Journal: Frontiers in Genetics

Article Title: Distinct Associations of BMI and Fatty Acids With DNA Methylation in Fasting and Postprandial States in Men

doi: 10.3389/fgene.2021.665769

Figure Lengend Snippet: DNA methylation trend in fasting and postprandial states across BMI classes. Open squares and solid circles, fasting and postprandial state, respectively. Gene name and EPIC array Ow-dmCpG ID are indicated above each graph. N, Ow, and Ob, normal weight, overweight and obese, respectively.

Article Snippet: Ow-dmCpG genomic distribution relative to gene compartments or CpG islands was significantly skewed in favor of promoters and first exons (∼1.8-fold enrichment, p = 0.006; Chi-square test) and CpG islands (∼2.3-fold, p = 9.7 × 10 –8 ), where enrichment was highest of any dmCpG set, compared to the distribution of the 736,741 Infinium methylation EPIC array reference probes ( ).

Techniques: DNA Methylation Assay

Journal: Nature Aging

Article Title: Universal DNA methylation age across mammalian tissues

doi: 10.1038/s43587-023-00462-6

Figure Lengend Snippet: The title of each panel lists the type of universal clock: a , Clock 1 = basic universal clock based on log(Age + 2), b, d, Clock 2 = universal clock for relative age, c, Clock 3 =universal clock for log-linear age. Leave-one-fraction-out (LOFO) methylation estimates versus a–c, chronological age or d, relative age for clock 2. The respective inverse transformations were applied to arrive at DNA methylation-based estimates of chronological age in years or relative age (y-axis).

Article Snippet: We devised a method to impute mammalian methylation array data from human Infinium array data (Supplementary Note ).

Techniques: Methylation, DNA Methylation Assay

Journal: Nature Aging

Article Title: Universal DNA methylation age across mammalian tissues

doi: 10.1038/s43587-023-00462-6

Figure Lengend Snippet: a – p , DNA methylation-based estimates of relative age (y-axis) versus actual relative age (x-axis). The specific tissue or cell type is reported in the title of each panel. Each sample is labeled by mammalian species index and colored by tissue type (Supplementary Data – ). The analysis is restricted to tissues that have at least 15 samples available. Leave-one-fraction-out cross-validation (LOFO) was used to arrive at unbiased estimates of predictive accuracy measures: median absolute error (MAE) and age correlation based on relative age. ‘Cor’ denotes the Pearson correlation coefficient based on all available samples. ‘med.Cor’ denotes the median values across all species for which at least 15 samples were available. Title is marked in blue if a tissue type was collected from a single species.

Article Snippet: We devised a method to impute mammalian methylation array data from human Infinium array data (Supplementary Note ).

Techniques: DNA Methylation Assay, Labeling, Biomarker Discovery

Journal: Nature Aging

Article Title: Universal DNA methylation age across mammalian tissues

doi: 10.1038/s43587-023-00462-6

Figure Lengend Snippet: a – d , g , h , Eutherian EWAS of age. a , Meta-analysis −log 10 ( P values) for age-related CpG sites (annotated by proximal genes) on chromosomes ( x axis in hg38). Top and bottom, CpG sites that gain or lose methylation with age, respectively. CpG sites in red and blue denote highly significant positive and negative age correlation ( P < 10 −200 ), respectively. The most significant CpG (cg12841266, P = 1.41 × 10 −1,001 ) resides in exon 2 on the LHFPL4 gene in humans and most mammals, followed by cg11084334 ( P = 2.59 × 10 −891 ). These two CpG sites and cg097720 ( P = 4.97 × 10 −787 ) located in the paralog gene LHFPL3 are marked with purple diamonds. b – d , Scatterplots of cg12841266 versus chronological age (years) in mini pigs ( Sus scrofa minusculus ) ( b ), Oldfield mice ( Peromyscus polionotus ) ( c ) and horses ( Equus caballus ) ( d ). Tissue samples are labeled by the mammalian species index and colored by tissue type as detailed in Supplementary Data – . e , f , Correlation analysis between Z scores of EWAS of age in eutherians versus marsupials ( e ) and eutherians versus monotremes ( f ). g , h , Annotations of the top 1,000 CpG sites with increased or decreased methylation with age that were identified in EWAS meta-analysis across all species and tissues (results in a ) (brain, cortex, blood, liver, muscle and skin tissues). g , The overlap of age-associated CpG sites across various organs, based on the top 1,000 CpG sites showing positive or negative age correlation in EWAS. The Venn diagram includes 51 age-associated CpG sites shared across all organs, adjacent to 38 genes (35 with positive and three with negative age correlation) categorized by protein family. The 35 positive genes are color coded based on their protein family: two in LHFPL, 12 in homeobox, three in paired box or T-box, three in bHLH, seven in zinc finger and eight in others. h , Selected universal chromatin state and polycomb group protein enrichment results. ORs ( P values) are presented in each cell. The color gradient is based on −log 10 (hypergeometric P value) times sign of OR > 1. The complete results are listed in Extended Data Fig. . State annotation can be found in Supplementary Data . HET denotes heterochromatin. Except for the hypergeometric analysis in h , all figure P values are unadjusted and two sided.

