátedra de Neuropediatría, Facultad de Medicina, Universidad de la República, Uruguay
| | - Martín Graña
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Uruguay
| | - Hugo Naya
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Uruguay; Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Uruguay
| | - Rodrigo Puentes
- Departamento de Patobiología, Unidad de Microbiología, Facultad de Veterinaria, Universidad de la República, Uruguay
| | | | - Víctor Raggio
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Uruguay
| | - Aída Lemes
- Centro de Referencia Nacional en Defectos Congénitos y Enfermedades Raras (CRENADECER) del Banco de Previsión Social (BPS), Uruguay
| | - Laura Castro
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Uruguay.
| | - Celia Quijano
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Uruguay.
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12
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Pandey A, Shah SJ, Butler J, Kellogg DL, Lewis GD, Forman DE, Mentz RJ, Borlaug BA, Simon MA, Chirinos JA, Fielding RA, Volpi E, Molina AJA, Haykowsky MJ, Sam F, Goodpaster BH, Bertoni AG, Justice JN, White JP, Ding J, Hummel SL, LeBrasseur NK, Taffet GE, Pipinos II, Kitzman D. Exercise Intolerance in Older Adults With Heart Failure With Preserved Ejection Fraction: JACC State-of-the-Art Review. J Am Coll Cardiol 2021; 78:1166-1187. [PMID: 34503685 PMCID: PMC8525886 DOI: 10.1016/j.jacc.2021.07.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/16/2022]
Abstract
Exercise intolerance (EI) is the primary manifestation of chronic heart failure with preserved ejection fraction (HFpEF), the most common form of heart failure among older individuals. The recent recognition that HFpEF is likely a systemic, multiorgan disorder that shares characteristics with other common, difficult-to-treat, aging-related disorders suggests that novel insights may be gained from combining knowledge and concepts from aging and cardiovascular disease disciplines. This state-of-the-art review is based on the outcomes of a National Institute of Aging-sponsored working group meeting on aging and EI in HFpEF. We discuss aging-related and extracardiac contributors to EI in HFpEF and provide the rationale for a transdisciplinary, "gero-centric" approach to advance our understanding of EI in HFpEF and identify promising new therapeutic targets. We also provide a framework for prioritizing future research, including developing a uniform, comprehensive approach to phenotypic characterization of HFpEF, elucidating key geroscience targets for treatment, and conducting proof-of-concept trials to modify these targets.
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Affiliation(s)
- Ambarish Pandey
- University of Texas Southwestern Medical Center, Dallas, Texas, USA. https://twitter.com/ambarish4786
| | - Sanjiv J Shah
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Javed Butler
- University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Dean L Kellogg
- University of Texas Health Science Center and GRECC, South Texas Veterans Affairs Health System, San Antonio, Texas, USA
| | | | - Daniel E Forman
- University of Pittsburgh and VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Robert J Mentz
- Duke Clinical Research Center, Durham, North Carolina, USA
| | | | - Marc A Simon
- University of Pittsburgh and VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | | | | | - Elena Volpi
- University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | | | | | - Flora Sam
- Boston University School of Medicine, Boston, Massachusetts, USA
| | - Bret H Goodpaster
- Advent Health Translational Research Institute, Orlando, Florida, USA
| | - Alain G Bertoni
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jamie N Justice
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | | | - Jingzhone Ding
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Scott L Hummel
- University of Michigan and the VA Ann Arbor Health System, Ann Arbor, Michigan, USA
| | | | | | | | - Dalane Kitzman
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
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13
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Methods for Characterization of Senescent Circulating and Tumor-Infiltrating T-Cells: An Overview from Multicolor Flow Cytometry to Single-Cell RNA Sequencing. Methods Mol Biol 2021; 2325:79-95. [PMID: 34053052 DOI: 10.1007/978-1-0716-1507-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Immunosenescence is the general term used to describe the aging-associated decline of immunological function that explains the higher susceptibility to infectious diseases and cancer, increased autoimmunity, or the reduced effectiveness of vaccinations. Senescence of CD8+ T-cells has been described in all these conditions.The most important classical markers of T senescent cells are the cell cycle inhibitors p16ink4a, p21, and p53, together with positivity for SA-βgal expression and the acquirement of a peculiar IFNγ -based secretory phenotype commonly defined SASP (Senescence Associated Secretory Phenotype). Other surface markers are the CD28 and CD27 loss together with gain of expression of CD45RA, CD57, TIGIT, and/or KLRG1. However, this characterization could not be sufficient to distinguish from truly senescent cells and exhausted T-cells. Furthermore, more complexity is added by the wide heterogeneity of T-cells subset in aged individuals or in the tumor microenvironment. A combined analysis by multicolor flow cytometry for surface and intracellular markers integrated with gene-expression arrays and single-cell RNA sequencing is required to develop effective interventions for therapeutic modulation of specific T-cell subsets. The RNASeq offers the great possibility to reveal at single-cell resolution the exact molecular hallmarks of senescent CD8+ T-cells without the limitations of bulk analysis. Furthermore, the comprehensive integration of multidimensional approaches (genomics, epigenomics, proteomics, metabolomics) will increase our global understanding of how immunosenescence of T-cells is interlinked to human aging.
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14
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Szymczak S, Dose J, Torres GG, Heinsen FA, Venkatesh G, Datlinger P, Nygaard M, Mengel-From J, Flachsbart F, Klapper W, Christensen K, Lieb W, Schreiber S, Häsler R, Bock C, Franke A, Nebel A. DNA methylation QTL analysis identifies new regulators of human longevity. Hum Mol Genet 2021; 29:1154-1167. [PMID: 32160291 PMCID: PMC7206852 DOI: 10.1093/hmg/ddaa033] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 01/01/2020] [Accepted: 02/11/2020] [Indexed: 12/14/2022] Open
Abstract
Human longevity is a complex trait influenced by both genetic and environmental factors, whose interaction is mediated by epigenetic mechanisms like DNA methylation. Here, we generated genome-wide whole-blood methylome data from 267 individuals, of which 71 were long-lived (90–104 years), by applying reduced representation bisulfite sequencing. We followed a stringent two-stage analysis procedure using discovery and replication samples to detect differentially methylated sites (DMSs) between young and long-lived study participants. Additionally, we performed a DNA methylation quantitative trait loci analysis to identify DMSs that underlie the longevity phenotype. We combined the DMSs results with gene expression data as an indicator of functional relevance. This approach yielded 21 new candidate genes, the majority of which are involved in neurophysiological processes or cancer. Notably, two candidates (PVRL2, ERCC1) are located on chromosome 19q, in close proximity to the well-known longevity- and Alzheimer’s disease-associated loci APOE and TOMM40. We propose this region as a longevity hub, operating on both a genetic (APOE, TOMM40) and an epigenetic (PVRL2, ERCC1) level. We hypothesize that the heritable methylation and associated gene expression changes reported here are overall advantageous for the LLI and may prevent/postpone age-related diseases and facilitate survival into very old age.
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Affiliation(s)
- Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Janina Dose
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Guillermo G Torres
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Femke-Anouska Heinsen
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Geetha Venkatesh
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | - Marianne Nygaard
- Research Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, DK-5000 Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, DK-5000 Odense C, Denmark
| | - Jonas Mengel-From
- Research Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, DK-5000 Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, DK-5000 Odense C, Denmark
| | - Friederike Flachsbart
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Wolfram Klapper
- Institute of Pathology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Kaare Christensen
- Research Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, DK-5000 Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, DK-5000 Odense C, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, DK-5000 Odense C, Denmark
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, A-1090 Vienna, Austria.,Max Planck Institute for Informatics, Saarland Informatics Campus, D-66123 Saarbrücken, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
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15
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Broustas CG, Duval AJ, Amundson SA. Impact of aging on gene expression response to x-ray irradiation using mouse blood. Sci Rep 2021; 11:10177. [PMID: 33986387 PMCID: PMC8119453 DOI: 10.1038/s41598-021-89682-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/27/2021] [Indexed: 02/07/2023] Open
Abstract
As a radiation biodosimetry tool, gene expression profiling is being developed using mouse and human peripheral blood models. The impact of dose, dose-rate, and radiation quality has been studied with the goal of predicting radiological tissue injury. In this study, we determined the impact of aging on the gene expression profile of blood from mice exposed to radiation. Young (2 mo) and old (21 mo) male mice were irradiated with 4 Gy x-rays, total RNA was isolated from whole blood 24 h later, and subjected to whole genome microarray analysis. Pathway analysis of differentially expressed genes revealed young mice responded to x-ray exposure by significantly upregulating pathways involved in apoptosis and phagocytosis, a process that eliminates apoptotic cells and preserves tissue homeostasis. In contrast, the functional annotation of senescence was overrepresented among differentially expressed genes from irradiated old mice without enrichment of phagocytosis pathways. Pathways associated with hematologic malignancies were enriched in irradiated old mice compared with irradiated young mice. The fibroblast growth factor signaling pathway was underrepresented in older mice under basal conditions. Similarly, brain-related functions were underrepresented in unirradiated old mice. Thus, age-dependent gene expression differences should be considered when developing gene signatures for use in radiation biodosimetry.
