14 results on '"Kyra Thrush"'
Search Results
2. Aging biomarkers and the brain
- Author
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Albert T. Higgins-Chen, Kyra Thrush, and Morgan E. Levine
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Aged, 80 and over ,0301 basic medicine ,Aging ,Brain ,Context (language use) ,Cognition ,Cell Biology ,Disease ,Biology ,Article ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Neuroimaging ,Humans ,Biomarker (medicine) ,Neuroscience ,Brain aging ,Biomarkers ,030217 neurology & neurosurgery ,Aged ,Developmental Biology - Abstract
Quantifying biological aging is critical for understanding why aging is the primary driver of morbidity and mortality and for assessing novel therapies to counter pathological aging. In the past decade, many biomarkers relevant to brain aging have been developed using various data types and modeling techniques. Aging involves numerous interconnected processes, and thus many complementary biomarkers are needed, each capturing a different slice of aging biology. Here we present a hierarchical framework highlighting how these biomarkers are related to each other and the underlying biological processes. We review those measures most studied in the context of brain aging: epigenetic clocks, proteomic clocks, and neuroimaging age predictors. Many studies have linked these biomarkers to cognition, mental health, brain structure, and pathology during aging. We also delve into the challenges and complexities in interpreting these biomarkers and suggest areas for further innovation. Ultimately, a robust mechanistic understanding of these biomarkers will be needed to effectively intervene in the aging process to prevent and treat age-related disease.
- Published
- 2021
3. Revisiting the bad luck hypothesis: Cancer risk and aging are linked to replication-driven changes to the epigenome
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Christopher J. Minteer, Kyra Thrush, Peter Niimi, Joel Rozowsky, Jason Liu, Mor Frank, Thomas McCabe, Erin Hofstatter, Mariya Rozenblit, Lajos Pusztai, Kenneth Beckman, Mark Gerstein, and Morgan E. Levine
- Abstract
Aging is the leading risk factor for cancer. While it’s been proposed that the age-related accumulation of somatic mutations drives this relationship, it is likely not the full story. Here, we show that both aging and cancer share a common epigenetic replication signature, which we modeled from DNA methylation data in extensively passaged immortalized human cells in vitro and tested on clinical tissues. This epigenetic signature of replication – termed CellDRIFT – increased with age across multiple tissues, distinguished tumor from normal tissue, and was escalated in normal breast tissue from cancer patients. Additionally, within-person tissue differences were correlated with both predicted lifetime tissue-specific stem cell divisions and tissue-specific cancer risk. Overall, our findings suggest that age-related replication drives epigenetic changes in cells, pushing them towards a more tumorigenic state.One sentence summaryCellular replication leaves an epigenetic fingerprint that may partially underly the age-associated increase in cancer risk.
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- 2022
4. Epigenetic Age Acceleration as a Risk Predictor of Hepatocellular Carcinoma
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Aesis Luna and Kyra Thrush
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Genetics ,Molecular Biology ,Biochemistry ,Biotechnology - Published
- 2022
5. Abstract PR009: Revisiting the bad luck hypothesis: Cancer risk and aging are linked to replication-driven changes to the epigenome
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Christopher J. Minteer, Kyra Thrush, Peter Niimi, Joel Rozowsky, Jason Liu, Mor Frank, Thomas McCabe, Erin Hofstatter, Mariya Rozenblit, Lajos Pusztai, Kenneth Beckman, Mark Gerstein, and Morgan E. Levine
- Subjects
Cancer Research ,Oncology - Abstract
Aging is the leading risk factor for cancer. While some have proposed that the age-related accumulation of somatic mutations drives this relationship, it is likely not the full story. Here, we show that both aging and cancer share a common epigenetic replication signature, which we modeled from DNA methylation data in extensively passaged immortalized human cells in vitro and tested on clinical tissues. This epigenetic signature of replication – termed CellDRIFT – increased with age across multiple tissues, distinguished tumor from normal tissue, and was escalated in normal breast tissue from cancer patients. Additionally, within-person tissue differences were correlated with both predicted lifetime tissue-specific stem cell divisions and tissue-specific cancer risk. Overall, our findings suggest that age-related replication drives epigenetic changes in cells, potentially pushing them towards a more tumorigenic state. Citation Format: Christopher J. Minteer, Kyra Thrush, Peter Niimi, Joel Rozowsky, Jason Liu, Mor Frank, Thomas McCabe, Erin Hofstatter, Mariya Rozenblit, Lajos Pusztai, Kenneth Beckman, Mark Gerstein, Morgan E. Levine. Revisiting the bad luck hypothesis: Cancer risk and aging are linked to replication-driven changes to the epigenome [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr PR009.