Article Snippet: We devised a method to impute mammalian methylation array data from human Infinium array data (Supplementary Note ).

Techniques: Methylation, Labeling, Protein Enrichment

Journal: Nature Aging

Article Title: Universal DNA methylation age across mammalian tissues

doi: 10.1038/s43587-023-00462-6

Figure Lengend Snippet: Meta-analysis p-value (-log base 10 transformed) versus chromosomal location (x-axis) according to human genome assembly 38 (hg38) in ( a ), brain tissues (across multiple brain regions), ( b ) cerebral cortex, ( c ) blood, ( d ) liver, ( e ) muscle and ( f ) skin tissues. The upper and lower panels of the Manhattan plot depict the CpG sites that gain/lose methylation with age. In panel a, P values were calculated via two-stage meta-analysis that combined EWAS results across strata formed by species/brain-tissue (with n ≥ 15 samples, Methods). CpGs are colored in red and blue if they exhibit highly significant positive and negative age correlations according to a meta analysis P < 1.0 × 10 −40 , 1.0 × 10 −30 , 1.0 × 10 −250 , 1.0 × 10 −50 , 1.0 × 10 −20 and 1.0 × 10 −150 for a–f, respectively. Red dashed horizontal lines denote Bonferroni correction. Gene names are annotated for the top 20 CpGs with positive and negative associations, respectively. CpGs are labeled by adjacent genes. Purple color and diamond shapes mark CpGs of particular interest: cg12841266 and cg11084334 in LHFPL4 and cg09710440 in LHFPL3 . All P-values presented in this figure are unadjusted and computed using two-sided tests.

Article Snippet: We devised a method to impute mammalian methylation array data from human Infinium array data (Supplementary Note ).

Techniques: Transformation Assay, Methylation, Labeling

Journal: Nature Aging

Article Title: Universal DNA methylation age across mammalian tissues

doi: 10.1038/s43587-023-00462-6

Figure Lengend Snippet: Results are reported for different tissues and age groups. a – g , Postnatal development (dev.) (from 1 week to 6 weeks). h – o , Age effects in adult mice. Mean ± s.d. of chronological age is 3.5 ± 1.7 (1.0–6.0) weeks in the developmental age group and 1.12 ± 0.72 (0.15–2.78) years in the post-developmental group. a , h , All tissues combined. Each dot (sample) is colored by the tissue type. o , Pearson correlations between the CpG site and age in additional mouse tissues and cell types from the Mammalian Methylation Consortium. Hemato.prog.LSK, hematopoietic progenitor cells with lineage − Sca-1 + c-Kit + phenotype; max, maximum; min, minimum; n , sample size; SVZ, subventricular zone. Pearson correlation coefficients and nominal (unadjusted) two-sided correlation test P values are shown.

Article Snippet: We devised a method to impute mammalian methylation array data from human Infinium array data (Supplementary Note ).