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Affiliation(s)
- Constantinos G Broustas
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W. 168th St., New York, NY, 10032, USA.
| | - Axel J Duval
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W. 168th St., New York, NY, 10032, USA
| | - Sally A Amundson
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W. 168th St., New York, NY, 10032, USA
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16
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Transcriptome alterations are enriched for synapse-associated genes in the striatum of subjects with obsessive-compulsive disorder. Transl Psychiatry 2021; 11:171. [PMID: 33723209 PMCID: PMC7961029 DOI: 10.1038/s41398-021-01290-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/24/2020] [Accepted: 02/25/2021] [Indexed: 12/20/2022] Open
Abstract
Obsessive-compulsive disorder (OCD) is a chronic and severe psychiatric disorder for which effective treatment options are limited. Structural and functional neuroimaging studies have consistently implicated the orbitofrontal cortex (OFC) and striatum in the pathophysiology of the disorder. Recent genetic evidence points to involvement of components of the excitatory synapse in the etiology of OCD. However, the transcriptional alterations that could link genetic risk to known structural and functional abnormalities remain mostly unknown. To assess potential transcriptional changes in the OFC and two striatal regions (caudate nucleus and nucleus accumbens) of OCD subjects relative to unaffected comparison subjects, we sequenced messenger RNA transcripts from these brain regions. In a joint analysis of all three regions, 904 transcripts were differentially expressed between 7 OCD versus 8 unaffected comparison subjects. Region-specific analyses highlighted a smaller number of differences, which concentrated in caudate and nucleus accumbens. Pathway analyses of the 904 differentially expressed transcripts showed enrichment for genes involved in synaptic signaling, with these synapse-associated genes displaying lower expression in OCD subjects relative to unaffected comparison subjects. Finally, we estimated that cell type fractions of medium spiny neurons were lower whereas vascular cells and astrocyte fractions were higher in tissue of OCD subjects. Together, these data provide the first unbiased examination of differentially expressed transcripts in both OFC and striatum of OCD subjects. These transcripts encoded synaptic proteins more often than expected by chance, and thus implicate the synapse as a vulnerable molecular compartment for OCD.
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17
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Dobbs KR, Embury P, Koech E, Ogolla S, Munga S, Kazura JW, Dent AE. Age-related differences in monocyte DNA methylation and immune function in healthy Kenyan adults and children. Immun Ageing 2021; 18:11. [PMID: 33685492 PMCID: PMC7938546 DOI: 10.1186/s12979-021-00223-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/23/2021] [Indexed: 01/16/2023]
Abstract
BACKGROUND Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profiles in monocytes from young adults and children from western Kenya. RESULTS We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles. CONCLUSIONS These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.
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Affiliation(s)
- Katherine R Dobbs
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC: 4983, Cleveland, OH, 44106, USA
- Division of Pediatric Infectious Diseases, University Hospitals Rainbow Babies and Children's Hospital, Cleveland, OH, USA
| | - Paula Embury
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC: 4983, Cleveland, OH, 44106, USA
| | - Emmily Koech
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Sidney Ogolla
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Stephen Munga
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC: 4983, Cleveland, OH, 44106, USA
| | - Arlene E Dent
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC: 4983, Cleveland, OH, 44106, USA.
- Division of Pediatric Infectious Diseases, University Hospitals Rainbow Babies and Children's Hospital, Cleveland, OH, USA.
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18
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Yan CC, Zhang XS, Zhou L, Yang Q, Zhou M, Zhang LW, Xing JC, Yan ZF, Price M, Li J, Yue BS, Fan ZX. Effects of aging on gene expression in blood of captive Tibetan macaques ( Macaca thibetana) and comparisons with expression in humans. Zool Res 2021; 41:557-563. [PMID: 32746507 PMCID: PMC7475009 DOI: 10.24272/j.issn.2095-8137.2020.092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Changes in gene expression occur as animals, including primates, age. Macaques have long been used as a model species for primate evolution and biomedical studies. Here, to study gene expression in Tibetan macaques (Macaca thibetana, TMs) and its differences to humans, we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs. In total, 2 523 age-associated differentially expressed genes (DEGs) were identified. Several pathways and processes that regulate aging, including the FoxO signaling pathway, autophagy, and platelet activation, were significantly enriched in the up-regulated DEGs. Two significantly age-related modules were identified by weighted gene co-expression network analysis (WGCNA). The TMs and humans shared 279 common DEGs, including 111 up-regulated and 141 down-regulated genes with advancing age in the same expression direction. However, 27 age-related DEGs presented the opposite expression direction in TMs as that in humans. For example, INPPL1, with inhibitory effects on the B cell receptor signaling pathway, was up-regulated in humans but down-regulated in TMs. In general, our study suggests that aging is a critical factor affecting gene expression in the captive TM population. The similarities and differences in gene expression patterns between TMs and humans could provide new insights into primate evolution and benefit TM model development.
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Affiliation(s)
- Chao-Chao Yan
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xin-Shang Zhang
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Liang Zhou
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Qiao Yang
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Min Zhou
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Lin-Wan Zhang
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jin-Chuan Xing
- Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Zhi-Feng Yan
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jing Li
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Bi-Song Yue
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhen-Xin Fan
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China. E-mail:
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19
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Shchukina I, Bagaitkar J, Shpynov O, Loginicheva E, Porter S, Mogilenko DA, Wolin E, Collins P, Demidov G, Artomov M, Zaitsev K, Sidorov S, Camell C, Bambouskova M, Arthur L, Swain A, Panteleeva A, Dievskii A, Kurbatsky E, Tsurinov P, Chernyatchik R, Dixit VD, Jovanovic M, Stewart SA, Daly MJ, Dmitriev S, Oltz EM, Artyomov MN. Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome. NATURE AGING 2021; 1:124-141. [PMID: 34796338 PMCID: PMC8597198 DOI: 10.1038/s43587-020-00002-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022]
Abstract
The impact of healthy aging on molecular programming of immune cells is poorly understood. Here, we report comprehensive characterization of healthy aging in human classical monocytes, with a focus on epigenomic, transcriptomic, and proteomic alterations, as well as the corresponding proteomic and metabolomic data for plasma, using healthy cohorts of 20 young and 20 older males (~27 and ~64 years old on average). For each individual, we performed eRRBS-based DNA methylation profiling, which allowed us to identify a set of age-associated differentially methylated regions (DMRs) - a novel, cell-type specific signature of aging in DNA methylome. Hypermethylation events were associated with H3K27me3 in the CpG islands near promoters of lowly-expressed genes, while hypomethylated DMRs were enriched in H3K4me1 marked regions and associated with age-related increase of expression of the corresponding genes, providing a link between DNA methylation and age-associated transcriptional changes in primary human cells.
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Affiliation(s)
- Irina Shchukina
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Juhi Bagaitkar
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, USA
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Oleg Shpynov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Ekaterina Loginicheva
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sofia Porter
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Denis A. Mogilenko
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Erica Wolin
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Patrick Collins
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - German Demidov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mykyta Artomov
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Konstantin Zaitsev
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- Present address: Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | - Sviatoslav Sidorov
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Christina Camell
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Monika Bambouskova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Laura Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alexandra Panteleeva
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | | | | | - Petr Tsurinov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
| | - Roman Chernyatchik
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
| | - Vishwa Deep Dixit
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sheila A. Stewart
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine, Helsinki, Finland
| | | | - Eugene M. Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maxim N. Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
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20
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Rivero-Segura NA, Bello-Chavolla OY, Barrera-Vázquez OS, Gutierrez-Robledo LM, Gomez-Verjan JC. Promising biomarkers of human aging: In search of a multi-omics panel to understand the aging process from a multidimensional perspective. Ageing Res Rev 2020; 64:101164. [PMID: 32977058 DOI: 10.1016/j.arr.2020.101164] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
Abstract
The aging process has been linked to the occurrence of chronic diseases and functional impairments, including cancer, sarcopenia, frailty, metabolic, cardiovascular, and neurodegenerative diseases. Nonetheless, aging is highly variable and heterogeneous and represents a challenge for its characterization. In this sense, intrinsic capacity (IC) stands as a novel perspective by the World Health Organization, which integrates the individual wellbeing, environment, and risk factors to understand aging. However, there is a lack of quantitative and qualitative attributes to define it objectively. Therefore, in this review we attempt to summarize the most relevant and promising biomarkers described in clinical studies at date over different molecular levels, including epigenomics, transcriptomics, proteomics, metabolomics, and the microbiome. To aid gerontologists, geriatricians, and biomedical researchers to understand the aging process through the IC. Aging biomarkers reflect the physiological state of individuals and the underlying mechanisms related to homeostatic changes throughout an individual lifespan; they demonstrated that aging could be measured independently of time (that may explain its heterogeneity) and to be helpful to predict age-related syndromes and mortality. In summary, we highlight the areas of opportunity and gaps of knowledge that must be addressed to fully integrate biomedical findings into clinically useful tools and interventions.
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Affiliation(s)
| | - O Y Bello-Chavolla
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico; Department of Physiology, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - O S Barrera-Vázquez
- Departamento de Famacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - J C Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico.
