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Goyal S, Tibrewal S, Ratna R, Vanita V. Genetic and environmental factors contributing to anophthalmia and microphthalmia: Current understanding and future directions. World J Clin Pediatr 2025; 14:101982. [DOI: 10.5409/wjcp.v14.i2.101982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 02/19/2025] [Accepted: 02/25/2025] [Indexed: 03/18/2025] Open
Abstract
Anophthalmia is defined as a complete absence of one eye or both the eyes, while microphthalmia represents the presence of a small eye within the orbit. The estimated birth prevalence for anophthalmia is approximately 3 per 100000 live births, and for microphthalmia, it is around 14 per 100000 live births. However, combined evidence suggests that the prevalence of these malformations could be as high as 30 per 100000 individuals. Microphthalmia is reported to occur in 3.2% to 11.2% of blind children. Anophthalmia and microphthalmia (A/M) are part of a phenotypic spectrum alongside ocular coloboma, hypothesized to share a common genetic basis. Both A/M can occur in isolation or as part of a syndrome. Their complex etiology involves chromosomal aberrations, monogenic inheritance pattern, and the contribution of environmental factors such as gestational-acquired infections, maternal vitamin A deficiency (VAD), exposure to X-rays, solvent misuse, and thalidomide exposure. A/M exhibit significant clinical and genetic heterogeneity with over 90 genes identified so far. Familial cases of A/M have a complex genetic basis, including all Mendelian modes of inheritance, i.e., autosomal dominant, recessive, and X-linked. Most cases arise sporadically due to de novo mutations. Examining gene expression during eye development and the effects of various environmental variables will help us better understand the phenotypic heterogeneity found in A/M, leading to more effective diagnosis and management strategies. The present review focuses on key genetic factors, developmental abnormalities, and environmental modifiers linked with A/M. It also emphasizes at potential research areas including multiomic methods and disease modeling with induced pluripotent stem cell technologies, which aim to create innovative treatment options.
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Affiliation(s)
- Shiwali Goyal
- Department of Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Rockville, MD 20852, United States
| | - Shailja Tibrewal
- Department of Pediatric Ophthalmology, Dr. Shroff’s Charity Eye Hospital, New Delhi 110002, Delhi, India
- Department of Ocular Genetics (Center for Unknown and Rare Eye Diseases), Dr. Shroff’s Charity Eye Hospital, New Delhi 110002, Delhi, India
| | - Ria Ratna
- Department of Ocular Genetics (Center for Unknown and Rare Eye Diseases), Dr. Shroff’s Charity Eye Hospital, New Delhi 110002, Delhi, India
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University, Amritsar 143005, Punjab, India
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Wolujewicz P, Steele JW, Kaltschmidt JA, Finnell RH, Ross ME. Unraveling the complex genetics of neural tube defects: From biological models to human genomics and back. Genesis 2021; 59:e23459. [PMID: 34713546 DOI: 10.1002/dvg.23459] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022]
Abstract
Neural tube defects (NTDs) are a classic example of preventable birth defects for which there is a proven-effective intervention, folic acid (FA); however, further methods of prevention remain unrealized. In the decades following implementation of FA nutritional fortification programs throughout at least 87 nations, it has become apparent that not all NTDs can be prevented by FA. In the United States, FA fortification only reduced NTD rates by 28-35% (Williams et al., 2015). As such, it is imperative that further work is performed to understand the risk factors associated with NTDs and their underlying mechanisms so that alternative prevention strategies can be developed. However, this is complicated by the sheer number of genes associated with neural tube development, the heterogeneity of observable phenotypes in human cases, the rareness of the disease, and the myriad of environmental factors associated with NTD risk. Given the complex genetic architecture underlying NTD pathology and the way in which that architecture interacts dynamically with environmental factors, further prevention initiatives will undoubtedly require precision medicine strategies that utilize the power of human genomics and modern tools for assessing genetic risk factors. Herein, we review recent advances in genomic strategies for discovering genetic variants associated with these defects, and new ways in which biological models, such as mice and cell culture-derived organoids, are leveraged to assess mechanistic functionality, the way these variants interact with other genetic or environmental factors, and their ultimate contribution to human NTD risk.