Techniques: Methylation

Journal: Nature Aging

Article Title: Universal DNA methylation age across mammalian tissues

doi: 10.1038/s43587-023-00462-6

Figure Lengend Snippet: For each species, the age groups were defined with respect to the average ASM obtained from the Animal Aging and Longevity Database (AnAge) (de Magalhaes et al. ). We defined the three age groups using intervals defined by multiples of ASM: young age is defined as age <1.5 × ASM, middle age is defined as age between 1.5ASM and 3.5ASM, and old age is defined by age ≥3.5ASM. Each axis reports a Z score from the meta-analysis EWAS of age across all mammalian species and tissues. Each dot corresponds to a CpG site. Labels are provided for the top ten hypermethylated or hypomethylated CpG sites according to the product of Z scores in x and y axes. CpG sites that are located in LHFPL4 and LHFPL3 are colored in purple. The Pearson correlation coefficient and corresponding nominal (unadjusted) two-sided correlation test P value can be found in the title. a , EWAS of age in young animals versus EWAS in middle-aged animals. b , EWAS of age in middle-aged animals versus EWAS in old animals. c , EWAS of age in young animals versus EWAS of age in old animals. The high pairwise correlations indicate that conserved aging effects in mammals are largely preserved in different age groups. Many of the top CpG sites for conserved aging effects in young mammals remain the top CpG sites for conserved aging effects in old mammals. Specifically, we analyzed the mean methylation levels in eutherians across the three age groups. d , Mean methylation ( y axis) across the top 1,000 CpG sites positively correlated with age according to the EWAS across all mammalian tissue types (Fig. ). The x axis denotes the distance to the closest TSS in a log 10 scale of bp. The positive TSS indicates the direction from 5′ to 3′, and the negative TSS indicates from the direction from 3′ to 5′. The horizontal phase is categorized into three regions: distal upstream → promoter → gene bodies. The mean methylation levels are bounded by 0.2, reflecting that fact that CpG sites beginning with lower methylation levels have higher propensity to increase with age.

Article Snippet: We devised a method to impute mammalian methylation array data from human Infinium array data (Supplementary Note ).

Techniques: Methylation

Journal: Epigenetics

Article Title: Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data

doi: 10.1080/15592294.2024.2375022

Figure Lengend Snippet: Integration of gene expression data with methylation pathways. (a,b) Euler diagrams showing the overlap in statistically significant pathways (FDR <0.05) from gene expression and GSA results (a) and LAM (b) results. (c) Multi-dimensional enrichment analysis of promoter and gene body methylation with gene expression using mitch. Top 20 gene sets shown with the largest absolute enrichment scores after FDR filtering at 0.05.

Article Snippet: Here we aim to develop and evaluate methods for two-tailed FCS of Infinium methylation array data that address these limitations.

Techniques: Gene Expression, Methylation

Journal: Epigenetics

Article Title: Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data

doi: 10.1080/15592294.2024.2375022

Figure Lengend Snippet: Pathway-level DNA methylation alterations with chronological age. (a) Contour heatmap showing the similarity in gene methylation score ranks in the discovery and replication studies. (b) Mitch pathway enrichment scores in discovery and replication studies. Pathways with MANOVA FDR < 0.05 are shown in red while others are shaded grey. (c) Heatmap of 30 pathways with largest absolute enrichment scores after FDR filtering at 0.05. Red indicates increasing methylation and blue shows lower methylation. (d) An example of a pathway identified with this method, ‘creation of C4 and C2 activators’ shows lower methylation of member genes in both discovery and replication studies.

Article Snippet: Here we aim to develop and evaluate methods for two-tailed FCS of Infinium methylation array data that address these limitations.

Techniques: DNA Methylation Assay, Methylation

Journal: Epigenetics

Article Title: Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data

doi: 10.1080/15592294.2024.2375022

Figure Lengend Snippet: Pathway-level DNA methylation differences in natural and IVF conceived infants. (a) Contour heatmap showing the similarity in gene methylation score ranks in the Estill (HM450K) and Novakovic (EPIC) studies. (b) Mitch pathway enrichment scores in Estil and Novakovic studies. Pathways with MANOVA FDR < 0.05 are shown in red while others are shaded grey. (c) Heatmap of 30 pathways with largest absolute enrichment score after FDR filtering at 0.05. Red indicates higher methylation and blue shows lower methylation. (d) An example of a pathway identified with this joint enrichment analysis method, ‘Adrenoreceptors’ shows lower methylation of member genes in both Estill and Novakovic studies.

