Neural tube defects (NTDs) are common, costly, and deadly human congenital anomalies whose etiologies remain largely unknown. One of the most promising clues to the causes of NTDs is that women who use vitamins containing folic acid in early pregnancy are at much lower risk for NTD-affected pregnancies. However, the underlying mechanisms by which folic acid contributes to these reduced risks are unknown. The most commonly held hypothesis is that folate intake prevents NTDs by compensating for individual genetic susceptibilities, although clear identification of genetic determinants through association studies has proven elusive. The approach we propose to further define the molecular genetic mechanisms behind neural tube defects and folate-prevention therapy is rooted in the results of a pilot study to identify nonsynonymous substitutions in vitamin-dependent enzymes that impair function, yet are augmentable by elevated vitamin concentration. This pilot has demonstrated that deep sequencing reveals a substantial amount of low frequency, nonsynonymous variation in folate pathway genes (frequencies <=1%) that has gone unnoticed thus far. Furthermore, using a robust assay platform based on complementation in S. cerevisiae, we have demonstrated that approximately one-half of these low frequency variants affect enzyme function and have identified novel folate-remedial alleles. We hypothesize that genetic susceptibilities in folate metabolism can be etiological for NTDs and that these susceptibilities can be conferred by both low-frequency and common variants and by the possible synergy between these. To test this hypothesis, we will resequence the coding regions in 19 folate metabolic genes from a population of 250 NTD-affected infants and 250 controls, for which we also have information on maternal nutritional intake. We will test all enzyme variants for functional impact and folate remediation, and correlate functional studies with clinical phenotype and nutritional data. We hope to better define the causality of NTDs, understand the remedial role of folate supplementation, and determine whether additional folate supplementation may be preventative. We have assembled a unique combination of scientific expertise to execute this research plan. Relevance: This proposal should reveal the causes of a common form of birth defect known as neural tube defects. Ultimately, this research may lead to better diagnostic and preventive strategies.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM072859-03
Application #
7614304
Study Section
Genetics of Health and Disease Study Section (GHD)
Project Start
2007-04-01
Project End
2011-03-31
Budget Start
2009-04-01
Budget End
2010-03-31
Support Year
3
Fiscal Year
2009
Total Cost
$487,089
Indirect Cost
Name
University of California Berkeley
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Asrani, Kripa; Shaw, Gary M; Rine, Jasper et al. (2017) DNA Methylome Profiling on the Infinium HumanMethylation450 Array from Limiting Quantities of Genomic DNA from a Single, Small Archived Bloodspot. Genet Test Mol Biomarkers 21:516-519
Marini, Nicholas J; Yang, Wei; Asrani, Kripa et al. (2016) Sequence variation in folate pathway genes and risks of human cleft lip with or without cleft palate. Am J Med Genet A 170:2777-2787
Sadhu, Meru J; Moresco, James J; Zimmer, Anjali D et al. (2014) Multiple inputs control sulfur-containing amino acid synthesis in Saccharomyces cerevisiae. Mol Biol Cell 25:1653-65
Sadhu, Meru J; Guan, Qiaoning; Li, Fei et al. (2013) Nutritional control of epigenetic processes in yeast and human cells. Genetics 195:831-44
Dimster-Denk, Dago; Tripp, Katherine W; Marini, Nicholas J et al. (2013) Mono and dual cofactor dependence of human cystathionine ?-synthase enzyme variants in vivo and in vitro. G3 (Bethesda) 3:1619-28
Marini, Nicholas J; Hoffmann, Thomas J; Lammer, Edward J et al. (2011) A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis. PLoS One 6:e28408
Hoffmann, Thomas J; Marini, Nicholas J; Witte, John S (2010) Comprehensive approach to analyzing rare genetic variants. PLoS One 5:e13584
Marini, Nicholas J; Thomas, Paul D; Rine, Jasper (2010) The use of orthologous sequences to predict the impact of amino acid substitutions on protein function. PLoS Genet 6:e1000968
Marini, Nicholas J; Gin, Jennifer; Ziegle, Janet et al. (2008) The prevalence of folate-remedial MTHFR enzyme variants in humans. Proc Natl Acad Sci U S A 105:8055-60