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Affiliation(s)
- Paul Wolujewicz
- Center for Neurogenetics, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
| | - John W Steele
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Julia A Kaltschmidt
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, USA
| | - Richard H Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Margaret Elizabeth Ross
- Center for Neurogenetics, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
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Seelan RS, Mukhopadhyay P, Philipose J, Greene RM, Pisano MM. Gestational folate deficiency alters embryonic gene expression and cell function. Differentiation 2020; 117:1-15. [PMID: 33302058 DOI: 10.1016/j.diff.2020.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 11/04/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022]
Abstract
Folic acid is a nutrient essential for embryonic development. Folate deficiency can cause embryonic lethality or neural tube defects and orofacial anomalies. Folate receptor 1 (Folr1) is a folate binding protein that facilitates the cellular uptake of dietary folate. To better understand the biological processes affected by folate deficiency, gene expression profiles of gestational day 9.5 (gd9.5) Folr1-/- embryos were compared to those of gd9.5 Folr1+/+ embryos. The expression of 837 genes/ESTs was found to be differentially altered in Folr1-/- embryos, relative to those observed in wild-type embryos. The 837 differentially expressed genes were subjected to Ingenuity Pathway Analysis. Among the major biological functions affected in Folr1-/- mice were those related to 'digestive system development/function', 'cardiovascular system development/function', 'tissue development', 'cellular development', and 'cell growth and differentiation', while the major canonical pathways affected were those associated with blood coagulation, embryonic stem cell transcription and cardiomyocyte differentiation (via BMP receptors). Cellular proliferation, apoptosis and migration were all significantly affected in the Folr1-/- embryos. Cranial neural crest cells (NCCs) and neural tube explants, grown under folate-deficient conditions, exhibited marked reduction in directed migration that can be attributed, in part, to an altered cytoskeleton caused by perturbations in F-actin formation and/or assembly. The present study revealed that several developmentally relevant biological processes were compromised in Folr1-/- embryos.
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Affiliation(s)
- R S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development & Anomalies, University of Louisville Dental School, 501 S. Preston St., Louisville, KY, 40292, USA
| | - P Mukhopadhyay
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development & Anomalies, University of Louisville Dental School, 501 S. Preston St., Louisville, KY, 40292, USA
| | - J Philipose
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development & Anomalies, University of Louisville Dental School, 501 S. Preston St., Louisville, KY, 40292, USA
| | - R M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development & Anomalies, University of Louisville Dental School, 501 S. Preston St., Louisville, KY, 40292, USA.
| | - M M Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development & Anomalies, University of Louisville Dental School, 501 S. Preston St., Louisville, KY, 40292, USA
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Lee S, Gleeson JG. Closing in on Mechanisms of Open Neural Tube Defects. Trends Neurosci 2020; 43:519-532. [PMID: 32423763 PMCID: PMC7321880 DOI: 10.1016/j.tins.2020.04.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/02/2020] [Accepted: 04/22/2020] [Indexed: 11/24/2022]
Abstract
Neural tube defects (NTDs) represent a failure of the neural plate to complete the developmental transition to a neural tube. NTDs are the most common birth anomaly of the CNS. Following mandatory folic acid fortification of dietary grains, a dramatic reduction in the incidence of NTDs was observed in areas where the policy was implemented, yet the genetic drivers of NTDs in humans, and the mechanisms by which folic acid prevents disease, remain disputed. Here, we discuss current understanding of human NTD genetics, recent advances regarding potential mechanisms by which folic acid might modify risk through effects on the epigenome and transcriptome, and new approaches to study refined phenotypes for a greater appreciation of the developmental and genetic causes of NTDs.
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Affiliation(s)
- Sangmoon Lee
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA 92025, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA 92025, USA.