Article Snippet: Here we aim to develop and evaluate methods for two-tailed FCS of Infinium methylation array data that address these limitations.

Techniques: DNA Methylation Assay, Methylation

Journal: Epigenetics

Article Title: Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data

doi: 10.1080/15592294.2024.2375022

Figure Lengend Snippet: Differential pathway methylation associated with prevalence of 14 common disease states. (a) A bar plot showing the number of statistically significant pathways with higher and lower methylation identified in each prevalent condition (FDR <0.05). (b) A heatmap of enrichment scores for selected pathways across 14 common prevalent disease states. Stars indicate that the pathway was identified as being among the top five differentially methylated pathways in each direction for each condition.

Article Snippet: Here we aim to develop and evaluate methods for two-tailed FCS of Infinium methylation array data that address these limitations.

Techniques: Methylation

Journal: Epigenetics

Article Title: Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data

doi: 10.1080/15592294.2024.2375022

Figure Lengend Snippet: Differential pathway methylation associated with incidence of 19 common disease states. (a) A bar plot showing the number of statistically significant pathways with higher and lower methylation identified in each incident condition (FDR <0.05). (b) A heatmap of enrichment scores for selected pathways across 19 common incident disease states. Stars indicate that the pathway was identified as being among the top three differentially methylated pathways in each direction for each condition.

Article Snippet: Here we aim to develop and evaluate methods for two-tailed FCS of Infinium methylation array data that address these limitations.

Techniques: Methylation

Journal: bioRxiv

Article Title: Functional and multi-omic aging rejuvenation with GLP-1R agonism

doi: 10.1101/2024.05.06.592653

Figure Lengend Snippet: a , Scatter plots showing DNA methylation level changes in aging ( x -axis) vs. exenatide treatment ( y -axis) in sites covered by the Illumina mouse 285k array (mm285k) across different tissue organs and circulating white blood cells (WBCs). Each dot represents one differentially methylated locus (DML), color-coded by treatment (Rx) effect categories as shown in the inset (rejuvenation: opposing aging and Rx effects; exacerbation: same aging and Rx effects; aging- or Rx-dominant: statistically significant in the respective comparison only; no additional label: significant for both aging and Rx effect comparisons, also see Methods ). For each plot, the line represents linear fit. The Spearman correlation coefficients ( R S ) and associated P -values are also shown. Inset of left upper panel: symbol for DNA methylation. b , Summary bar plot of the proportions of DML among the mm285k array sites under different categories (as specified in the inset of a ). c , Similar to b , but for DML among the imputed mammalian conserved sites covered by the mammalian 40k array (mm40k). Sample sizes for the various tissue organs (young adult vehicle, aged vehicle, aged exenatide): hypothalamus (4, 4, 5), frontal cortex (8, 8, 8), hippocampus (8, 8, 8), adipose tissue (8, 8, 8), liver (8, 8, 8), circulating WBCs (5, 9, 6), heart (8, 8, 8), kidney (7, 9, 8), skeletal muscle (8, 8, 8), colon (7, 9, 8), spleen (8, 8, 8).

Article Snippet: DNA methylation assays were carried out by the Clock Foundation using a custom BeadChip array containing loci from the Infinium Mouse Methylation BeadChip (i.e., mm285k array ) and the mammalian methylation array (i.e., mm40k array ).