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21
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The transcriptome of CMML monocytes is highly inflammatory and reflects leukemia-specific and age-related alterations. Blood Adv 2020; 3:2949-2961. [PMID: 31648319 DOI: 10.1182/bloodadvances.2019000585] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/23/2019] [Indexed: 12/19/2022] Open
Abstract
Chronic myelomonocytic leukemia (CMML) is an aggressive myeloid neoplasm of older individuals characterized by persistent monocytosis. Somatic mutations in CMML are heterogeneous and only partially explain the variability in clinical outcomes. Recent data suggest that cardiovascular morbidity is increased in CMML and contributes to reduced survival. Clonal hematopoiesis of indeterminate potential (CHIP), the presence of mutated blood cells in hematologically normal individuals, is a precursor of age-related myeloid neoplasms and associated with increased cardiovascular risk. To isolate CMML-specific alterations from those related to aging, we performed RNA sequencing and DNA methylation profiling on purified monocytes from CMML patients and from age-matched (old) and young healthy controls. We found that the transcriptional signature of CMML monocytes is highly proinflammatory, with upregulation of multiple inflammatory pathways, including tumor necrosis factor and interleukin (IL)-6 and -17 signaling, whereas age per se does not significantly contribute to this pattern. We observed no consistent correlations between aberrant gene expression and CpG island methylation, suggesting that proinflammatory signaling in CMML monocytes is governed by multiple and complex regulatory mechanisms. We propose that proinflammatory monocytes contribute to cardiovascular morbidity in CMML patients and promote progression by selection of mutated cell clones. Our data raise questions of whether asymptomatic patients with CMML benefit from monocyte-depleting or anti-inflammatory therapies.
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22
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Piber D, Olmstead R, Cho JHJ, Witarama T, Perez C, Dietz N, Seeman TE, Breen EC, Cole SW, Irwin MR. Inflammaging: Age and Systemic, Cellular, and Nuclear Inflammatory Biology in Older Adults. J Gerontol A Biol Sci Med Sci 2020; 74:1716-1724. [PMID: 31107949 DOI: 10.1093/gerona/glz130] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Indexed: 12/31/2022] Open
Abstract
Systemic inflammation is associated with increasing age. Yet, there are limited data about the association between age and systemic inflammation within older adults, and whether older age is also associated with cellular and nuclear signaling markers of inflammation. In community-dwelling older adults (N = 262, 60-88 years), systemic levels of C-reactive protein, interleukin-6, and soluble tumor necrosis factor receptor II; levels of toll-like receptor-4-stimulated monocytic production of interleukin-6 and tumor necrosis factor α; and resting nuclear levels of activated nuclear factor kappa B and signal transducer and activator of transcription (STAT1, STAT3, STAT5) were evaluated. Adjusting for demographic and clinical factors, multivariate linear regression tested the association between age and each inflammatory marker. Age was positively associated with increased levels of interleukin-6 and soluble tumor necrosis factor receptor II (p's < .05) and with increases in STAT1, STAT3, and STAT5 activation (p's < .05). However, no relationship was found between age and C-reactive protein, toll-like receptor-4-stimulated interleukin-6/tumor necrosis factor alpha α production, or nuclear factor kappa B. Within a community-dwelling sample of older adults, older age is associated with increases in STAT activation, along with increases of systemic inflammatory cytokines. In older adults, heterogeneity in age-related increases in inflammatory disease risk may be related to individual variability in inflammation.
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Affiliation(s)
- Dominique Piber
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles.,Department of Psychiatry, Charité-Universitätsmedizin Berlin, Germany
| | - Richard Olmstead
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Joshua Hyong-Jin Cho
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Tuff Witarama
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Christian Perez
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Nicholas Dietz
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Teresa E Seeman
- Division of Geriatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Elizabeth C Breen
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Steve W Cole
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Michael R Irwin
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
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23
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Saare M, Tserel L, Haljasmägi L, Taalberg E, Peet N, Eimre M, Vetik R, Kingo K, Saks K, Tamm R, Milani L, Kisand K, Peterson P. Monocytes present age-related changes in phospholipid concentration and decreased energy metabolism. Aging Cell 2020; 19:e13127. [PMID: 32107839 PMCID: PMC7189998 DOI: 10.1111/acel.13127] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 01/21/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
Age‐related changes at the cellular level include the dysregulation of metabolic and signaling pathways. Analyses of blood leukocytes have revealed a set of alterations that collectively lower their ability to fight infections and resolve inflammation later in life. We studied the transcriptomic, epigenetic, and metabolomic profiles of monocytes extracted from younger adults and individuals over the age of 65 years to map major age‐dependent changes in their cellular physiology. We found that the monocytes from older persons displayed a decrease in the expression of ribosomal and mitochondrial protein genes and exhibited hypomethylation at the HLA class I locus. Additionally, we found elevated gene expression associated with cell motility, including the CX3CR1 and ARID5B genes, which have been associated with the development of atherosclerosis. Furthermore, the downregulation of two genes, PLA2G4B and ALOX15B, which belong to the arachidonic acid metabolism pathway involved in phosphatidylcholine conversion to anti‐inflammatory lipoxins, correlated with increased phosphatidylcholine content in monocytes from older individuals. We found age‐related changes in monocyte metabolic fitness, including reduced mitochondrial function and increased glycose consumption without the capacity to upregulate it during increased metabolic needs, and signs of increased oxidative stress and DNA damage. In conclusion, our results complement existing findings and elucidate the metabolic alterations that occur in monocytes during aging.
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Affiliation(s)
- Mario Saare
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Liina Tserel
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Liis Haljasmägi
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Egon Taalberg
- Department of Biochemistry Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Nadežda Peet
- Department of Pathophysiology Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Margus Eimre
- Department of Pathophysiology Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Rait Vetik
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Külli Kingo
- Department of Dermatology and Venereology Institute of Clinical Medicine University of Tartu Tartu Estonia
- Clinic of Dermatology Tartu University Hospital Tartu Estonia
| | - Kai Saks
- Department of Internal Medicine Institute of Clinical Medicine University of Tartu Tartu Estonia
| | - Riin Tamm
- Laboratory of Immune Analysis, United Laboratories Tartu University Hospital Tartu Estonia
| | - Lili Milani
- Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia
| | - Kai Kisand
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
| | - Pärt Peterson
- Molecular Pathology Research Group Institute of Biomedicine and Translational Medicine University of Tartu Tartu Estonia
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24
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Kicic A, de Jong E, Ling KM, Nichol K, Anderson D, Wark PAB, Knight DA, Bosco A, Stick SM. Assessing the unified airway hypothesis in children via transcriptional profiling of the airway epithelium. J Allergy Clin Immunol 2020; 145:1562-1573. [PMID: 32113981 DOI: 10.1016/j.jaci.2020.02.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Emerging evidence suggests that disease vulnerability is expressed throughout the airways, the so-called unified airway hypothesis, but the evidence to support this is predominantly indirect. OBJECTIVES We sought to establish the transcriptomic profiles of the upper and lower airways and determine their level of similarity irrespective of airway symptoms (wheeze) and allergy. METHODS We performed RNA sequencing on upper and lower airway epithelial cells from 63 children with or without wheeze and accompanying atopy, using differential gene expression and gene coexpression analyses to determine transcriptional similarity. RESULTS We observed approximately 91% homology in the expressed genes between the 2 sites. When coexpressed genes were grouped into modules relating to biological functions, all were found to be conserved between the 2 regions, resulting in a consensus network containing 16 modules associated with ribosomal function, metabolism, gene expression, mitochondrial activity, and antiviral responses through IFN activity. Although symptom-associated gene expression changes were more prominent in the lower airway, they were reflected in nasal epithelium and included IL-1 receptor like 1, prostaglandin-endoperoxide synthase 1, CCL26, and periostin. Through network analysis we identified a cluster of coexpressed genes associated with atopic wheeze in the lower airway, which could equally distinguish atopic and nonatopic phenotypes in upper airway samples. CONCLUSIONS We show that the upper and lower airways are significantly conserved in their transcriptional composition, and that variations associated with disease are present in both nasal and tracheal epithelium. Findings from this study supporting a unified airway imply that clinical insight regarding the lower airway in health and disease can be gained from studying the nasal epithelium.
