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Narad P, Kulshrestha S, Chikara A, Gupta V, Kakrania M, Saxena R, Gupta P, Gupta L, Vijayaraghavan P, Sengupta A. Systems-wide analysis of A. fumigatus using kinetic modeling of metabolic pathways to identify putative drug targets. J Biomol Struct Dyn 2024; 42:4379-4394. [PMID: 37334711 DOI: 10.1080/07391102.2023.2223726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
Aspergillosis is a major causative factor for morbidity in those with impaired immune systems, often caused by Aspergillus fumigatus. The diagnosis and treatment are difficult due to the diversity of individuals and risk factors and still pose a challenge for medical professionals. To understand the pathogenicity of any organism, it is critical to identify the significant metabolic pathways that are involved. Our work focused on developing kinetic models of critical pathways crucial for the survival of A. fumigatus using COPASI. While focusing on the folate biosynthesis, ergosterol biosynthesis and glycolytic pathway; sensitivity, time-course and steady-state analysis were performed to find the proteins/enzymes that are essential in the pathway and can be considered as potential drug targets. For further analysis of the interaction of drug targets identified, a protein-protein interaction (PPI) network was built, and hub nodes were identified using the Cytohubba package from Cytoscape. Based on the findings, dihydropteroate-synthase, dihydrofolate-reductase, 4-amino-4-deoxychorismate synthase, HMG-CoA-reductase, PG-isomerase and hexokinase could act as potential drug targets. Further, molecular docking and MM-GBSA analysis were performed with ligands chosen from DrugBank, and PubChem, and validated by experimental evidence and existing literature based on results from kinetic modeling and PPI network analysis. Based on docking scores and MM-GBSA results, molecular simulations were carried out for 1AJ2-dapsone, 1DIS-sulfamethazine, 1T02-lovastatin and 70YL-3-bromopyruvic acid complexes, which validated our findings. Our study provides a deeper insight into the mechanisms of A. fumigatus's metabolism to reveal dapsone, sulfamethazine, lovastatin and 3-bromopyruvic acid as potential drugs for the treatment of Aspergillosis.
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Affiliation(s)
- Priyanka Narad
- Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Sudeepti Kulshrestha
- Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Aryan Chikara
- Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Vinayak Gupta
- Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Mahi Kakrania
- Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Ritika Saxena
- Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Payal Gupta
- Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Lovely Gupta
- Anti-mycotic Drug Susceptibility Laboratory, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Pooja Vijayaraghavan
- Anti-mycotic Drug Susceptibility Laboratory, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Abhishek Sengupta
- Systems Biology and Data Analytics Research Lab, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
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2
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Nguyen TN, Ingle C, Thompson S, Reynolds KA. The genetic landscape of a metabolic interaction. Nat Commun 2024; 15:3351. [PMID: 38637543 PMCID: PMC11026382 DOI: 10.1038/s41467-024-47671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
While much prior work has explored the constraints on protein sequence and evolution induced by physical protein-protein interactions, the sequence-level constraints emerging from non-binding functional interactions in metabolism remain unclear. To quantify how variation in the activity of one enzyme constrains the biochemical parameters and sequence of another, we focus on dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), a pair of enzymes catalyzing consecutive reactions in folate metabolism. We use deep mutational scanning to quantify the growth rate effect of 2696 DHFR single mutations in 3 TYMS backgrounds under conditions selected to emphasize biochemical epistasis. Our data are well-described by a relatively simple enzyme velocity to growth rate model that quantifies how metabolic context tunes enzyme mutational tolerance. Together our results reveal the structural distribution of epistasis in a metabolic enzyme and establish a foundation for the design of multi-enzyme systems.
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Affiliation(s)
- Thuy N Nguyen
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- The Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- The Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Form Bio, Dallas, TX, 75226, USA
| | - Christine Ingle
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- The Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- The Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Samuel Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94158, USA
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Kimberly A Reynolds
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- The Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- The Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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3
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Xia Y, Huang L, Long Z, Chen Y, Gao L, Hua R, Li S, Wang Y. The association of preconceptional folic acid supplementation with gestational age and preterm birth risk in twin pregnancies: a prospective cohort study in China. Eur J Nutr 2024; 63:107-119. [PMID: 37733259 DOI: 10.1007/s00394-023-03223-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 07/24/2023] [Indexed: 09/22/2023]
Abstract
PURPOSE This study aims to explore the association of maternal preconceptional folic acid (FA) supplementation with gestational age and preterm birth in twin pregnancies, and whether the association varies by chorionicity or conception mode. METHODS From November 2018 to December 2021, the information of FA supplementation and pregnancy outcomes were collected in twin pregnant women. The linear regression models and the logistic regression were used to test the association of preconceptional FA supplementation with gestational age at delivery and preterm birth and premature rupture of membranes (PROM). RESULTS A total of 416 twin pregnancies were included. Compared with no use in twins, maternal preconceptional FA use was associated with a 0.385-week longer gestational age (95% CI 0.019-0.751) and lower risk of preterm birth < 36 weeks (adjusted OR 0.519; 95% CI 0.301-0.895) and PROM (adjusted OR 0.426; 95% CI 0.215-0.845). The protective effect on preterm birth < 36 weeks and PROM is similar whether taking FA supplements alone or multivitamins. However, the associations varied by chorionicity and conception mode of twins or compliance with supplementation. The positive associations between preconceptional FA use and gestational age only remained significant among twins via assisted reproductive technology or dichorionic diamniotic twins. Significant protective effects on preterm birth < 36 weeks and PROM were only found among women who took FA at least 4 times a week before conception. CONCLUSION Maternal preconceptional FA supplementation was associated with longer gestation duration and lower risk of preterm birth < 36 weeks and PROM in twin pregnancies. To improve the success of their pregnancies, reproductive women should start taking FA supplements well before conception and with good compliance.
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Affiliation(s)
- Yuanqing Xia
- Division of Maternal-Fetal Fetal Medicine, Prenatal Diagnosis Department, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Xuhui District, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, 200030, China
| | - Lili Huang
- School of Public Health, Shanghai Jiao Tong University, 227 South Chongqing Road, Huangpu District, Shanghai, 200025, China
| | - Zichong Long
- School of Public Health, Shanghai Jiao Tong University, 227 South Chongqing Road, Huangpu District, Shanghai, 200025, China
| | - Yiting Chen
- School of Public Health, Shanghai Jiao Tong University, 227 South Chongqing Road, Huangpu District, Shanghai, 200025, China
| | - Li Gao
- Division of Maternal-Fetal Fetal Medicine, Prenatal Diagnosis Department, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Xuhui District, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, 200030, China
| | - Renyi Hua
- Division of Maternal-Fetal Fetal Medicine, Prenatal Diagnosis Department, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Xuhui District, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
- Shanghai Municipal Key Clinical Specialty, Shanghai, 200030, China
| | - Shenghui Li
- School of Public Health, Shanghai Jiao Tong University, 227 South Chongqing Road, Huangpu District, Shanghai, 200025, China.
| | - Yanlin Wang
- Division of Maternal-Fetal Fetal Medicine, Prenatal Diagnosis Department, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Xuhui District, Shanghai, 200030, China.
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
- Shanghai Municipal Key Clinical Specialty, Shanghai, 200030, China.
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4
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Morgan AE, Salcedo-Sora JE, Mc Auley MT. A new mathematical model of folate homeostasis in E. coli highlights the potential importance of the folinic acid futile cycle in cell growth. Biosystems 2024; 235:105088. [PMID: 38000545 DOI: 10.1016/j.biosystems.2023.105088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Folate (vitamin B9) plays a central role in one-carbon metabolism in prokaryotes and eukaryotes. This pathway mediates the transfer of one-carbon units, playing a crucial role in nucleotide synthesis, methylation, and amino acid homeostasis. The folinic acid futile cycle adds a layer of intrigue to this pathway, due to its associations with metabolism, cell growth, and dormancy. It also introduces additional complexity to folate metabolism. A logical way to deal with such complexity is to examine it by using mathematical modelling. This work describes the construction and analysis of a model of folate metabolism, which includes the folinic acid futile cycle. This model was tested under three in silico growth conditions. Model simulations revealed: 1) the folate cycle behaved as a stable biochemical system in three growth states (slow, standard, and rapid); 2) the initial concentration of serine had the greatest impact on metabolite concentrations; 3) 5-formyltetrahydrofolate cyclo-ligase (5-FCL) activity had a significant impact on the levels of the 7 products that carry the one-carbon donated from folates, and the redox couple NADP/NADPH; this was particularly evident in the rapid growth state; 4) 5-FCL may be vital to the survival of the cells by maintaining low levels of homocysteine, as high levels can induce toxicity; and 5) the antifolate therapeutic trimethoprim had a greater impact on folate metabolism with higher nutrient availability. These results highlight the important role of 5-FCL in intracellular folate homeostasis and mass generation under different metabolic scenarios.
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Affiliation(s)
- Amy E Morgan
- School of Health & Sport Sciences, Hope Park, Liverpool Hope University, Liverpool, L16 9JD, UK.
| | - J Enrique Salcedo-Sora
- Liverpool Shared Research Facilities, GeneMill, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Mark T Mc Auley
- School of Science, Engineering and Environment, University of Salford, Manchester, M5 4NT, UK
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5
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Korasick DA, Owuocha LF, Kandoth PK, Tanner JJ, Mitchum MG, Beamer LJ. Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance. FEBS J 2024; 291:323-337. [PMID: 37811683 DOI: 10.1111/febs.16971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Two amino acid variants in soybean serine hydroxymethyltransferase 8 (SHMT8) are associated with resistance to the soybean cyst nematode (SCN), a devastating agricultural pathogen with worldwide economic impacts on soybean production. SHMT8 is a cytoplasmic enzyme that catalyzes the pyridoxal 5-phosphate-dependent conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylenetetrahydrofolate. A previous study of the P130R/N358Y double variant of SHMT8, identified in the SCN-resistant soybean cultivar (cv.) Forrest, showed profound impairment of folate binding affinity and reduced THF-dependent enzyme activity, relative to the highly active SHMT8 in cv. Essex, which is susceptible to SCN. Given the importance of SCN-resistance in soybean agriculture, we report here the biochemical and structural characterization of the P130R and N358Y single variants to elucidate their individual effects on soybean SHMT8. We find that both single variants have reduced THF-dependent catalytic activity relative to Essex SHMT8 (10- to 50-fold decrease in kcat /Km ) but are significantly more active than the P130R/N368Y double variant. The kinetic data also show that the single variants lack THF-substrate inhibition as found in Essex SHMT8, an observation with implications for regulation of the folate cycle. Five crystal structures of the P130R and N358Y variants in complex with various ligands (resolutions from 1.49 to 2.30 Å) reveal distinct structural impacts of the mutations and provide new insights into allosterism. Our results support the notion that the P130R/N358Y double variant in Forrest SHMT8 produces unique and unexpected effects on the enzyme, which cannot be easily predicted from the behavior of the individual variants.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Luckio F Owuocha
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Pramod K Kandoth
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Melissa G Mitchum
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Plant Pathology, Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, USA
| | - Lesa J Beamer
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
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6
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Ussishkin N, Nachmani D. A Bloody Feast-Nutritional Regulation of Hematopoiesis. Exp Hematol 2023; 127:1-7. [PMID: 37582454 DOI: 10.1016/j.exphem.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023]
Abstract
Hematopoietic stem cells provide us with a lifelong supply of blood cells. Hence, their proper function is absolutely essential for life, and their dysfunction can lead to infectious and malignant diseases. These cells have specific metabolic requirements to enable their lifelong function and blood-producing capacity. With the words of the Roman poet Juvenal "a healthy mind in a healthy body" in mind, it is intriguing to understand the connection between our daily diet and the quality of our blood, with the hope that through specific dietary adjustments we can improve our hematopoietic stem cell function and prevent disease. Nowadays, dietary supplements are an expanding market filled with potential and promises for better health. However, the link between many of those supplements and human physiology is obscure. Several groups have begun to shed light on this by investigating the metabolic regulation of hematopoiesis by specific nutrients. Beyond the link to dietary supplementation, these studies have also significantly improved our understanding of basic hematopoietic stem cell biology. Herein we summarize recent knowledge on the effect of specific vitamins and amino acids, which might be considered as dietary supplements, on normal hematopoiesis and hematopoietic stem cell function. We propose that improving our understanding of the link between nutrition in general and blood physiology can ultimately lead to the optimization of health-care policies, protocols, and standards of care.