Techniques: DNA Methylation Assay, Methylation, Comparison

Journal: bioRxiv

Article Title: Functional and multi-omic aging rejuvenation with GLP-1R agonism

doi: 10.1101/2024.05.06.592653

Figure Lengend Snippet: a , Schematic of experimental design for the aged short-term treatment cohort. The animals either received hypothalamic injection of adeno-associated virus vector (AAV) for the expression of shRNA to knockdown Glp1r or scramble shRNA, and either received vehicle, exenatide, or rapamycin treatment. Abbreviations: HTH, hypothalamus. KD, knockdown. OGTT: oral glucose tolerance test. b , Mean (±S.D.) hypothalamic Glp1r transcript expression levels measured with quantitative PCR ( n = 3 mice from each group used for the comparison), relative to the mean of aged control group (i.e., hypothalamic scramble shRNA-AAV injection, treated with vehicle). c , Scatter plots showing transcriptomic changes in aging ( x -axis) vs. exenatide treatment ( y -axis) in different tissue organs and circulating white blood cells (WBCs). Each dot represents one differentially expressed gene (DEG), color-coded by treatment (Rx) effect categories as shown in the inset (rejuvenation: opposing aging and Rx effects; exacerbation: same aging and Rx effects; aging- or Rx-dominant: statistically significant in the respective comparison only; no additional label: significant for both aging and Rx effect comparisons, also see Methods ). Inset of left panel: symbol for transcript. d , Summary bar plot of the proportions of DEGs under different categories (as specified in the inset of c ). e and f , Similar to c and d , but for showing exenatide treatment effects in aged animals with hypothalamic Glp1r knockdown. g , Scatter plots showing DNA methylation level changes in aging ( x -axis) vs. exenatide treatment ( y -axis) in sites covered by the Illumina mouse 285k array (mm285k) across different tissue organs and circulating WBCs. Each dot represents one differentially methylated locus (DML), color-coded by treatment (Rx) effect categories (as shown in the inset of c ). Inset of left panel: symbol for DNA methylation. h , Similar to g , but for showing exenatide treatment effects in aged animals with hypothalamic Glp1r knockdown. i , Scatter plot showing plasma metabolomic changes in aging ( x -axis) vs. exenatide treatment ( y -axis). Each dot represents one metabolite. j , Similar to i , but for showing exenatide treatment effects in aged animals with hypothalamic Glp1r knockdown. In c , e , and g – j , the lines represent linear fits (with confidence interval (grey) in i and j ). The Spearman correlation coefficients ( R S ) and associated P -values are also shown. Sample sizes for data in c – j : n = 5 mice for each experimental group for the various tissues, except n = 4 aged exenatide-treated mice (src group) for circulating WBCs transcriptomic profiling.

Article Snippet: DNA methylation assays were carried out by the Clock Foundation using a custom BeadChip array containing loci from the Infinium Mouse Methylation BeadChip (i.e., mm285k array ) and the mammalian methylation array (i.e., mm40k array ).

Techniques: Injection, Virus, Plasmid Preparation, Expressing, shRNA, Real-time Polymerase Chain Reaction, Comparison, DNA Methylation Assay, Methylation

Journal: bioRxiv

Article Title: Functional and multi-omic aging rejuvenation with GLP-1R agonism

doi: 10.1101/2024.05.06.592653

Figure Lengend Snippet: a , Longitudinal changes in average daily food intake per mouse for animals in the different experimental groups (monitored weekly). Abbreviations: scr, scramble shRNA group; KD, knockdown group. b , Mean (±S.D.) body weight of the animal groups throughout the treatment period (monitored weekly). c , Oral glucose tolerance test (OGTT) results for the different experimental groups at the end of 13-week treatment (Rx) period. P -value: one-way ANOVA with Holm-Sidak’s post-hoc multiple comparisons test for area under the curve (AUC). d , Gonadal fat weight as percentage of body weight in the different experimental groups. P -value: one-way ANOVA with Tukey’s post-hoc test for multiple comparisons. e , Scatter plots showing transcriptomic changes with exenatide treatment in aged control (scramble shRNA) mice ( x -axis) vs. hypothalamic (HTH) Glp1r knockdown ( y -axis) mice across the different tissue organs and circulating white blood cells (WBCs). Each dot represents one differentially expressed gene (DEG), color-coded by treatment (Rx) effect categories as shown in the inset (same or opposite Rx effects; dominant in scr or KD: statistically significant in the respective comparison only; no additional label: significant for both comparisons, also see Methods ). Inset of left panel: symbol for transcript. f , Similar to e , but showing the results for exenatide treatment-induced differentially methylated loci (DML) covered by the Illumina mouse 285k array (mm285k) across different tissue organs and circulating WBCs. Inset of left panel: symbol for DNA methylation. g , Scatter plot showing plasma metabolomic changes with exenatide treatment in aged control (scramble shRNA) mice ( x -axis) vs. HTH Glp1r knockdown ( y -axis) mice. For each plot in e – g , the line represents linear fit (with confidence interval (grey) in g ). The Spearman correlation coefficients ( R S ) and associated P -values are also shown. Sample sizes for data in all plots: n = 5 mice for each experimental group for the various tissues, except n = 4 aged exenatide-treated mice for circulating WBCs transcriptomic profiling.