- Published
- 2023
6. Clock Work: Deconstructing the Epigenetic Clock Signals in Aging, Disease, and Reprogramming
- Author
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Morgan E Levine, Albert Higgins-Chen, Kyra Thrush, Christopher Minteer, and Peter Niimi
- Abstract
Epigenetic clocks have come to be regarded as powerful tools for estimating aging. However, a major drawback in their application is our lack of mechanistic understanding. We hypothesize that uncovering the underlying biology is difficult due to the fact that epigenetic clocks are multifactorial composites: They are comprised of disparate parts, each with their own causal mechanism and functional consequences. Thus, only by deconstructing epigenetic clock signals will it be possible to glean biological insight. Here we clustered 5,717 clock CpGs into twelve distinct modules using multi-tissue and in-vitro datasets. We show that epigenetic clocks are comprised of different proportions of modules, which may explain their discordance when simultaneously applied in a given study. We also observe that epigenetic reprogramming does not ‘reset’ the entire clock and instead the observed rejuvenation is driven by a subset of modules. Overall, two modules stand-out in terms of their unique features. The first is one of the most responsive to epigenetic reprogramming; is the strongest predictor of all-cause mortality; and shows increases with in vitro passaging up until senescence burden begins to emerge. The light-second module is moderately responsive to reprogramming; is very accelerated in tumor vs. normal tissues; and tracks with passaging in vitro even as population doublings decelerate. Overall, we show that clock deconstruction can identify unique DNAm alterations and facilitate our mechanistic understanding of epigenetic clocks.
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- 2022
7. A computational solution for bolstering reliability of epigenetic clocks: Implications for clinical trials and longitudinal tracking
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Stefania Bandinelli, Yunzhang Wang, Elbert Geuze, Eileen M. Crimmins, Christopher Minteer, Meng Wang, Stefanie Schreiter, Marco P. Boks, Albert T. Higgins-Chen, Ann Zenobia Moore, Pei-Lun Kuo, Morgan E. Levine, Jurjen J. Luykx, Marte Z. van der Horst, Bart P. F. Rutten, Sara Hägg, Kyra Thrush, Eric Vermetten, Luigi Ferrucci, Cynthia Okhuijsen-Pfeifer, Stefan Gutwinski, Christiaan H. Vinkers, and Tina T. Hu-Seliger
- Subjects
business.industry ,Computer science ,dNaM ,Machine learning ,computer.software_genre ,Clinical trial ,Noise ,Random noise ,Principal component analysis ,Personalized medicine ,Epigenetics ,Artificial intelligence ,business ,computer ,Reliability (statistics) - Abstract
Epigenetic clocks are widely used aging biomarkers calculated from DNA methylation data. Unfortunately, measurements for individual CpGs can be surprisingly unreliable due to technical noise, and this may limit the utility of epigenetic clocks. We report that noise produces deviations up to 3 to 9 years between technical replicates for six major epigenetic clocks. The elimination of low-reliability CpGs does not ameliorate this issue. Here, we present a novel computational multi-step solution to address this noise, involving performing principal component analysis on the CpG-level data followed by biological age prediction using principal components as input. This method extracts shared systematic variation in DNAm while minimizing random noise from individual CpGs. Our novel principal-component versions of six clocks show agreement between most technical replicates within 0 to 1.5 years, equivalent or improved prediction of outcomes, and more stable trajectories in longitudinal studies and cell culture. This method entails only one additional step compared to traditional clocks, does not require prior knowledge of CpG reliabilities, and can improve the reliability of any existing or future epigenetic biomarker. The high reliability of principal component-based epigenetic clocks will make them particularly useful for applications in personalized medicine and clinical trials evaluating novel aging interventions.
