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Opsasnick LA, Zhao W, Schmitz LL, Ratliff SM, Faul JD, Zhou X, Needham BL, Smith JA. Epigenome-wide association study of long-term psychosocial stress in older adults. Epigenetics 2024; 19:2323907. [PMID: 38431869 PMCID: PMC10913704 DOI: 10.1080/15592294.2024.2323907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Long-term psychosocial stress is strongly associated with negative physical and mental health outcomes, as well as adverse health behaviours; however, little is known about the role that stress plays on the epigenome. One proposed mechanism by which stress affects DNA methylation is through health behaviours. We conducted an epigenome-wide association study (EWAS) of cumulative psychosocial stress (n = 2,689) from the Health and Retirement Study (mean age = 70.4 years), assessing DNA methylation (Illumina Infinium HumanMethylationEPIC Beadchip) at 789,656 CpG sites. For identified CpG sites, we conducted a formal mediation analysis to examine whether smoking, alcohol use, physical activity, and body mass index (BMI) mediate the relationship between stress and DNA methylation. Nine CpG sites were associated with psychosocial stress (all p < 9E-07; FDR q < 0.10). Additionally, health behaviours and/or BMI mediated 9.4% to 21.8% of the relationship between stress and methylation at eight of the nine CpGs. Several of the identified CpGs were in or near genes associated with cardiometabolic traits, psychosocial disorders, inflammation, and smoking. These findings support our hypothesis that psychosocial stress is associated with DNA methylation across the epigenome. Furthermore, specific health behaviours mediate only a modest percentage of this relationship, providing evidence that other mechanisms may link stress and DNA methylation.
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Affiliation(s)
- Lauren A. Opsasnick
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Lauren L. Schmitz
- Robert M. La Follette School of Public Affairs, University of Wisconsin-Madison, Madison, WI, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Belinda L. Needham
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
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2
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Tang L, Zhao P, Pan C, Song Y, Zheng J, Zhu R, Wang F, Tang Y. Epigenetic molecular underpinnings of brain structural-functional connectivity decoupling in patients with major depressive disorder. J Affect Disord 2024; 363:249-257. [PMID: 39029702 DOI: 10.1016/j.jad.2024.07.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Major depressive disorder (MDD) is progressively recognized as a stress-related disorder characterized by aberrant brain network dynamics, encompassing both structural and functional domains. Yet, the intricate interplay between these dynamic networks and their molecular underpinnings remains predominantly unexplored. METHODS Both structural and functional networks were constructed using multimodal neuroimaging data from 183 MDD patients and 300 age- and gender-matched healthy controls (HC). structural-functional connectivity (SC-FC) coupling was evaluated at both the connectome- and nodal-levels. Methylation data of five HPA axis key genes, including NR3C1, FKBP5, CRHBP, CRHR1, and CRHR2, were analyzed using Illumina Infinium Methylation EPIC BeadChip. RESULTS We observed a significant reduction in SC-FC coupling at the connectome-level in patients with MDD compared to HC. At the nodal level, we found an imbalance in SC-FC coupling, with reduced coupling in cortical regions and increased coupling in subcortical regions. Furthermore, we identified 23 differentially methylated CpG sites on the HPA axis, following adjustment for multiple comparisons and control of age, gender, and medication status. Notably, three CpG sites on NR3C1 (cg01294526, cg19457823, and cg23430507), one CpG site on FKBP5 (cg25563198), one CpG site on CRHR1 (cg26656751), and one CpG site on CRHR2 (cg18351440) exhibited significant associations with SC-FC coupling in MDD patients. CONCLUSIONS These findings provide valuable insights into the connection between micro-scale epigenetic changes in the HPA axis and SC-FC coupling at macro-scale connectomes. They unveil the mechanisms underlying increased susceptibility to MDD resulting from chronic stress and may suggest potential pharmacological targets within the HPA-axis for MDD treatment.
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Affiliation(s)
- Lili Tang
- Early Intervention Unit, Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China; Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, PR China
| | - Pengfei Zhao
- Early Intervention Unit, Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China
| | - Chunyu Pan
- School of Computer Science and Engineering, Northeastern University, Shenyang, PR China
| | - Yanzhuo Song
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, PR China
| | - Junjie Zheng
- Early Intervention Unit, Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China
| | - Rongxin Zhu
- Early Intervention Unit, Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China
| | - Fei Wang
- Early Intervention Unit, Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, PR China.
| | - Yanqing Tang
- Department of Psychiatry, Shengjing Hospital of China Medical University, Shenyang, Liaoning, PR China.