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López‐Escobar B, Wlodarczyk BJ, Caro‐Vega J, Lin Y, Finnell RH, Ybot‐González P. The interaction of maternal diabetes with mutations that affect folate metabolism and how they affect the development of neural tube defects in mice. Dev Dyn 2019; 248:900-917. [DOI: 10.1002/dvdy.92] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 07/18/2019] [Accepted: 07/21/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Beatriz López‐Escobar
- Neurodevelopment Research GroupInstitute of Biomedicine of Seville/Hospital Virgen del Rocio/US/CSIC Sevilla Spain
- Department of Nutritional SciencesDell Pediatric Research Institute, The University of Texas at Austin Austin Texas USA
| | - Bogdan J. Wlodarczyk
- Department of Nutritional SciencesDell Pediatric Research Institute, The University of Texas at Austin Austin Texas USA
- Departments of Molecular and Cellular Biology and MedicineBaylor College of Medicine Houston Texas USA
| | - Jose Caro‐Vega
- Neurodevelopment Research GroupInstitute of Biomedicine of Seville/Hospital Virgen del Rocio/US/CSIC Sevilla Spain
| | - Ying Lin
- Department of Nutritional SciencesDell Pediatric Research Institute, The University of Texas at Austin Austin Texas USA
- Departments of Molecular and Cellular Biology and MedicineBaylor College of Medicine Houston Texas USA
| | - Richard H. Finnell
- Department of Nutritional SciencesDell Pediatric Research Institute, The University of Texas at Austin Austin Texas USA
- Departments of Molecular and Cellular Biology and MedicineBaylor College of Medicine Houston Texas USA
| | - Patricia Ybot‐González
- Neurodevelopment Research GroupInstitute of Biomedicine of Seville/Hospital Virgen del Rocio/US/CSIC Sevilla Spain
- Department of Neurology and NeurofisiologyHospital Virgen de Macarena Sevilla Spain
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Mohanty V, Shah A, Allender E, Siddiqui MR, Monick S, Ichi S, Mania-Farnell B, G McLone D, Tomita T, Mayanil CS. Folate Receptor Alpha Upregulates Oct4, Sox2 and Klf4 and Downregulates miR-138 and miR-let-7 in Cranial Neural Crest Cells. Stem Cells 2016; 34:2721-2732. [PMID: 27300003 DOI: 10.1002/stem.2421] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/09/2016] [Accepted: 05/28/2016] [Indexed: 12/20/2022]
Abstract
Prenatal folic acid (FA) supplementation prevents neural tube defects. Folate receptor alpha (FRα) is critical for embryonic development, including neural crest (NC) development. Previously we showed that FRα translocates to the nucleus in response to FA, where it acts as a transcription factor. In this study, we examined if FA through interaction with FRα regulates stem cell characteristics of cranial neural crest cells (CNCCs)-critical for normal development. We hypothesized that FRα upregulates coding genes and simultaneously downregulates non-coding miRNA which targets coding genes in CNCCs. Quantitative RT-PCR and chromatin immunoprecipitation showed that FRα upregulates Oct4, Sox2, and Klf4 by binding to their cis-regulator elements-5' enhancer/promoters defined by H3K27Ac and p300 occupancy. FA via FRα downregulates miRNAs, miR-138 and miR-let-7, which target Oct4 and Trim71 (an Oct4 downstream effector), respectively. Co-immunoprecipitation data suggests that FRα interacts with the Drosha-DGCR8 complex to affect pre-miRNA processing. Transfecting anti-miR-138 or anti-miR-let-7 into non-proliferating neural crest cells (NCCs) derived from Splotch (Sp-/- ), restored their proliferation potential. In summary, these results suggest a novel pleiotropic role of FRα: (a) direct activation of Oct4, Sox2, and Klf4 genes; and (b) repression of biogenesis of miRNAs that target these genes or their effector molecules. Stem Cells 2016;34:2721-2732.
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Affiliation(s)
- Vineet Mohanty
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amar Shah
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elise Allender
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - M Rizwan Siddiqui
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sarah Monick
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shunsuke Ichi
- Department of Neurosurgery, Japanese Red Cross Medical Center, Shibuya-Ku, Tokyo, Japan
| | | | - David G McLone
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tadanori Tomita
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chandra Shekhar Mayanil
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Kappen C. Modeling anterior development in mice: diet as modulator of risk for neural tube defects. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2013; 163C:333-56. [PMID: 24124024 PMCID: PMC4149464 DOI: 10.1002/ajmg.c.31380] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Head morphogenesis is a complex process that is controlled by multiple signaling centers. The most common defects of cranial development are craniofacial defects, such as cleft lip and cleft palate, and neural tube defects, such as anencephaly and encephalocoele in humans. More than 400 genes that contribute to proper neural tube closure have been identified in experimental animals, but only very few causative gene mutations have been identified in humans, supporting the notion that environmental influences are critical. The intrauterine environment is influenced by maternal nutrition, and hence, maternal diet can modulate the risk for cranial and neural tube defects. This article reviews recent progress toward a better understanding of nutrients during pregnancy, with particular focus on mouse models for defective neural tube closure. At least four major patterns of nutrient responses are apparent, suggesting that multiple pathways are involved in the response, and likely in the underlying pathogenesis of the defects. Folic acid has been the most widely studied nutrient, and the diverse responses of the mouse models to folic acid supplementation indicate that folic acid is not universally beneficial, but that the effect is dependent on genetic configuration. If this is the case for other nutrients as well, efforts to prevent neural tube defects with nutritional supplementation may need to become more specifically targeted than previously appreciated. Mouse models are indispensable for a better understanding of nutrient-gene interactions in normal pregnancies, as well as in those affected by metabolic diseases, such as diabetes and obesity.
