scholarly journals Impact of large granular lymphocyte leukemia on blood DNA methylation and epigenetic clock modeling in Fischer 344 rats

2021 ◽  
Author(s):  
Giovanni E Finesso ◽  
Ross A McDevitt ◽  
Roshni Roy ◽  
Lauren R Brinster ◽  
Andrea Di Francesco ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Large Granular Lymphocyte ◽  
Epigenetic Clock ◽  
Selection Probability ◽  
Large Granular Lymphocyte Leukemia ◽  
Reduced Representation ◽  
Fischer 344 ◽  
Adverse Health Outcomes ◽  
Epigenetic Age ◽  
F344 Rats

Abstract Age-dependent differences in methylation at specific cytosine-guanosine sites (CpGs) have been used in “epigenetic clock” formulas to predict age. Deviations of epigenetic age from chronological age are informative of health status and are associated with adverse health outcomes, including mortality. In most cases, epigenetic clocks are performed on methylation from DNA extracted from circulating blood cells. However, the effect of neoplastic cells in the circulation on estimation and interpretation of epigenetic clocks is not well understood. Here, we explored this using Fischer 344 (F344) rats, a strain that often develops large granular lymphocyte leukemia (LGL). We found clear histological markers of LGL pathology in the spleens and livers of 27 out of 61 rats aged 17-27 months. We assessed DNA methylation by reduced representation bisulfite sequencing with coverage of 3 million cytosine residues. Although LGL broadly increased DNA methylation variability, it did not change epigenetic aging. Despite this, inclusion of rats with LGL in clock training sets significantly altered predictor selection probability at 83 of 121 commonly utilized CpGs. Furthermore, models trained on rat samples that included individuals with LGL had greater absolute age error than those trained exclusively on LGL-free rats (39% increase; p<0.0001). We conclude that the epigenetic signals for aging and LGL are distinct, such that LGL assessment is not necessary for valid measures of epigenetic age in F344 rats. The precision and architecture of constructed epigenetic clock formulas, however, can be influenced by the presence of neoplastic hematopoietic cells in training set populations.

scholarly journals A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Morgan Levine ◽  
Ross A McDevitt ◽  
Margarita Meer ◽  
Kathy Perdue ◽  
Andrea Di Francesco ◽  
...  
Keyword(s):  
Epigenetic Clock ◽  
Reduced Representation ◽  
Fischer 344 ◽  
Biomarkers Of Aging ◽  
Cell Counts ◽  
Reduced Representation Bisulfite Sequencing ◽  
Epigenetic Age ◽  
Intergenic Regions ◽  
F344 Rats ◽  
Physiological And Biochemical

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.

scholarly journals A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin-associated histone modifications

2020 ◽  
Author(s):  
Morgan Levine ◽  
Ross McDevitt ◽  
Margarita Meer ◽  
Kathy Perdue ◽  
Andrea Di Francesco ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Network Analysis ◽  
Experimental Studies ◽  
Model Systems ◽  
Lung Fibroblasts ◽  
Epigenetic Clock ◽  
Complex Signals ◽  
Reduced Representation ◽  
Cell Counts ◽  
F344 Rats

ABSTRACTAging 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.

scholarly journals Epigenetic clock and DNA methylation studies of roe deer in the wild

2020 ◽  
Author(s):  
Jean-François Lemaître ◽  
Benjamin Rey ◽  
Jean-Michel Gaillard ◽  
Corinne Régis ◽  
Emmanuelle Gilot ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Evolutionary Biology ◽  
Roe Deer ◽  
Chronological Age ◽  
Epigenetic Clock ◽  
Aging Effects ◽  
Methylation Array ◽  
Biomarkers Of Aging ◽  
Epigenetic Age ◽  
The Relationship

