Research in the Molecular Pathogenesis Section is focused on defining changes in the genes that underlie inherited susceptibilities to common diseases such as cancer and birth defects. Changes in folate and vitamin B12 metabolism are associated with tumor formation, birth defects and cognitive decline. Folate and vitamin B12 genes are also involved in the methylation of DNA and normal brain function. We are searching for genetic variants in genes related to folate, methionine and homocysteine metabolism. Individuals affected with cancer or spina bifida (one form of neural tube defects) will be tested for these variants. Variants found at higher frequency in individuals with disease will help us identify genes associated with risk. In the past we found that variants in two genes, TCN2 and TCN2R, appear to affect the levels of vitamin B12 in the blood during pregnancy. In addition, variants in TCN2R are associated the risk of neural tube defects. These findings may be related to birth defects and also may help to explain why some elderly individuals become anemic and suffer neurological symptoms from vitamin B12 deficiency. We also found that mothers carrying a specific variant in a second gene, MTHFD1, have a 50% increased risk bearing a child with a neural tube defect. This previously un-described variant may be responsible for up to 25% of all neural tube defects. Approximately one in five individuals in the population carry one of these risk factors. We recently determined that this particular variant was also an risk factor for placental abruption a common cause of miscarriage and for miscarriages that occur in the second trimester. We have synthesized copies of these genes in the laboratory and are currently using an experimental system to determine exactly how these variants alter the function of these proteins. We have tested more than 64 additional genes for variants that might perturb folate metabolism and therefore be associated with an increased risk of having a child with an neural tube defect. This was carried out by genotyping more than 1,200 single nucleotide polymorphisms in a large number of families affected with neural tube defects and unaffected controls. This large experiment has allowed us to exclude most of the genes on this list. Results for approximately a dozen genes suggest that they are associated with neural tube defects. Over the past year we have carried out second series of experiments to determine if the genes identified in the first stage of these are definitively associated with neural tube defects. These data are currently being analyzed. One of these genes has already passed through our stage 2 validation. This gene produces a protein that binds vitamin B12 and transports it from the blood into the tissues. We have published data demonstrating that several variants in this transporter are associated with a risk of having a child with an NTD. While we now know which variants are associated with risk, we do not yet know if they are actually causing the risk or are linked to additional variants that change the function of the protein. To screen for additional variants, we sequenced the DNA containing this transporter gene in a large number of individuals. This sequencing experiment uncovered a number of previously unidentified variants in this gene. We measured the impact of these variants on the function of the transporter. The majority of variants tested do not appear to have an adverse effect of the function of the receptor. However, we have found that several of the variants are associated with changes in vitamin B12 levels in a large sample of healthy individuals. We plan to test these variants in a large sample of elderly individuals to determine if these changes are associated with human disease conditions. When we perform the same test in pregnant women, the variant is associated with decreased levels of vitamin B12. This result is consistent with the association of the same variant and adverse outcomes in pregnancy. We have also carried out experiments aimed at determining the relationship between folate, vitamin B12 and DNA methylation. These experiments are difficult to carry out in humans. We have used zebrafish as a model organism for these studies and have produced a whole genome methylation map of the zebrafish genome covering important developmental stages. We have also characterized the genes in the folate/ vitamin B12 pathway in zebrafish. During this work we were able to assign a predicted function to a number of genes that had not been characterized. We also discovered that the disruption of folate metabolism produces developmental defects in zebrafish. By using a number of methods, we conclude that the defects are due to a lack of cell division not a change in developmental signaling. Completion of this work will allow us disrupt these genes in developing zebrafish and observe how these disruptions affect early development. A benefit of our work is that a detailed knowledge of the function of the the genes in the folate vitamin B12 metabolic pathways will add to our understanding of neural tube defects and potentially help guide public health policy in the area of nutritional supplementation.

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Project End
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Budget End
Support Year
13
Fiscal Year
2012
Total Cost
$1,697,350
Indirect Cost
Name
National Human Genome Research Institute
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Szymczak, Silke; Holzinger, Emily; Dasgupta, Abhijit et al. (2016) r2VIM: A new variable selection method for random forests in genome-wide association studies. BioData Min 9:7
Sobczyńska-Malefora, Agata; Pangilinan, Faith; Plant, Gordon T et al. (2016) Association of a transcobalamin II genetic variant with falsely low results for the holotranscobalamin immunoassay. Eur J Clin Invest 46:434-9
Molloy, Anne M; Pangilinan, Faith; Mills, James L et al. (2016) A Common Polymorphism in HIBCH Influences Methylmalonic Acid Concentrations in Blood Independently of Cobalamin. Am J Hum Genet 98:869-82
Deac, Oana M; Mills, James L; Gardiner, Clair M et al. (2016) Serum Immune System Biomarkers Neopterin and Interleukin-10 Are Strongly Related to Tryptophan Metabolism in Healthy Young Adults. J Nutr 146:1801-6
Ozaki, Mari; Molloy, Anne M; Mills, James L et al. (2015) The Dihydrofolate Reductase 19 bp Polymorphism Is Not Associated with Biomarkers of Folate Status in Healthy Young Adults, Irrespective of Folic Acid Intake. J Nutr 145:2207-11
Deac, Oana M; Mills, James L; Shane, Barry et al. (2015) Tryptophan catabolism and vitamin B-6 status are affected by gender and lifestyle factors in healthy young adults. J Nutr 145:701-7
Kurnat-Thoma, Emma L; Pangilinan, Faith; Matteini, Amy M et al. (2015) Association of Transcobalamin II (TCN2) and Transcobalamin II-Receptor (TCblR) Genetic Variations With Cobalamin Deficiency Parameters in Elderly Women. Biol Res Nurs 17:444-54
Rigler, Shannon L; Kay, Denise M; Sicko, Robert J et al. (2015) Novel copy-number variants in a population-based investigation of classic heterotaxy. Genet Med 17:348-57
Carter, Tonia C; Pangilinan, Faith; Molloy, Anne M et al. (2015) Common Variants at Putative Regulatory Sites of the Tissue Nonspecific Alkaline Phosphatase Gene Influence Circulating Pyridoxal 5'-Phosphate Concentration in Healthy Adults. J Nutr 145:1386-93
McGaughey, David M; Abaan, Hatice Ozel; Miller, Ryan M et al. (2014) Genomics of CpG methylation in developing and developed zebrafish. G3 (Bethesda) 4:861-9

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