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Zhao ZG, Niu CY, Qiu JF, Chen XD, Li JC. Effect of mesenteric lymph duct ligation on gene expression profiles of renal tissue in hemorrhagic shock rats with fluid resuscitation. Ren Fail 2013; 36:271-7. [DOI: 10.3109/0886022x.2013.844623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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PCMT1 gene polymorphisms, maternal folate metabolism, and neural tube defects: a case-control study in a population with relatively low folate intake. GENES AND NUTRITION 2013; 8:581-7. [PMID: 23918616 DOI: 10.1007/s12263-013-0355-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 07/26/2013] [Indexed: 12/29/2022]
Abstract
The PCMT1 gene encodes the protein repair enzyme protein-L-isoaspartate (D-aspartate) O-methyltransferase, which is known to protect certain neural cells against Bax-induced apoptosis. Previous studies have produced inconsistent results regarding the effects of PCMT1 (rs4816 and rs4552) polymorphisms on neural tube defects (NTDs). Reduced maternal plasma folate levels and/or elevated homocysteine (Hcy) levels are considered to be risk factors for NTDs. In order to clarify the key factors contributing to the apparent discrepancy and investigate gene-environment interaction, we conducted a case-control study including 121 cases and 146 matched controls to investigate the association between the two PCMT1 polymorphisms in fetuses and the risk of NTDs in the Chinese population of Lvliang, which has low folate intake. Maternal plasma folate and Hcy levels were also measured, and the interaction between fetal PCMT1 gene status and maternal folate metabolites was assessed. Maternal plasma folate concentrations in the NTD group were lower than in controls (10.23 vs. 13.08 nmol/L, adjusted P = 0.059), and Hcy concentrations were significantly higher (14.46 vs. 11.65 μmol/L, adjusted P = 0.026). Fetuses carrying the rs4816 AG + GG genotype, combined with higher maternal plasma Hcy, had a 6.46-fold (95 % CI 1.15-36.46) increased risk of anencephaly. The results of this study imply that the fetal PCMT1 rs4816 polymorphism may play only a weak role in NTD formation and that gene-environment interactions might be more significant.
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Zhao H, Wang F, Wang J, Xie H, Guo J, Liu C, Wang L, Lu X, Bao Y, Wang G, Zhong R, Niu B, Zhang T. Maternal PCMT1 gene polymorphisms and the risk of neural tube defects in a Chinese population of Lvliang high-risk area. Gene 2012; 505:340-4. [PMID: 22647835 DOI: 10.1016/j.gene.2012.05.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 04/26/2012] [Accepted: 05/15/2012] [Indexed: 11/17/2022]
Abstract
Protein-L-isoaspartate (D-aspartate) O-methyltransferase 1 (PCMT1) gene encodes for the protein repair enzyme L-isoaspartate (D-aspartate) O-methyltransferase (PIMT), which is known to protect certain neural cells from Bax-induced apoptosis. Previous study has shown that PCMT1 polymorphisms rs4552 and rs4816 of infant are associated with spina bifida in the Californian population. The association between maternal polymorphism and neural tube defects is still uncovered. A case-control study was conducted to investigate a possible association between maternal PCMT1 and NTDs in Lvliang high-risk area of Shanxi Province in China, using a high-resolution DNA melting analysis genotyping method. We found that increased risk for anencephaly in isolated NTDs compared with the normal control group was observed for the G (vs. A) allele (p=0.034, OR=1.896, 95% CI, 1.04-3.45) and genotypes GG+GA (p=0.025, OR=2.237, 95% CI, 1.09-4.57). Although the significance was lost after multiple comparison correction, the results implied that maternal polymorphisms in PCMT1 might be a potential genetic risk factor for isolated anencephaly in this Chinese population.