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Affiliation(s)
- Anthony Kicic
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia; Occupation and Environment, School of Public Health, Curtin University, Perth, Australia; School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Australia; Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, Australia.
| | - Emma de Jong
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia
| | - Kak-Ming Ling
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Kristy Nichol
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, Australia
| | - Denise Anderson
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia
| | - Peter A B Wark
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, Australia
| | - Darryl A Knight
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, Australia; Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Anthony Bosco
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia
| | - Stephen M Stick
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia; School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Australia; Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, Australia
| | -
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia
| | -
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia; Robinson Research Institute, University of Adelaide, Adelaide, Australia; Hunter Medical Research Institute, Priority Research Centre for Asthma and Respiratory Disease, New Lambton Heights, Australia
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25
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Marttila S, Chatsirisupachai K, Palmer D, de Magalhães JP. Ageing-associated changes in the expression of lncRNAs in human tissues reflect a transcriptional modulation in ageing pathways. Mech Ageing Dev 2020; 185:111177. [PMID: 31706952 PMCID: PMC6961210 DOI: 10.1016/j.mad.2019.111177] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/18/2022]
Abstract
Ageing-associated changes in the protein coding transcriptome have been extensively characterised, but less attention has been paid to the non-coding portion of the human genome, especially to long non-coding RNAs (lncRNAs). Only a minority of known lncRNAs have been functionally characterised; however, a handful of these lncRNAs have already been linked to ageing-associated processes. To gain more information on the effects of ageing on lncRNAs, we identified from GTEx data lncRNAs that show ageing-associated expression patterns (age-lncRNAs) in 29 human tissues in 20-79-year-old individuals. The age-lncRNAs identified were highly tissue-specific, but the protein coding genes co-expressed with the age-lncRNAs and the functional categories associated with the age-lncRNAs showed significant overlap across tissues. Functions associated with the age-lncRNAs, including immune system processes and transcription, were similar to what has previously been reported for protein coding genes with ageing-associated expression pattern. As the tissue-specific age-lncRNAs were associated with shared functions across tissues, they may reflect the tissue-specific fine-tuning of the common ageing-associated processes. The present study can be utilised as a resource when selecting and prioritising lncRNAs for further functional analyses.
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Affiliation(s)
- Saara Marttila
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Daniel Palmer
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
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26
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Bektas A, Schurman SH, Gonzalez-Freire M, Dunn CA, Singh AK, Macian F, Cuervo AM, Sen R, Ferrucci L. Age-associated changes in human CD4 + T cells point to mitochondrial dysfunction consequent to impaired autophagy. Aging (Albany NY) 2019; 11:9234-9263. [PMID: 31707363 PMCID: PMC6874450 DOI: 10.18632/aging.102438] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022]
Abstract
To gain understanding on the mechanisms that drive immunosenescence in humans, we examined CD4+ T cells obtained from younger (20-39 years-old) and older (70+ years-old) healthy participants of the Baltimore Longitudinal Study on Aging (BLSA). We found that mitochondrial proteins involved in the electron transport chain were overrepresented in cells from older participants, with prevalent dysregulation of oxidative phosphorylation and energy metabolism molecular pathways. Surprisingly, gene transcripts coding for mitochondrial proteins pertaining to oxidative phosphorylation and electron transport chain pathways were underrepresented in older individuals. Paralleling the observed decrease in gene expression, mitochondrial respiration was impaired in CD4+ T cells from older subjects. Though mitochondrial number in both naïve and memory cells visualized with electron microcopy was similar in older versus younger participants, there were a significantly higher number of autophagosomes, many of them containing undegraded mitochondria, in older individuals. The presence of mitochondria inside the accumulated autophagic compartments in CD4+ T cells from older individuals was confirmed by immunofluorescence. These findings suggest that older age is associated with persistence of dysfunctional mitochondria in CD4+ T lymphocytes caused by defective mitochondrial turnover by autophagy, which may trigger chronic inflammation and contribute to the impairment of immune defense in older persons.
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Affiliation(s)
- Arsun Bektas
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shepherd H. Schurman
- Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Marta Gonzalez-Freire
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Christopher A. Dunn
- Flow Cytometry Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Amit K. Singh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Fernando Macian
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ana Maria Cuervo
- Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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27
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The role of DNA methylation and hydroxymethylation in immunosenescence. Ageing Res Rev 2019; 51:11-23. [PMID: 30769150 DOI: 10.1016/j.arr.2019.01.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 12/12/2022]
Abstract
A healthy functioning immune system is critical to stave off infectious diseases, but as humans and other organisms age, their immune systems decline. As a result, diseases that were readily thwarted in early life pose nontrivial harm and can even be deadly in late life. Immunosenescence is defined as the general deterioration of the immune system with age, and it is characterized by functional changes in hematopoietic stem cells (HSCs) and specific blood cell types as well as changes in levels of numerous factors, particularly those involved in inflammation. Potential mechanisms underlying immunosenescence include epigenetic changes such as changes in DNA methylation (DNAm) and DNA hydroxymethylation (DNAhm) that occur with age. The purpose of this review is to describe what is currently known about the relationship between immunosenescence and the age-related changes to DNAm and DNAhm, and to discuss experimental approaches best suited to fill gaps in our understanding.
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28
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Keenan CR, Allan RS. Epigenomic drivers of immune dysfunction in aging. Aging Cell 2019; 18:e12878. [PMID: 30488545 PMCID: PMC6351880 DOI: 10.1111/acel.12878] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/26/2018] [Accepted: 10/18/2018] [Indexed: 12/17/2022] Open
Abstract
Aging inevitably leads to reduced immune function, leaving the elderly more susceptible to infections, less able to respond to pathogen challenges, and less responsive to preventative vaccinations. No cell type is exempt from the ravages of age, and extensive studies have found age-related alterations in the frequencies and functions of both stem and progenitor cells, as well as effector cells of both the innate and adaptive immune systems. The intrinsic functional reduction in immune competence is also associated with low-grade chronic inflammation, termed "inflamm-aging," which further perpetuates immune dysfunction. While many of these age-related cellular changes are well characterized, understanding the molecular changes that underpin the functional decline has proven more difficult. Changes in chromatin are increasingly appreciated as a causative mechanism of cellular and organismal aging across species. These changes include increased genomic instability through loss of heterochromatin and increased DNA damage, telomere attrition, and epigenetic alterations. In this review, we discuss the connections between chromatin, immunocompetence, and the loss of function associated with mammalian immune aging. Through understanding the molecular events which underpin the phenotypic changes observed in the aged immune system, it is hoped that the aged immune system can be restored to provide youthful immunity once more.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
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29
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Payán-Gómez C, Rodríguez D, Amador-Muñoz D, Ramírez-Clavijo S. Integrative Analysis of Global Gene Expression Identifies Opposite Patterns of Reactive Astrogliosis in Aged Human Prefrontal Cortex. Brain Sci 2018; 8:brainsci8120227. [PMID: 30572619 PMCID: PMC6317157 DOI: 10.3390/brainsci8120227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
The prefrontal cortex (PFC) is one of the brain regions with more prominent changes in human aging. The molecular processes related to the cognitive decline and mood changes during aging are not completely understood. To improve our knowledge, we integrated transcriptomic data of four studies of human PFC from elderly people (58–80 years old) compared with younger people (20–40 years old) using a meta-analytic approximation combined with molecular signature analysis. We identified 1817 differentially expressed genes, 561 up-regulated and 1256 down-regulated. Pathway analysis revealed down-regulation of synaptic genes with conservation of gene expression of other neuronal regions. Additionally, we identified up-regulation of markers of astrogliosis with transcriptomic signature compatible with A1 neurotoxic astrocytes and A2 neuroprotective astrocytes. Response to interferon is related to A1 astrocytes and the A2 phenotype is mediated in aging by activation of sonic hedgehog (SHH) pathway and up-regulation of metallothioneins I and genes of the family ERM (ezrin, radixin, and moesin). The main conclusions of our study are the confirmation of a global dysfunction of the synapses in the aged PFC and the evidence of opposite phenotypes of astrogliosis in the aging brain, which we report for the first time in the present article.
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Affiliation(s)
- César Payán-Gómez
- Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá 111221, Colombia.
| | - Diego Rodríguez
- Neuroscience (NEUROS) Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá 111221, Colombia.
| | - Diana Amador-Muñoz
- Neuroscience (NEUROS) Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá 111221, Colombia.
| | - Sandra Ramírez-Clavijo
- Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá 111221, Colombia.
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30
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Gomez-Verjan JC, Vazquez-Martinez ER, Rivero-Segura NA, Medina-Campos RH. The RNA world of human ageing. Hum Genet 2018; 137:865-879. [DOI: 10.1007/s00439-018-1955-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
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31
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McCall CE, Zabalawi M, Liu T, Martin A, Long DL, Buechler NL, Arts RJW, Netea M, Yoza BK, Stacpoole PW, Vachharajani V. Pyruvate dehydrogenase complex stimulation promotes immunometabolic homeostasis and sepsis survival. JCI Insight 2018; 3:99292. [PMID: 30089711 PMCID: PMC6129136 DOI: 10.1172/jci.insight.99292] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/21/2018] [Indexed: 12/22/2022] Open
Abstract
Limited understanding of the mechanisms responsible for life-threatening organ and immune failure hampers scientists' ability to design sepsis treatments. Pyruvate dehydrogenase kinase 1 (PDK1) is persistently expressed in immune-tolerant monocytes of septic mice and humans and deactivates mitochondrial pyruvate dehydrogenase complex (PDC), the gate-keeping enzyme for glucose oxidation. Here, we show that targeting PDK with its prototypic inhibitor dichloroacetate (DCA) reactivates PDC; increases mitochondrial oxidative bioenergetics in isolated hepatocytes and splenocytes; promotes vascular, immune, and organ homeostasis; accelerates bacterial clearance; and increases survival. These results indicate that the PDC/PDK axis is a druggable mitochondrial target for promoting immunometabolic and organ homeostasis during sepsis.