Article Snippet: DNA methylation assays were carried out by the Clock Foundation using a custom BeadChip array containing loci from the Infinium Mouse Methylation BeadChip (i.e., mm285k array ) and the mammalian methylation array (i.e., mm40k array ).

Techniques: shRNA, Comparison, Methylation, DNA Methylation Assay

Journal: bioRxiv

Article Title: Functional and multi-omic aging rejuvenation with GLP-1R agonism

doi: 10.1101/2024.05.06.592653

Figure Lengend Snippet: a , Scatter plots showing transcriptomic changes in aging ( x -axis) vs. rapamycin treatment ( y -axis) in different tissue organs and circulating white blood cells (WBCs). Each dot represents one differentially expressed gene (DEG), color-coded by treatment (Rx) effect categories as shown in the inset (rejuvenation: opposing aging and Rx effects; exacerbation: same aging and Rx effects; aging- or Rx-dominant: statistically significant in the respective comparison only; no additional label: significant for both aging and Rx effect comparisons, also see Methods ). Inset of left panel: symbol for transcript. b , Summary bar plot of the proportions of differentially expressed genes (DEGs) under different categories (as specified in the inset of a ). c , Scatter plots showing DNA methylation level changes in aging ( x -axis) vs. exenatide treatment ( y -axis) in sites covered by the Illumina mouse 285k array (mm285k) across different tissue organs and circulating WBCs. Each dot represents one differentially methylated locus (DML), color-coded by treatment Rx effect categories (as shown in the inset of a ). Inset of left panel: symbol for DNA methylation. d , Scatter plot showing plasma metabolomic changes in aging ( x -axis) vs. rapamycin treatment ( y -axis). Each dot represents one metabolite. e , f , and g , Scatter plots showing transcriptomic ( e ), DNA methylation level ( f ), and plasma metabolomic ( g ) changes with rapamycin ( x -axis) vs. exenatide ( y -axis) treatment. Inset of e , DEG and DML categories, indicating: same or opposite Rx effects; GLP-1RA- or mTORi-dominant: statistically significant in the respective comparison only; no additional label: significant for both Rx effect comparisons (also see Methods ). Inset of left panels of e and f : symbols for transcript and DNA methylation, respectively. In a , c – g , the lines represent linear fits (with confidence interval (grey) in d and g ). The Spearman correlation coefficients ( R S ) and associated P -values are also shown. h , Heatmap showing the normalized expression (Norm. exp.) levels of significant differentially expressed gene modules with exenatide and/or rapamycin treatment. Inset (left) shows the color coding for tissue origin and Rx effect category (i.e., significant with exenatide, rapamycin, or both treatments). i , Bubble chart showing the gene ontology–biological process (GO:BP) pathways with significant enrichment among the different treatment-upregulated gene modules with exenatide and/or rapamycin treatment (top 3 for each tissue organ/circulating WBCs plotted). Gene count is represented with bubble size. Tissue origin and Rx effect category are color-coded as per the inset. j , Similar to i , but for treatment-downregulated gene modules. Sample sizes for all plots: n = 5 mice for each experimental group for the various tissues, except n = 4 aged exenatide- and 4 rapamycin-treated mice for circulating WBCs transcriptomic profiling.

Article Snippet: DNA methylation assays were carried out by the Clock Foundation using a custom BeadChip array containing loci from the Infinium Mouse Methylation BeadChip (i.e., mm285k array ) and the mammalian methylation array (i.e., mm40k array ).

Techniques: Comparison, DNA Methylation Assay, Methylation, Expressing