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- 2021
8. Author response: A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin
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Andrea Di Francesco, Luigi Ferrucci, Margarita Meer, Theresa Meade, Colin Farrell, Ross A. McDevitt, Kyra Thrush, Matteo Pellegrini, Christopher Dunn, Kathy A Perdue, Meng Wang, Rafael de Cabo, and Morgan E. Levine
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Heterochromatin ,Epigenetics ,Biology ,Phenotype ,Cell biology - Published
- 2020
9. A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin
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Kathy A Perdue, Meng Wang, Christopher Dunn, Rafael de Cabo, Luigi Ferrucci, Ross A. McDevitt, Andrea Di Francesco, Kyra Thrush, Margarita Meer, Colin Farrell, Theresa Meade, Matteo Pellegrini, and Morgan E. Levine
- Subjects
0301 basic medicine ,Male ,Aging ,Mouse ,Inbred C57BL ,Epigenesis, Genetic ,Mice ,computational biology ,0302 clinical medicine ,Biomarkers of aging ,Heterochromatin ,E2F1 ,rat ,Biology (General) ,Genetics ,Inbred F344 ,DNA methylation ,General Neuroscience ,systems biology ,General Medicine ,Phenotype ,030220 oncology & carcinogenesis ,Reduced representation bisulfite sequencing ,Medicine ,caloric restriction ,Research Article ,Computational and Systems Biology ,QH301-705.5 ,Science ,1.1 Normal biological development and functioning ,Genomics ,Biology ,Basic Behavioral and Social Science ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Genetic ,Underpinning research ,Biological Clocks ,Behavioral and Social Science ,genomics ,Animals ,Epigenetics ,mouse ,General Immunology and Microbiology ,Human Genome ,Genetics and Genomics ,Rats, Inbred F344 ,Rats ,biological age ,Mice, Inbred C57BL ,030104 developmental biology ,Rat ,Generic health relevance ,Biochemistry and Cell Biology ,Biomarkers ,epigenetic clock ,Epigenesis ,Unsupervised Machine Learning - Abstract
Robust biomarkers of aging have been developed from DNA methylation in humans and more recently, in mice. This study aimed to generate a novel epigenetic clock in rats—a model with unique physical, physiological, and biochemical advantages—by incorporating behavioral data, unsupervised machine learning, and network analysis to identify epigenetic signals that not only track with age, but also relates to phenotypic aging. Reduced representation bisulfite sequencing (RRBS) data was used to train an epigenetic age (DNAmAge) measure in Fischer 344 CDF (F344) rats. This measure correlated with age at (r = 0.93) in an independent sample, and related to physical functioning (p=5.9e-3), after adjusting for age and cell counts. DNAmAge was also found to correlate with age in male C57BL/6 mice (r = 0.79), and was decreased in response to caloric restriction. Our signatures driven by CpGs in intergenic regions that showed substantial overlap with H3K9me3, H3K27me3, and E2F1 transcriptional factor binding.
