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Diaz-Garcia H, Vilchis-Gil J, Castro-Cerritos KV, Rivera-Susunaga LE, Klünder-Klünder M, Granados-Riveron JT, Gómez-López J, López-Torres A, Sánchez-Urbina R. Association between maternal diet, smoking, and the placenta MTHFR 677C/T genotype and global placental DNA methylation. Placenta 2024; 146:17-24. [PMID: 38160599 DOI: 10.1016/j.placenta.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
INTRODUCTION The placenta provides nutrients to the fetus, and it has protective effects against harmful substances. Unhealthy maternal diets and toxic agents might increase free radical (FR) production. Elevated FR levels are associated with a high risk of oxidative stress, which may cause DNA damage. DNA might be oxidized in the placenta, occasionally affecting its methylation profile due to 8-hidroxy-2'-deoxyguanosine formation. METHODS This study assessed 130 mothers and their children. The maternal's nutritional patterns were determined using the Food Frequency Questionnaire. Information on smoking and alcohol consumption was collected during the medical examination. Data on placental DNA were obtained to determine the MTHFR 677C/T genotype and the proportion of placental DNA methylation (pDNAm). RESULTS Consumption of vitamins and folic acid was above 85%. The pDNAm was found to be correlated with gestational age and coffee intake. Mothers with a smoking history had a low pDNAm. Placentas with the TT genotype had a higher but not significant pDNAm. In the placentas with the CC/CT genotype, the pDNAm was positively associated with carbohydrate and biotin intake. However, the TT genotype was negatively associated with folate and vegetable intake. DISCUSSION The pDNAm was positively associated with coffee intake, but not with macro-, and micronutrient intake. However, it was negatively associated with cigarette smoking. The placentas with the CC/CT genotype had a lower pDNAm than those with the TT genotype. In the placentas with the CC/CT or TT genotype, methylation was positively, and negatively associated with micro- or macronutrients, respectively.
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Affiliation(s)
- Hector Diaz-Garcia
- Centro de Investigación en Malformaciones Congénitas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; Escuela Superior de Enfermería y Obstetricia, Instituto Politécnico Nacional, Mexico City 07738, Mexico
| | - Jenny Vilchis-Gil
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | | | - Luis E Rivera-Susunaga
- Centro de Investigación en Malformaciones Congénitas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; Escuela Superior de Medicina del Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Miguel Klünder-Klünder
- Subdirección de la Gestión de la Investigación, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Javier T Granados-Riveron
- Centro de Investigación en Malformaciones Congénitas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Jaqueline Gómez-López
- Hospital Militar de Especialidades de la Mujer y Neonatología, Secretaria de la Defensa Nacional, Mexico City 11200, Mexico
| | - Adolfo López-Torres
- Instituto de Química Aplicada, Universidad del Papaloapan, Tuxtepec, Oaxaca 68301, Mexico
| | - Rocío Sánchez-Urbina
- Centro de Investigación en Malformaciones Congénitas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; Escuela Superior de Medicina del Instituto Politécnico Nacional, Mexico City 11340, Mexico.
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Granados-Riveron JT, Aquino-Jarquin G. Engineering of the current nucleoside-modified mRNA-LNP vaccines against SARS-CoV-2. Biomed Pharmacother 2021; 142:111953. [PMID: 34343897 PMCID: PMC8299225 DOI: 10.1016/j.biopha.2021.111953] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Currently, there are over 230 different COVID-19 vaccines under development around the world. At least three decades of scientific development in RNA biology, immunology, structural biology, genetic engineering, chemical modification, and nanoparticle technologies allowed the accelerated development of fully synthetic messenger RNA (mRNA)-based vaccines within less than a year since the first report of a SARS-CoV-2 infection. mRNA-based vaccines have been shown to elicit broadly protective immune responses, with the added advantage of being amenable to rapid and flexible manufacturing processes. This review recapitulates current advances in engineering the first two SARS-CoV-2-spike-encoding nucleoside-modified mRNA vaccines, highlighting the strategies followed to potentiate their effectiveness and safety, thus facilitating an agile response to the current COVID-19 pandemic.
