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Stover, Patrick

Patrick Stover

Professor, Biochemistry and Biophysics
Focus Area:  one-carbon metabolism; genome stability; folate, B-vitamins; metabolic networks
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Education

Undergraduate Education
B.S. Chemistry, Saint Joseph’s University (1986)
Graduate Education
Ph.D. Biochemistry and Biophysics, Medical College of Virginia (1990)
Postdoc. Nutritional Sciences, University of California, Berkeley (1991-1994)

Areas of Expertise

  • Metabolism, metabolic tracers, nutrition, developmental anomalies

Professional Summary

Our research has two overarching goals: 1) to understand the role of nuclear The essential B-vitamins folate, vitamin B12 and pyridoxal phosphate function in a metabolic network known as one-carbon metabolism, which is essential for the faithful replication of the genome and maintenance of genome stability. It is also required for the provision of activated methyl groups for cellular methylation reactions. Aberrations in one-carbon metabolism, due to interactions among nutrition and common gene variants, are tightly linked to several common human pathologies. The Stover research group investigates the fundamental chemical, biochemical, genetic and epigenetic mechanisms, and their associated pathways within the one-carbon metabolic network, that underlie the relationships among nutrition, metabolism and risk for birth defects, cancer and neurodegenerative diseases.

Cellular compartmentation of de novo thymidylate biosynthesis to sites of DNA replication

A MTHFD1-GFP fusion protein localizes to the nucleus at S-phase in HeLa cells where it co-localizes with a laminB-RFP fusion protein (upper panel).  Co-lhe localization of MTHFD1-GFP with LaminB-RFP requires SHMT1 expression (lower panel), as the SHMT1 protein is the scaffold that connects the thymidylate de novo synthesis multi-enzyme complex to the nuclear lamina

A MTHFD1-GFP fusion protein localizes to the nucleus at S-phase in HeLa cells where it co-localizes with a laminB-RFP fusion protein (upper panel).  Co-lhe localization of MTHFD1-GFP with LaminB-RFP requires SHMT1 expression (lower panel), as the SHMT1 protein is the scaffold that connects the thymidylate de novo synthesis multi-enzyme complex to the nuclear lamina

Through a combination of isotope tracer studies, immunoprecipitation experiments, genetic manipulations of human cells and mouse embryonic stem cells, and imaging technologies, we have demonstrated that de novo thymidylate biosynthesis occurs at sites of DNA replication in the nucleus and mitochondria. We have established the mechanism whereby the enzymes that constitute this pathway translocate to the nucleus through SUMO-dependent processes, where the enzymes form a multienzyme complex associated with the nuclear lamina.  This nuclear trafficking of the pathway is regulated by the cell cycle, DNA damage, as well as dietary and other environmental factors.  The current focus is to reconstitute the metabolic complex in vitro, determine the structure of the complex and investigate evidence for metabolic channeling of folate cofactors within the complex.

  1. Field MS, Kamynina E, Watkins D, Rosenblatt DD, and Stover PJ. 2015. Human Mutations in Methylenetetrahydrofolate Dehydrogenase 1 Impair Nuclear de novo Thymidylate Biosynthesis. Proc Natl Acad Sci. 112(2): 400-5.. PMCID: PMC4299200.
  2. Field MS, Kamynina E, Agunloye OC, Liebenthal RP, Lamarre SG, Brosnan ME, Brosnan JT, Stover PJ. 2014. Nuclear enrichment of folate cofactors and methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) protect de novo thymidylate biosynthesis during folate deficiency. J Biol Chem. 289: 29642-50. PMID: 25213861. PMCID: PMC4207979.

 

Mechanisms of folic-acid responsive neural tube defects

Neural tube defects in Shmt1-deficient embryos. A, B: At gestational day 11.5 (E11.5),Shmt1 +/-embryos from dams fed diets lacking folate exhibited failure of rostral neural tube closure at the midbrain/hindbrain boundary (B). All wild-type littermates (A) were unaffected. Arrows indicate extent of lesions. C, D: At E14.5, affected Shmt1+/- embryos (D) exhibited prominent exencephaly. Wild-type littermates (C) were unaffected.

Neural tube defects in Shmt1-deficient embryos. A, B: At gestational day 11.5 (E11.5),Shmt1 +/-embryos from dams fed diets lacking folate exhibited failure of rostral neural tube closure at the midbrain/hindbrain boundary (B). All wild-type littermates (A) were unaffected. Arrows indicate extent of lesions. C, D: At E14.5, affected Shmt1+/- embryos (D) exhibited prominent exencephaly. Wild-type littermates (C) were unaffected.

Clinical trials and experiences with national folic acid fortification programs have definitely established that dietary folic acid consumed by women of childbearing age decreases risk for neural tube defects during early development. However, the mechanisms by which folic acid prevents neural tube defects have remained elusive. Furthermore, not all neural tube defect-affected pregnancies are prevented by folic acid. We have established the only mouse model of folic acid-responsive neural tube defects resulting from disruption of one-carbon metabolism that mirrors the human condition including folic acid responsiveness, subtle alterations in metabolism, and low penetrance. The Shmt1 mouse model provides strong evidence that impairments in de novo thymidylate biosynthesis underlie folic-acid responsive neural tube defects, and provides the opportunity to explore novel dietary approaches to prevent more effectively neural tube defects, including nucleotide and vitamin B12 supplementation.  Current efforts are focused on the mechanism underlying folic acid-responsive neural tube defects in mice.

Martiniova L, Field MS, Finkelstein JL, Perry CA, and Stover, PJ. 2015. Maternal dietary uridine causes, and deoxyuridine prevents, neural tube closure defects in a mouse model of folate-responsive neural tube defects. Amer J Clin Nutr. 101:860-9.PMID: 25833982 PMCID: PMC4381776

Computational simulations of folate-mediated one-carbon metabolism (FOCM)

Folate-mediated one-carbon metabolism. The figure shows the reaction-based specification of the model. Orange rectangles identify model variables, non-boxed substrates indicate model constants, green circles identify enzymes. Solid blue arcs identify matter transformation, while dashed blue arcs identify regulatory events (T shaped arrows identify inhibitions and standard arrows identify activations).

Folate-mediated one-carbon metabolism. The figure shows the reaction-based specification of the model. Orange rectangles identify model variables, non-boxed substrates indicate model constants, green circles identify enzymes. Solid blue arcs identify matter transformation, while dashed blue arcs identify regulatory events (T shaped arrows identify inhibitions and standard arrows identify activations).

With our collaborators at the Microsoft Research – University of Trento Centre for Computational and Systems Biology, we have developed a hybrid stochastic model of FOCM. The model provides a description of FOCM as well as its regulation of key biological processes related to de novo dTMP synthesis, de novo purine synthesis and remethylation of homocysteine to methionine.  The model is composed of 14 variables and 20 (reversible and irreversible) reactions, most of which have been parametrized by means of Michaelis-Menten kinetics with one or two substrates, with an overlay stochastic simulation.  Current efforts are focused on extending the model to include the nuclear metabolic compartment, to include other intersecting metabolic networks, and to test hypotheses related to network function through biological simulations.

Misselbeck, K., Marchetti, L., Priami, C., Stover, P.J. and Field, M.S. 2019. The 5-formyltetrahydrofolate futile cycle reduces pathway stochasticity in an extended hybrid-stochastic model of folate-mediated one-carbon metabolism. Sci Rep. 9(1): 4322.

 

Publications