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Affiliation(s)
- Huizhi Zhao
- Capital Institute of Pediatrics, Beijing 100020, China
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Pavlinkova G, Salbaum JM, Kappen C. Maternal diabetes alters transcriptional programs in the developing embryo. BMC Genomics 2009; 10:274. [PMID: 19538749 PMCID: PMC2715936 DOI: 10.1186/1471-2164-10-274] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 06/18/2009] [Indexed: 02/06/2023] Open
Abstract
Background Maternal diabetes is a well-known risk factor for birth defects, such as heart defects and neural tube defects. The causative molecular mechanisms in the developing embryo are currently unknown, and the pathogenesis of developmental abnormalities during diabetic pregnancy is not well understood. We hypothesized that the developmental defects are due to alterations in critical developmental pathways, possibly as a result of altered gene expression. We here report results from gene expression profiling of exposed embryos from a mouse diabetes model. Results In comparison to normal embryos at mid-gestation, we find significantly altered gene expression levels in diabetes-exposed embryos. Independent validation of altered expression was obtained by quantitative Real Time Polymerase Chain Reaction. Sequence motifs in the promoters of diabetes-affected genes suggest potential binding of transcription factors that are involved in responses to oxidative stress and/or to hypoxia, two conditions known to be associated with diabetic pregnancies. Functional annotation shows that a sixth of the de-regulated genes have known developmental phenotypes in mouse mutants. Over 30% of the genes we have identified encode transcription factors and chromatin modifying proteins or components of signaling pathways that impinge on transcription. Conclusion Exposure to maternal diabetes during pregnancy alters transcriptional profiles in the developing embryo. The enrichment, within the set of de-regulated genes, of those encoding transcriptional regulatory molecules provides support for the hypothesis that maternal diabetes affects specific developmental programs.
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Affiliation(s)
- Gabriela Pavlinkova
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198-5455, USA.
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Bliek BJB, Steegers-Theunissen RPM, Blok LJ, Santegoets LAM, Lindemans J, Oostra BA, Steegers EAP, de Klein A. Genome-wide pathway analysis of folate-responsive genes to unravel the pathogenesis of orofacial clefting in man. ACTA ACUST UNITED AC 2008; 82:627-35. [PMID: 18655124 DOI: 10.1002/bdra.20488] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND A cleft of the lip with or without the palate (CLP) is a frequent congenital malformation with a heterogeneous etiology, for which folic acid supplementation has a protective effect. To gain more insight into the molecular pathways affected by natural folate, we examined gene expression profiles of cultured B-lymphoblasts from CLP patients before and after the addition of 5-methyltetrahydrofolate (5-mTHF) to the cultures. METHODS Immortalized B-lymphoblasts from five children with CLP were cultured in folate-deficient medium for 5 days. 5-mTHF was added to a concentration of 30 nM. Gene expression patterns were then evaluated before and after supplementation using Human Genome U133 Plus 2.0 arrays. Data analysis was performed with Omniviz and the GEPAS analysis suite. Differential genes were categorized into biological pathways with Ingenuity Pathway systems. Differential expression was validated by quantitative RT-PCR. RESULTS Using supervised clustering, with a false discovery rate <1%, we identified 144 and 409 significantly up-regulated and down-regulated probesets, respectively, after 5-mTHF addition. The regulated genes were involved in a variety of biological pathways, including one carbon pool and cell cycle regulation, biosynthesis of amino acids and DNA/RNA nucleotides, protein processing, apoptosis, and DNA repair. CONCLUSIONS The large variety of the identified folate responsive pathways fits with the modifying role of folate via the methylation pathway. From the present data we may conclude that folate deficiency deranges normal cell development, which might contribute to the development of CLP. The role of these folate responsive genes in CLP development is intriguing and needs further investigation.