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Affiliation(s)
- Javier T Granados-Riveron
- Laboratorio de Investigación en Patogénesis Molecular, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico
| | - Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico.
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Martínez-Saucedo M, Ornelas-Fuentes C, Dedden M, Sánchez-Urbina R, Díaz-García H, Aquino-Jarquin G, Moreno-Salgado R, Granados-Riveron JT. Implementation of high-resolution melting analysis of the porcupine (PORCN) gene for molecular diagnosis of focal dermal hypoplasia: Identification of a novel mutation. J Gene Med 2020; 22:e3165. [PMID: 31984575 DOI: 10.1002/jgm.3165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/18/2020] [Accepted: 01/19/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Focal dermal hypoplasia (FDH) is rare X-linked dominant disease characterized by atrophy and linear pigmentation of the skin, split hand/foot deformities and ocular anomalies. FDH is caused by mutations of the Porcupine (PORCN) gene, which encodes an enzyme that catalyzes the palmitoylation of Wnt ligands required for their secretion. High resolution melting analysis (HRM) is a technique that allows rapid, labor-efficient, low-cost detection of genomic variants. In the present study, we report the successful implementation of HRM in the molecular diagnosis of FDH. METHODS Polymerase chain reaction and HRM assays were designed and optimized for each of the coding exons of the PORCN gene, processing genomic DNA samples form a non-affected control and a patient complying with the FDH diagnostic criteria. The causal mutation was characterized by Sanger sequencing from an amplicon showing a HRM trace suggesting heterozygous variation and was validated using an amplification-refractory mutation system (ARMS) assay. RESULTS The melting profiles suggested the presence of a variant in the patient within exon 1. Sanger sequencing revealed a previously unknown C to T transition replacing a glutamine codon for a premature stop codon at position 28, which was validated using ARMS. CONCLUSIONS Next-generation sequencing facilitates the molecular diagnosis of monogenic disorders; however, its cost-benefit ratio is not optimal when a single, small or medium size causal gene is already identified and the clinical diagnostic presumption is strong. Under those conditions, as it is the case for FDH, HRM represents a cost- and labor-effective approach.
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Affiliation(s)
- Mirna Martínez-Saucedo
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Carolina Ornelas-Fuentes
- Department of Medical Genetics and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Mark Dedden
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rocío Sánchez-Urbina
- Laboratory of Developmental Biology and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez,, Mexico City, México
| | - Héctor Díaz-García
- Laboratory of Developmental Biology and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez,, Mexico City, México
| | - Guillermo Aquino-Jarquin
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rodrigo Moreno-Salgado
- Department of Medical Genetics and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Javier T Granados-Riveron
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Martínez-Saucedo M, Bárcenas-Gómez Y, Baeza-Capetillo P, Dedden M, Aguirre-Hernandez J, Téllez-Camacho SA, Sánchez-Urbina R, Aquino-Jarquin G, Granados-Riveron JT. Identification of human miR-1839-5p by small RNA-seq, a miRNA enriched in neoplastic tissues. J Gene Med 2019; 21:e3117. [PMID: 31408249 DOI: 10.1002/jgm.3117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/19/2019] [Accepted: 08/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) modulate gene expression through destabilization or translational inhibition of cytoplasmic transcripts or by transcriptional regulation through binding to genomic DNA. Although miRNAs are globally down-regulated in cancer, some are overexpressed in neoplastic tissues, playing key roles in tumorigenesis (oncomiRs), sometimes behaving as effective cancer markers. METHODS Using total RNA from human uterus adenocarcinoma and non-neoplastic uterus, we conducted a small RNA-sequencing experiment followed by prediction of novel miRNAs using MirDeep* software. Synteny analysis and whole genome alignments were performed using BLAST. We also evaluated expression by a reverse transcriptase-polymerase chain reaction (RT-PCR) in normal tissues of the FSD2 gene, which spans the human miR-1839-5p gene in the opposite direction. RESULTS MirDeep* analysis predicted a miRNA not previously annotated in databases, identical to and likely the orthologue of mouse miR-1839-5p. Whole-genome local alignments of this miRNA revealed a single perfect hit that is indeed syntenic to mouse miR-1839-5p. Alignments with other mammalian orthologues showed considerable conservation. We validated the prediction via a stem-loop RT-PCR assay, also employed to screen RNA samples from several additional normal and cancer tissues, showing increased expression in neoplastic tissues compared to their respective non neoplastic counterparts. Human heart tissue expresses both miR-1839-5p and FSD2. CONCLUSIONS Human tissues express an orthologue of mouse miR-1839-5p and, given its expression pattern, we suggest that this miRNA could be explored as a potential oncomiR or cancer marker. Also, according to the genomic organization of miR-1839-5p and FSD2, perfect complementarity exists between the two elements, making possible miRNA-directed cleavage in human cardiac tissue.
