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Ford ML, Cooley JM, Sripada V, Xu Z, Erickson JS, Bennett KP, Crawford DR. Eat4Genes: a bioinformatic rational gene targeting app and prototype model for improving human health. Front Nutr 2023; 10:1196520. [PMID: 37305078 PMCID: PMC10250663 DOI: 10.3389/fnut.2023.1196520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/04/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction and aims Dietary Rational Gene Targeting (DRGT) is a therapeutic dietary strategy that uses healthy dietary agents to modulate the expression of disease-causing genes back toward the normal. Here we use the DRGT approach to (1) identify human studies assessing gene expression after ingestion of healthy dietary agents with an emphasis on whole foods, and (2) use this data to construct an online dietary guide app prototype toward eventually aiding patients, healthcare providers, community and researchers in treating and preventing numerous health conditions. Methods We used the keywords "human", "gene expression" and separately, 51 different dietary agents with reported health benefits to search GEO, PubMed, Google Scholar, Clinical trials, Cochrane library, and EMBL-EBI databases for related studies. Studies meeting qualifying criteria were assessed for gene modulations. The R-Shiny platform was utilized to construct an interactive app called "Eat4Genes". Results Fifty-one human ingestion studies (37 whole food related) and 96 key risk genes were identified. Human gene expression studies were found for 18 of 41 searched whole foods or extracts. App construction included the option to select either specific conditions/diseases or genes followed by food guide suggestions, key target genes, data sources and links, dietary suggestion rankings, bar chart or bubble chart visualization, optional full report, and nutrient categories. We also present user scenarios from physician and researcher perspectives. Conclusion In conclusion, an interactive dietary guide app prototype has been constructed as a first step towards eventually translating our DRGT strategy into an innovative, low-cost, healthy, and readily translatable public resource to improve health.
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Affiliation(s)
- Morgan L. Ford
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Jessica M. Cooley
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Veda Sripada
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, United States
| | - Zhengwen Xu
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - John S. Erickson
- Rensselaer Institute for Data Exploration and Applications, Renssalaer Polytechnic Institute, Troy, NY, United States
| | - Kristin P. Bennett
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
- Rensselaer Institute for Data Exploration and Applications, Renssalaer Polytechnic Institute, Troy, NY, United States
| | - Dana R. Crawford
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, United States
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Fatty Acids: A Safe Tool for Improving Neurodevelopmental Alterations in Down Syndrome? Nutrients 2022; 14:nu14142880. [PMID: 35889838 PMCID: PMC9323400 DOI: 10.3390/nu14142880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023] Open
Abstract
The triplication of chromosome 21 causes Down syndrome (DS), a genetic disorder that is characterized by intellectual disability (ID). The causes of ID start in utero, leading to impairments in neurogenesis, and continue into infancy, leading to impairments in dendritogenesis, spinogenesis, and connectivity. These defects are associated with alterations in mitochondrial and metabolic functions and precocious aging, leading to the early development of Alzheimer’s disease. Intense efforts are currently underway, taking advantage of DS mouse models to discover pharmacotherapies for the neurodevelopmental and cognitive deficits of DS. Many treatments that proved effective in mouse models may raise safety concerns over human use, especially at early life stages. Accumulating evidence shows that fatty acids, which are nutrients present in normal diets, exert numerous positive effects on the brain. Here, we review (i) the knowledge obtained from animal models regarding the effects of fatty acids on the brain, by focusing on alterations that are particularly prominent in DS, and (ii) the progress recently made in a DS mouse model, suggesting that fatty acids may indeed represent a useful treatment for DS. This scenario should prompt the scientific community to further explore the potential benefit of fatty acids for people with DS.
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Bayona-Bafaluy MP, Garrido-Pérez N, Meade P, Iglesias E, Jiménez-Salvador I, Montoya J, Martínez-Cué C, Ruiz-Pesini E. Down syndrome is an oxidative phosphorylation disorder. Redox Biol 2021; 41:101871. [PMID: 33540295 PMCID: PMC7859316 DOI: 10.1016/j.redox.2021.101871] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/29/2020] [Accepted: 01/13/2021] [Indexed: 02/07/2023] Open
Abstract
Down syndrome is the most common genomic disorder of intellectual disability and is caused by trisomy of chromosome 21. Several genes in this chromosome repress mitochondrial biogenesis. The goal of this study was to evaluate whether early overexpression of these genes may cause a prenatal impairment of oxidative phosphorylation negatively affecting neurogenesis. Reduction in the mitochondrial energy production and a lower mitochondrial function have been reported in diverse tissues or cell types, and also at any age, including early fetuses, suggesting that a defect in oxidative phosphorylation is an early and general event in Down syndrome individuals. Moreover, many of the medical conditions associated with Down syndrome are also frequently found in patients with oxidative phosphorylation disease. Several drugs that enhance mitochondrial biogenesis are nowadays available and some of them have been already tested in mouse models of Down syndrome restoring neurogenesis and cognitive defects. Because neurogenesis relies on a correct mitochondrial function and critical periods of brain development occur mainly in the prenatal and early neonatal stages, therapeutic approaches intended to improve oxidative phosphorylation should be provided in these periods.
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Affiliation(s)
- M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza. C/ Mariano Esquillor (Edificio I+D), 50018, Zaragoza, Spain.
| | - Nuria Garrido-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza. C/ Mariano Esquillor (Edificio I+D), 50018, Zaragoza, Spain.
| | - Patricia Meade
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza. C/ Mariano Esquillor (Edificio I+D), 50018, Zaragoza, Spain.
| | - Eldris Iglesias
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain.
| | - Irene Jiménez-Salvador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain.