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Affiliation(s)
- Noga Ussishkin
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Daphna Nachmani
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel.
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7
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Nguyen TN, Ingle C, Thompson S, Reynolds KA. The Genetic Landscape of a Metabolic Interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.28.542639. [PMID: 37645784 PMCID: PMC10461916 DOI: 10.1101/2023.05.28.542639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Enzyme abundance, catalytic activity, and ultimately sequence are all shaped by the need of growing cells to maintain metabolic flux while minimizing accumulation of deleterious intermediates. While much prior work has explored the constraints on protein sequence and evolution induced by physical protein-protein interactions, the sequence-level constraints emerging from non-binding functional interactions in metabolism remain unclear. To quantify how variation in the activity of one enzyme constrains the biochemical parameters and sequence of another, we focused on dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), a pair of enzymes catalyzing consecutive reactions in folate metabolism. We used deep mutational scanning to quantify the growth rate effect of 2,696 DHFR single mutations in 3 TYMS backgrounds under conditions selected to emphasize biochemical epistasis. Our data are well-described by a relatively simple enzyme velocity to growth rate model that quantifies how metabolic context tunes enzyme mutational tolerance. Together our results reveal the structural distribution of epistasis in a metabolic enzyme and establish a foundation for the design of multi-enzyme systems.
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Affiliation(s)
- Thuy N. Nguyen
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, USA, 75390
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, USA, 75390
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, USA, 75390
| | - Christine Ingle
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, USA, 75390
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, USA, 75390
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, USA, 75390
| | - Samuel Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Kimberly A. Reynolds
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, USA, 75390
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, USA, 75390
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, USA, 75390
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8
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Craciun G, Deshpande A. Homeostasis and injectivity: a reaction network perspective. J Math Biol 2022; 85:67. [PMID: 36380248 DOI: 10.1007/s00285-022-01795-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/02/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Homeostasis represents the idea that a feature may remain invariant despite changes in some external parameters. We establish a connection between homeostasis and injectivity for reaction network models. In particular, we show that a reaction network cannot exhibit homeostasis if a modified version of the network (which we call homeostasis-associated network) is injective. We provide examples of reaction networks which can or cannot exhibit homeostasis by analyzing the injectivity of their homeostasis-associated networks.
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Affiliation(s)
- Gheorghe Craciun
- Department of Mathematics and Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, USA
| | - Abhishek Deshpande
- Department of Mathematics, University of Wisconsin-Madison, Madison, USA.
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9
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Kim R, Nijhout HF, Reed MC. One-carbon metabolism during the menstrual cycle and pregnancy. PLoS Comput Biol 2021; 17:e1009708. [PMID: 34914693 PMCID: PMC8741061 DOI: 10.1371/journal.pcbi.1009708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/07/2022] [Accepted: 12/01/2021] [Indexed: 11/18/2022] Open
Abstract
Many enzymes in one-carbon metabolism (OCM) are up- or down-regulated by the sex hormones which vary diurnally and throughout the menstrual cycle. During pregnancy, estradiol and progesterone levels increase tremendously to modulate physiological changes in the reproductive system. In this work, we extend and improve an existing mathematical model of hepatic OCM to understand the dynamic metabolic changes that happen during the menstrual cycle and pregnancy due to estradiol variation. In particular, we add the polyamine drain on S-adenosyl methionine and the direct effects of estradiol on the enzymes cystathionine β-synthase (CBS), thymidylate synthase (TS), and dihydrofolate reductase (DHFR). We show that the homocysteine concentration varies inversely with estradiol concentration, discuss the fluctuations in 14 other one-carbon metabolites and velocities throughout the menstrual cycle, and draw comparisons with the literature. We then use the model to study the effects of vitamin B12, vitamin B6, and folate deficiencies and explain why homocysteine is not a good biomarker for vitamin deficiencies. Additionally, we compute homocysteine throughout pregnancy, and compare the results with experimental data. Our mathematical model explains how numerous homeostatic mechanisms in OCM function and provides new insights into how homocysteine and its deleterious effects are influenced by estradiol. The mathematical model can be used by others for further in silico experiments on changes in one-carbon metabolism during the menstrual cycle and pregnancy.
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Affiliation(s)
- Ruby Kim
- Department of Mathematics, Duke University, Durham, North Carolina, United States of America
| | - H Frederik Nijhout
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Michael C Reed
- Department of Mathematics, Duke University, Durham, North Carolina, United States of America
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10
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Cui L, Zhao X, Jin Z, Wang H, Yang SF, Hu S. Melatonin modulates metabolic remodeling in HNSCC by suppressing MTHFD1L-formate axis. J Pineal Res 2021; 71:e12767. [PMID: 34533844 DOI: 10.1111/jpi.12767] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022]
Abstract
Metabolic remodeling is now widely recognized as a hallmark of cancer, yet its role in head and neck squamous cell carcinoma (HNSCC) remains largely unknown. In this study, metabolomic analysis of melatonin-treated HNSCC cell lines revealed that exogenous melatonin inhibited many important metabolic pathways including folate cycle in HNSCC cells. Methylenetetrahydrofolate dehydrogenase 1 like (MTHFD1L), a metabolic enzyme of the folate cycle regulating the production of formate, was identified as a downstream target of melatonin. MTHFD1L was found to be markedly upregulated in HNSCC, and MTHFD1L overexpression was significantly associated with unfavorable clinical outcome of HNSCC patients. In addition, MTHFD1L promoted HNSCC progression in vitro and in vivo and reversed the oncostatic effects of exogenous melatonin. More importantly, the malignant phenotypes suppressed by knockdown of MTHFD1L or exogenous melatonin could be partially rescued by formate. Furthermore, we found that melatonin inhibited the expression of MTHFD1L in HNSCC cells through the downregulation of cyclic AMP-responsive element-binding protein 1 (CREB1) phosphorylation. Lastly, this novel regulatory axis of melatonin-p-CREB1-MTHFD1L-formate was also verified in HNSCC tissues. Collectively, our findings have demonstrated that MTHFD1L-formate axis promotes HNSCC progression and melatonin inhibits HNSCC progression through CREB1-mediated downregulation of MTHFD1L and formate. These findings have revealed new metabolic mechanisms in HNSCC and may provide novel insights on the therapeutic intervention of HNSCC.
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Affiliation(s)
- Li Cui
- School of Dentistry, University of California, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, USA
| | - Xinyuan Zhao
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhenning Jin
- School of Dentistry, University of California, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, USA
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shen Hu
- School of Dentistry, University of California, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, USA
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11
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Induri SNR, Kansara P, Thomas SC, Xu F, Saxena D, Li X. The Gut Microbiome, Metformin, and Aging. Annu Rev Pharmacol Toxicol 2021; 62:85-108. [PMID: 34449247 DOI: 10.1146/annurev-pharmtox-051920-093829] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metformin has been extensively used for the treatment of type 2 diabetes, and it may also promote healthy aging. Despite its widespread use and versatility, metformin's mechanisms of action remain elusive. The gut typically harbors thousands of bacterial species, and as the concentration of metformin is much higher in the gut as compared to plasma, it is plausible that microbiome-drug-host interactions may influence the functions of metformin. Detrimental perturbations in the aging gut microbiome lead to the activation of the innate immune response concomitant with chronic low-grade inflammation. With the effectiveness of metformin in diabetes and antiaging varying among individuals, there is reason to believe that the gut microbiome plays a role in the efficacy of metformin. Metformin has been implicated in the promotion and maintenance of a healthy gut microbiome and reduces many age-related degenerative pathologies. Mechanistic understanding of metformin in the promotion of a healthy gut microbiome and aging will require a systems-level approach. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sri Nitya Reddy Induri
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA;
| | - Payalben Kansara
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA;
| | - Scott C Thomas
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA;
| | - Fangxi Xu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA;
| | - Deepak Saxena
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; .,Department of Surgery, New York University School of Medicine, New York, NY 10016, USA
| | - Xin Li
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA;
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12
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Mendes CC, Zampieri BL, Arantes LMRB, Melendez ME, Biselli JM, Carvalho AL, Eberlin MN, Riccio MF, Vannucchi H, Carvalho VM, Goloni-Bertollo EM, Pavarino ÉC. One-carbon metabolism and global DNA methylation in mothers of individuals with Down syndrome. Hum Cell 2021; 34:1671-1681. [PMID: 34410622 DOI: 10.1007/s13577-021-00586-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Down syndrome (DS) is the most common chromosomal disorder, resulting from the failure of normal chromosome 21 segregation. Studies have suggested that impairments within the one-carbon metabolic pathway can be of relevance for the global genome instability observed in mothers of individuals with DS. Based on the association between global DNA hypomethylation, genome instability, and impairments within the one-carbon metabolic pathway, the present study aimed to identify possible predictors, within the one-carbon metabolism, of global DNA methylation, measured by methylation patterns of LINE-1 and Alu repetitive sequences, in mothers of individuals with DS and mothers of individuals without the syndrome. In addition, we investigated one-carbon genetic polymorphisms and metabolites as maternal predisposing factors for the occurrence of trisomy 21 in children. Eighty-three samples of mothers of children with DS with karyotypically confirmed free trisomy 21 (case group) and 84 of mothers who had at least one child without DS or any other aneuploidy were included in the study. Pyrosequencing assays were performed to access global methylation. The results showed that group affiliation (case or control), betaine-homocysteine methyltransferase (BHMT) G742A and transcobalamin 2 (TCN2) C776G polymorphisms, and folate concentration were identified as predictors of global Alu DNA methylation values. In addition, thymidylate synthase (TYMS) 28-bp repeats 2R/3R or 3R/3R genotypes are independent maternal predisposing factors for having a child with DS. This study adds evidence that supports the association of impairments in the one-carbon metabolism, global DNA methylation, and the possibility of having a child with DS.