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Affiliation(s)
- Mirna Martínez-Saucedo
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Yolanda Bárcenas-Gómez
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Patricia Baeza-Capetillo
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Mark Dedden
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Jesus Aguirre-Hernandez
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Samara A Téllez-Camacho
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rocío Sánchez-Urbina
- Laboratory of Developmental Biology and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Guillermo Aquino-Jarquin
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Javier T Granados-Riveron
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico.,Laboratory of Developmental Biology and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Granados-Riveron JT, Aquino-Jarquin G. Reversal of multidrug resistance of leukemia cells is not necessarily induced by direct miR-138/MDR1 promoter interaction. Leuk Res 2017; 57:55-56. [PMID: 28288324 DOI: 10.1016/j.leukres.2017.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Javier T Granados-Riveron
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez. Dr. Márquez No 162, Col. Doctores, Delegación Cuauhtémoc, Ciudad de México, C.P 06720, Mexico, Mexico
| | - Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez. Dr. Márquez No 162, Col. Doctores, Delegación Cuauhtémoc, Ciudad de México, C.P 06720, Mexico, Mexico.
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Granados-Riveron JT, Aquino-Jarquin G. The complexity of the translation ability of circRNAs. Biochim Biophys Acta 2016; 1859:1245-51. [PMID: 27449861 DOI: 10.1016/j.bbagrm.2016.07.009] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/21/2016] [Accepted: 07/15/2016] [Indexed: 12/12/2022]
Abstract
Circular RNAs (circRNAs) are a new class of long non-coding RNAs that play a potential role in gene expression regulation, acting as efficient microRNAs sponges. The latest surprise concerning circRNAs is that we now know that they can serve as transcriptional activators in human cells, indicating that circRNAs are involved in important regulatory tasks. Recently, new insight has been gained about the coding potential of circular viroid RNAs, as well as the presence of Internal Ribosomal Entry Sites (IRES) allowing the formation of peptides or proteins from circular RNA. Here, we discuss the current state of our knowledge regarding evidence supporting the hypothesis that circRNAs serve as protein-coding sequences in vitro and in vivo. Also, we remark on the difficulties of their identification and highlight some tools currently available for exploring the coding potential of circRNA.
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Affiliation(s)
- Javier T Granados-Riveron
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, 4to Piso, Sección 2, Hospital Infantil de México, Federico Gómez, Mexico
| | - Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, 4to Piso, Sección 2, Hospital Infantil de México, Federico Gómez, Mexico.
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Granados-Riveron JT, Aquino-Jarquin G. The TATA-box motif and its impact on transcriptional gene regulation by miRNAs. Biomol Concepts 2015; 6:157-61. [PMID: 25898396 DOI: 10.1515/bmc-2015-0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/22/2015] [Indexed: 11/15/2022] Open
Abstract
Emerging evidence suggests that components of the small RNAs pathway interact with chromatin to regulate nuclear events, such as gene transcription. However, it has recently been reported that in some cases, gene transcription regulation by cellular miRNAs can occur via targeting the TATA-box motif without altering epigenetic modifications. This observation supports the notion that multiple mechanisms of miRNA-based transcriptional regulation exist, enhancing our understanding of the complexity of small RNA-mediated gene regulatory pathways. Here, we remark that miRNA-mediated transcriptional modulation, through the TATA-box motif, may be a synergistic approach for transcriptional control.
