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We collected published datasets of human blood samples for gene expression, DNA methylation, and single-cell transcriptomic data. The analysis aimed to study the relation between the expression and DNA methylation of retrotransposons (RTEs) versus chronological and biological aging in large human cohorts. The single-cell transcriptomic datasets were employed for cell type-specific analysis of RTEs in peripheral blood mononuclear cell (PBMC) to identify the relation between RTE expression and aging events for annotated cell types within old versus young PBMC samples.

Journal: eLife

Article Title: Expression of most retrotransposons in human blood correlates with biological aging

doi: 10.7554/eLife.96575

Figure Lengend Snippet: We collected published datasets of human blood samples for gene expression, DNA methylation, and single-cell transcriptomic data. The analysis aimed to study the relation between the expression and DNA methylation of retrotransposons (RTEs) versus chronological and biological aging in large human cohorts. The single-cell transcriptomic datasets were employed for cell type-specific analysis of RTEs in peripheral blood mononuclear cell (PBMC) to identify the relation between RTE expression and aging events for annotated cell types within old versus young PBMC samples.

Article Snippet: By overlapping Illumina microarray expression and methylation probe locations to RTE locations in RepeatMasker , we were able to identify a sufficient number of probes to calculate the expression and methylation levels of RTE classes and families.

Techniques: Gene Expression, DNA Methylation Assay, Expressing

(a, b), Methylation levels of RTE classes inversely correlated with chronological age in monocyte (Multi-Ethnic Study of Atherosclerosis, MESA) and whole blood (WB) (BSGS, SATSA, and GMPWAR) samples. Satellite DNA was included as a control group. ( c ), Methylation levels versus low (first quartile), medium (second and third quartile), and high (fourth quartile) expressions of RTE classes in monocytes (MESA). Wilcoxon test; ns: not significant. ( d ), Correlation matrix for RTE expressions and methylation levels, and chronological age. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001, Pearson’s correlation. MESA, n=1202; BSGS, n=614; GMPWAR, n=656; SATSA, n=1072.

Journal: eLife

Article Title: Expression of most retrotransposons in human blood correlates with biological aging

doi: 10.7554/eLife.96575

Figure Lengend Snippet: (a, b), Methylation levels of RTE classes inversely correlated with chronological age in monocyte (Multi-Ethnic Study of Atherosclerosis, MESA) and whole blood (WB) (BSGS, SATSA, and GMPWAR) samples. Satellite DNA was included as a control group. ( c ), Methylation levels versus low (first quartile), medium (second and third quartile), and high (fourth quartile) expressions of RTE classes in monocytes (MESA). Wilcoxon test; ns: not significant. ( d ), Correlation matrix for RTE expressions and methylation levels, and chronological age. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001, Pearson’s correlation. MESA, n=1202; BSGS, n=614; GMPWAR, n=656; SATSA, n=1072.

Article Snippet: By overlapping Illumina microarray expression and methylation probe locations to RTE locations in RepeatMasker , we were able to identify a sufficient number of probes to calculate the expression and methylation levels of RTE classes and families.

Techniques: Methylation, Control

(a, b), Methylation levels of long terminal repeats (LTR) and LINE/SINE families negatively correlate with chronological age in monocytes (MESA) and the WB (BSGS, SATSA, and GMPWAR). **p≤0.01, ***p≤0.001, Wilcoxon test.

Journal: eLife

Article Title: Expression of most retrotransposons in human blood correlates with biological aging

doi: 10.7554/eLife.96575

Figure Lengend Snippet: (a, b), Methylation levels of long terminal repeats (LTR) and LINE/SINE families negatively correlate with chronological age in monocytes (MESA) and the WB (BSGS, SATSA, and GMPWAR). **p≤0.01, ***p≤0.001, Wilcoxon test.

Article Snippet: By overlapping Illumina microarray expression and methylation probe locations to RTE locations in RepeatMasker , we were able to identify a sufficient number of probes to calculate the expression and methylation levels of RTE classes and families.

Techniques: Methylation

While LINE families, MIR, and long terminal repeats (LTR) families except ERVK show lower levels of methylation in higher expression groups, this pattern is not seen in Alu, CR1, and ERVl. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001, ns: not significant, Wilcoxon test.

Journal: eLife

Article Title: Expression of most retrotransposons in human blood correlates with biological aging

doi: 10.7554/eLife.96575

Figure Lengend Snippet: While LINE families, MIR, and long terminal repeats (LTR) families except ERVK show lower levels of methylation in higher expression groups, this pattern is not seen in Alu, CR1, and ERVl. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001, ns: not significant, Wilcoxon test.

Article Snippet: By overlapping Illumina microarray expression and methylation probe locations to RTE locations in RepeatMasker , we were able to identify a sufficient number of probes to calculate the expression and methylation levels of RTE classes and families.

Techniques: Methylation, Expressing

Set Enrichment Analysis (GSEA) of A549 Cell Line Treated with 5-Aza. The running ES indicates the degree to which this gene set is overrepresented at the top or bottom of the entire ranked list of genes. GSEA plots are a ranked list of genes from microarray analysis, sorted by their correlation with treatment effect. The color code bar (red to blue) represents the correlation of gene expression with the phenotype of interest, with red indicating a positive correlation and blue indicating a negative correlation. The leading-edge subset of genes, those contributing most to the ES, are highlighted within this list.

Journal: Medicine and Pharmacy Reports

Article Title: 5-Azacytidine treatment inhibits the development of lung cancer models via epigenetic reprogramming and activation of cellular pathways with anti-tumor activity

doi: 10.15386/mpr-2777

Figure Lengend Snippet: Set Enrichment Analysis (GSEA) of A549 Cell Line Treated with 5-Aza. The running ES indicates the degree to which this gene set is overrepresented at the top or bottom of the entire ranked list of genes. GSEA plots are a ranked list of genes from microarray analysis, sorted by their correlation with treatment effect. The color code bar (red to blue) represents the correlation of gene expression with the phenotype of interest, with red indicating a positive correlation and blue indicating a negative correlation. The leading-edge subset of genes, those contributing most to the ES, are highlighted within this list.

Article Snippet: Prior to hybridizatiion, the microarray probes (cRNA-Cy3) underwent purification using the RNeasy Mini Kit (Qiagen, Germany).

Techniques: Microarray, Gene Expression

Comparative analysis of gene expression changes from microarray and qPCR analysis.

Journal: Medicine and Pharmacy Reports

Article Title: 5-Azacytidine treatment inhibits the development of lung cancer models via epigenetic reprogramming and activation of cellular pathways with anti-tumor activity

doi: 10.15386/mpr-2777

Figure Lengend Snippet: Comparative analysis of gene expression changes from microarray and qPCR analysis.

Article Snippet: Prior to hybridizatiion, the microarray probes (cRNA-Cy3) underwent purification using the RNeasy Mini Kit (Qiagen, Germany).

Techniques: Gene Expression, Microarray, Biomarker Discovery