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3
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Eachus H, Choi MK, Tochwin A, Kaspareit J, Ho M, Ryu S. Elevated glucocorticoid alters the developmental dynamics of hypothalamic neurogenesis in zebrafish. Commun Biol 2024; 7:416. [PMID: 38580727 PMCID: PMC10997759 DOI: 10.1038/s42003-024-06060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/16/2024] [Indexed: 04/07/2024] Open
Abstract
Exposure to excess glucocorticoid (GC) during early development is implicated in adult dysfunctions. Reduced adult hippocampal neurogenesis is a well-known consequence of exposure to early life stress or elevated GC, however the effects on neurogenesis during development and effects on other brain regions are not well understood. Using an optogenetic zebrafish model, here we analyse the effects of GC exposure on neurogenesis during development in the whole brain. We identify that the hypothalamus is a highly GC-sensitive region where elevated GC causes precocious development. This is followed by failed maturation and early decline accompanied by impaired feeding, growth, and survival. In GC-exposed animals, the developmental trajectory of hypothalamic progenitor cells is strikingly altered, potentially mediated by direct regulation of transcription factors such as rx3 by GC. Our data provide cellular and molecular level insight into GC-induced alteration of the hypothalamic developmental trajectory, a process crucial for health across the life-course.
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Affiliation(s)
- Helen Eachus
- Living Systems Institute & Department of Clinical and Biomedical Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Institute of Health and Neurodevelopment & Aston Pharmacy School, Aston University, Birmingham, B4 7ET, UK
| | - Min-Kyeung Choi
- Living Systems Institute & Department of Clinical and Biomedical Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Anna Tochwin
- Living Systems Institute & Department of Clinical and Biomedical Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Johanna Kaspareit
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - May Ho
- Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Soojin Ryu
- Living Systems Institute & Department of Clinical and Biomedical Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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4
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Fraccarollo D, Geffers R, Galuppo P, Bauersachs J. Mineralocorticoid receptor promotes cardiac macrophage inflammaging. Basic Res Cardiol 2024; 119:243-260. [PMID: 38329499 PMCID: PMC11008080 DOI: 10.1007/s00395-024-01032-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Inflammaging, a pro-inflammatory status that characterizes aging and primarily involving macrophages, is a master driver of age-related diseases. Mineralocorticoid receptor (MR) activation in macrophages critically regulates inflammatory and fibrotic processes. However, macrophage-specific mechanisms and the role of the macrophage MR for the regulation of inflammation and fibrotic remodeling in the aging heart have not yet been elucidated. Transcriptome profiling of cardiac macrophages from male/female young (4 months-old), middle (12 months-old) and old (18 and 24 months-old) mice revealed that myeloid cell-restricted MR deficiency prevents macrophage differentiation toward a pro-inflammatory phenotype. Pathway enrichment analysis showed that several biological processes related to inflammation and cell metabolism were modulated by the MR in aged macrophages. Further, transcriptome analysis of aged cardiac fibroblasts revealed that macrophage MR deficiency reduced the activation of pathways related to inflammation and upregulation of ZBTB16, a transcription factor involved in fibrosis. Phenotypic characterization of macrophages showed a progressive replacement of the TIMD4+MHC-IIneg/low macrophage population by TIMD4+MHC-IIint/high and TIMD4-MHC-IIint/high macrophages in the aging heart. By integrating cell sorting and transwell experiments with TIMD4+/TIMD4-macrophages and fibroblasts from old MRflox/MRLysMCre hearts, we showed that the inflammatory crosstalk between TIMD4- macrophages and fibroblasts may imply the macrophage MR and the release of mitochondrial superoxide anions. Macrophage MR deficiency reduced the expansion of the TIMD4- macrophage population and the emergence of fibrotic niches in the aging heart, thereby protecting against cardiac inflammation, fibrosis, and dysfunction. This study highlights the MR as an important mediator of cardiac macrophage inflammaging and age-related fibrotic remodeling.