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Affiliation(s)
- Javier T Granados-Riveron
- Institute of Genetics, School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom.
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Granados-Riveron JT, Pope M, Bu'lock FA, Thornborough C, Eason J, Setchfield K, Ketley A, Kirk EP, Fatkin D, Feneley MP, Harvey RP, Brook JD. Combined mutation screening of NKX2-5, GATA4, and TBX5 in congenital heart disease: multiple heterozygosity and novel mutations. CONGENIT HEART DIS 2011; 7:151-9. [PMID: 22011241 PMCID: PMC3370385 DOI: 10.1111/j.1747-0803.2011.00573.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background. Variants of several genes encoding transcription modulators, signal transduction, and structural proteins are known to cause Mendelian congenital heart disease (CHD). NKX2-5 and GATA4 were the first CHD-causing genes identified by linkage analysis in large affected families. Mutations of TBX5 cause Holt-Oram syndrome, which includes CHD as a clinical feature. All three genes have a well-established role in cardiac development. Design. In order to investigate the possible role of multiple mutations in CHD, a combined mutation screening was performed in NKX2-5, GATA4, and TBX5 in the same patient cohort. Samples from a cohort of 331 CHD patients were analyzed by polymerase chain reaction, double high-performance liquid chromatography and sequencing in order to identify changes in the NKX2-5, GATA4, and TBX5 genes. Results. Two cases of multiple heterozygosity of putative disease-causing mutations were identified. One patient was found with a novel L122P NKX2-5 mutation in combination with the private A1443D mutation of MYH6. A patient heterozygote for a D425N GATA4 mutation carries also a private mutation of the MYH6 gene (V700M). Conclusions. In addition to reporting two novel mutations of NKX2-5 in CHD, we describe families where multiple individual mutations seem to have an additive effect over the pathogenesis of CHD. Our findings highlight the usefulness of multiple gene mutational analysis of large CHD cohorts.
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Affiliation(s)
- Javier T Granados-Riveron
- Institute of Genetics, School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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Granados-Riveron JT, Ghosh TK, Pope M, Bu'Lock F, Thornborough C, Eason J, Kirk EP, Fatkin D, Feneley MP, Harvey RP, Armour JAL, David Brook J. Alpha-cardiac myosin heavy chain (MYH6) mutations affecting myofibril formation are associated with congenital heart defects. Hum Mol Genet 2010; 19:4007-16. [PMID: 20656787 DOI: 10.1093/hmg/ddq315] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Congenital heart defects (CHD) are collectively the most common form of congenital malformation. Studies of human cases and animal models have revealed that mutations in several genes are responsible for both familial and sporadic forms of CHD. We have previously shown that a mutation in MYH6 can cause an autosomal dominant form of atrial septal defect (ASD), whereas others have identified mutations of the same gene in patients with hypertrophic and dilated cardiomyopathy. In the present study, we report a mutation analysis of MYH6 in patients with a wide spectrum of sporadic CHD. The mutation analysis of MYH6 was performed in DNA samples from 470 cases of isolated CHD using denaturing high-performance liquid chromatography and sequence analysis to detect point mutations and small deletions or insertions, and multiplex amplifiable probe hybridization to detect partial or complete copy number variations. One non-sense mutation, one splicing site mutation and seven non-synonymous coding mutations were identified. Transfection of plasmids encoding mutant and non-mutant green fluorescent protein-MYH6 fusion proteins in mouse myoblasts revealed that the mutations A230P and A1366D significantly disrupt myofibril formation, whereas the H252Q mutation significantly enhances myofibril assembly in comparison with the non-mutant protein. Our data indicate that functional variants of MYH6 are associated with cardiac malformations in addition to ASD and provide a novel potential mechanism. Such phenotypic heterogeneity has been observed in other genes mutated in CHD.
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Affiliation(s)
- Javier T Granados-Riveron
- Institute of Genetics, School of Biology, Queen’s Medical Centre, University of Nottingham, Nottingham, UK
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