Distinct DNA methylation signatures associated with blood lipids as exposures or outcomes among survivors of childhood cancer: a report from the St. Jude lifetime cohort

How to cite our paper:

Dong, Q., Chen, C., Song, N. et al. Distinct DNA methylation signatures associated with blood lipids as exposures or outcomes among survivors of childhood cancer: a report from the St. Jude lifetime cohort. Clin Epigenet 15, 32 (2023). https://doi.org/10.1186/s13148-023-01447-3

Abstract:

Background

DNA methylation (DNAm) plays an important role in lipid metabolism, however, no epigenome-wide association study (EWAS) of lipid levels has been conducted among childhood cancer survivors. Here, we performed EWAS analysis with longitudinally collected blood lipid data from survivors in the St. Jude lifetime cohort study.

Methods

Among 2052 childhood cancer survivors of European ancestry (EA) and 370 survivors of African ancestry (AA), four types of blood lipids, including high-density lipoprotein (HDL), low-density lipoprotein (LDL), total cholesterol (TC), and triglycerides (TG), were measured during follow-up beyond 5-years from childhood cancer diagnosis. For the exposure EWAS (i.e., lipids measured before blood draw for DNAm), the DNAm level was an outcome variable and each of the blood lipid level was an exposure variable; vice versa for the outcome EWAS (i.e., lipids measured after blood draw for DNAm).

Results

Among EA survivors, we identified 43 lipid-associated CpGs in the HDL (n =&thinsp;7), TC (n =&thinsp;3), and TG (n =&thinsp;33) exposure EWAS, and 106 lipid-associated CpGs in the HDL (n =&thinsp;5), LDL (n =&thinsp;3), TC (n =&thinsp;4), and TG (n =&thinsp;94) outcome EWAS. Among AA survivors, we identified 15 lipid-associated CpGs in TG exposure (n =&thinsp;6), HDL (n =&thinsp;1), LDL (n =&thinsp;1), TG (n =&thinsp;5) and TC (n =&thinsp;2) outcome EWAS with epigenome-wide significance (P < 9 × 10⁻⁸). There were no overlapping lipids-associated CpGs between exposure and outcome EWAS among EA and AA survivors, suggesting that the DNAm changes of different CpGs could be the cause or consequence of blood lipid levels. In the meta-EWAS, 12 additional CpGs reached epigenome-wide significance. Notably, 32 out of 74 lipid-associated CpGs showed substantial heterogeneity (P_het < 0.1 or I² > 70%) between EA and AA survivors, highlighting differences in DNAm markers of blood lipids between populations with diverse genetic ancestry. Ten lipid-associated CpGs were cis-expression quantitative trait methylation with their DNAm levels associated with the expression of corresponding genes, out of which seven were negatively associated.

Conclusions

We identified distinct signatures of DNAm for blood lipids as exposures or outcomes and between EA and AA survivors, revealing additional genes involved in lipid metabolism and potential novel targets for controlling blood lipids in childhood cancer survivors.

Upload file descriptions:

1. Upload_Table1_ST1_Lipids_EWAS_data.csv: derived variables in Tables 1, 2, and 3, and Supplementary Table 1.

2. Upload_Table2_Lipids_EWAS.csv: other derived variables used in the lipid EWAS among survivors of European ancestry in Table 2.

3. Upload_Table4_eQTM_Lipids_EWAS.csv: derived variables (CpG levels and normalized gene expression) in Table 4.

4. Upload_ST4_AA_EWAS.csv: other derived variables used in the lipid EWAS among survivors of African ancestry in Table 2.

5. Upload_SF5.Gene_summary_GWAS_EWAS_catalog.xlsx: known lipids-related gene lists from GWAS Catalog (P<5x10^-8) and EWAS Catalog (P<9x10^-8) for Supplementary Figure 5.

6. AA_HDL/LDL/TG/TC_exposure/outcome_EWAS_result.txt: lipid EWAS results among survivors of African ancestry.

7. EA_HDL/LDL/TG/TC_exposure/outcome_EWAS_result.txt: lipid EWAS results among survivors of European ancestry.

8. meta_HDL/LDL/TG/TC_exposure/outcome_P_anno: meta-EWAS results of lipid levels.

*The DNA methylation data of the 2052 survivors of European ancestry are accessible at NCBI Gene Expression Omnibus database under the accession number GSE169156 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169156