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Affiliation(s)
- Cristiani Cortez Mendes
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil
| | | | | | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Joice Matos Biselli
- Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências, Letras e Ciências Exatas de São José do Rio Preto, Departamento de Ciências Biológicas, São José do Rio Preto, São Paulo, Brazil
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Marcos Nogueira Eberlin
- Universidade Presbiteriana Mackenzie, Discovery-Mackenzie-Núcleo Mackenzie de Pesquisa, Núcleo Mackenzie de Pesquisas em Ciência, Fé e Sociedade, São Paulo, São Paulo, Brazil
| | | | - Hélio Vannucchi
- Laboratório de Nutrição, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto-USP, Ribeirão Preto, São Paulo, Brazil
| | | | - Eny Maria Goloni-Bertollo
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil
| | - Érika Cristina Pavarino
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil.
- , Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, São Paulo, 15090-000, Brazil.
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Metformin Is a Pyridoxal-5'-phosphate (PLP)-Competitive Inhibitor of SHMT2. Cancers (Basel) 2021; 13:cancers13164009. [PMID: 34439169 PMCID: PMC8393646 DOI: 10.3390/cancers13164009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/18/2021] [Accepted: 08/05/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The mitochondrial enzyme serine hydroxymethyltransferase (SHMT2), which converts serine into glycine and generates 1C units for cell growth, is one of the most consistently overexpressed metabolic enzymes in cancer. Here, we reveal that the anti-diabetic biguanide metformin operates as a novel class of non-catalytic SHMT2 inhibitor that disrupts the pyridoxal-5′-phosphate (PLP)-dependent SHMT2 oligomerization process and ultimately SHMT2 activity. As SHMT2 inhibitors have not yet reached the clinic, these findings may aid the rational design of PLP-competitive SHMT2 inhibitors based on the biguanide skeleton of metformin. Abstract The anticancer actions of the biguanide metformin involve the functioning of the serine/glycine one-carbon metabolic network. We report that metformin directly and specifically targets the enzymatic activity of mitochondrial serine hydroxymethyltransferase (SHMT2). In vitro competitive binding assays with human recombinant SHMT1 and SHMT2 isoforms revealed that metformin preferentially inhibits SHMT2 activity by a non-catalytic mechanism. Computational docking coupled with molecular dynamics simulation predicted that metformin could occupy the cofactor pyridoxal-5′-phosphate (PLP) cavity and destabilize the formation of catalytically active SHMT2 oligomers. Differential scanning fluorimetry-based biophysical screening confirmed that metformin diminishes the capacity of PLP to promote the conversion of SHMT2 from an inactive, open state to a highly ordered, catalytically competent closed state. CRISPR/Cas9-based disruption of SHMT2, but not of SHMT1, prevented metformin from inhibiting total SHMT activity in cancer cell lines. Isotope tracing studies in SHMT1 knock-out cells confirmed that metformin decreased the SHMT2-channeled serine-to-formate flux and restricted the formate utilization in thymidylate synthesis upon overexpression of the metformin-unresponsive yeast equivalent of mitochondrial complex I (mCI). While maintaining its capacity to inhibit mitochondrial oxidative phosphorylation, metformin lost its cytotoxic and antiproliferative activity in SHMT2-null cancer cells unable to produce energy-rich NADH or FADH2 molecules from tricarboxylic acid cycle (TCA) metabolites. As currently available SHMT2 inhibitors have not yet reached the clinic, our current data establishing the structural and mechanistic bases of metformin as a small-molecule, PLP-competitive inhibitor of the SHMT2 activating oligomerization should benefit future discovery of biguanide skeleton-based novel SHMT2 inhibitors in cancer prevention and treatment.
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14
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Wang Y, Huang Z, Antoneli F, Golubitsky M. The structure of infinitesimal homeostasis in input-output networks. J Math Biol 2021; 82:62. [PMID: 34021398 PMCID: PMC8139887 DOI: 10.1007/s00285-021-01614-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/23/2021] [Accepted: 05/03/2021] [Indexed: 11/30/2022]
Abstract
Homeostasis refers to a phenomenon whereby the output [Formula: see text] of a system is approximately constant on variation of an input [Formula: see text]. Homeostasis occurs frequently in biochemical networks and in other networks of interacting elements where mathematical models are based on differential equations associated to the network. These networks can be abstracted as digraphs [Formula: see text] with a distinguished input node [Formula: see text], a different distinguished output node o, and a number of regulatory nodes [Formula: see text]. In these models the input-output map [Formula: see text] is defined by a stable equilibrium [Formula: see text] at [Formula: see text]. Stability implies that there is a stable equilibrium [Formula: see text] for each [Formula: see text] near [Formula: see text] and infinitesimal homeostasis occurs at [Formula: see text] when [Formula: see text]. We show that there is an [Formula: see text] homeostasis matrix [Formula: see text] for which [Formula: see text] if and only if [Formula: see text]. We note that the entries in H are linearized couplings and [Formula: see text] is a homogeneous polynomial of degree [Formula: see text] in these entries. We use combinatorial matrix theory to factor the polynomial [Formula: see text] and thereby determine a menu of different types of possible homeostasis associated with each digraph [Formula: see text]. Specifically, we prove that each factor corresponds to a subnetwork of [Formula: see text]. The factors divide into two combinatorially defined classes: structural and appendage. Structural factors correspond to feedforward motifs and appendage factors correspond to feedback motifs. Finally, we discover an algorithm for determining the homeostasis subnetwork motif corresponding to each factor of [Formula: see text] without performing numerical simulations on model equations. The algorithm allows us to classify low degree factors of [Formula: see text]. There are two types of degree 1 homeostasis (negative feedback loops and kinetic or Haldane motifs) and there are two types of degree 2 homeostasis (feedforward loops and a degree two appendage motif).
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Affiliation(s)
- Yangyang Wang
- Department of Mathematics, The University of Iowa, Iowa City, IA 52242 USA
| | | | - Fernando Antoneli
- Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04039-032 Brazil
| | - Martin Golubitsky
- Department of Mathematics, The Ohio State University, Columbus, OH 43210 USA
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15
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Folylpoly-ɣ-glutamate synthetase association to the cytoskeleton: Implications to folate metabolon compartmentalization. J Proteomics 2021; 239:104169. [PMID: 33676037 DOI: 10.1016/j.jprot.2021.104169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/03/2021] [Accepted: 02/19/2021] [Indexed: 11/23/2022]
Abstract
Folates are essential for nucleotide biosynthesis, amino acid metabolism and cellular proliferation. Following carrier-mediated uptake, folates are polyglutamylated by folylpoly-ɣ-glutamate synthetase (FPGS), resulting in their intracellular retention. FPGS appears as a long isoform, directed to mitochondria via a leader sequence, and a short isoform reported as a soluble cytosolic protein (cFPGS). However, since folates are labile and folate metabolism is compartmentalized, we herein hypothesized that cFPGS is associated with the cytoskeleton, to couple folate uptake and polyglutamylation and channel folate polyglutamates to metabolon compartments. We show that cFPGS is a cytoskeleton-microtubule associated protein: Western blot analysis revealed that endogenous cFPGS is associated with the insoluble cellular fraction, i.e., cytoskeleton and membranes, but not with the cytosol. Mass spectrometry analysis identified the putative cFPGS interactome primarily consisting of microtubule subunits and cytoskeletal motor proteins. Consistently, immunofluorescence microscopy with cytosol-depleted cells demonstrated the association of cFPGS with the cytoskeleton and unconventional myosin-1c. Furthermore, since anti-microtubule, anti-actin cytoskeleton, and coatomer dissociation-inducing agents yielded perinuclear pausing of cFPGS, we propose an actin- and microtubule-dependent transport of cFPGS between the ER-Golgi and the plasma membrane. These novel findings support the coupling of folate transport with polyglutamylation and folate channeling to intracellular metabolon compartments. SIGNIFICANCE: FPGS, an essential enzyme catalyzing intracellular folate polyglutamylation and efficient retention, was described as a soluble cytosolic enzyme in the past 40 years. However, based on the lability of folates and the compartmentalization of folate metabolism and nucleotide biosynthesis, we herein hypothesized that cytoplasmic FPGS is associated with the cytoskeleton, to couple folate transport and polyglutamylation as well as channel folate polyglutamates to biosynthetic metabolon compartments. Indeed, using complementary techniques including Mass-spectrometry proteomics and fluorescence microscopy, we show that cytoplasmic FPGS is associated with the cytoskeleton and unconventional myosin-1c. This novel cytoskeletal localization of cytoplasmic FPGS supports the dynamic channeling of polyglutamylated folates to metabolon compartments to avoid oxidation and intracellular dilution of folates, while enhancing folate-dependent de novo biosynthesis of nucleotides and DNA/protein methylation.
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16
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Identifying metabolic pathway intermediates that modulate the gallate dioxygenase (DesB) from Sphingobium sp. strain SYK-6. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Ouyang Y, Wu Q, Li J, Sun S, Sun S. S-adenosylmethionine: A metabolite critical to the regulation of autophagy. Cell Prolif 2020; 53:e12891. [PMID: 33030764 PMCID: PMC7653241 DOI: 10.1111/cpr.12891] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/21/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023] Open
Abstract
Autophagy is a mechanism that enables cells to maintain cellular homeostasis by removing damaged materials and mobilizing energy reserves in conditions of starvation. Although nutrient availability strongly impacts the process of autophagy, the specific metabolites that regulate autophagic responses have not yet been determined. Recent results indicate that S-adenosylmethionine (SAM) represents a critical inhibitor of methionine starvation-induced autophagy. SAM is primarily involved in four key metabolic pathways: transmethylation, transsulphuration, polyamine synthesis and 5'-deoxyadenosyl 5'-radical-mediated biochemical transformations. SAM is the sole methyl group donor involved in the methylation of DNA, RNA and histones, modulating the autophagic process by mediating epigenetic effects. Moreover, the metabolites of SAM, such as homocysteine, glutathione, decarboxylated SAM and spermidine, also exert important influences on the regulation of autophagy. From our perspective, nuclear-cytosolic SAM is a conserved metabolic inhibitor that connects cellular metabolic status and the regulation of autophagy. In the future, SAM might be a new target of autophagy regulators and be widely used in the treatment of various diseases.