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Affiliation(s)
| | | | - Tiefu Liu
- Department of Internal Medicine/Molecular Medicine and
| | - Ayana Martin
- Department of Internal Medicine/Molecular Medicine and
| | - David L. Long
- Department of Internal Medicine/Molecular Medicine and
| | - Nancy L. Buechler
- Department of Anesthesiology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Rob J. W. Arts
- Department in Internal Medicine and Radboud Center for Infectious Diseases, Radboud Medical Center, Nijmegen, Netherlands
| | - Mihai Netea
- Department in Internal Medicine and Radboud Center for Infectious Diseases, Radboud Medical Center, Nijmegen, Netherlands
| | - Barbara K. Yoza
- Department of Surgery/General Surgery and Trauma, Wake Forest Medical School, Winston- Salem, North Carolina, USA
| | - Peter W. Stacpoole
- Department of Medicine, Division of Endocrinology, Diabetes & Metabolism, and Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Vidula Vachharajani
- Department of Internal Medicine/Molecular Medicine and
- Department of Anesthesiology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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32
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Abstract
Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing. These encompass widely reported features of ageing such as increased senescence and inflammation, reduced electron transport chain activity and reduced ribosome synthesis, but also reveal a surprising lack of gene expression responses to known age-linked cellular stresses. We discuss how the existence of conserved transcriptomic hallmarks relates to genome-wide epigenetic differences underlying ageing clocks, and how the changing transcriptome results in proteomic alterations where data is available and to variations in cell physiology characteristic of ageing. Identification of gene expression events that occur during ageing across distant organisms should be informative as to conserved underlying mechanisms of ageing, and provide additional biomarkers to assess the effects of diet and other environmental factors on the rate of ageing.
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Affiliation(s)
- Stephen Frenk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
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33
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Shao Y, Shaw M, Todd K, Khrestian M, D'Aleo G, Barnard PJ, Zahratka J, Pillai J, Yu CE, Keene CD, Leverenz JB, Bekris LM. DNA methylation of TOMM40-APOE-APOC2 in Alzheimer's disease. J Hum Genet 2018; 63:459-471. [PMID: 29371683 DOI: 10.1038/s10038-017-0393-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
Abstract
The apolipoprotein E (APOE) ε4 allele is the major genetic risk factor for Alzheimer's disease (AD). Multiple regulatory elements, spanning the extended TOMM40-APOE-APOC2 region, regulate gene expression at this locus. Regulatory element DNA methylation changes occur under different environmental conditions, such as disease. Our group and others have described an APOE CpG island as hypomethylated in AD, compared to cognitively normal controls. However, little is known about methylation of the larger TOMM40-APOE-APOC2 region. The hypothesis of this investigation was that regulatory element methylation levels of the larger TOMM40-APOE-APOC2 region are associated with AD. The aim was to determine whether DNA methylation of the TOMM40-APOE-APOC2 region differs in AD compared to cognitively normal controls in post-mortem brain and peripheral blood. DNA was extracted from human brain (n = 12) and peripheral blood (n = 67). A methylation array was used for this analysis. Percent methylation within the TOMM40-APOE-APOC2 region was evaluated for differences according to tissue type, disease state, AD-related biomarkers, and gene expression. Results from this exploratory analysis suggest that regulatory element methylation levels within the larger TOMM40-APOE-APOC2 gene region correlate with AD-related biomarkers and TOMM40 or APOE gene expression in AD.
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Affiliation(s)
- Yvonne Shao
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - McKenzie Shaw
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Kaitlin Todd
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Maria Khrestian
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Giana D'Aleo
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - P John Barnard
- Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jeff Zahratka
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Jagan Pillai
- Lou Ruvo Center for Brain Health, Cleveland Clinic, Cleveland, OH, USA
| | - Chang-En Yu
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - C Dirk Keene
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - James B Leverenz
- Lou Ruvo Center for Brain Health, Cleveland Clinic, Cleveland, OH, USA
| | - Lynn M Bekris
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, USA.
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Declerck K, Vanden Berghe W. Back to the future: Epigenetic clock plasticity towards healthy aging. Mech Ageing Dev 2018; 174:18-29. [PMID: 29337038 DOI: 10.1016/j.mad.2018.01.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/22/2022]
Abstract
Aging is the most important risk factor for major human lifestyle diseases, including cancer, neurological and cardiometabolic disorders. Due to the complex interplay between genetics, lifestyle and environmental factors, some individuals seem to age faster than others, whereas centenarians seem to have a slower aging process. Therefore, a biochemical biomarker reflecting the relative biological age would be helpful to predict an individual's health status and aging disease risk. Although it is already known for years that cumulative epigenetic changes occur upon aging, DNA methylation patterns were only recently used to construct an epigenetic clock predictor for biological age, which is a measure of how well your body functions compared to your chronological age. Moreover, the epigenetic DNA methylation clock signature is increasingly applied as a biomarker to estimate aging disease susceptibility and mortality risk. Finally, the epigenetic clock signature could be used as a lifestyle management tool to monitor healthy aging, to evaluate preventive interventions against chronic aging disorders and to extend healthy lifespan. Dissecting the mechanism of the epigenetic aging clock will yield valuable insights into the aging process and how it can be manipulated to improve health span.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Belgium.
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Witkowski JM, Mikosik A, Bryl E, Fulop T. Proteodynamics in aging human T cells - The need for its comprehensive study to understand the fine regulation of T lymphocyte functions. Exp Gerontol 2017; 107:161-168. [PMID: 29038026 DOI: 10.1016/j.exger.2017.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022]
Abstract
Cellular life depends mostly on the creation, modification, interactions and destruction of proteins. This is true for every cell, including human T lymphocytes. One way these cells can ascertain the fidelity and at least partial functionality of their proteomes under constant attack of irreversible modulations (e.g., ROS- or glycation-dependent) is proteostasis. However, with cellular aging proteostasis progressively fails and proteostenosis (decreased amounts and functionalities of remaining proteins) occurs. There are several mechanisms involved in the modulation and protection of the proteome in the T cells which include mainly multiple layers of vesicle-bound and cytoplasmic proteases (e.g., lysosomal and proteasomal ones) acting mostly by degradation of obsolete and age-modified proteins. Recently it was shown that another not yet so widely known system consisting of obligatorily calcium-dependent cysteine proteases, the calpains and their inhibitor, the calpastatin serves in T cells as a dual switch, either activating or inactivating different proteins depending on intracellular conditions. Thus the proteolytic elimination of altered proteins as well as modulation of activity of those remaining leads to dynamic change of proteome composition and function (proteodynamics) in aging lymphocytes, so far in an almost unknown way. Aging T cell proteodynamics requires further comprehensive analysis of the resulting lysoproteomic patterns and their changes.
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Affiliation(s)
- Jacek M Witkowski
- Department of Pathophysiology, Medical University of Gdańsk, Poland.
| | - Anna Mikosik
- Department of Pathophysiology, Medical University of Gdańsk, Poland
| | - Ewa Bryl
- Department of Pathology and Experimental Rheumatology, Medical University of Gdańsk, Poland
| | - Tamas Fulop
- Centre for Aging Research, University of Sherbrooke, QC, Canada
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36
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Blood-Based Bioenergetic Profiling Reflects Differences in Brain Bioenergetics and Metabolism. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:7317251. [PMID: 29098063 PMCID: PMC5643153 DOI: 10.1155/2017/7317251] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/09/2017] [Accepted: 07/20/2017] [Indexed: 11/18/2022]
Abstract
Blood-based bioenergetic profiling provides a minimally invasive assessment of mitochondrial health shown to be related to key features of aging. Previous studies show that blood cells recapitulate mitochondrial alterations in the central nervous system under pathological conditions, including the development of Alzheimer's disease. In this study of nonhuman primates, we focus on mitochondrial function and bioenergetic capacity assessed by the respirometric profiling of monocytes, platelets, and frontal cortex mitochondria. Our data indicate that differences in the maximal respiratory capacity of brain mitochondria are reflected by CD14+ monocyte maximal respiratory capacity and platelet and monocyte bioenergetic health index. A subset of nonhuman primates also underwent [18F] fluorodeoxyglucose positron emission tomography (FDG-PET) imaging to assess brain glucose metabolism. Our results indicate that platelet respiratory capacity positively correlates to measures of glucose metabolism in multiple brain regions. Altogether, the results of this study provide early evidence that blood-based bioenergetic profiling is related to brain mitochondrial metabolism. While these measures cannot substitute for direct measures of brain metabolism, provided by measures such as FDG-PET, they may have utility as a metabolic biomarker and screening tool to identify individuals exhibiting systemic bioenergetic decline who may therefore be at risk for the development of neurodegenerative diseases.