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Carmen Martínez-Cué
- Departamento de Fisiología y Farmacología. Facultad de Medicina, Universidad de Cantabria. Av. Herrera Oría, 39011, Santander, Spain.
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet, 177. 50013, Zaragoza, Spain and C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Rd de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
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García-Cerro S, Rueda N, Vidal V, Puente A, Campa V, Lantigua S, Narcís O, Velasco A, Bartesaghi R, Martínez-Cué C. Prenatal Administration of Oleic Acid or Linolenic Acid Reduces Neuromorphological and Cognitive Alterations in Ts65dn Down Syndrome Mice. J Nutr 2020; 150:1631-1643. [PMID: 32243527 DOI: 10.1093/jn/nxaa074] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/17/2019] [Accepted: 03/02/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The cognitive impairments that characterize Down syndrome (DS) have been attributed to brain hypocellularity due to neurogenesis impairment during fetal stages. Thus, enhancing prenatal neurogenesis in DS could prevent or reduce some of the neuromorphological and cognitive defects found in postnatal stages. OBJECTIVES As fatty acids play a fundamental role in morphogenesis and brain development during fetal stages, in this study, we aimed to enhance neurogenesis and the cognitive abilities of the Ts65Dn (TS) mouse model of DS by administering oleic or linolenic acid. METHODS In total, 85 pregnant TS females were subcutaneously treated from Embryonic Day (ED) 10 until Postnatal Day (PD) 2 with oleic acid (400 mg/kg), linolenic acid (500 mg/kg), or vehicle. All analyses were performed on their TS and Control (CO) male and female progeny. At PD2, we evaluated the short-term effects of the treatments on neurogenesis, cellularity, and brain weight, in 40 TS and CO pups. A total of 69 TS and CO mice were used to test the long-term effects of the prenatal treatments on cognition from PD30 to PD45, and on neurogenesis, cellularity, and synaptic markers, at PD45. Data were compared by ANOVAs. RESULTS Prenatal administration of oleic or linolenic acid increased the brain weight (+36.7% and +45%, P < 0.01), the density of BrdU (bromodeoxyuridine)- (+80% and +115%; P < 0.01), and DAPI (4',6-diamidino-2-phenylindole)-positive cells (+64% and +22%, P < 0.05) of PD2 TS mice with respect to the vehicle-treated TS mice. Between PD30 and PD45, TS mice prenatally treated with oleic or linolenic acid showed better cognitive abilities (+28% and +25%, P < 0.01) and a higher density of the postsynaptic marker PSD95 (postsynaptic density protein 95) (+65% and +44%, P < 0.05) than the vehicle-treated TS animals. CONCLUSION The beneficial cognitive and neuromorphological effects induced by oleic or linolenic acid in TS mice suggest that they could be promising pharmacotherapies for DS-associated cognitive deficits.
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Affiliation(s)
- Susana García-Cerro
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Cantabria, Spain
| | - Noemí Rueda
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Cantabria, Spain
| | - Verónica Vidal
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Cantabria, Spain
| | - Alba Puente
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Cantabria, Spain
| | - Víctor Campa
- Institute of Molecular Biology and Biomedicine (IBTECC), Santander, Cantabria, Spain
| | - Sara Lantigua
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Cantabria, Spain
| | - Oriol Narcís
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Cantabria, Spain
| | - Ana Velasco
- Department of Biochemistry and Molecular Biology, Institute of Neurosciences of Castilla and Leon (INCYL), University of Salamanca, Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Renata Bartesaghi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Carmen Martínez-Cué
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Cantabria, Spain
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Saxena AR, Ilic Z, Sripada V, Crawford DR. Lower concentrations of curcumin inhibit Her2-Akt pathway components in human breast cancer cells, and other dietary botanicals potentiate this and lapatinib inhibition. Nutr Res 2020; 78:93-104. [PMID: 32563955 DOI: 10.1016/j.nutres.2020.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/23/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022]
Abstract
Her2-dependent breast cancer is treated with pharmacological drugs (eg, Herceptin, lapatinib) that target Her2 signaling. Curcumin has emerged as a potential co-treatment for this and other cancers, but prior studies have focused on non-attainable concentrations. Here we test the hypothesis that attainable in vivo levels of dietary curcumin can reduce Her2 signaling. Consistent with previous studies, higher dose curcumin (18 μmol/L) inhibits Her2-Akt pathway signaling (pHer2, total Her2 and pAkt levels) and cell growth using AU565 human breast cancer cells. We then examined lower, more physiologically relevant concentrations of curcumin, alone and in combination with other dietary botanicals (quercetin and OptiBerry fruit extract). At 4 μmol/L, curcumin reduced Her2 signaling, and even more when combined with quercetin or OptiBerry. At 1.5 μmol/L curcumin, pHer2 and Her2 (but not pAkt) were reduced, with all three pathway markers reduced more in the presence of quercetin. We also found that 1.5 μmol/L curcumin strongly potentiated lapatinib inhibition of Her2-Akt pathway signaling, and more so for pAkt, when combined with quercetin plus OptiBerry (CQO). Parallel analyses revealed cell growth inhibition at 18 and 4 μmol/L but not 1.5 μmol/L curcumin, and potentiation of 1.5 μmol/L curcumin growth arrest with other botanicals +/- lapatinib. These studies demonstrate that a physiological attainable level of curcumin (1.5 μmol/L) can reduce some components of the critical Her2-Akt pathway; that even more complete inhibition can be achieved by combination with other dietary botanicals; and that curcumin and other botanicals can potentiate the action of the Her2-cancer metastatic drug lapatinib, in turn suggesting the potential anti-cancer clinical use of these botanicals.
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Affiliation(s)
- Abhinav R Saxena
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Zoran Ilic
- Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Veda Sripada
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Dana R Crawford
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208.
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