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Affiliation(s)
- Daniela Fraccarollo
- Department of Cardiology and Angiology, Hannover Medical School, Carl-Neuberg-Str.1 30625, Hannover, Germany.
| | - Robert Geffers
- Research Group Genome Analytics, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Paolo Galuppo
- Department of Cardiology and Angiology, Hannover Medical School, Carl-Neuberg-Str.1 30625, Hannover, Germany
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, Carl-Neuberg-Str.1 30625, Hannover, Germany.
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5
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Welter EM, Benavides S, Archer TK, Kosyk O, Zannas AS. Machine learning-based morphological quantification of replicative senescence in human fibroblasts. GeroScience 2024; 46:2425-2439. [PMID: 37985642 PMCID: PMC10828145 DOI: 10.1007/s11357-023-01007-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/28/2023] [Indexed: 11/22/2023] Open
Abstract
Although aging has been investigated extensively at the organismal and cellular level, the morphological changes that individual cells undergo along their replicative lifespan have not been precisely quantified. Here, we present the results of a readily accessible machine learning-based pipeline that uses standard fluorescence microscope and open access software to quantify the minute morphological changes that human fibroblasts undergo during their replicative lifespan in culture. Applying this pipeline in a widely used fibroblast cell line (IMR-90), we find that advanced replicative age robustly increases (+28-79%) cell surface area, perimeter, number and total length of pseudopodia, and nuclear surface area, while decreasing cell circularity, with phenotypic changes largely occurring as replicative senescence is reached. These senescence-related morphological changes are recapitulated, albeit to a variable extent, in primary dermal fibroblasts derived from human donors of different ancestry, age, and sex groups. By performing integrative analysis of single-cell morphology, our pipeline further classifies senescent-like cells and quantifies how their numbers increase with replicative senescence in IMR-90 cells and in dermal fibroblasts across all tested donors. These findings provide quantitative insights into replicative senescence, while demonstrating applicability of a readily accessible computational pipeline for high-throughput cell phenotyping in aging research.
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Affiliation(s)
- Emma M Welter
- Department of Psychiatry, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Sofia Benavides
- Department of Psychiatry, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - Oksana Kosyk
- Department of Psychiatry, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Anthony S Zannas
- Department of Psychiatry, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, 438 Taylor Hall, 109 Mason Farm Road, Chapel Hill, NC, 27599, USA.
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6
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Zannas AS. Emerging evidence linking stress and glucocorticoid signaling with cancer phenotypes. J Transl Med 2024; 22:147. [PMID: 38347561 PMCID: PMC10863226 DOI: 10.1186/s12967-024-04962-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024] Open
Affiliation(s)
- Anthony S Zannas
- Department of Psychiatry, University of North Carolina, 438 Taylor Hall, 109 Mason Farm Rd, Chapel Hill, NC, 27599-7096, USA.
- Department of Genetics, University of North Carolina, 438 Taylor Hall, 109 Mason Farm Rd, Chapel Hill, NC, 27599-7096, USA.
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7
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Zannas AS, Linnstaedt SD, An X, Stevens JS, Harnett NG, Roeckner AR, Oliver KI, Rubinow DR, Binder EB, Koenen KC, Ressler KJ, McLean SA. Epigenetic aging and PTSD outcomes in the immediate aftermath of trauma. Psychol Med 2023; 53:7170-7179. [PMID: 36951141 DOI: 10.1017/s0033291723000636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
BACKGROUND Psychological trauma exposure and posttraumatic stress disorder (PTSD) have been associated with advanced epigenetic age. However, whether epigenetic aging measured at the time of trauma predicts the subsequent development of PTSD outcomes is unknown. Moreover, the neural substrates underlying posttraumatic outcomes associated with epigenetic aging are unclear. METHODS We examined a multi-ancestry cohort of women and men (n = 289) who presented to the emergency department (ED) after trauma. Blood DNA was collected at ED presentation, and EPIC DNA methylation arrays were used to assess four widely used metrics of epigenetic aging (HorvathAge, HannumAge, PhenoAge, and GrimAge). PTSD symptoms were evaluated longitudinally at the time of ED presentation and over the ensuing 6 months. Structural and functional neuroimaging was performed 2 weeks after trauma. RESULTS After covariate adjustment and correction for multiple comparisons, advanced ED GrimAge predicted increased risk for 6-month probable PTSD diagnosis. Secondary analyses suggested that the prediction of PTSD by GrimAge was driven by worse trajectories for intrusive memories and nightmares. Advanced ED GrimAge was also associated with reduced volume of the whole amygdala and specific amygdala subregions, including the cortico-amygdaloid transition and the cortical and accessory basal nuclei. CONCLUSIONS Our findings shed new light on the relation between biological aging and trauma-related phenotypes, suggesting that GrimAge measured at the time of trauma predicts PTSD trajectories and is associated with relevant brain alterations. Furthering these findings has the potential to enhance early prevention and treatment of posttraumatic psychiatric sequelae.