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37
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Ucar D, Márquez EJ, Chung CH, Marches R, Rossi RJ, Uyar A, Wu TC, George J, Stitzel ML, Palucka AK, Kuchel GA, Banchereau J. The chromatin accessibility signature of human immune aging stems from CD8 + T cells. J Exp Med 2017; 214:3123-3144. [PMID: 28904110 PMCID: PMC5626401 DOI: 10.1084/jem.20170416] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/22/2017] [Accepted: 07/06/2017] [Indexed: 12/14/2022] Open
Abstract
Ucar et al. describe a novel chromatin accessibility signature of aging that is borne by memory CD8+ T cells but is detectable from PBMCs. This signature harbors the IL7R gene as a potential biomarker of aging-associated immunodeficiency. Aging is linked to deficiencies in immune responses and increased systemic inflammation. To unravel the regulatory programs behind these changes, we applied systems immunology approaches and profiled chromatin accessibility and the transcriptome in PBMCs and purified monocytes, B cells, and T cells. Analysis of samples from 77 young and elderly donors revealed a novel and robust aging signature in PBMCs, with simultaneous systematic chromatin closing at promoters and enhancers associated with T cell signaling and a potentially stochastic chromatin opening mostly found at quiescent and repressed sites. Combined analyses of chromatin accessibility and the transcriptome uncovered immune molecules activated/inactivated with aging and identified the silencing of the IL7R gene and the IL-7 signaling pathway genes as potential biomarkers. This signature is borne by memory CD8+ T cells, which exhibited an aging-related loss in binding of NF-κB and STAT factors. Thus, our study provides a unique and comprehensive approach to identifying candidate biomarkers and provides mechanistic insights into aging-associated immunodeficiency.
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Affiliation(s)
- Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT .,Institute for Systems Genomics, University of Connecticut, Farmington, CT.,Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT
| | | | - Cheng-Han Chung
- The Jackson Laboratory for Genomic Medicine, Farmington, CT.,Department of Biomedical Studies, Baylor University, Waco, TX
| | - Radu Marches
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Robert J Rossi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Asli Uyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Te-Chia Wu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT.,Institute for Systems Genomics, University of Connecticut, Farmington, CT.,Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT
| | | | - George A Kuchel
- University of Connecticut Center on Aging, University of Connecticut, Farmington, CT
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38
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Goronzy JJ, Weyand CM. Successful and Maladaptive T Cell Aging. Immunity 2017; 46:364-378. [PMID: 28329703 DOI: 10.1016/j.immuni.2017.03.010] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 02/27/2017] [Accepted: 03/07/2017] [Indexed: 12/21/2022]
Abstract
Throughout life, the T cell system adapts to shifting resources and demands, resulting in a fundamentally restructured immune system in older individuals. Here we review the cellular and molecular features of an aged immune system and discuss the trade-offs inherent to these adaptive mechanisms. Processes include homeostatic proliferation that maintains compartment size at the expense of partial loss in stemness and incomplete differentiation and the activation of negative regulatory programs, which constrain effector T cell expansion and prevent increasing oligoclonality but also interfere with memory cell generation. We propose that immune failure occurs when adaptive strategies developed by the aging T cell system fail and also discuss how, in some settings, the programs associated with T cell aging culminates in a maladaptive response that directly contributes to chronic inflammatory disease.
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Affiliation(s)
- Jörg J Goronzy
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Health Care System, Palo Alto, CA 94304, USA.
| | - Cornelia M Weyand
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Health Care System, Palo Alto, CA 94304, USA.
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39
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Liu Y, Reynolds LM, Ding J, Hou L, Lohman K, Young T, Cui W, Huang Z, Grenier C, Wan M, Stunnenberg HG, Siscovick D, Hou L, Psaty BM, Rich SS, Rotter JI, Kaufman JD, Burke GL, Murphy S, Jacobs DR, Post W, Hoeschele I, Bell DA, Herrington D, Parks JS, Tracy RP, McCall CE, Stein JH. Blood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosis. Nat Commun 2017; 8:393. [PMID: 28855511 PMCID: PMC5577184 DOI: 10.1038/s41467-017-00517-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/05/2017] [Indexed: 12/20/2022] Open
Abstract
Little is known regarding the epigenetic basis of atherosclerosis. Here we present the CD14+ blood monocyte transcriptome and epigenome signatures associated with human atherosclerosis. The transcriptome signature includes transcription coactivator, ARID5B, which is known to form a chromatin derepressor complex with a histone H3K9Me2-specific demethylase and promote adipogenesis and smooth muscle development. ARID5B CpG (cg25953130) methylation is inversely associated with both ARID5B expression and atherosclerosis, consistent with this CpG residing in an ARID5B enhancer region, based on chromatin capture and histone marks data. Mediation analysis supports assumptions that ARID5B expression mediates effects of cg25953130 methylation and several cardiovascular disease risk factors on atherosclerotic burden. In lipopolysaccharide-stimulated human THP1 monocytes, ARID5B knockdown reduced expression of genes involved in atherosclerosis-related inflammatory and lipid metabolism pathways, and inhibited cell migration and phagocytosis. These data suggest that ARID5B expression, possibly regulated by an epigenetically controlled enhancer, promotes atherosclerosis by dysregulating immunometabolism towards a chronic inflammatory phenotype.The molecular mechanisms mediating the impact of environmental factors in atherosclerosis are unclear. Here, the authors examine CD14+ blood monocyte's transcriptome and epigenome signatures to find differential methylation and expression of ARID5B to be associated with human atherosclerosis.
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Affiliation(s)
- Yongmei Liu
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
| | - Lindsay M Reynolds
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Jingzhong Ding
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Li Hou
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Kurt Lohman
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Tracey Young
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Wei Cui
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | | | | | - Ma Wan
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences (NCMLS), 6525, GA, Nijmegen, The Netherlands
| | | | - Lifang Hou
- Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, 60208, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Joel D Kaufman
- Department of Environmental and Occupational Health Sciences, Medicine and Epidemiology, University of Washington, Seattle, WA, 98104, USA
| | - Gregory L Burke
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | | | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wendy Post
- Department of Pathology and Cardiology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Ina Hoeschele
- Biocomplexity Institute and Department of Statistics, Virginia Tech, VA, 24061, USA
| | - Douglas A Bell
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - David Herrington
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - John S Parks
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Russell P Tracy
- Department of Pathology, University of Vermont, Colchester, VT, 05446, USA
| | - Charles E McCall
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - James H Stein
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA
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40
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Bektas A, Schurman SH, Sen R, Ferrucci L. Human T cell immunosenescence and inflammation in aging. J Leukoc Biol 2017; 102:977-988. [PMID: 28733462 DOI: 10.1189/jlb.3ri0716-335r] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 05/25/2017] [Accepted: 06/19/2017] [Indexed: 12/28/2022] Open
Abstract
The aging process is driven by a finite number of inter-related mechanisms that ultimately lead to the emergence of characteristic phenotypes, including increased susceptibility to multiple chronic diseases, disability, and death. New assays and analytical tools have become available that start to unravel some of these mechanisms. A prevailing view is that aging leads to an imbalance between stressors and stress-buffering mechanisms that causes loss of compensatory reserve and accumulation of unrepaired damage. Central to this paradigm are changes in the immune system and the chronic low-grade proinflammatory state that affect many older individuals, even when they are apparently healthy and free of risk factors. Independent of chronological age, high circulating levels of proinflammatory markers are associated with a high risk of multiple adverse health outcomes in older persons. In this review, we discuss current theories about causes and consequences of the proinflammatory state of aging, with a focus on changes in T cell function. We examine the role of NF-κB activation and its dysregulation and how NF-κB activity differs among subgroups of T cells. We explore emerging hypotheses about immunosenescence and changes in T cell behavior with age, including consideration of the T cell antigen receptor and regulatory T cells (Tregs). We conclude by illustrating how research using advanced technology is uncovering clues at the core of inflammation and aging. Some of the preliminary work in this field is already improving our understanding of the complex mechanisms by which immunosenescence of T cells is intertwined during human aging.
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Affiliation(s)
- Arsun Bektas
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Shepherd H Schurman
- Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA; and
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA;
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41
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Identification of a T cell gene expression clock obtained by exploiting a MZ twin design. Sci Rep 2017; 7:6005. [PMID: 28729616 PMCID: PMC5519672 DOI: 10.1038/s41598-017-05694-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/01/2017] [Indexed: 02/02/2023] Open
Abstract
Many studies investigated age-related changes in gene expression of different tissues, with scarce agreement due to the high number of affecting factors. Similarly, no consensus has been reached on which genes change expression as a function of age and not because of environment. In this study we analysed gene expression of T lymphocytes from 27 healthy monozygotic twin couples, with ages ranging over whole adult lifespan (22 to 98 years). This unique experimental design allowed us to identify genes involved in normative aging, which expression changes independently from environmental factors. We obtained a transcriptomic signature with 125 genes, from which chronological age can be estimated. This signature has been tested in two datasets of same cell type hybridized over two different platforms, showing a significantly better performance compared to random signatures. Moreover, the same signature was applied on a dataset from a different cell type (human muscle). A lower performance was obtained, indicating the possibility that the signature is T cell-specific. As a whole our results suggest that this approach can be useful to identify age-modulated genes.