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Affiliation(s)
- Yang Ouyang
- Department of Breast and Thyroid SurgeryRenmin Hospital of Wuhan UniversityWuhanChina
| | - Qi Wu
- Department of Breast and Thyroid SurgeryRenmin Hospital of Wuhan UniversityWuhanChina
| | - Juanjuan Li
- Department of Breast and Thyroid SurgeryRenmin Hospital of Wuhan UniversityWuhanChina
| | - Si Sun
- Department of Clinical LaboratoryRenmin Hospital of Wuhan UniversityWuhanChina
| | - Shengrong Sun
- Department of Breast and Thyroid SurgeryRenmin Hospital of Wuhan UniversityWuhanChina
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18
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Vezzoli A, Dellanoce C, Maria Caimi T, Vietti D, Montorsi M, Mrakic-Sposta S, Accinni R. Influence of Dietary Supplementation for Hyperhomocysteinemia Treatments. Nutrients 2020; 12:E1957. [PMID: 32630031 PMCID: PMC7400212 DOI: 10.3390/nu12071957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 11/17/2022] Open
Abstract
Hyperhomocysteinemia is recognized as risk factor for cardiovascular and age-associated diseases. Folic acid supplementation efficiently lowers plasma homocysteine (Hcy) levels, but high intake may negatively affect health because of unnatural levels of unmetabolized folic acid in the systemic circulation. Oxoproline (Oxo) provides by glutamic acid production an increase of intracellular folic acid trapping. Aim of this study was to compare the efficacy of three supplementation protocols: (1) traditional therapy (5-methyl-tetrahydrofolate: 15 mg/day); (2) 5 mL/day of Oxo with 300 μg folic acid (oxifolic); (3) 5 mL/day of Oxo alone (magnesio+) in a 90 days randomized trial on thirty-two moderate hyperhomocysteinemic (18.6 ± 2.4 μmol.L-1) patients (age 48 ± 14 yrs). Thiols: cysteine (Cys), cysteinylglycine (Cys-Gly) and glutathione levels were assessed too. Every supplementation induced significant (p range <0.05-0.0001) reductions of Hcy level and Cys concentration after the three protocols adopted. Otherwise glutathione concentration significantly increased after oxifolic (p < 0.01) and traditional (p < 0.05) supplementation. The integration of Oxo resulted an interesting alternative to traditional therapy because absence or minimal number of folates in the integrator eliminates any chance of excess that can constitute a long-term risk.
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Affiliation(s)
- Alessandra Vezzoli
- Institute of Clinical Physiology, National Council of Research (IFC-CNR), ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.V.); (C.D.); (R.A.)
| | - Cinzia Dellanoce
- Institute of Clinical Physiology, National Council of Research (IFC-CNR), ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.V.); (C.D.); (R.A.)
| | - Teresa Maria Caimi
- S.S Emostasi, S.C. Ematologia ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy;
| | | | - Michela Montorsi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, 20122 Milan, Italy;
| | - Simona Mrakic-Sposta
- Institute of Clinical Physiology, National Council of Research (IFC-CNR), ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.V.); (C.D.); (R.A.)
| | - Roberto Accinni
- Institute of Clinical Physiology, National Council of Research (IFC-CNR), ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.V.); (C.D.); (R.A.)
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19
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Gatica-Domínguez G, Rothenberg SJ, Torres-Sánchez L, Schnaas L, Stein AD, Schmidt RJ, López-Carrillo L. The association of prenatal folate and vitamin B12 levels with postnatal neurodevelopment varies by maternal MTHFR 677C>T genotype. INTERNATIONAL JOURNAL OF BEHAVIORAL DEVELOPMENT 2020. [DOI: 10.1177/0165025419853379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Prenatal folate and vitamin B12 status have been linked to child neuropsychological development, but less is known about maternal genetic influences on this association. We conducted an exploratory longitudinal study of 181 mother–child pairs to assess whether maternal MTHFR 677C>T genotype modifies the association between maternal plasma folate and vitamin B12 in the first trimester of pregnancy and child neuropsychological development. Maternal plasma folate and vitamin B12 were determined by radioimmunoassay, and MTHFR 677C>T genotypes by PCR. We evaluated child neuropsychological development at 1, 3, 6, 12, 18, 24, and 30 month old using the Bayley Scales of Infant Development II. We analyzed the data using mixed-effects multivariate linear regression. The MTHFR 677C>T genotype distribution among the mothers was 18.2% CC, 49.8% CT, and 32.0% TT. The Mental Development Index (MDI) was inversely associated with maternal plasma folate among offspring of MTHFR 677CC mothers (β = -2.18 per twofold increase, 95% CI -4.07; -0.30, corrected P value = 0.02); no significant associations were observed among children born to women of other genotypes. The Motor Development Index (PDI) was not significantly associated with maternal plasma folate in any maternal MTHFR 677C>T genotype group, nor were MDI or PDI significantly associated with maternal plasma vitamin B12 in any maternal MTHFR 677C>T genotype group. This study suggests that maternal MTHFR 677CC genotype interacts with first-trimester plasma folate to influence offspring mental development.
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Affiliation(s)
| | | | | | - Lourdes Schnaas
- Subdirección de Investigación en Intervenciones Comunitarias, Instituto Nacional de Perinatología, Mexico
| | - Aryeh D. Stein
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, USA
| | - Rebecca J. Schmidt
- Department of Public Health Science and the MIND Institute, University of California Davis School of Medicine, USA
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20
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Golubitsky M, Wang Y. Infinitesimal homeostasis in three-node input-output networks. J Math Biol 2020; 80:1163-1185. [PMID: 31919651 DOI: 10.1007/s00285-019-01457-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 10/08/2019] [Indexed: 12/17/2022]
Abstract
Homeostasis occurs in a system where an output variable is approximately constant on an interval on variation of an input variable [Formula: see text]. Homeostasis plays an important role in the regulation of biological systems, cf. Ferrell (Cell Syst 2:62-67, 2016), Tang and McMillen (J Theor Biol 408:274-289, 2016), Nijhout et al. (BMC Biol 13:79, 2015), and Nijhout et al. (Wiley Interdiscip Rev Syst Biol Med 11:e1440, 2018). A method for finding homeostasis in mathematical models is given in the control theory literature as points where the derivative of the output variable with respect to [Formula: see text] is identically zero. Such points are called perfect homeostasis or perfect adaptation. Alternatively, Golubitsky and Stewart (J Math Biol 74:387-407, 2017) use an infinitesimal notion of homeostasis (namely, the derivative of the input-output function is zero at an isolated point) to introduce singularity theory into the study of homeostasis. Reed et al. (Bull Math Biol 79(9):1-24, 2017) give two examples of infinitesimal homeostasis in three-node chemical reaction systems: feedforward excitation and substrate inhibition. In this paper we show that there are 13 different three-node networks leading to 78 three-node input-output network configurations, under the assumption that there is one input node, one output node, and they are distinct. The different configurations are based on which node is the input node and which node is the output node. We show nonetheless that there are only three basic mechanisms for three-node input-output networks that lead to infinitesimal homeostasis and we call them structural homeostasis, Haldane homeostasis, and null-degradation homeostasis. Substantial parts of this classification are given in Ma et al. (Cell 138:760-773, 2009) and Ferrell (2016) among others. Our contributions include giving a complete classification using general admissible systems (Golubitsky and Stewart in Bull Am Math Soc 43:305-364, 2006) rather than specific biochemical models, relating the types of infinitesimal homeostasis to the graph theoretic existence of simple paths, and providing the basis to use singularity theory to study higher codimension homeostasis singularities such as the chair singularities introduced in Nijhout and Reed (Integr Comp Biol 54(2):264-275, 2014. https://doi.org/10.1093/icb/icu010) and Nijhout et al. (Math Biosci 257:104-110, 2014). See Golubitsky and Stewart (2017). The first two of these mechanisms are illustrated by feedforward excitation and substrate inhibition. Structural homeostasis occurs only when the network has a feedforward loop as a subnetwork; that is, when there are two distinct simple paths connecting the input node to the output node. Moreover, when the network is just the feedforward loop motif itself, one of the paths must be excitatory and one inhibitory to support infinitesimal homeostasis. Haldane homeostasis occurs when there is a single simple path from the input node to the output node and then only when one of the couplings along this path has strength 0. Null-degradation homeostasis is illustrated by a biochemical example from Ma et al. (2009); this kind of homeostasis can occur only when the degradation constant of the third node is 0. The paper ends with an analysis of Haldane homeostasis infinitesimal chair singularities.
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Affiliation(s)
- Martin Golubitsky
- Department of Mathematics, The Ohio State University, Columbus, OH, 43210, USA.
| | - Yangyang Wang
- Department of Mathematics, The University of Iowa, Iowa City, IA, 52242, USA
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21
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Li H, Fu X, Yao F, Tian T, Wang C, Yang A. MTHFD1L-Mediated Redox Homeostasis Promotes Tumor Progression in Tongue Squamous Cell Carcinoma. Front Oncol 2019; 9:1278. [PMID: 31867267 PMCID: PMC6906156 DOI: 10.3389/fonc.2019.01278] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 11/04/2019] [Indexed: 12/15/2022] Open
Abstract
Background: Routine changes in cell metabolism can drive tumor development, as the cellular program develops to promote glycolysis and redox homeostasis during tumor progression; however, the associated mechanisms in tongue squamous cell carcinoma (TSCC) remain unclear. Methods: We investigated methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L) expression, its clinical relevance, redox modification, and molecular mechanisms using TSCC cells and tissues. The anti-tumor effects of MTHFD1L knockdown on TSCC tumorigenesis were evaluated in vitro and in vivo. Kaplan-Meier curves and the log-rank test were used to analyze disease-free survival and overall survival. Results: TSCC patients with high expression levels of MTHFD1L had shorter overall survival (P < 0.05) and disease-free survival (P < 0.05). Knockdown of MTHFD1L reduced nicotinamide adenine dinucleotide phosphate (NADPH) levels and increased reactive oxygen species (ROS), which accelerated cell death under oxidative stress, such as hypoxia or glucose deprivation. Additionally, inhibition of MTHFD1L suppressed TSCC cell growth and delayed the cell cycle, including in xenograft experiments. Conclusions: MTHFD1L confers redox homeostasis and promotes TSCC cell growth, which provides a great opportunity to study tumor metabolism in head and neck cancer. The mTORC1-4EBP1-eIF4E axis may affect the expression of MTHFD1L in TSCC. Inhibition of the expression of MTHFD1L may be an actionable and effective therapeutic target in TSCC.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Head and Neck Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoyan Fu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Head and Neck Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fan Yao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Head and Neck Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tian Tian
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunyang Wang
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Ankui Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Head and Neck Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
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Li B, Zhang X, Peng X, Zhang S, Wang X, Zhu C. Folic Acid and Risk of Preterm Birth: A Meta-Analysis. Front Neurosci 2019; 13:1284. [PMID: 31849592 PMCID: PMC6892975 DOI: 10.3389/fnins.2019.01284] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
The results from epidemiologic studies linking blood folate concentrations, folic acid supplementation, or dietary folate to the risk of preterm birth are inconsistent. In this study, we aimed to summarize the available evidence on these associations. A systematic search of the PubMed/MEDLINE, Google Scholar, Web of Science, and Cochrane Library databases up to October 20, 2018 was performed and reference lists of retrieved articles were screened. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) for the highest vs. the lowest levels of folate concentrations, folic acid supplementation, and dietary folate were calculated using random-effects models. Subgroup analyses and univariate meta-regression were performed to explore the sources of heterogeneity. Ten studies (six prospective cohort studies and four case-control studies) were included on folate concentrations, 13 cohort studies were included about folic acid supplementation, and 4 cohort studies were included regarding dietary folate intake. Higher maternal folate levels were associated with a 28% reduction in the risk of preterm birth (OR 0.72, 95% CI 0.56–0.93). Higher folic acid supplementation was associated with 10% lower risk of preterm birth (OR 0.90, 95% CI 0.85–0.95). In addition, a significant negative association was observed between dietary folate intake and the risk of preterm birth (OR 0.68, 95% CI 0.55–0.84), but no significant relation was seen between dietary folate and the risk of spontaneous preterm birth (OR 0.89, 95% CI 0.57–1.41). In the subgroup analysis, higher maternal folate levels in the third trimester were associated with a lower risk of preterm birth (OR 0.58, 95% CI 0.36–0.94). To initiate taking folic acid supplementation early before conception was adversely associated with preterm birth risk (OR 0.89, 95% CI 0.83–0.95). In conclusion, higher maternal folate levels and folic acid supplementation were significantly associated with a lower risk of preterm birth. The limited data currently available suggest that dietary folate is associated with a significantly decreased risk of preterm birth.