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Affiliation(s)
- Anthony S Zannas
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Stress Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah D Linnstaedt
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Anesthesiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xinming An
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Anesthesiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer S Stevens
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Nathaniel G Harnett
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Boston, MA, USA
| | - Alyssa R Roeckner
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Katelyn I Oliver
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - David R Rubinow
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Karestan C Koenen
- Department of Epidemiology, Harvard School of Public Health, Harvard University, Boston, MA, USA
- Department of Social and Behavioral Sciences, Harvard School of Public Health, Harvard University, Boston, MA, USA
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel A McLean
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Anesthesiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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8
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Herrera-Martínez AD, Rebollo Román Á, Pascual Corrales E, Idrobo C, Parra Ramírez P, Martín Rojas-Marcos P, Robles Lázaro C, Marginean DL, Araujo-Castro M. Adrenal Incidentalomas and Other Endocrine-Related Adenomas: How Much Does Cortisol Secretion Matter? Cancers (Basel) 2023; 15:4735. [PMID: 37835429 PMCID: PMC10572012 DOI: 10.3390/cancers15194735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Background: Adrenal incidentalomas (AI) are frequent findings in clinical practice. About 40% of AIs are associated with hypercortisolism of variable severity. Although mild autonomous cortisol secretion (MACS) has been associated with the impaired clinical outcome of several diseases, its effect on the development of benign neoplasms is unknown. Aim: To compare the prevalence of adenomas (thyroid, parathyroid, pituitary and other locations) in patients with nonfunctioning AIs (NFAIs) and MACS. Methods: A multicenter, retrospective study of patients with AIs evaluated in four tertiary hospitals was performed. Results: A total of 923 patients were included. Most patients were male (53.6%), with a mean age at diagnosis of 62.4 ± 11.13 years; 21.7% presented with bilateral AIs. MACS was observed in 29.9% (n = 276) of patients, while 69.9% (n = 647) were NFAIs. Adenomas in locations other than the adrenal gland were observed in 36% of the studied population, with a similar distribution in patients with MACS and NFAIs (33% vs. 32%; p > 0.05). There were no statistically significant differences in the prevalence of pituitary, thyroid, parathyroid or other endocrine-related adenomas between both groups, but the prevalence of metabolic comorbidities and mortality was increased in patients with MACS, specifically in patients with thyroid and other endocrine-related adenomas (p < 0.05). Conclusions: Adenomas in locations other than the adrenal glands occur in one third of patients with AIs. Mild autonomous hypercortisolism does not affect the prevalence of other endocrine-related adenomas but is associated with increased metabolic comorbidities and mortality, especially in patients with thyroid adenomas and adenomas in other locations.
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Affiliation(s)
- Aura D. Herrera-Martínez
- Endocrinology & Nutrition Department, Hospital Reina Sofia, 14004 Córdoba, Spain; (Á.R.R.); (D.L.M.)
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain
| | - Ángel Rebollo Román
- Endocrinology & Nutrition Department, Hospital Reina Sofia, 14004 Córdoba, Spain; (Á.R.R.); (D.L.M.)
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain
| | - Eider Pascual Corrales
- Endocrinology & Nutrition Department, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain (C.I.)
- Instituto de Investigación Biomédica Ramón y Cajal (IRYCIS), 28034 Madrid, Spain
| | - Cindy Idrobo
- Endocrinology & Nutrition Department, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain (C.I.)
- Instituto de Investigación Biomédica Ramón y Cajal (IRYCIS), 28034 Madrid, Spain
| | - Paola Parra Ramírez
- Endocrinology & Nutrition Department, Hospital La Paz, 28034 Madrid, Spain (P.M.R.-M.)
| | | | | | - Delia Lavinia Marginean
- Endocrinology & Nutrition Department, Hospital Reina Sofia, 14004 Córdoba, Spain; (Á.R.R.); (D.L.M.)
