Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke

Authors: WILLIAMS, STEPHEN - University Of Virginia; YAN, QIONG - Boston University; CHEN, FANG - University Of Virginia; LIU, XUAN - Boston University; KEENE, KEITH - University Of Virginia; JACQUES, PAUL - Jean Mayer Human Nutrition Research Center On Aging At Tufts University; CHEN, WEI-MIN - University Of Virginia; WEINSTEIN, GALIT - Boston University; HSU, FANG-CHI - Wake Forest University; BEISER, ALEXA - Boston University; WANG, LIEWEI - Mayo Clinic; BOOKMAN, EBONY - National Institutes Of Health (NIH); DOHENY, KIMBERLY - Johns Hopkins University; WOLF, PHILIP - Boston University; ZILKA, MICHELLE - Johns Hopkins University; SELHUB, JACOB - Jean Mayer Human Nutrition Research Center On Aging At Tufts University; NELSON, SARAH - University Of Washington; GOGARTEN, STEPHANIE - University Of Washington; WORRALL, BRADFORD - University Of Virginia; SESHADRI, SUDHA - Boston University; SALE, MICHELE - University Of Virginia

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/14/2014
Publication Date: 3/20/2014
Citation: Williams, S.R., Yan, Q., Chen, F., Liu, X., Keene, K.L., Jacques, P.F., Chen, W., Weinstein, G., Hsu, F., Beiser, A., Wang, L., Bookman, E., Doheny, K.F., Wolf, P.A., Zilka, M., Selhub, J., Nelson, S., Gogarten, S.M., Worrall, B.B., Seshadri, S., Sale, M.M. 2014. Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke. PLoS Genetics. 10(3):e1004214.

Interpretive Summary: Stroke is the fourth leading cause of death and the leading cause of disability in American adults. Previous research has suggested that higher levels of homocysteine (tHcy), an amino acid found in the blood, may be associated with risk of stroke, heart disease, and dementia. Folate and vitamin B12 help to metabolize tHcy in the body through the folate one-carbon metabolism pathway (FOCM), and, thus, some clinical trials have examined whether providing individuals with folate and vitamin B12 supplements help to lower tHcy and reduce risk of disease. These studies have shown varying and unclear results, indicating that the relationship between tHcy and disease risk is complicated. It is known that the amount of tHcy in the blood is a heritable (genetic) trait; however, specific genetic determinants and underlying biological processes are not known. Previous research has identified genes that may be associated with tHcy levels. We examined these genes, along with tHcy levels, among participants from two large studies, the Framingham Heart Study and the Vitamin Intervention for Stroke Prevention clinical trial. Our results showed that five genes in the FOCM pathway were strongly associated with differences in tHcy levels in the blood. Of these five genes, one particular genetic variant was associated with higher risk of ischemic stroke. We have shown that understanding genetic variation in the FOCM pathway may provide a link to functional differences in the population that, in turn, tie the FOCM pathway to a broad range of disease risk factors. Our study also highlights the importance of working to further understand the FOCM pathway and potential ways to target the pathway with therapeutic interventions to reduce disease risk.

Technical Abstract: Circulating homocysteine levels (tHcy), a product of the folate one carbon metabolism pathway (FOCM) through the demethylation of methionine, are heritable and are associated with an increased risk of common diseases such as stroke, cardiovascular disease (CVD), cancer and dementia. The FOCM is the sole source of de novo methyl group synthesis, impacting many biological and epigenetic pathways. However, the genetic determinants of elevated tHcy (hyperhomocysteinemia), dysregulation of methionine metabolism and the underlying biological processes remain unclear. We conducted independent genome-wide association studies and a meta-analysis of methionine metabolism, characterized by post-methionine load test tHcy, in 2,710 participants from the Framingham Heart Study (FHS) and 2,100 participants from the Vitamin Intervention for Stroke Prevention (VISP) clinical trial, and then examined the association of the identified loci with incident stroke in FHS. Five genes in the FOCM pathway (GNMT [p = 1.60x10**-63], CBS [p = 3.15x10**-26], CPS1 [p = 9.10x10**-13], ALDH1L1 [p = 7.3x10**-13] and PSPH [p = 1.17x10**-16]) were strongly associated with the difference between pre- and post-methionine load test tHcy levels (deltaPOST). Of these, one variant in the ALDH1L1 locus, rs2364368, was associated with incident ischemic stroke. Promoter analyses reveal genetic and epigenetic differences that may explain a direct effect on GNMT transcription and a downstream effect on methionine metabolism. Additionally, a genetic-score consisting of the five significant loci explains 13% of the variance of deltaPOST in FHS and 6% of the variance in VISP. Association between variants in FOCM genes with deltaPOST suggest novel mechanisms that lead to differences in methionine metabolism, and possibly the epigenome, impacting disease risk. These data emphasize the importance of a concerted effort to understand regulators of one carbon metabolism as potential therapeutic targets.