AbstractDNA methylation-based biomarkers of aging (epigenetic clocks) promise to lead to new insights in the evolutionary biology of ageing. Relatively little is known about how the natural environment affects epigenetic aging effects in wild species. In this study, we took advantage of a unique long-term (>40 years) longitudinal monitoring of individual roe deer (Capreolus capreolus) living in two wild populations (Chizé and Trois Fontaines, France) facing different ecological contexts to investigate the relationship between chronological age and levels of DNA methylation (DNAm). We generated novel DNA methylation data from n=90 blood samples using a custom methylation array (HorvathMammalMethylChip40). We present three DNA methylation-based estimators of age (DNAm or epigenetic age), which were trained in males, females, and both sexes combined. We investigated how sex differences influenced the relationship between DNAm age and chronological age through the use of sex-specific epigenetic clocks. Our results highlight that both populations and sex influence the epigenetic age, with the bias toward a stronger male average age acceleration (i.e. differences between epigenetic age and chronological ages) particularly pronounced in the population facing harsh environmental conditions. Further, we identify the main sites of epigenetic alteration that have distinct aging patterns across the two sexes. These findings open the door to promising avenues of research at the crossroad of evolutionary biology and biogerontology.

Transplantation of Large Granular Lymphocyte Leukemia in Congenitally Athymic Rats

1992 ◽  
Vol 29 (3) ◽  
pp. 216-222 ◽  
Author(s):  
P. C. Stromberg ◽  
T. J. Rosol ◽  
I. S. Grants ◽  
L. E. Mezza
Keyword(s):  
Tumor Cells ◽  
Hemolytic Anemia ◽  
Cell Function ◽  
Leukemia Cell ◽  
Large Granular Lymphocyte ◽  
White Pulp ◽  
Spleen Cells ◽  
Cell Width ◽  
Large Granular Lymphocyte Leukemia ◽  
F344 Rats

Twenty-two congenitally athymic nude ( rnu/rnu) rats were transplanted with large granular lymphocyte leukemia derived from F344 rats and then compared with ten similar rats inoculated with a suspension of normal F344 rat spleen cells. The normal spleen cells and tumor cells from a spontaneous, naturally occurring leukemia did not grow or cause clinical disease in any of the rats. All rats inoculated with a serially passaged leukemia cell inoculum had local growth at the inoculation site that spread widely and resulted in progressive tumor growth. Death occurred between 16 and 38 days after inoculation. The 22 rats that received passaged tumor cells developed leukemia and splenomegaly. Spleens were diffusely infiltrated by tumor cells and had severe depletion of lymphocytes in the white pulp. Leukemic rats were thrombocytopenic and had hemolytic anemia characterized by increased osmotic fragility, red cell width, and many nucleated erythrocytes. The disease syndrome appears similar to that of F344 rats transplanted with the same inoculum. Because the host rats lacked T cells, it is concluded that the hemolytic anemia and thrombocytopenia that develop in transplanted rats are independent of T cell function.

scholarly journals Novel Epigenetic Clock for Fetal Brain Development Predicts Fetal Epigenetic Age for iPSCs and iPSC-Derived Neurons.

2020 ◽  
Author(s):  
Leonard C Steg ◽  
Gemma L Shireby ◽  
Jennifer Imm ◽  
Jonathan P Davies ◽  
Robert Flynn ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brain Development ◽  
Fetal Brain ◽  
Cell Types ◽  
Biological Research ◽  
Epigenetic Clock ◽  
Cellular Model ◽  
Neuronal Precursor Cells ◽  
Age Related ◽  
Epigenetic Age

Abstract Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the early stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age, and is has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons, here, we establish the fetal brain clock (FBC), a bespoke epigenetic clock trained in prenatal neurodevelopmental samples. Our data show that the FBC outperforms other established epigenetic clocks in predicting the age of fetal brain samples. We then applied the FBC to DNA methylation data of cellular datasets that have profiled iPSCs and iPSC-derived neuronal precursor cells and neurons and find that these cell types are characterized by a fetal epigenetic age. Furthermore, while differentiation from iPSCs to neurons significantly increases the epigenetic age, iPSC-neurons are still predicted as having fetal epigenetic age. Together our findings reiterate the need for better understanding of the limitations of existing epigenetic clocks for answering biological research questions and highlight a potential limitation of iPSC-neurons as a cellular model for the research of age-related diseases as they might not fully recapitulate an aged phenotype.