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Affiliation(s)
- Bart J B Bliek
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
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Shaw GM, Carmichael SL, Laurent C, Louik C, Finnell RH, Lammer EJ. Nutrient intakes in women and risks of anophthalmia and microphthalmia in their offspring. ACTA ACUST UNITED AC 2007; 79:708-13. [PMID: 17847120 DOI: 10.1002/bdra.20398] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND There is a paucity of information about risk factors for the human eye anomalies anophthalmia and microphthalmia. In this population-based case-control study we investigated whether periconceptional intakes of supplemental folic acid, dietary folate, vitamin A, and several other nutrients were associated with these eye defects. METHODS This study included data on deliveries that had estimated due dates from 1997-2002 and were part of the National Birth Defects Prevention Study (the National Birth Defects Prevention Study is a population-based case-control study of a wide spectrum of birth defects, incorporating data from 10 birth defects surveillance systems in the United States [Arkansas, California, Georgia/Centers for Disease Control and Prevention, Iowa, Massachusetts, New Jersey, New York, North Carolina, Texas, and Utah]). Cases were those infants or fetuses born with either anophthalmia or microphthalmia. Liveborn infants without major malformations were eligible as controls. Maternal interviews were conducted, primarily by telephone, in English or Spanish. Participation in the interview was 71% among case mothers and 68% among control mothers. Interviews were completed with 89 case mothers and 4,143 control mothers. A shortened version of the food frequency questionnaire from the Nurse's Health Study was used to assess frequency of intake of 58 food items during the year before pregnancy. RESULTS Our results did not indicate reduced risks for these eye malformations associated with maternal intake of vitamin supplements containing folic acid. The data did not show an association between malformation risk and higher or lower intakes of vitamin A. We also did not observe strong evidence that an abundance or a lack of dietary intake of any other nutrient was associated with increased risk of the studied eye malformations. CONCLUSIONS Our observations contribute to a limited body of findings on these rare eye defects.
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Affiliation(s)
- Gary M Shaw
- March of Dimes Birth Defects Foundation, California Research Division, Oakland, California, USA.
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Harris MJ, Juriloff DM. Mouse mutants with neural tube closure defects and their role in understanding human neural tube defects. ACTA ACUST UNITED AC 2007; 79:187-210. [PMID: 17177317 DOI: 10.1002/bdra.20333] [Citation(s) in RCA: 238] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND The number of mouse mutants and strains with neural tube closure defects (NTDs) now exceeds 190, including 155 involving known genes, 33 with unidentified genes, and eight "multifactorial" strains. METHODS The emerging patterns of mouse NTDs are considered in relation to the unknown genetics of the common human NTDs, anencephaly, and spina bifida aperta. RESULTS Of the 150 mouse mutants that survive past midgestation, 20% have risk of either exencephaly and spina bifida aperta or both, parallel to the majority of human NTDs, whereas 70% have only exencephaly, 5% have only spina bifida, and 5% have craniorachischisis. The primary defect in most mouse NTDs is failure of neural fold elevation. Most null mutations (>90%) produce syndromes of multiple affected structures with high penetrance in homozygotes, whereas the "multifactorial" strains and several null-mutant heterozygotes and mutants with partial gene function (hypomorphs) have low-penetrance nonsyndromic NTDs, like the majority of human NTDs. The normal functions of the mutated genes are diverse, with clusters in pathways of actin function, apoptosis, and chromatin methylation and structure. The female excess observed in human anencephaly is found in all mouse exencephaly mutants for which gender has been studied. Maternal agents, including folate, methionine, inositol, or alternative commercial diets, have specific preventative effects in eight mutants and strains. CONCLUSIONS If the human homologs of the mouse NTD mutants contribute to risk of common human NTDs, it seems likely to be in multifactorial combinations of hypomorphs and low-penetrance heterozygotes, as exemplified by mouse digenic mutants and the oligogenic SELH/Bc strain.
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Affiliation(s)
- Muriel J Harris
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
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Katula KS, Heinloth AN, Paules RS. Folate deficiency in normal human fibroblasts leads to altered expression of genes primarily linked to cell signaling, the cytoskeleton and extracellular matrix. J Nutr Biochem 2007; 18:541-52. [PMID: 17320366 DOI: 10.1016/j.jnutbio.2006.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 11/06/2006] [Accepted: 11/22/2006] [Indexed: 11/22/2022]
Abstract
The molecular basis linking folate deficiency to certain health conditions and developmental defects is not fully understood. We examined the consequences of folate deficiency on global gene expression by microarray and compared transcript levels in normal human fibroblast cells (GM03349) grown in folate-deficient and -sufficient medium. The largest represented groups from the selected genes functioned in cell signaling, the cytoskeleton and the extracellular matrix and included the Wnt pathway genes DKK1, WISP1 and WNT5A. Twelve selected genes were further validated by qRT-PCR. Analysis of six genes at 4, 7, 10 and 14 days indicated that the relative differences in transcript levels between folate-sufficient and -deficient cells increases with time. Transcripts for 7 of the 12 selected genes were detected in the human lymphoblast cell line GM02257, and of these, changes in 4 genes corresponded to the results with fibroblast cells. Fibroblast cells were treated with the compounds homocysteine, methotrexate and the MEK1/2 inhibitor U0126, and relative transcript levels of six genes were determined. U0126 caused changes that more closely mimicked those detected in folate-deficient cells. The response of the DKK1 and TAGLN gene promoters to folate deficiency and compounds was examined in NIH3T3 cells using luciferase reporter plasmids. Promoter activity for both genes was decreased by folate deficiency and methotrexate and unaffected by homocysteine. U0126 caused a decrease in DKK1 promoter activity at 50 microM and had no effect on TAGLN promoter activity. These findings suggest an alternative mechanism for how folate deficiency leads to changes in gene expression and altered cell function.