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42
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Liu H, Smith TPL, Nonneman DJ, Dekkers JCM, Tuggle CK. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics 2017. [PMID: 28646867 PMCID: PMC5483264 DOI: 10.1186/s12864-017-3863-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes and/or transcriptomes. However, neither the reference genome nor the peripheral blood transcriptome of the pig have been sufficiently assembled and annotated to support such profiling assays in this emerging biomedical model organism. We aimed to assemble published and novel RNA-seq data to provide a comprehensive, well-annotated blood transcriptome for pigs by integrating a de novo assembly with a genome-guided assembly. Results A de novo and a genome-guided transcriptome of porcine whole peripheral blood was assembled with ~162 million pairs of paired-end and ~183 million single-end, trimmed and normalized Illumina RNA-seq reads (~6 billion initial reads from 146 RNA-seq libraries) from five independent studies by using the Trinity and Cufflinks software, respectively. We then removed putative transcripts (PTs) of low confidence from both assemblies and merged the remaining PTs into an integrated transcriptome consisting of 132,928 PTs, with 126,225 (~95%) PTs from the de novo assembly and more than 91% of PTs spliced. In the integrated transcriptome, ~90% and 63% of PTs had significant sequence similarity to sequences in the NCBI NT and NR databases, respectively; 68,754 (~52%) PTs were annotated with 15,965 unique gene ontology (GO) terms; and 7618 PTs annotated with Enzyme Commission codes were assigned to 134 pathways curated by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Full exon-intron junctions of 17,528 PTs were validated by PacBio IsoSeq full-length cDNA reads from 3 other porcine tissues, NCBI pig RefSeq mRNAs and transcripts from Ensembl Sscrofa10.2 annotation. Completeness of the 5’ termini of 37,569 PTs was validated by public cap analysis of gene expression (CAGE) data. By comparison to the Ensembl transcripts, we found that (1) the deduced precursors of 54,402 PTs shared at least one intron or exon with those of 18,437 Ensembl transcripts; (2) 12,262 PTs had both longer 5’ and 3’ termini than their maximally overlapping Ensembl transcripts; and (3) 41,838 spliced PTs were totally missing from the Sscrofa10.2 annotation. Similar results were obtained when the PTs were compared to the pig NCBI RefSeq mRNA collection. Conclusions We built, validated and annotated a comprehensive porcine blood transcriptome with significant improvement over the annotation of Ensembl Sscrofa10.2 and the pig NCBI RefSeq mRNAs, and laid a foundation for blood-based high throughput transcriptomic assays in pigs and for advancing annotation of the pig genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3863-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haibo Liu
- Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, 2258 Kildee Hall, Ames, IA, 50011, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Dan J Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 239 Kildee Hall, Ames, IA, 50011, USA
| | - Christopher K Tuggle
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
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43
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Abstract
Background CD4+ T cells can be broadly divided into naïve and memory subsets, each of which are differentially impaired by the aging process. It is unclear if and how these differences are reflected at the transcriptomic level. We performed microarray profiling on RNA derived from naïve (CD44low) and memory (CD44high) CD4+ T cells derived from young (2–3 month) and old (28 month) mice, in order to better understand the mechanisms of age-related functional alterations in both subsets. We also performed follow-up bioinformatic analyses in order to determine the functional consequences of gene expression changes in both of these subsets, and identify regulatory factors potentially responsible for these changes. Results We found 185 and 328 genes differentially expressed (FDR ≤ 0.05) in young vs. old naïve and memory cells, respectively, with 50 genes differentially expressed in both subsets. Functional annotation analyses highlighted an increase in genes involved in apoptosis specific to aged naïve cells. Both subsets shared age-related increases in inflammatory signaling genes, along with a decrease in oxidative phosphorylation genes. Cis-regulatory analyses revealed enrichment of multiple transcription factor binding sites near genes with age-associated expression, in particular NF-κB and several forkhead box transcription factors. Enhancer associated histone modifications were enriched near genes down-regulated in naïve cells. Comparison of our results with previous mouse and human datasets indicates few overlapping genes overall, but suggest consistent up-regulation of Casp1 and Il1r2, and down-regulation of Foxp1 in both mouse and human CD4+ T cells. Conclusions The transcriptomes of naïve and memory CD4+ T cells are distinctly affected by the aging process. However, both subsets exhibit a common increase inflammatory genes and decrease in oxidative phosphorylation genes. NF-κB, forkhead box, and Myc transcription factors are implicated as upstream regulators of these gene expression changes in both subsets, with enhancer histone modifications potentially driving unique changes unique to naïve cells. Finally we conclude that there is little overlap in age-related gene expression changes between humans and mice; however, age-related alterations in a small subset of genes may be conserved. Electronic supplementary material The online version of this article (doi:10.1186/s12979-017-0092-5) contains supplementary material, which is available to authorized users.
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44
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Mu F, Rich-Edwards J, Rimm EB, Spiegelman D, Forman JP, Missmer SA. Association Between Endometriosis and Hypercholesterolemia or Hypertension. Hypertension 2017; 70:59-65. [PMID: 28559401 DOI: 10.1161/hypertensionaha.117.09056] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 01/22/2017] [Accepted: 04/26/2017] [Indexed: 02/01/2023]
Abstract
An altered hormonal or chronic systemic inflammatory milieu characterizing endometriosis may result in a higher risk of hypercholesterolemia and hypertension. Conversely, elevated low-density lipoprotein in hypercholesterolemia and chronic systemic inflammation resulting from hypertension may increase the risk of endometriosis. We assessed the association of laparoscopically confirmed endometriosis with hypercholesterolemia and hypertension in a large prospective cohort study. In 1989, 116 430 registered female nurses aged 25 to 42 completed the baseline questionnaire and were followed for 20 years. Multivariable Cox proportional hazards models were applied. In 1989, there were 4244 women with laparoscopically confirmed endometriosis and 91 554 women without. After adjusting for demographic, anthropometric, family history, reproductive, dietary, and lifestyle risk factors prospectively, comparing women with laparoscopically confirmed endometriosis to women without, the relative risks were 1.25 (95% confidence interval, 1.21-1.30) for development of hypercholesterolemia and 1.14 (95% confidence interval, 1.09-1.18) for hypertension. Conversely, the relative risks of developing laparoscopically confirmed endometriosis were 1.22 (95% confidence interval, 1.15-1.31) comparing women with hypercholesterolemia to women without and 1.29 (95% confidence interval, 1.18-1.41) comparing women with hypertension to women without. The strength of associations of laparoscopically confirmed endometriosis with hypercholesterolemia or hypertension was strongest among women aged ≤40 and weakened as age increased (P values for interaction <0.001). We observed that ≈45% of the associations between endometriosis and hypercholesterolemia and hypertension could be accounted for by treatment factors after endometriosis diagnosis, including greater frequency of hysterectomy/oophorectomy and earlier age for this surgery. In this large cohort study, laparoscopically confirmed endometriosis was prospectively associated with increased risk of hypercholesterolemia and hypertension. Conversely, hypercholesterolemia and hypertension were prospectively associated with higher risk of laparoscopically confirmed endometriosis.