scholarly journals Alcohol consumption and methylation-based measures of biological age

2021 ◽  
Author(s):  
Jacob K Kresovich ◽  
Alexandra M Martinez Lopez ◽  
Emma L Garval ◽  
Zongli Xu ◽  
Alexandra J White ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Alcohol Consumption ◽  
Biological Age ◽  
Average Lifetime ◽  
Epigenetic Clock ◽  
Genome Wide ◽  
Epigenetic Age ◽  
Epigenetic Age Acceleration ◽  
The Mean ◽  
Average Consumption

Abstract Epigenetic age acceleration is considered a measure of biological aging based on genome-wide patterns of DNA methylation. Although age acceleration has been associated with incidence of diseases and death, less is known about how it is related to lifestyle behaviors. Among 2,316 women, we evaluate associations between self-reported alcohol consumption and various metrics of epigenetic age acceleration. Recent average alcohol consumption was defined as the mean number of drinks consumed per week within the past year; lifetime average consumption was estimated as the mean number of drinks per year drinking. Whole blood genome-wide DNA methylation was measured with HumanMethylation450 BeadChips and used to assess four epigenetic clocks (Hannum, Horvath, PhenoAge, GrimAge) and their corresponding metrics of epigenetic age acceleration (Hannum AgeAccel, Horvath AgeAccel, PhenoAgeAccel, GrimAgeAccel). Although alcohol consumption showed little association with most age acceleration metrics, both lifetime and recent average consumption measures were positively associated with GrimAgeAccel (lifetime, per additional 135 drinks/year: β=0.30 years, 95% CI: 0.11, 0.48, p=0.002; recent, per additional 5 drinks/week: β=0.19 years, 95% CI: 0.01, 0.37, p=0.04). In a mutually adjusted model, only average lifetime alcohol consumption remained associated with GrimAgeAccel (lifetime, per additional 135 drinks/year: β=0.27 years, 95% CI: 0.04, 0.50, p=0.02; recent, per 5 additional drinks/week: β=0.05 years, 95% CI: -0.16, 0.26, p=0.64). Although alcohol use does not appear to be strongly associated with biological age measured by most epigenetic clocks, lifetime average consumption is associated with higher biological age assessed by the GrimAge epigenetic clock.

scholarly journals Novel epigenetic clock for fetal brain development predicts fetal epigenetic age for iPSCs and iPSC-derived neurons

2020 ◽  
Author(s):  
Leonard C. Steg ◽  
Gemma L. Shireby ◽  
Jennifer Imm ◽  
Jonathan P. Davies ◽  
Robert Flynn ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brain Development ◽  
Fetal Brain ◽  
Cell Types ◽  
Biological Research ◽  
Epigenetic Clock ◽  
Cellular Model ◽  
Neuronal Precursor Cells ◽  
Age Related ◽  
Epigenetic Age

AbstractInduced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the early stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age, and is has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons, here, we establish the fetal brain clock (FBC), a bespoke epigenetic clock trained in prenatal neurodevelopmental samples. Our data show that the FBC outperforms other established epigenetic clocks in predicting the age of fetal brain samples. We then applied the FBC to DNA methylation data of cellular datasets that have profiled iPSCs and iPSC-derived neuronal precursor cells and neurons and find that these cell types are characterized by a fetal epigenetic age. Furthermore, while differentiation from iPSCs to neurons significantly increases the epigenetic age, iPSC-neurons are still predicted as having fetal epigenetic age. Together our findings reiterate the need for better understanding of the limitations of existing epigenetic clocks for answering biological research questions and highlight a potential limitation of iPSC-neurons as a cellular model for the research of age-related diseases as they might not fully recapitulate an aged phenotype.

scholarly journals Dysfunctional epigenetic aging of the normal colon and colorectal cancer risk