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- 2020
10. A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin-associated histone modifications
- Author
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Ross A. McDevitt, Kathy A Perdue, Kyra Thrush, Andrea Di Francesco, Matteo Pellegrini, Luigi Ferrucci, Meng Wang, Christopher A. Dunn, Theresa Meade, Rafael de Cabo, Margarita Meer, Colin Farrell, and Morgan E. Levine
- Subjects
Histone ,biology ,Heterochromatin ,Reduced representation bisulfite sequencing ,DNA methylation ,biology.protein ,dNaM ,Epigenetics ,Induced pluripotent stem cell ,Gene ,Cell biology - Abstract
Aging has been shown to be a strong driver of DNA methylation changes, leading to the development of robust biomarkers in humans and more recently, in mice. This study aimed to generate a novel epigenetic clock in rats—a model with unique physical, physiological, and biochemical advantages for studying mammalian aging. Additionally, we incorporated behavioral data, unsupervised machine learning, and network analysis to identify epigenetic signals that not only track with age, but also relate to phenotypic aging and reflect higher-order molecular aging changes. We used DNAm data from reduced representation bisulfite sequencing (RRBS) to train an epigenetic age (DNAmAge) measure in Fischer 344 CDF (F344) rats. In an independent sample of n=32 F344 rats, we found that this measure correlated with age at (r=0.93), and related to physical functioning (5.9e-3), after adjusting for age and differential cell counts. DNAmAge was also found to correlate with age in C57BL/6 mice (r=0.79), and was decreased in response to caloric restriction (CR), such that the longer the animal was on a CR diet, the greater the decrease in DNAm. We also observed resetting of DNAm when kidney and lung fibroblasts when converted to induced pluripotent stem cells (iPSCs). Using weighted gene correlation network analysis (WGCNA) we identified two modules that appeared to drive our DNAmAge measure. These two modules contained CpGs in intergenic regions that showed substantial overlap with histone marks H3K9me3, H3K27me3, and E2F1 transcriptional factor binding. In moving forward, our ability to unravel the complex signals linking DNA methylation changes to functional aging would require experimental studies in model systems in which longitudinal epigenetic changes can be related to other molecular and physiological hallmarks of aging.
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- 2020
11. Underlying features of epigenetic aging clocks in vivo and in vitro
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Wei Zhao, Luigi Ferrucci, Diana Leung, Jennifer A. Smith, Kyra Thrush, Scott M. Ratliff, Zuyun Liu, Toshiko Tanaka, Lauren Schmitz, and Morgan E. Levine
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0301 basic medicine ,Senescence ,Epigenomics ,Male ,Aging ,CD14 ,Computational biology ,Mitochondrion ,Biology ,03 medical and health sciences ,0302 clinical medicine ,In vivo ,Biological Clocks ,Humans ,cellular senescence ,Epigenetics ,DNA methylation ,Autophagy ,Cell Biology ,Original Articles ,In vitro ,mitochondria ,030104 developmental biology ,biological aging ,Female ,Original Article ,030217 neurology & neurosurgery ,epigenetic clock - Abstract
Epigenetic clocks, developed using DNA methylation data, have been widely used to quantify biological aging in multiple tissues/cells. However, many existing epigenetic clocks are weakly correlated with each other, suggesting they may capture different biological processes. We utilize multi‐omics data from diverse human tissue/cells to identify shared features across eleven existing epigenetic clocks. Despite the striking lack of overlap in CpGs, multi‐omics analysis suggested five clocks (Horvath1, Horvath2, Levine, Hannum, and Lin) share transcriptional associations conserved across purified CD14+ monocytes and dorsolateral prefrontal cortex. The pathways enriched in the shared transcriptional association suggested links between epigenetic aging and metabolism, immunity, and autophagy. Results from in vitro experiments showed that two clocks (Levine and Lin) were accelerated in accordance with two hallmarks of aging—cellular senescence and mitochondrial dysfunction. Finally, using multi‐tissue data to deconstruct the epigenetic clock signals, we developed a meta‐clock that demonstrated improved prediction for mortality and robustly related to hallmarks of aging in vitro than single clocks., We compared 11 existing epigenetic clocks on the basis of their functional characteristics, transcriptional associations, and ability to capture hallmarks of aging. We then decomposed their signals and recombined them into a “meta‐clock.” This meta‐clock showed stronger prediction of all‐cause mortality than any one epigenetic clock and was able to distinguish tumor from normal tissue and capture epigenetic changes in two types of senescence (replicative and oncogene induced).