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Affiliation(s)
- Fan Mu
- From the Department of Epidemiology (F.M., J.R.-E., E.B.R., D.S., S.A.M.), Department of Nutrition (E.B.R., D.S.), and Department of Biostatistics (D.S.), Harvard T.H. Chan School of Public Health, Boston, MA; Connors Center for Women's Health and Gender Biology, Brigham and Women's Hospital, Boston, MA (J.R.-E.); and Channing Division of Network Medicine, Department of Medicine (E.B.R., J.P.F., S.A.M.), Renal Division, Department of Medicine (J.P.F.), and Department of Obstetrics, Gynecology, and Reproductive Biology (S.A.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
| | - Janet Rich-Edwards
- From the Department of Epidemiology (F.M., J.R.-E., E.B.R., D.S., S.A.M.), Department of Nutrition (E.B.R., D.S.), and Department of Biostatistics (D.S.), Harvard T.H. Chan School of Public Health, Boston, MA; Connors Center for Women's Health and Gender Biology, Brigham and Women's Hospital, Boston, MA (J.R.-E.); and Channing Division of Network Medicine, Department of Medicine (E.B.R., J.P.F., S.A.M.), Renal Division, Department of Medicine (J.P.F.), and Department of Obstetrics, Gynecology, and Reproductive Biology (S.A.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Eric B Rimm
- From the Department of Epidemiology (F.M., J.R.-E., E.B.R., D.S., S.A.M.), Department of Nutrition (E.B.R., D.S.), and Department of Biostatistics (D.S.), Harvard T.H. Chan School of Public Health, Boston, MA; Connors Center for Women's Health and Gender Biology, Brigham and Women's Hospital, Boston, MA (J.R.-E.); and Channing Division of Network Medicine, Department of Medicine (E.B.R., J.P.F., S.A.M.), Renal Division, Department of Medicine (J.P.F.), and Department of Obstetrics, Gynecology, and Reproductive Biology (S.A.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Donna Spiegelman
- From the Department of Epidemiology (F.M., J.R.-E., E.B.R., D.S., S.A.M.), Department of Nutrition (E.B.R., D.S.), and Department of Biostatistics (D.S.), Harvard T.H. Chan School of Public Health, Boston, MA; Connors Center for Women's Health and Gender Biology, Brigham and Women's Hospital, Boston, MA (J.R.-E.); and Channing Division of Network Medicine, Department of Medicine (E.B.R., J.P.F., S.A.M.), Renal Division, Department of Medicine (J.P.F.), and Department of Obstetrics, Gynecology, and Reproductive Biology (S.A.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - John P Forman
- From the Department of Epidemiology (F.M., J.R.-E., E.B.R., D.S., S.A.M.), Department of Nutrition (E.B.R., D.S.), and Department of Biostatistics (D.S.), Harvard T.H. Chan School of Public Health, Boston, MA; Connors Center for Women's Health and Gender Biology, Brigham and Women's Hospital, Boston, MA (J.R.-E.); and Channing Division of Network Medicine, Department of Medicine (E.B.R., J.P.F., S.A.M.), Renal Division, Department of Medicine (J.P.F.), and Department of Obstetrics, Gynecology, and Reproductive Biology (S.A.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Stacey A Missmer
- From the Department of Epidemiology (F.M., J.R.-E., E.B.R., D.S., S.A.M.), Department of Nutrition (E.B.R., D.S.), and Department of Biostatistics (D.S.), Harvard T.H. Chan School of Public Health, Boston, MA; Connors Center for Women's Health and Gender Biology, Brigham and Women's Hospital, Boston, MA (J.R.-E.); and Channing Division of Network Medicine, Department of Medicine (E.B.R., J.P.F., S.A.M.), Renal Division, Department of Medicine (J.P.F.), and Department of Obstetrics, Gynecology, and Reproductive Biology (S.A.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Liu D, Wang R, Grant AR, Zhang J, Gordon PM, Wei Y, Chen P. Immune adaptation to chronic intense exercise training: new microarray evidence. BMC Genomics 2017; 18:29. [PMID: 28056786 PMCID: PMC5216585 DOI: 10.1186/s12864-016-3388-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/07/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Endurance exercise training, especially the high-intensity training, exhibits a strong influence on the immune system. However, the mechanisms underpinning the immune-regulatory effect of exercise remain unclear. Consequently, we chose to investigate the alterations in the transcriptional profile of blood leukocytes in young endurance athletes as compared with healthy sedentary controls, using Affymetrix human gene 1.1 ST array. RESULTS Group differences in the transcriptome were analyzed using Intensity-based Hierarchical Bayes method followed by a Logistic Regression-based gene set enrichment method. We identified 72 significant transcripts differentially expressed in the leukocyte transcriptome of young endurance athletes as compared with non-athlete controls with a false discovery rate (FDR) < 0.05, comprising mainly the genes encoding ribosomal proteins and the genes involved in mitochondrial oxidative phosphorylation. Gene set enrichment analysis identified three major gene set clusters: two were up-regulated in athletes including gene translation and ribosomal protein production, and mitochondria oxidative phosphorylation and biogenesis; one gene set cluster identified as transcriptionally downregulated in athletes was related to inflammation and immune activity. CONCLUSION Our data indicates that in young healthy individuals, intense endurance exercise training (exemplifed by athletic training) can chronically induce transcriptional changes in the peripheral blood leukocytes, upregulating genes related to protein production and mitochondrial energetics, and downregulating genes involved in inflammatory response. The findings of the study also provide support for the notion that peripheral blood can be used as a surrogate tissue to study the systemic effect of exercise training.
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Affiliation(s)
- Dongmei Liu
- School of Kinesiology, Shanghai University of Sport, Qinyuanhuan Road, #650, Yangpu District, Shanghai, China
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Qinyuanhuan Road, #650, Yangpu District, Shanghai, China
| | - Ana R. Grant
- Department of Computational Medicine & Bioinformatics / Bioinformatics Core, University of Michigan Medical School, Ann Arbor, MI USA
| | - Jinming Zhang
- College of sports medicine and rehabilitation, Taishan Medical University, Shandong Province, China
| | - Paul M. Gordon
- Department of Health, Human Performance and Recreation, Baylor University, Waco, TX USA
| | - Yuqin Wei
- School of Kinesiology, Shanghai University of Sport, Qinyuanhuan Road, #650, Yangpu District, Shanghai, China
| | - Peijie Chen
- School of Kinesiology, Shanghai University of Sport, Qinyuanhuan Road, #650, Yangpu District, Shanghai, China
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Distinct epigenomes in CD4 + T cells of newborns, middle-ages and centenarians. Sci Rep 2016; 6:38411. [PMID: 27917918 PMCID: PMC5137168 DOI: 10.1038/srep38411] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022] Open
Abstract
Age-related variations in genes and microRNAs expression and DNA methylation have been reported respectively; however, their interactions during aging are unclear. We therefore investigated alterations in the transcriptomes, miRNAomes and DNA methylomes in the same CD4+T cells from newborn (NB), middle-aged (MA) and long-lived (LL) individuals to elucidate the molecular changes and their interactions. A total 659 genes showed significantly expression changes across NB, MA and LL individuals, in which we identified four age-related co-expression modules with three hub networks of co-expressed genes and non-coding RNAs. Moreover, we identified 9835 differentially methylated regions (DMRs) including 7015 hypermethylated and 2820 hypomethylated DMRs in the NB compared with the MA, and 12,362 DMRs including 4809 hypermethylated and 7553 hypomethylated DMRs in the MA compared with the LL. The integrated analysis revealed a potential relationship between genes transcription and DNA methylation for many age- or immune-related genes, suggesting that DNA methylation-dependent transcription regulation is involved in development and functions of T cells during aging. Our results reveals age-related transcription and methylation changes and their interactions in human T cells from the cradle to the grave. Longitudinal work is required to establish the relationship between identified age-associated genes/DNA methylation and T cells aging phenotypes.
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da Costa JP, Rocha-Santos T, Duarte AC. Analytical tools to assess aging in humans: The rise of geri-omics. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Tyrrell DJ, Bharadwaj MS, Van Horn CG, Marsh AP, Nicklas BJ, Molina AJA. Blood-cell bioenergetics are associated with physical function and inflammation in overweight/obese older adults. Exp Gerontol 2015; 70:84-91. [PMID: 26226578 DOI: 10.1016/j.exger.2015.07.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 01/25/2023]
Abstract
BACKGROUND Physical function and strength decline with age and lead to limited mobility and independence in older adults. Alterations in mitochondrial function are thought to underlie numerous age-related changes, including declining physical ability. Recent studies suggest that systemic changes in bioenergetic capacity may be reported by analyzing mitochondrial function in circulating cells. The objective of this study was to determine whether the bioenergetic capacity of peripheral blood mononuclear cells (PBMCs) is related to differences in physical function among older, overweight/obese, adults. To address this, we tested the hypothesis that greater PBMC respirometric capacity would be associated with better physical function, muscular strength, leg lean mass, and muscle quality. Furthermore, we tested whether the respirometric capacity of PBMCs is related to cellular composition and inflammatory status reported by interleukin-6 (IL-6). METHODS Fasted PBMC respiration (pmol/min/500,000 cells), expanded short physical performance battery (Ex-SPPB), peak knee extensor (KE) strength (Nm), grip strength (kg), leg lean mass (kg, via dual energy X-ray absorptiometry [DXA]), muscle quality (Nm/kg), and plasma IL-6 (pg/mL) were analyzed in 15 well-functioning, community-dwelling, sedentary overweight/obese older men (n=9) and women (n=6) aged 65 to 78 (mean 68.3 ± 3.5 years). Pearson and partial correlations were calculated to determine associations between PBMC respiration and these variables. RESULTS Higher maximal respiration of PBMCs was associated with better Ex-SPPB (r=0.58, p=0.02), greater KE strength (r=0.60, p=0.02), greater grip strength (r=0.52, p=0.05) and lower IL-6 (r=-0.58, p=0.04). Higher spare respiratory capacity was associated with better Ex-SPPB (r=0.59, p=0.02), greater KE strength (r=0.60, p=0.02), greater grip strength (r=0.54, p=0.04), greater leg muscle quality (r=0.56, p=0.04), and lower IL-6 (r=-0.55, p=0.05). Monocyte and lymphocyte counts were not related to PBMC respiratory capacity. CONCLUSIONS Our results indicate that respirometric profiles of readily obtainable blood cells are associated with physical function and strength. Future studies should be undertaken in order to determine whether blood-based bioenergetic profiling can provide an objective index of systemic mitochondrial health.
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Affiliation(s)
- Daniel J Tyrrell
- Sticht Center on Aging and Department of Internal Medicine, Section on Gerontology and Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Manish S Bharadwaj
- Sticht Center on Aging and Department of Internal Medicine, Section on Gerontology and Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Cynthia G Van Horn
- Sticht Center on Aging and Department of Internal Medicine, Section on Gerontology and Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Anthony P Marsh
- Department of Health and Exercise Science, Wake Forest University, Winston-Salem, NC 27109, United States
| | - Barbara J Nicklas
- Sticht Center on Aging and Department of Internal Medicine, Section on Gerontology and Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Anthony J A Molina
- Sticht Center on Aging and Department of Internal Medicine, Section on Gerontology and Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States.
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