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Affiliation(s)
- Bingbing Li
- Henan Key Laboratory of Child Brain Injury, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Henan Key Laboratory of Child Brain Injury, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xirui Peng
- Henan Key Laboratory of Child Brain Injury, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Shan Zhang
- Henan Key Laboratory of Child Brain Injury, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China
| | - Xiaoyang Wang
- Henan Key Laboratory of Child Brain Injury, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China.,Perinatal Center, Institute of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury, Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou, China.,Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
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Stan RC, Bhatt DK, Camargo MM. Cellular Adaptation Relies on Regulatory Proteins Having Episodic Memory. Bioessays 2019; 42:e1900115. [DOI: 10.1002/bies.201900115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/06/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Razvan C. Stan
- Cantacuzino National Military‐Medical Institute for Research‐Development Bucharest 050096 Romania
- Department of ImmunologyUniversity of São Paulo São Paulo 05508‐900 Brazil
| | - Darshak K. Bhatt
- Faculty of Medical SciencesGroningen University Groningen 9700 AB The Netherlands
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Wang J, Asante I, Baron JA, Figueiredo JC, Haile R, Joan Levine A, Newcomb PA, Templeton AS, Schumacher FR, Louie SG, Casey G, Conti DV. Genome-wide association study of circulating folate one-carbon metabolites. Genet Epidemiol 2019; 43:1030-1045. [PMID: 31502714 DOI: 10.1002/gepi.22249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/16/2019] [Accepted: 07/11/2019] [Indexed: 12/31/2022]
Abstract
Experimental, observational, and clinical trials support a critical role of folate one-carbon metabolism (FOCM) in colorectal cancer (CRC) development. In this report, we focus on understanding the relationship between common genetic variants and metabolites of FOCM. We conducted a genome-wide association study of FOCM biomarkers among 1,788 unaffected (without CRC) individuals of European ancestry from the Colon Cancer Family Registry. Twelve metabolites, including 5-methyltetrahydrofolate, vitamin B2 (flavin mononucleotide and riboflavin), vitamin B6 (4-pyridoxic acid, pyridoxal, and pyridoxamine), total homocysteine, methionine, S-adenosylmethionine, S-adenosylhomocysteine, cystathionine, and creatinine were measured from plasma using liquid chromatography-mass spectrometry (LC-MS) or LC-MS/MS. For each individual biomarker, we estimated genotype array-specific associations followed by a fixed-effect meta-analysis. We identified the variant rs35976024 (at 2p11.2 and intronic of ATOH8) associated with total homocysteine (p = 4.9 × 10-8 ). We found a group of six highly correlated variants on chromosome 15q14 associated with cystathionine (all p < 5 × 10-8 ), with the most significant variant rs28391580 (p = 2.8 × 10-8 ). Two variants (rs139435405 and rs149119426) on chromosome 14q13 showed significant (p < 5 × 10-8 ) associations with S-adenosylhomocysteine. These three biomarkers with significant associations are closely involved in homocysteine metabolism. Furthermore, when assessing the principal components (PCs) derived from seven individual biomarkers, we identified the variant rs12665366 (at 6p25.3 and intronic of EXOC2) associated with the first PC (p = 2.3 × 10-8 ). Our data suggest that common genetic variants may play an important role in FOCM, particularly in homocysteine metabolism.
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Affiliation(s)
- Jun Wang
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Isaac Asante
- Department of Clinical Pharmacy and Pharmaceutical Economics and Policy, School of Pharmacy, University of Southern California, Los Angeles, California
| | - John A Baron
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Jane C Figueiredo
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California
| | - Robert Haile
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - A Joan Levine
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Allyson S Templeton
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Stan G Louie
- Department of Clinical Pharmacy and Pharmaceutical Economics and Policy, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
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25
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Rat liver folate metabolism can provide an independent functioning of associated metabolic pathways. Sci Rep 2019; 9:7657. [PMID: 31113966 PMCID: PMC6529478 DOI: 10.1038/s41598-019-44009-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/30/2019] [Indexed: 11/27/2022] Open
Abstract
Folate metabolism in mammalian cells is essential for multiple vital processes, including purine and pyrimidine synthesis, histidine catabolism, methionine recycling, and utilization of formic acid. It remains unknown, however, whether these processes affect each other via folate metabolism or can function independently based on cellular needs. We addressed this question using a quantitative mathematical model of folate metabolism in rat liver cytoplasm. Variation in the rates of metabolic processes associated with folate metabolism (i.e., purine and pyrimidine synthesis, histidine catabolism, and influxes of formate and methionine) in the model revealed that folate metabolism is organized in a striking manner that enables activation or inhibition of each individual process independently of the metabolic fluxes in others. In mechanistic terms, this independence is based on the high activities of a group of enzymes involved in folate metabolism, which efficiently maintain close-to-equilibrium ratios between substrates and products of enzymatic reactions.
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26
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Naninck EFG, Stijger PC, Brouwer-Brolsma EM. The Importance of Maternal Folate Status for Brain Development and Function of Offspring. Adv Nutr 2019; 10:502-519. [PMID: 31093652 PMCID: PMC6520042 DOI: 10.1093/advances/nmy120] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/18/2018] [Accepted: 11/27/2018] [Indexed: 12/25/2022] Open
Abstract
The importance of an adequate periconceptional maternal folate status to prevent fetal neural tube defects has been well demonstrated and resulted in the recommendation for women to use folic acid supplements during the periconception period. The importance of maternal folate status for offspring neurodevelopment and brain health is less well described. We reviewed the current evidence linking maternal folate status before conception and during pregnancy with neurodevelopment and cognition of the offspring. We discuss both animal and human studies. Preclinical research revealed the importance of maternal folate status for several key processes required for normal neurodevelopment and brain functioning in the offspring, including DNA synthesis, regulation of gene expression, synthesis of phospholipids and neurotransmitters, and maintenance of healthy plasma homocysteine concentrations. Human observational studies are inconclusive; about half have shown a positive association between maternal folate status and cognitive performance of offspring. Whereas some studies suggest a positive association between maternal folate intake and cognition of offspring during childhood, data from interventional studies are too limited to conclude that there is a direct effect. Future preclinical studies are needed to help us characterize the behavioral effects, understand the underlying mechanisms, and to establish an optimal dosage and time window of folate supplementation. Moreover, more conclusive data from well-designed human observational studies and randomized controlled trials are needed to determine whether current recommendations for folic acid supplementation during pregnancy cover the needs for normal cognitive development in the offspring.
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Affiliation(s)
- Eva F G Naninck
- Swammerdam Institute for Life Sciences, Center for Neuroscience, Brain plasticity group, University of Amsterdam, Amsterdam, Netherlands
| | - Pascalle C Stijger
- Division of Human Nutrition and Health, Wageningen University, Wageningen, Netherlands
| | - Elske M Brouwer-Brolsma
- Division of Human Nutrition and Health, Wageningen University, Wageningen, Netherlands,Address correspondence to EMB-B (e-mail: )
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27
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Mc Auley MT, Mooney KM, Salcedo-Sora JE. Computational modelling folate metabolism and DNA methylation: implications for understanding health and ageing. Brief Bioinform 2019; 19:303-317. [PMID: 28007697 DOI: 10.1093/bib/bbw116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 11/12/2022] Open
Abstract
Dietary folates have a key role to play in health, as deficiencies in the intake of these B vitamins have been implicated in a wide variety of clinical conditions. The reason for this is folates function as single carbon donors in the synthesis of methionine and nucleotides. Moreover, folates have a vital role to play in the epigenetics of mammalian cells by supplying methyl groups for DNA methylation reactions. Intriguingly, a growing body of experimental evidence suggests that DNA methylation status could be a central modulator of the ageing process. This has important health implications because the methylation status of the human genome could be used to infer age-related disease risk. Thus, it is imperative we further our understanding of the processes which underpin DNA methylation and how these intersect with folate metabolism and ageing. The biochemical and molecular mechanisms, which underpin these processes, are complex. However, computational modelling offers an ideal framework for handling this complexity. A number of computational models have been assembled over the years, but to date, no model has represented the full scope of the interaction between the folate cycle and the reactions, which governs the DNA methylation cycle. In this review, we will discuss several of the models, which have been developed to represent these systems. In addition, we will present a rationale for developing a combined model of folate metabolism and the DNA methylation cycle.