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), 14004 Córdoba, Spain
| | - Marta Araujo-Castro
- Endocrinology & Nutrition Department, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain (C.I.)
- Instituto de Investigación Biomédica Ramón y Cajal (IRYCIS), 28034 Madrid, Spain
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9
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Bobba-Alves N, Sturm G, Lin J, Ware SA, Karan KR, Monzel AS, Bris C, Procaccio V, Lenaers G, Higgins-Chen A, Levine M, Horvath S, Santhanam BS, Kaufman BA, Hirano M, Epel E, Picard M. Cellular allostatic load is linked to increased energy expenditure and accelerated biological aging. Psychoneuroendocrinology 2023; 155:106322. [PMID: 37423094 PMCID: PMC10528419 DOI: 10.1016/j.psyneuen.2023.106322] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/08/2023] [Accepted: 06/10/2023] [Indexed: 07/11/2023]
Abstract
Stress triggers anticipatory physiological responses that promote survival, a phenomenon termed allostasis. However, the chronic activation of energy-dependent allostatic responses results in allostatic load, a dysregulated state that predicts functional decline, accelerates aging, and increases mortality in humans. The energetic cost and cellular basis for the damaging effects of allostatic load have not been defined. Here, by longitudinally profiling three unrelated primary human fibroblast lines across their lifespan, we find that chronic glucocorticoid exposure increases cellular energy expenditure by ∼60%, along with a metabolic shift from glycolysis to mitochondrial oxidative phosphorylation (OxPhos). This state of stress-induced hypermetabolism is linked to mtDNA instability, non-linearly affects age-related cytokines secretion, and accelerates cellular aging based on DNA methylation clocks, telomere shortening rate, and reduced lifespan. Pharmacologically normalizing OxPhos activity while further increasing energy expenditure exacerbates the accelerated aging phenotype, pointing to total energy expenditure as a potential driver of aging dynamics. Together, our findings define bioenergetic and multi-omic recalibrations of stress adaptation, underscoring increased energy expenditure and accelerated cellular aging as interrelated features of cellular allostatic load.
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Affiliation(s)
- Natalia Bobba-Alves
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Sarah A Ware
- Department of Medicine, Vascular Medicine Institute and Center for Metabolic and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kalpita R Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Anna S Monzel
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Céline Bris
- Department of Genetics, Angers Hospital, Angers, France; MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Guy Lenaers
- Department of Genetics, Angers Hospital, Angers, France; MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France; Department of Neurology, Angers Hospital, Angers, France
| | - Albert Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven CT, United States
| | - Morgan Levine
- Altos Labs, San Diego Institute of Science, San Diego, CA United States
| | - Steve Horvath
- Altos Labs, San Diego Institute of Science, San Diego, CA United States
| | - Balaji S Santhanam
- Departments of Biological Sciences, Systems Biology, and Biochemistry and Molecular Biophysics, Institute for Cancer Dynamics, Columbia University, New York, NY, United States
| | - Brett A Kaufman
- Department of Medicine, Vascular Medicine Institute and Center for Metabolic and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Michio Hirano
- Department of Neurology, Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, United States
| | - Elissa Epel
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States; Department of Neurology, Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, United States; New York State Psychiatric Institute, New York, NY, United States.
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10
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Budkina A, Medvedeva YA, Stupnikov A. Assessing the Differential Methylation Analysis Quality for Microarray and NGS Platforms. Int J Mol Sci 2023; 24:ijms24108591. [PMID: 37239934 DOI: 10.3390/ijms24108591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/28/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Differential methylation (DM) is actively recruited in different types of fundamental and translational studies. Currently, microarray- and NGS-based approaches for methylation analysis are the most widely used with multiple statistical models designed to extract differential methylation signatures. The benchmarking of DM models is challenging due to the absence of gold standard data. In this study, we analyze an extensive number of publicly available NGS and microarray datasets with divergent and widely utilized statistical models and apply the recently suggested and validated rank-statistic-based approach Hobotnica to evaluate the quality of their results. Overall, microarray-based methods demonstrate more robust and convergent results, while NGS-based models are highly dissimilar. Tests on the simulated NGS data tend to overestimate the quality of the DM methods and therefore are recommended for use with caution. Evaluation of the top 10 DMC and top 100 DMC in addition to the not-subset signature also shows more stable results for microarray data. Summing up, given the observed heterogeneity in NGS methylation data, the evaluation of newly generated methylation signatures is a crucial step in DM analysis. The Hobotnica metric is coordinated with previously developed quality metrics and provides a robust, sensitive, and informative estimation of methods' performance and DM signatures' quality in the absence of gold standard data solving a long-existing problem in DM analysis.
