Genetic Variants and Haplotypes of TOMM40, APOE, and APOC1 are Related to the Age of Onset of Late-onset Alzheimer Disease in a Colombian Population.

BACKGROUND: The Apolipoprotein E (APOE) gene is the main risk factor for late-onset Alzheimer disease (LOAD). Genetic variants and haplotypes in regions near the APOE locus may be associated with LOAD in the Colombian population. OBJECTIVE: We evaluated frequencies and risk of genetic variants and haplotypes in APOE, TOMM40, and APOC1 promoters, also in putative regulatory enhancer elements (TOMM40 IVS2-4 and TOMM40 IVS6), and in cis-regulatory elements (ME1 and BCR). MATERIALS AND METHODS: Our case-control association study was carried out in 50 patients with LOAD and 50 controls. We determined frequencies and odd ratios for genetic variants and haplotypes. RESULTS: We found a significant association between LOAD and genetic variants at the TOMM40 promoter, at TOMM40 IVS2-4 and TOMM40 IVS6 regulatory enhancer elements, and at the APOC1 promoter. Particularly, variants of Poly-T and APOC1 promoter could anticipate the age of onset of LOAD in our population. We identified three risk haplotypes in TOMM40 (ACGGAG, ACGGGG, and ATAGGC) related to LOAD's age of onset. We also found other risk or protection haplotypes at the TOMM40 and APOE promoters, at TOMM40 IVS2-4, TOMM40 IVS6 regulatory enhancer elements, and at ME1. CONCLUSION: Genetic variants and haplotypes near the APOE locus are related to LOAD risk and accelerated onset of LOAD in the Colombian population.

Differential Methylation Levels in CpGs of the BIN1 Gene in Individuals With Alzheimer Disease.

INTRODUCTION: Late-onset Alzheimer disease (LOAD) is the most common dementia worldwide. APOE-[Latin Small Letter Open E]4 and BIN1 (Bridging Integrator 1) have been implicated in the pathogenesis of this disease, but, although DNA methylation of dinucleotide CpGs in the BIN1 gene influences alterations, it has not been studied in Hispanics. OBJECTIVE: The objective of this study was to evaluate the BIN1 3' intergenic region DNA methylation patterns in a Colombian sample of LOAD patients. METHODS: A case-control study was conducted in 50 individuals with LOAD and 50 age-sex matched controls to determine associations of LOAD with DNA methylation. DNA was isolated from peripheral blood, and methylation levels of 8 CpGs were estimated by bisulfite conversion followed by Sanger sequencing with direct PCR analysis. Logistic regression models adjusted by age, sex, and APOE were used to calculate risk associations between methylation levels and LOAD. RESULTS: Overall, participants with LOAD had significantly lower methylation levels on CpG26 (0.86±0.11 vs. 0.95±0.05; P>0.001), CpG44 (0.84±0.09 vs. 0.94±0.06; P=0.001), and CpG87 (0.64±0.12 vs. 0.82±0.10; P>0.001). Adjusted regression models showed that decreased methylation levels of these CpGs remained as risk factors for LOAD (P<0.05). CONCLUSIONS: Hypomethylation of CpGs in BIN1 might play an important role in the expression of BIN1 and may be a biomarker for identifying individuals at high risk of developing LOAD.

Differential Methylation in APOE (Chr19; Exon Four; from 44,909,188 to 44,909,373/hg38) and Increased Apolipoprotein E Plasma Levels in Subjects with Mild Cognitive Impairment.

BACKGROUND: Biomarkers are essential for identification of individuals at high risk of mild cognitive impairment (MCI) for potential prevention of dementia. We investigated DNA methylation in the APOE gene and apolipoprotein E (ApoE) plasma levels as MCI biomarkers in Colombian subjects with MCI and controls. METHODS: In total, 100 participants were included (71% women; average age, 70 years; range, 43⁻91 years). MCI was diagnosed by neuropsychological testing, medical and social history, activities of daily living, cognitive symptoms and neuroimaging. Using multivariate logistic regression models adjusted by age and gender, we examined the risk association of MCI with plasma ApoE and APOE methylation. RESULTS: MCI was diagnosed in 41 subjects (average age, 66.5 ± 9.6 years) and compared with 59 controls. Elevated plasma ApoE and APOE methylation of CpGs 165, 190, and 198 were risk factors for MCI (p < 0.05). Higher CpG-227 methylation correlated with lower risk for MCI (p = 0.002). Only CpG-227 was significantly correlated with plasma ApoE levels (correlation coefficient = -0.665; p = 0.008). CONCLUSION: Differential APOE methylation and increased plasma ApoE levels were correlated with MCI. These epigenetic patterns require confirmation in larger samples but could potentially be used as biomarkers to identify early stages of MCI.

The p.R47H Variant of TREM2 Gene is Associated With Late-onset Alzheimer Disease in Colombian Population.