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Affiliation(s)
- Mark T Mc Auley
- Department of Chemical Engineering, Thornton Science Park, University of Chester, UK
| | - Kathleen M Mooney
- Faculty of Health and Social Care, Edge Hill University, Ormskirk, Lancashire, UK
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28
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Duff MR, Desai N, Craig MA, Agarwal PK, Howell EE. Crowders Steal Dihydrofolate Reductase Ligands through Quinary Interactions. Biochemistry 2019; 58:1198-1213. [PMID: 30724552 DOI: 10.1021/acs.biochem.8b01110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) reduces dihydrofolate (DHF) to tetrahydrofolate using NADPH as a cofactor. Due to its role in one carbon metabolism, chromosomal DHFR is the target of the antibacterial drug, trimethoprim. Resistance to trimethoprim has resulted in a type II DHFR that is not structurally related to the chromosomal enzyme target. Because of its metabolic significance, understanding DHFR kinetics and ligand binding behavior in more cell-like conditions, where the total macromolecule concentration can be as great as 300 mg/mL, is important. The progress-curve kinetics and ligand binding properties of the drug target (chromosomal E. coli DHFR) and the drug resistant (R67 DHFR) enzymes were studied in the presence of macromolecular cosolutes. There were varied effects on NADPH oxidation and binding to the two DHFRs, with some cosolutes increasing affinity and others weakening binding. However, DHF binding and reduction in both DHFRs decreased in the presence of all cosolutes. The decreased binding of ligands is mostly attributed to weak associations with the macromolecules, as opposed to crowder effects on the DHFRs. Computer simulations found weak, transient interactions for both ligands with several proteins. The net charge of protein cosolutes correlated with effects on NADP+ binding, with near neutral and positively charged proteins having more detrimental effects on binding. For DHF binding, effects correlated more with the size of binding pockets on the protein crowders. These nonspecific interactions between DHFR ligands and proteins predict that the in vivo efficiency of DHFRs may be much lower than expected from their in vitro rates.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Nidhi Desai
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Michael A Craig
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
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29
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Zagkos L, Auley MM, Roberts J, Kavallaris NI. Mathematical models of DNA methylation dynamics: Implications for health and ageing. J Theor Biol 2019; 462:184-193. [DOI: 10.1016/j.jtbi.2018.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 11/01/2018] [Accepted: 11/09/2018] [Indexed: 12/24/2022]
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30
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Nijhout HF, Best JA, Reed MC. Systems biology of robustness and homeostatic mechanisms. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1440. [DOI: 10.1002/wsbm.1440] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/30/2018] [Accepted: 09/21/2018] [Indexed: 12/30/2022]
Affiliation(s)
| | - Janet A. Best
- Department of Mathematics Ohio State University Columbus Ohio
| | - Michael C. Reed
- Department of Mathematics Duke University Durham North Carolina
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31
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Sadre-Marandi F, Dahdoul T, Reed MC, Nijhout HF. Sex differences in hepatic one-carbon metabolism. BMC SYSTEMS BIOLOGY 2018; 12:89. [PMID: 30355281 PMCID: PMC6201565 DOI: 10.1186/s12918-018-0621-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022]
Abstract
Background There are large differences between men and women of child-bearing age in the expression level of 5 key enzymes in one-carbon metabolism almost certainly caused by the sex hormones. These male-female differences in one-carbon metabolism are greatly accentuated during pregnancy. Thus, understanding the origin and consequences of sex differences in one-carbon metabolism is important for precision medicine. Results We have created a mathematical model of hepatic one-carbon metabolism based on the underlying physiology and biochemistry. We use the model to investigate the consequences of sex differences in gene expression. We give a mechanistic understanding of observed concentration differences in one-carbon metabolism and explain why women have lower S-andenosylmethionine, lower homocysteine, and higher choline and betaine. We give a new explanation of the well known phenomenon that folate supplementation lowers homocysteine and we show how to use the model to investigate the effects of vitamin deficiencies, gene polymorphisms, and nutrient input changes. Conclusions Our model of hepatic one-carbon metabolism is a useful platform for investigating the mechanistic reasons that underlie known associations between metabolites. In particular, we explain how gene expression differences lead to metabolic differences between males and females. Electronic supplementary material The online version of this article (doi:10.1186/s12918-018-0621-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Farrah Sadre-Marandi
- Mathematical Biosciences Institute, The Ohio State University, Columbus, 43210, OH, USA
| | - Thabat Dahdoul
- Department of Mathematics, Cal-State Fullerton, Fullerton, 92831, CA, USA
| | - Michael C Reed
- Department of Mathematics, Duke University, 120 Science Drive, Box 90320, Durham, 27708, NC, USA.
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32
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In Vivo Titration of Folate Pathway Enzymes. Appl Environ Microbiol 2018; 84:AEM.01139-18. [PMID: 30030232 DOI: 10.1128/aem.01139-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022] Open
Abstract
How enzymes behave in cells is likely different from how they behave in the test tube. Previous in vitro studies find that osmolytes interact weakly with folate. Removal of the osmolyte from the solvation shell of folate is more difficult than removal of water, which weakens binding of folate to its enzyme partners. To examine if this phenomenon occurs in vivo, osmotic stress titrations were performed with Escherichia coli Two strategies were employed: resistance to an antibacterial drug and complementation of a knockout strain by the appropriate gene cloned into a plasmid that allows tight control of expression levels as well as labeling by a degradation tag. The abilities of the knockout and complemented strains to grow under osmotic stress were compared. Typically, the knockout strain could grow to high osmolalities on supplemented medium, while the complemented strain stopped growing at lower osmolalities on minimal medium. This pattern was observed for an R67 dihydrofolate reductase clone rescuing a ΔfolA strain, for a methylenetetrahydrofolate reductase clone rescuing a ΔmetF strain, and for a serine hydroxymethyltransferase clone rescuing a ΔglyA strain. Additionally, an R67 dihydrofolate reductase clone allowed E. coli DH5α to grow in the presence of trimethoprim until an osmolality of ∼0.81 is reached, while cells in a control titration lacking antibiotic could grow to 1.90 osmol.IMPORTANCEE. coli can survive in drought and flooding conditions and can tolerate large changes in osmolality. However, the cell processes that limit bacterial growth under high osmotic stress conditions are not known. In this study, the dose of four different enzymes in E. coli was decreased by using deletion strains complemented by the gene carried in a tunable plasmid. Under conditions of limiting enzyme concentration (lower than that achieved by chromosomal gene expression), cell growth can be blocked by osmotic stress conditions that are normally tolerated. These observations indicate that E. coli has evolved to deal with variations in its osmotic environment and that normal protein levels are sufficient to buffer the cell from environmental changes. Additional factors involved in the osmotic pressure response may include altered protein concentration/activity levels, weak solute interactions with ligands which can make it more difficult for proteins to bind their substrates/inhibitors/cofactors in vivo, and/or viscosity effects.
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33
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Mishra M, Jayal P, Karande AA, Chandra N. Identification of a co-target for enhancing efficacy of sorafenib in HCC through a quantitative modeling approach. FEBS J 2018; 285:3977-3992. [PMID: 30136368 DOI: 10.1111/febs.14641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/07/2018] [Accepted: 08/20/2018] [Indexed: 12/22/2022]
Abstract
Sorafenib (SFB), a multi-kinase inhibitor, is the only approved drug for treating hepatocellular carcinoma (HCC). However, SFB shows low efficacy in many cases. HCC related mortality therefore remains to be high worldwide. SFB, a multi-kinase inhibitor is also known to modulate the redox homeostasis in cancer cells. To understand the effect of SFB on the redox status, a quantitative understanding of the system is necessary. Kinetic modeling of the relevant pathways is a useful approach for obtaining a quantitative understanding of the pathway dynamics and to rank the individual factors based on the extent of influence they wield on the pathway. Here, we report a comprehensive model of the glutathione reaction network (GSHnet ), consisting of four modules and includes SFB-induced redox stress. We compared GSHnet simulations for HCC of six different etiologies with healthy liver, and correctly identified the expected variations in cancer. Next, we studied alterations induced in the system upon SFB treatment and observed differential H2 O2 dynamics in all the conditions. Using metabolic control analysis, we identified glutathione S-transferase (GST) as the enzyme with the highest selective control coefficient, making it an attractive co-target for potentiating the action of SFB across all six etiologies. As a proof-of-concept, we selected ethacrynic acid (EA), a known inhibitor of GST, and verified ex vivo that EA synergistically potentiates the cytotoxic effect of SFB. Being an FDA approved drug, EA is a promising candidate for repurposing as a combination therapy with SFB for HCC treatment.
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Affiliation(s)
- Madhulika Mishra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Priyanka Jayal
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Anjali A Karande
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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34
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Abstract
Systems composed of many components which interact with each other and lead to unpredictable global behaviour, are considered as complex systems. In a biological context, complex systems represent living systems composed of a large number of interacting elements. In order to study these systems, a precise mathematical modelling was typically used in this context. However, this modelling has limitations in the structural understanding and the behavioural study. In this sense, formal computational modelling is an approach that allows to model and to simulate dynamical properties of these particular systems. In this paper, we use Hybrid Functional Petri Net (HFPN), a Petri net extension dedicated to study and verify biopathways, to model and study the Methionine metabolic pathway. Methionine and its derivatives play significant roles in human bodies. We propose a set of simulations for the purpose of studying and analysing the Methionine pathway’s behaviour. Our simulation results have shown that several important abnormalities in this pathway are related to sever diseases such as Alzheimer’s disease, cardiovascular disease, cancers and others.
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35
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Affiliation(s)
- Rose Schrott
- University Program in Environmental Health, Duke Nicholas School of the Environment, and Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC
| | - Susan K Murphy
- University Program in Environmental Health, Duke Nicholas School of the Environment, and Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC,Address correspondence to SKM (e-mail: )
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36
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Selected B vitamins and their possible link to the aetiology of age-related sarcopenia: relevance of UK dietary recommendations. Nutr Res Rev 2018; 31:204-224. [DOI: 10.1017/s0954422418000045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
AbstractThe possible roles of selected B vitamins in the development and progression of sarcopenia are reviewed. Age-related declines in muscle mass and function are associated with huge and increasing costs to healthcare providers. Falls and loss of mobility and independence due to declining muscle mass/function are associated with poor clinical outcomes and their prevention and management are attractive research targets. Nutritional status appears a key modifiable and affordable intervention. There is emerging evidence of sarcopenia being the result not only of diminished anabolic activity but also of declining neurological integrity in older age, which is emerging as an important aspect of the development of age-related decline in muscle mass/function. In this connection, several B vitamins can be viewed as not only cofactors in muscle synthetic processes, but also as neurotrophic agents with involvements in both bioenergetic and trophic pathways. The B vitamins thus selected are examined with respect to their relevance to multiple aspects of neuromuscular function and evidence is considered that requirements, intakes or absorption may be altered in the elderly. In addition, the evidence base for recommended intakes (UK recommended daily allowance) is examined with particular reference to original datasets and their relevance to older individuals. It is possible that inconsistencies in the literature with respect to the nutritional management of sarcopenia may, in part at least, be the result of compromised micronutrient status in some study participants. It is suggested that in order, for example, for intervention with amino acids to be successful, underlying micronutrient deficiencies must first be addressed/eliminated.