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Ting Wang ◽  
Sean K. Maden ◽  
Georg E. Luebeck ◽  
Christopher I. Li ◽  
Polly A. Newcomb ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Risk Group ◽  
Risk Groups ◽  
Biological Age ◽  
Chronological Age ◽  
Epigenetic Clock ◽  
Normal Colon ◽  
Epigenetic Aging ◽  
Epigenetic Age ◽  
Epigenetic Age Acceleration

Abstract Background Chronological age is a prominent risk factor for many types of cancers including colorectal cancer (CRC). Yet, the risk of CRC varies substantially between individuals, even within the same age group, which may reflect heterogeneity in biological tissue aging between people. Epigenetic clocks based on DNA methylation are a useful measure of the biological aging process with the potential to serve as a biomarker of an individual’s susceptibility to age-related diseases such as CRC. Methods We conducted a genome-wide DNA methylation study on samples of normal colon mucosa (N = 334). Subjects were assigned to three cancer risk groups (low, medium, and high) based on their personal adenoma or cancer history. Using previously established epigenetic clocks (Hannum, Horvath, PhenoAge, and EpiTOC), we estimated the biological age of each sample and assessed for epigenetic age acceleration in the samples by regressing the estimated biological age on the individual’s chronological age. We compared the epigenetic age acceleration between different risk groups using a multivariate linear regression model with the adjustment for gender and cell-type fractions for each epigenetic clock. An epigenome-wide association study (EWAS) was performed to identify differential methylation changes associated with CRC risk. Results Each epigenetic clock was significantly correlated with the chronological age of the subjects, and the Horvath clock exhibited the strongest correlation in all risk groups (r > 0.8, p < 1 × 10−30). The PhenoAge clock (p = 0.0012) revealed epigenetic age deceleration in the high-risk group compared to the low-risk group. Conclusions Among the four DNA methylation-based measures of biological age, the Horvath clock is the most accurate for estimating the chronological age of individuals. Individuals with a high risk for CRC have epigenetic age deceleration in their normal colons measured by the PhenoAge clock, which may reflect a dysfunctional epigenetic aging process.

scholarly journals Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Leonard C. Steg ◽  
Gemma L. Shireby ◽  
Jennifer Imm ◽  
Jonathan P. Davies ◽  
Alice Franklin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Brain Development ◽  
Embryonic Stem ◽  
Fetal Brain ◽  
Biological Research ◽  
Epigenetic Clock ◽  
Cellular Model ◽  
Neuronal Precursor Cells ◽  
Epigenetic Age

AbstractInduced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and embryonic stem cells and their derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.

scholarly journals Reversing age: dual species measurement of epigenetic age with a single clock

2020 ◽  
Author(s):  
Steve Horvath ◽  
Kavita Singh ◽  
Ken Raj ◽  
Shraddha Khairnar ◽  
Akshay Sanghavi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Training Data ◽  
Rat Tissues ◽  
Epigenetic Clock ◽  
Tissue Samples ◽  
Beneficial Effects ◽  
Biomarkers Of Aging ◽  
Plasma Fraction ◽  
Epigenetic Aging ◽  
Epigenetic Age

AbstractYoung blood plasma is known to confer beneficial effects on various organs in mice. However, it was not known whether young plasma rejuvenates cells and tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly-accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n=593 tissue samples. As indicated by their respective names, the rat pan-tissue clock can be applied to DNA methylation profiles from all rat tissues, while the rat brain-, liver-, and blood clocks apply to the corresponding tissue types. We also developed two epigenetic clocks that apply to both human and rat tissues by adding n=850 human tissue samples to the training data. We employed these six clocks to investigate the rejuvenation effects of a plasma fraction treatment in different rat tissues. The treatment more than halved the epigenetic ages of blood, heart, and liver tissue. A less pronounced, but statistically significant, rejuvenation effect could be observed in the hypothalamus. The treatment was accompanied by progressive improvement in the function of these organs as ascertained through numerous biochemical/physiological biomarkers and behavioral responses to assess cognitive functions. Cellular senescence, which is not associated with epigenetic aging, was also considerably reduced in vital organs. Overall, this study demonstrates that a plasma-derived treatment markedly reverses aging according to epigenetic clocks and benchmark biomarkers of aging.

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