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Affiliation(s)
- Anna Budkina
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Yulia A Medvedeva
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia
| | - Alexey Stupnikov
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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Dee G, Ryznar R, Dee C. Epigenetic Changes Associated with Different Types of Stressors and Suicide. Cells 2023; 12:cells12091258. [PMID: 37174656 PMCID: PMC10177343 DOI: 10.3390/cells12091258] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Stress is associated with various epigenetic changes. Some stress-induced epigenetic changes are highly dynamic, whereas others are associated with lasting marks on the epigenome. In our study, a comprehensive narrative review of the literature was performed by investigating the epigenetic changes that occur with acute stress, chronic stress, early childhood stress, and traumatic stress exposures, along with examining those observed in post-mortem brains or blood samples of suicide completers and attempters. In addition, the transgenerational effects of these changes are reported. For all types of stress studies examined, the genes Nr3c1, OXTR, SLC6A4, and BDNF reproducibly showed epigenetic changes, with some modifications observed to be passed down to subsequent generations following stress exposures. The aforementioned genes are known to be involved in neuronal development and hormonal regulation and are all associated with susceptibility to mental health disorders including depression, anxiety, personality disorders, and PTSD (post-traumatic stress disorder). Further research is warranted in order to determine the scope of epigenetic actionable targets in individuals suffering from the long-lasting effects of stressful experiences.
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Affiliation(s)
- Garrett Dee
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA
| | - Rebecca Ryznar
- Molecular Biology, Department of Biomedical Sciences, Rocky Vista University, Parker, CO 80112, USA
| | - Colton Dee
- College of Osteopathic Medicine, Des Moines University, Des Moines, IA 50312, USA
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Zhou W, Karan KR, Gu W, Klein HU, Sturm G, De Jager PL, Bennett DA, Hirano M, Picard M, Mills RE. Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527065. [PMID: 36778249 PMCID: PMC9915708 DOI: 10.1101/2023.02.03.527065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species 1-3 and recently demonstrated to occur in rare instances from one human generation to the next 4. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 post-mortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging 5. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kalpita R. Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Wenjin Gu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612 USA
| | - Michio Hirano
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Neurology, H. Houston Merritt Center, Columbia University Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, USA
- New York State Psychiatric Institute, New York, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Zannas AS. Molecular integrators of stress and aging: the example of FKBP5. Acta Neuropathol 2023; 145:713-715. [PMID: 37020089 DOI: 10.1007/s00401-023-02572-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023]
Affiliation(s)
- Anthony S Zannas
- Department of Psychiatry, University of North Carolina, 438 Taylor Hall, 109 Mason Farm Rd, Chapel Hill, NC, 27599-7096, USA.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
- Carolina Stress Initiative, University of North Carolina, Chapel Hill, NC, USA.
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Welter EM, Kosyk O, Zannas AS. An open access, machine learning pipeline for high-throughput quantification of cell morphology. STAR Protoc 2023; 4:101947. [PMID: 36527712 PMCID: PMC9792532 DOI: 10.1016/j.xpro.2022.101947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Cell morphology is influenced by many factors and can be used as a phenotypic marker. Here we describe a machine-learning-based protocol for high-throughput morphological measurement of human fibroblasts using a standard fluorescence microscope and the pre-existing, open access software ilastik for cell body identification, ImageJ/Fiji for image overlay, and CellProfiler for morphological quantification. Because this protocol overlays nuclei with their cell bodies and relies on coloration differences, it can be broadly applied to other cell types beyond fibroblasts. For details on the use and execution of this protocol, please also refer to Leung et al. (2022).1.
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Affiliation(s)
- Emma M Welter
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Oksana Kosyk
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anthony S Zannas
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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