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Affiliation(s)
- Karen S Katula
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402, USA.
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Blom HJ, Shaw GM, den Heijer M, Finnell RH. Neural tube defects and folate: case far from closed. Nat Rev Neurosci 2006; 7:724-31. [PMID: 16924261 PMCID: PMC2970514 DOI: 10.1038/nrn1986] [Citation(s) in RCA: 334] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neural tube closure takes place during early embryogenesis and requires interactions between genetic and environmental factors. Failure of neural tube closure is a common congenital malformation that results in morbidity and mortality. A major clinical achievement has been the use of periconceptional folic acid supplements, which prevents approximately 50-75% of cases of neural tube defects. However, the mechanism underlying the beneficial effects of folic acid is far from clear. Biochemical, genetic and epidemiological observations have led to the development of the methylation hypothesis, which suggests that folic acid prevents neural tube defects by stimulating cellular methylation reactions. Exploring the methylation hypothesis could direct us towards additional strategies to prevent neural tube defects.
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Affiliation(s)
- Henk J Blom
- Laboratory of Pediatrics and Neurology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Post Office Box 9101, 6500 HB Nijmegen, The Netherlands.
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Zhu H, Yang W, Lu W, Zhang J, Shaw GM, Lammer EJ, Finnell RH. A known functional polymorphism (Ile120Val) of the human PCMT1 gene and risk of spina bifida. Mol Genet Metab 2006; 87:66-70. [PMID: 16256389 PMCID: PMC2947858 DOI: 10.1016/j.ymgme.2005.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Revised: 08/30/2005] [Accepted: 09/02/2005] [Indexed: 10/25/2022]
Abstract
Folate binding protein 1 (Folr1) knockout mice with low maternal folate concentrations have been shown to be excellent animal models for human folate-responsive neural tube defects (NTDs). Previous studies using the Folr1 knockout mice revealed that maternal folate supplementation up-regulates the expression of the PCMT1 gene in Folr1 nullizygous neural tube tissue during neural tube closure. PCMT1 encodes the protein repair enzyme l-isoaspartate (d-aspartate) O-methyltransferase (PIMT) that converts abnormal d-aspartyl and l-isoaspartyl residues to the normal l-aspartyl form. PIMT is known to protect certain neural cells from Bax-induced apoptosis. Pcmt1-deficient mice present with abnormal AdoMet/AdoHcy homeostasis. We hypothesized that a known functional polymorphism (Ile120Val) in the human PCMT1 gene is associated with an increased risk of folate-responsive human NTDs. A case-control study was conducted to investigate a possible association between this polymorphism and risk of spina bifida. Compared to the Ile/Ile and Ile/Val genotypes, the homozygous Val/Val genotype showed decreased risk for spina bifida (adjusted odds ratio=0.6, 95% confidence interval: 0.4-0.9). Our results showed that the Ile120Val polymorphism of PCMT1 gene is a genetic modifier for the risk of spina bifida. Val/Val genotype was associated with a reduction in risk for spina bifida.
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Affiliation(s)
- Huiping Zhu
- Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, TX 77030, USA
| | - Wei Yang
- California Birth Defects Monitoring Program, Berkeley, CA, USA
| | - Wei Lu
- Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, TX 77030, USA
| | - Jing Zhang
- Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, TX 77030, USA
| | - Gary M. Shaw
- California Birth Defects Monitoring Program, Berkeley, CA, USA
| | - Edward J. Lammer
- Children’s Hospital Oakland Research Institute, Oakland, CA, USA
| | - Richard H. Finnell
- Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, TX 77030, USA
- Center for Environmental and Rural Health, Texas A&M University, College Station, TX 77843, USA
- Corresponding author. Fax: +1 713 677 7790. (R.H. Finnell)
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