Open AccessEpigenome‐Wide Association Study for All‐Cause Mortality in a Cardiovascular Cohort Identifies Differential Methylation in Castor Zinc Finger 1 ( CASZ 1 )
Author(s) -
Abdulrahim Jawan W.,
Kwee Lydia Coulter,
Grass Elizabeth,
Siegler Ilene C.,
Williams Redford,
Karra Ravi,
Kraus William E.,
Gregory Simon G.,
Shah Svati H.
Publication year - 2019
Publication title -
journal of the american heart association
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.494
H-Index - 85
ISSN - 2047-9980
DOI - 10.1161/jaha.119.013228
Subject(s) - medicine , epigenome , cohort , dna methylation , methylation , zinc , bioinformatics , physiology , genetics , gene , gene expression , biology , materials science , metallurgy
Background DNA methylation is implicated in many chronic diseases and may contribute to mortality. Therefore, we conducted an epigenome‐wide association study ( EWAS ) for all‐cause mortality with whole‐transcriptome data in a cardiovascular cohort ( CATHGEN [Catheterization Genetics]). Methods and Results Cases were participants with mortality≥7 days postcatheterization whereas controls were alive with≥2 years of follow‐up. The Illumina Human Methylation 450K and EPIC arrays (Illumina, San Diego, CA) were used for the discovery and validation sets, respectively. A linear model approach with empirical Bayes estimators adjusted for confounders was used to assess difference in methylation (Δβ). In the discovery set (55 cases, 49 controls), 25 629 (6.5%) probes were differently methylated ( P <0.05). In the validation set (108 cases, 108 controls), 3 probes were differentially methylated with a false discovery rate–adjusted P <0.10: cg08215811 ( SLC 4A9 ; log 2 fold change=−0.14); cg17845532 ( MATK ; fold change=−0.26); and cg17944110 (castor zinc finger 1 [ CASZ1 ]; FC =0.26; P <0.0001; false discovery rate–adjusted P =0.046–0.080). Meta‐analysis identified 6 probes (false discovery rate–adjusted P <0.05): the 3 above, cg20428720 (intergenic), cg17647904 ( NCOR 2 ), and cg23198793 ( CAPN 3 ). Messenger RNA expression of 2 MATK isoforms was lower in cases (fold change=−0.24 [ P =0.007] and fold change=−0.61 [ P =0.009]). The CASZ 1 , NCOR 2 , and CAPN 3 transcripts did not show differential expression ( P >0.05); the SLC 4A9 transcript did not pass quality control. The cg17944110 probe is located within a potential regulatory element; expression of predicted targets (using GeneHancer) of the regulatory element, UBIAD 1 ( P =0.01) and CLSTN 1 ( P =0.03), were lower in cases. Conclusions We identified 6 novel methylation sites associated with all‐cause mortality. Methylation in CASZ 1 may serve as a regulatory element associated with mortality in cardiovascular patients. Larger studies are necessary to confirm these observations.