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37
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Goodrich AJ, Volk HE, Tancredi DJ, McConnell R, Lurmann FW, Hansen RL, Schmidt RJ. Joint effects of prenatal air pollutant exposure and maternal folic acid supplementation on risk of autism spectrum disorder. Autism Res 2018; 11:69-80. [PMID: 29120534 PMCID: PMC5777535 DOI: 10.1002/aur.1885] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 06/27/2017] [Accepted: 09/24/2017] [Indexed: 12/14/2022]
Abstract
Independent studies report that periconceptional folic acid (FA) may decrease the risk of autism spectrum disorder (ASD) while exposure to air pollution may increase ASD risk. We examined the joint effects of gestational FA and air pollution exposures in association with ASD. We studied 346 ASD cases and 260 typically developing controls from the CHARGE case-control study. Self-reported FA intake for each month of pregnancy was quantified. Estimates of exposure to near roadway air pollution (NRP) and criteria air pollutant measures were assigned based on maternal residential history. Among mothers with high FA intake (>800 μg) in the first pregnancy month, exposure to increasing levels of all air pollutants, except ozone, during the first trimester was associated with decreased ASD risk, while increased ASD risk was observed for the same pollutant among mothers with low FA intake (≤800 μg). This difference was statistically significant for NO2 (e.g., NO2 and low FA intake: OR = 1.53 (0.91, 2.56) vs NO2 and high FA intake: OR = 0.74 (0.46, 1.19), P-interaction = 0.04). Mothers exposed to higher levels (≥ median) of any air pollutant during the first trimester of pregnancy and who reported low FA intake were at a higher ASD risk compared to mothers exposed to lower levels of that air pollutant and who reported high first month FA intake. Joint effects showed significant (alpha < 0.10) departures from expected interaction for NRP and NO2 . Our results suggest that periconceptional FA intake may reduce ASD risk in those with high prenatal air pollution exposure. Further study is needed to replicate these findings in larger sample sizes and to understand mechanisms of this potential relationship.. Autism Res 2018, 11: 69-80. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY We examined interactions between periconceptional folic acid (FA) and air pollution exposure on risk of ASD. Mothers exposed to higher levels of air pollution during the first trimester of pregnancy and who reported low supplemental FA intake during the first pregnancy month were at a higher ASD risk compared to mothers exposed to lower levels of air pollution and who reported high first month FA intake. Our results suggest that periconceptional FA intake may reduce ASD risk in those with high prenatal air pollution exposure.
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Affiliation(s)
- Amanda J Goodrich
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Heather E Volk
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Mental Health, Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Daniel J Tancredi
- Department of Pediatrics, University of California Davis, Sacramento, CA
| | - Rob McConnell
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Robin L Hansen
- Department of Pediatrics, University of California Davis, Sacramento, CA
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA
| | - Rebecca J Schmidt
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA
- Department of Public Health Sciences, University of California Davis, Davis, CA
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38
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Reed M, Best J, Golubitsky M, Stewart I, Nijhout HF. Analysis of Homeostatic Mechanisms in Biochemical Networks. Bull Math Biol 2017; 79:2534-2557. [PMID: 28884446 PMCID: PMC5842936 DOI: 10.1007/s11538-017-0340-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 08/25/2017] [Indexed: 12/18/2022]
Abstract
Cell metabolism is an extremely complicated dynamical system that maintains important cellular functions despite large changes in inputs. This "homeostasis" does not mean that the dynamical system is rigid and fixed. Typically, large changes in external variables cause large changes in some internal variables so that, through various regulatory mechanisms, certain other internal variables (concentrations or velocities) remain approximately constant over a finite range of inputs. Outside that range, the mechanisms cease to function and concentrations change rapidly with changes in inputs. In this paper we analyze four different common biochemical homeostatic mechanisms: feedforward excitation, feedback inhibition, kinetic homeostasis, and parallel inhibition. We show that all four mechanisms can occur in a single biological network, using folate and methionine metabolism as an example. Golubitsky and Stewart have proposed a method to find homeostatic nodes in networks. We show that their method works for two of these mechanisms but not the other two. We discuss the many interesting mathematical and biological questions that emerge from this analysis, and we explain why understanding homeostatic control is crucial for precision medicine.
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Affiliation(s)
- Michael Reed
- Department of Mathematics, Duke University, Durham, NC, 27708, USA.
| | - Janet Best
- Department of Mathematics, The Ohio State University, Columbus, OH, 43210, USA
| | - Martin Golubitsky
- Department of Mathematics, The Ohio State University, Columbus, OH, 43210, USA
| | - Ian Stewart
- Mathematics Institute, University of Warwick, Coventry, CV47AL, UK
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Henry CJ, Nemkov T, Casás-Selves M, Bilousova G, Zaberezhnyy V, Higa KC, Serkova NJ, Hansen KC, D'Alessandro A, DeGregori J. Folate dietary insufficiency and folic acid supplementation similarly impair metabolism and compromise hematopoiesis. Haematologica 2017; 102:1985-1994. [PMID: 28883079 PMCID: PMC5709097 DOI: 10.3324/haematol.2017.171074] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/06/2017] [Indexed: 12/11/2022] Open
Abstract
While dietary folate deficiency is associated with increased risk for birth defects and other diseases, evidence suggests that supplementation with folic acid can contribute to predisposition to some diseases, including immune dysfunction and cancer. Herein, we show that diets supplemented with folic acid both below and above the recommended levels led to significantly altered metabolism in multiple tissues in mice. Surprisingly, both low and excessive dietary folate induced similar metabolic changes, which were particularly evident for nucleotide biosynthetic pathways in B-progenitor cells. Diet-induced metabolic changes in these cells partially phenocopied those observed in mice treated with anti-folate drugs, suggesting that both deficiency and excessive levels of dietary folic acid compromise folate-dependent biosynthetic pathways. Both folate deficiency and excessive dietary folate levels compromise hematopoiesis, resulting in defective cell cycle progression, persistent DNA damage, and impaired production of lymphocytes. These defects reduce the reconstitution potential in transplantation settings and increase radiation-induced mortality. We conclude that excessive folic acid supplementation can metabolically mimic dietary folate insufficiency, leading to similar functional impairment of hematopoiesis.
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Affiliation(s)
- Curtis J Henry
- Department of Biochemistry and Molecular Genetics, University of Colorado AMC, Aurora, CO, USA.,Department of Immunology and Microbiology, University of Colorado AMC, Aurora, CO, USA
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado AMC, Aurora, CO, USA
| | - Matias Casás-Selves
- Department of Biochemistry and Molecular Genetics, University of Colorado AMC, Aurora, CO, USA
| | - Ganna Bilousova
- Department of Dermatology and Charles C. Gates Center for Regenerative Medicine, University of Colorado AMC, Aurora, CO, USA
| | - Vadym Zaberezhnyy
- Department of Biochemistry and Molecular Genetics, University of Colorado AMC, Aurora, CO, USA
| | - Kelly C Higa
- Department of Immunology and Microbiology, University of Colorado AMC, Aurora, CO, USA
| | - Natalie J Serkova
- Department of Anesthesiology, University of Colorado AMC, Aurora, CO, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado AMC, Aurora, CO, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado AMC, Aurora, CO, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado AMC, Aurora, CO, USA .,Department of Immunology and Microbiology, University of Colorado AMC, Aurora, CO, USA.,Department of Medicine, Section of Hematology, University of Colorado AMC, Aurora, CO, USA.,Department of Pediatrics, Section of Hematology/Oncology, University of Colorado AMC, Aurora, CO, USA
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Abstract
OBJECTIVES Children with celiac disease (CD) may experience deficiencies of several micronutrients. The objectives of the present study were to determine the prevalence of micronutrient deficiencies in children with CD at diagnosis, 6 months, and 18 months after the start of a gluten-free diet (GFD), and examine any correlation between micronutrient deficiencies, serum tissue transglutaminase (TtG) immunoglobulin A (IgA) antibody titers, and the degree of mucosal damage at diagnosis. METHODS Children (<17 years) with CD had their serum vitamins, minerals, and anti-TtG IgA antibodies measured at diagnosis, 6 and 18 months after starting a GFD. Histopathological changes of duodenal biopsies at diagnosis were documented using modified MARSH classification. RESULTS The medical records of 140 children (mean age at diagnosis 7.8 ± 4.01 years, 87 girls [621%]) with CD were examined. At diagnosis, serum vitamin D was the most commonly deficient vitamin in 70% of children. Serum ferritin was subnormal in 34.5% with zinc in 18.6% children but only 12 (10.9%) children had iron deficiency anemia. There was no correlation between micronutrient deficiencies at diagnosis and serum TtG IgA antibody titers or the degree of villous atrophy. The majority of serum levels of measured micronutrients had normalized after 6 months of starting GFD except for vitamin D, which improved but remained subnormal. CONCLUSIONS At diagnosis, most children with CD have vitamin D deficiency. The degree of micronutrient deficiencies does not correlate with the degree of villous atrophy or serum titers of anti-TtG IgA antibodies.
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Nijhout HF, Sadre-Marandi F, Best J, Reed MC. Systems Biology of Phenotypic Robustness and Plasticity. Integr Comp Biol 2017; 57:171-184. [DOI: 10.1093/icb/icx076] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Lyttle DN, Gill JP, Shaw KM, Thomas PJ, Chiel HJ. Robustness, flexibility, and sensitivity in a multifunctional motor control model. BIOLOGICAL CYBERNETICS 2017; 111:25-47. [PMID: 28004255 PMCID: PMC5326633 DOI: 10.1007/s00422-016-0704-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 10/07/2016] [Indexed: 05/25/2023]
Abstract
Motor systems must adapt to perturbations and changing conditions both within and outside the body. We refer to the ability of a system to maintain performance despite perturbations as "robustness," and the ability of a system to deploy alternative strategies that improve fitness as "flexibility." Different classes of pattern-generating circuits yield dynamics with differential sensitivities to perturbations and parameter variation. Depending on the task and the type of perturbation, high sensitivity can either facilitate or hinder robustness and flexibility. Here we explore the role of multiple coexisting oscillatory modes and sensory feedback in allowing multiphasic motor pattern generation to be both robust and flexible. As a concrete example, we focus on a nominal neuromechanical model of triphasic motor patterns in the feeding apparatus of the marine mollusk Aplysia californica. We find that the model can operate within two distinct oscillatory modes and that the system exhibits bistability between the two. In the "heteroclinic mode," higher sensitivity makes the system more robust to changing mechanical loads, but less robust to internal parameter variations. In the "limit cycle mode," lower sensitivity makes the system more robust to changes in internal parameter values, but less robust to changes in mechanical load. Finally, we show that overall performance on a variable feeding task is improved when the system can flexibly transition between oscillatory modes in response to the changing demands of the task. Thus, our results suggest that the interplay of sensory feedback and multiple oscillatory modes can allow motor systems to be both robust and flexible in a variable environment.