- Published
- 2020
12. A Computational Solution to Bolster Epigenetic Clock Reliability for Clinical Trials and Longitudinal Tracking
- Author
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Albert Higgins-Chen, Kyra Thrush, Tina Hu-Seliger, Yunzhang Wang, Sara Hagg, and Morgan Levine
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Abstracts ,Session 1015 (Symposium) ,Health (social science) ,Life-span and Life-course Studies ,AcademicSubjects/SOC02600 ,Health Professions (miscellaneous) - Abstract
Epigenetic clocks are widely used aging biomarkers, but they are calculated from methylation data for individual CpGs that can be surprisingly unreliable. We report that technical noise causes six major epigenetic clocks to deviate by 3 to 9 years between replicates. We present a novel computational solution: we perform principal component analysis followed by biological age prediction using principal components, extracting shared age-related changes across CpGs while ignoring noise from individual CpGs. Our novel principal-component versions of six clocks show agreement between most technical replicates within 1 year, and increased stability in short- and long-term longitudinal studies. This requires only one additional step compared to traditional clocks, does not require prior knowledge of CpG reliabilities, and can improve the reliability of any existing or future epigenetic biomarker. The extremely high reliability of principal component epigenetic clocks makes them particularly useful for personalized medicine and clinical trials evaluating novel aging interventions.
- Published
- 2021
13. Multiscale Brain Aging in the Context of Neurodegeneration and Alzheimer's Disease
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Kyra Thrush and Yaroslav Markov
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Health (social science) ,Life-span and Life-course Studies ,Health Professions (miscellaneous) - Abstract
The brain, with a diverse array of specialized cells, regional substructures, and a relatively isolated microenvironment, represents a uniquely challenging organ system for aging research. The brain can experience physical trauma, interact with the periphery, and is responsible for cognitive and behavioral modifications that can feed back into the molecular processes of aging both within and external to the brain. Advances to our understanding and ability to intervene in the complexity that personifies brain aging and associated neurodegeneration will require integrated, multiscale approaches operating in tandem. Therefore, we have organized this symposium to highlight promising new approaches to study brain aging through the lens of multiple biological levels of organization. We will provide insight not only into normal brain aging, but will also suggest key spurious processes that may drive neurodegeneration and functional decline.
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- 2021
14. Deep Learning Methods Capture Non-Linear Brain Aging Patterns Underlying Alzheimer’s Disease and Resilience
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Kyra Thrush, Albert Higgins-Chen, Yaroslav Markov, Raghav Sehgal, and Morgan Levine
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Health (social science) ,Life-span and Life-course Studies ,Health Professions (miscellaneous) - Abstract
The current era of multi-omics data collection has enabled researchers to obtain exceptionally comprehensive profiling of disease subjects. However, exceptionally high dimensionality can ultimately be an obstacle to biological insight. Previously, we presented a method in which penalized regression of methylation principal components reduces noise and improves prediction of age, disease, and Alzheimer’s Disease (AD) pathophysiology. However, strictly linear methods may overly simplify the complex epigenetic aging landscape. We hypothesized that non-linear deep learning methods could identify molecular signatures that better reflect individual resilience to AD. Through the use of an autoencoder to represent high dimensional methylation array data, and supplemental machine learning methods, we connect latent nonlinear representations of the brain to aging, resilience, and indications of AD. In particular, resultant age-predicting representations of methylation were correlated with enrichment of methylation regions and biological pathways. Contextualized within AD pathology, this work provides valuable, ongoing insight into resilience in AD.
- Published
- 2021
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