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Affiliation(s)
- David N Lyttle
- Department of Mathematics and Biology, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
| | - Jeffrey P Gill
- Department of Biology, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Kendrick M Shaw
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Peter J Thomas
- Department of Mathematics, Applied Mathematics, and Statistics, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Hillel J Chiel
- Department of Biology, Neurosciences and Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA
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Methylfolate Trap Promotes Bacterial Thymineless Death by Sulfa Drugs. PLoS Pathog 2016; 12:e1005949. [PMID: 27760199 PMCID: PMC5070874 DOI: 10.1371/journal.ppat.1005949] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 09/22/2016] [Indexed: 01/16/2023] Open
Abstract
The methylfolate trap, a metabolic blockage associated with anemia, neural tube defects, Alzheimer’s dementia, cardiovascular diseases, and cancer, was discovered in the 1960s, linking the metabolism of folate, vitamin B12, methionine and homocysteine. However, the existence or physiological significance of this phenomenon has been unknown in bacteria, which synthesize folate de novo. Here we identify the methylfolate trap as a novel determinant of the bacterial intrinsic death by sulfonamides, antibiotics that block de novo folate synthesis. Genetic mutagenesis, chemical complementation, and metabolomic profiling revealed trap-mediated metabolic imbalances, which induced thymineless death, a phenomenon in which rapidly growing cells succumb to thymine starvation. Restriction of B12 bioavailability, required for preventing trap formation, using an “antivitamin B12” molecule, sensitized intracellular bacteria to sulfonamides. Since boosting the bactericidal activity of sulfonamides through methylfolate trap induction can be achieved in Gram-negative bacteria and mycobacteria, it represents a novel strategy to render these pathogens more susceptible to existing sulfonamides. Sulfonamides were the first agents to successfully treat bacterial infections, but their use later declined due to the emergence of resistant organisms. Restoration of these drugs may be achieved through inactivation of molecular mechanisms responsible for resistance. A chemo-genomic screen first identified 50 chromosomal loci representing the whole-genome antifolate resistance determinants in Mycobacterium smegmatis. Interestingly, many determinants resembled components of the methylfolate trap, a metabolic blockage exclusively described in mammalian cells. Targeted mutagenesis, genetic and chemical complementation, followed by chemical analyses established the methylfolate trap as a novel mechanism of sulfonamide sensitivity, ubiquitously present in mycobacteria and Gram-negative bacterial pathogens. Furthermore, metabolomic analyses revealed trap-mediated interruptions in folate and related metabolic pathways. These metabolic imbalances induced thymineless death, which was reversible with exogenous thymine supplementation. Chemical restriction of vitamin B12, an important molecule required for prevention of the methylfolate trap, sensitized intracellular bacteria to sulfonamides. Thus, pharmaceutical promotion of the methylfolate trap represents a novel folate antagonistic strategy to render pathogenic bacteria more susceptible to available, clinically approved sulfonamides.
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Golubitsky M, Stewart I. Homeostasis, singularities, and networks. J Math Biol 2016; 74:387-407. [PMID: 27255135 DOI: 10.1007/s00285-016-1024-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 04/17/2016] [Indexed: 12/15/2022]
Abstract
Homeostasis occurs in a biological or chemical system when some output variable remains approximately constant as an input parameter [Formula: see text] varies over some interval. We discuss two main aspects of homeostasis, both related to the effect of coordinate changes on the input-output map. The first is a reformulation of homeostasis in the context of singularity theory, achieved by replacing 'approximately constant over an interval' by 'zero derivative of the output with respect to the input at a point'. Unfolding theory then classifies all small perturbations of the input-output function. In particular, the 'chair' singularity, which is especially important in applications, is discussed in detail. Its normal form and universal unfolding [Formula: see text] is derived and the region of approximate homeostasis is deduced. The results are motivated by data on thermoregulation in two species of opossum and the spiny rat. We give a formula for finding chair points in mathematical models by implicit differentiation and apply it to a model of lateral inhibition. The second asks when homeostasis is invariant under appropriate coordinate changes. This is false in general, but for network dynamics there is a natural class of coordinate changes: those that preserve the network structure. We characterize those nodes of a given network for which homeostasis is invariant under such changes. This characterization is determined combinatorially by the network topology.
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Affiliation(s)
- Martin Golubitsky
- Mathematical Biosciences Institute, Ohio State University, 364 Jennings Hall, Columbus, OH, 43210, USA.
| | - Ian Stewart
- Mathematics Institute, University of Warwick, Coventry, CV4 7AL, UK
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Ishiguro L, Yang M, Sohn KJ, Streutker CJ, Grin A, Croxford R, Kim YI. Folic Acid Supplementation Adversely Affects Chemosensitivity of Colon Cancer Cells to 5-fluorouracil. Nutr Cancer 2016; 68:780-90. [DOI: 10.1080/01635581.2016.1170168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Maternal folic acid supplementation modulates DNA methylation and gene expression in the rat offspring in a gestation period-dependent and organ-specific manner. J Nutr Biochem 2016; 33:103-10. [PMID: 27152636 DOI: 10.1016/j.jnutbio.2016.03.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 12/31/2022]
Abstract
Maternal folic acid supplementation can alter DNA methylation and gene expression in the developing fetus, which may confer disease susceptibility later in life. We determined which gestation period and organ were most sensitive to the modifying effect of folic acid supplementation during pregnancy on DNA methylation and gene expression in the offspring. Pregnant rats were randomized to a control diet throughout pregnancy; folic acid supplementation at 2.5× the control during the 1st, 2nd or 3rd week of gestation only; or folic acid supplementation throughout pregnancy. The brain, liver, kidney and colon from newborn pups were analyzed for folate concentrations, global DNA methylation and gene expression of the Igf2, Er-α, Gr, Ppar-α and Ppar-γ genes. Folic acid supplementation during the 2nd or 3rd week gestation or throughout pregnancy significantly increased brain folate concentrations (P<.001), while only folic acid supplementation throughout pregnancy significantly increased liver folate concentrations (P=.005), in newborn pups. Brain global DNA methylation incrementally decreased from early to late gestational folic acid supplementation and was the lowest with folic acid supplementation throughout pregnancy (P=.026). Folic acid supplementation in late gestation or throughout pregnancy significantly decreased Er-α, Gr and Ppar-α gene expression in the liver (P<.05). The kidney and colon were resistant to the effect of folic acid supplementation. Maternal folic acid supplementation affects tissue folate concentrations, DNA methylation and gene expression in the offspring in a gestation-period-dependent and organ-specific manner.
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Karamshetty V, Acharya JD, Ghaskadbi S, Goel P. Mathematical Modeling of Glutathione Status in Type 2 Diabetics with Vitamin B12 Deficiency. Front Cell Dev Biol 2016; 4:16. [PMID: 27047940 PMCID: PMC4803754 DOI: 10.3389/fcell.2016.00016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/22/2016] [Indexed: 01/11/2023] Open
Abstract
Deficiencies in vitamin B12 and glutathione (GSH) are associated with a number of diseases including type 2 diabetes mellitus. We tested newly diagnosed Indian diabetic patients for correlation between their vitamin B12 and GSH, and found it to be weak. Here we seek to examine the theoretical dependence of GSH on vitamin B12 with a mathematical model of 1-carbon metabolism due to Reed and co-workers. We study the methionine cycle of the Reed-Nijhout model by developing a simple "stylized model" that captures its essential topology and whose kinetics are analytically tractable. The analysis shows-somewhat counter-intuitively-that the flux responsible for the homeostasis of homocysteine is, in fact, peripheral to the methionine cycle. Elevation of homocysteine arises from reduced activity of methionine synthase, a vitamin B12-dependent enzyme, however, this does not increase GSH biosynthesis. The model suggests that the lack of vitamin B12-GSH correlation is explained by suppression of activity in the trans-sulfuration pathway that limits the synthesis of cysteine and GSH from homocysteine. We hypothesize this "cysteine-block" is an essential consequence of vitamin B12 deficiency. It can be clinically relevant to appreciate that these secondary effects of vitamin B12 deficiency could be central to its pathophysiology.
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Affiliation(s)
- Varun Karamshetty
- Department of Mathematics, Indian Institute of Science Education and Research Pune, India
| | | | | | - Pranay Goel
- Department of Biology, Indian Institute of Science Education and Research Pune, India
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Metabolic vitamin B12 deficiency: a missed opportunity to prevent dementia and stroke. Nutr Res 2016; 36:109-16. [DOI: 10.1016/j.nutres.2015.10.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 12/17/2022]
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Salcedo-Sora JE, Mc Auley MT. A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development. MOLECULAR BIOSYSTEMS 2016; 12:923-33. [PMID: 26794619 DOI: 10.1039/c5mb00801h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The metabolic biochemistry of folate biosynthesis and utilisation has evolved into a complex network of reactions. Although this complexity represents challenges to the field of folate research it has also provided a renewed source for antimetabolite targets. A range of improved folate chemotherapy continues to be developed and applied particularly to cancer and chronic inflammatory diseases. However, new or better antifolates against infectious diseases remain much more elusive. In this paper we describe the assembly of a generic deterministic mathematical model of microbial folate metabolism. Our aim is to explore how a mathematical model could be used to explore the dynamics of this inherently complex set of biochemical reactions. Using the model it was found that: (1) a particular small set of folate intermediates are overrepresented, (2) inhibitory profiles can be quantified by the level of key folate products, (3) using the model to scan for the most effective combinatorial inhibitions of folate enzymes we identified specific targets which could complement current antifolates, and (4) the model substantiates the case for a substrate cycle in the folinic acid biosynthesis reaction. Our model is coded in the systems biology markup language and has been deposited in the BioModels Database (MODEL1511020000), this makes it accessible to the community as a whole.
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Mathematical analysis of the regulation of competing methyltransferases. BMC SYSTEMS BIOLOGY 2015; 9:69. [PMID: 26467983 PMCID: PMC4606511 DOI: 10.1186/s12918-015-0215-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/22/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Methyltransferase (MT) reactions, in which methyl groups are attached to substrates, are fundamental to many aspects of cell biology and human physiology. The universal methyl donor for these reactions is S-adenosylmethionine (SAM) and this presents the cell with an important regulatory problem. If the flux along one pathway is changed then the SAM concentration will change affecting all the other MT pathways, so it is difficult for the cell to regulate the pathways independently. METHODS We created a mathematical model, based on the known biochemistry of the folate and methionine cycles, to study the regulatory mechanisms that enable the cell to overcome this difficulty. Some of the primary mechanisms are long-range allosteric interactions by which substrates in one part of the biochemical network affect the activity of enzymes at distant locations in the network (not distant in the cell). Because of these long-range allosteric interactions, the dynamic behavior of the network is very complicated, and so mathematical modeling is a useful tool for investigating the effects of the regulatory mechanisms and understanding the complicated underlying biochemistry and cell biology. RESULTS We study the allosteric binding of 5-methyltetrahydrofolate (5 mTHF) to glycine-N-methyltransferase (GNMT) and explain why data in the literature implies that when one molecule binds, GNMT retains half its activity. Using the model, we quantify the effects of different regulatory mechanisms and show how cell processes would be different if the regulatory mechanisms were eliminated. In addition, we use the model to interpret and understand data from studies in the literature. Finally, we explain why a full understanding of how competing MTs are regulated is important for designing intervention strategies to improve human health. CONCLUSIONS We give strong computational evidence that once bound GNMT retains half its activity. The long-range allosteric interactions enable the cell to regulate the MT reactions somewhat independently. The low K m values of many MTs also play a role because the reactions then run near saturation and changes in SAM have little effect. Finally, the inhibition of the MTs by the product S-adenosylhomocysteine also stabilizes reaction rates against changes in SAM.
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