OBJECTIVE: We evaluated the association of several single-nucleotide polymorphisms in the triggering receptor expressed on myeloid cells 2 (TREM2) gene in a Colombian sample of late-onset Alzheimer disease (LOAD). METHODS: The p.Q33* (rs104894002), p.R47H (rs75932628), p.R62H (rs143332484), and p.D87N (rs142232675) variants of TREM2 gene were directly genotyped using KASPar technology in 358 cases and 329 healthy controls. Sanger sequencing was used to validate >10% of KASPar's results. The Fisher exact test was used to compare the distribution of allelic and genotype frequency between cases and controls, and the Bonferroni correction was set at P<0.05. RESULTS: The minor allele frequency of rs75932628-T was 0.009 in cases and was not found in any healthy controls which suggests a significant association between rs75932628-T and LOAD risk in our sample (P=0.010). The rs143332484-T variant did not exhibit a significant association (P=0.160), whereas rs104894002 and rs142232675 were not found. CONCLUSIONS: Our findings suggest that the rs75932628-T variant of TREM2 is an important risk factor for LOAD in the Colombian population.

Study of mutations in IDH1 and IDH2 genes in a sample of gliomas from Colombian population

Introduction: Gliomas are the most common primary tumors of the central nervous system and, according to their malignancy, they are graded from I to IV. Recent studies have found that there is an association between gliomas and mutations in exon 4 of genes that codify for isocitrate dehydrogenases 1 and 2 (IDH1: codon 132; IDH2: codon 172). Objective: To establish the frequency of mutations in IDH1 and IDH2 in a sample of gliomas from Colombian population. Materials and methods: DNA was extracted from tumor tissue. The exon 4 of IDH1 and IDH2 was amplified by PCR using specific primers and subsequently sequenced. Mutations were determined using the 4Peaks MAFFT programs. Results: We found mutations in the IDH1 gene in 34% of the glioma samples, with a predominance of the nonsynonymous mutation R132H. Mutations in the IDH2 gene were found in 7.5% of cases, with a predominance of the nonsynonymous R172K and R172W mutations. Conclusions: The frequency of mutations in the IDH1 and IDH2 genes in the sample was similar to that reported in other studies. The analysis of these mutations may be important to establish prognostic factors and for the development of future therapeutic targets in gliomas.

Estudio de mutaciones en los genes IDH1 e IDH2 en una muestra de gliomas de población colombiana / Study of mutations in IDH1 and IDH2 genes in a sample of gliomas from Colombian population

Resumen Introducción. Los gliomas son los tumores primarios más comunes del sistema nervioso central y se clasifican de I a IV según su grado de malignidad. En recientes investigaciones se ha encontrado que su aparición está relacionada con mutaciones en el exón 4 de los genes que codifican las deshidrogenasas de isocitrato 1 y 2 (IDH1: codón 132; IDH2: codón 172). Objetivo. Determinar la frecuencia de mutaciones en los genes IDH1 e IDH2 en una muestra de gliomas de pacientes colombianos. Materiales y métodos. La extracción de ADN se hizo a partir de tejido tumoral. El exón 4 de los genes IDH1 e IDH2 se amplificó mediante PCR utilizando iniciadores específicos y, posteriormente, se secuenciaron. Para la determinación de las mutaciones, se emplearon los programas 4Peaksy MAFFT. Resultados. Se determinó la presencia de mutaciones en el gen IDH1 en el 34 % de las muestras, con predominio de la mutación no sinónima R132H. En el 7,5 % de los casos se detectaron mutaciones en el gen IDH2, principalmente las mutaciones no sinónimas R172K y R172W. Conclusiones. La frecuencia de mutaciones en los genes IDH1 e IDH2 en la muestra fue similar a la reportada en otros estudios. El análisis de estas mutaciones puede ser importante como factor pronóstico y para su uso como potenciales blancos terapéuticos en gliomas.

Abstract Introduction: Gliomas are the most common primary tumors of the central nervous system and, according to their malignancy, they are graded from I to IV. Recent studies have found that there is an association between gliomas and mutations in exon 4 of genes that codify for isocitrate dehydrogenases 1 and 2 (IDH1: codon 132; IDH2: codon 172). Objective: To establish the frequency of mutations in IDH1 and IDH2 in a sample of gliomas from Colombian population. Materials and methods: DNA was extracted from tumor tissue. The exon 4 of IDH1 and IDH2 was amplified by PCR using specific primers and subsequently sequenced. Mutations were determined using the 4Peaks MAFFT programs. Results: We found mutations in the IDH1 gene in 34% of the glioma samples, with a predominance of the nonsynonymous mutation R132H. Mutations in the IDH2 gene were found in 7.5% of cases, with a predominance of the nonsynonymous R172K and R172W mutations. Conclusions: The frequency of mutations in the IDH1 and IDH2 genes in the sample was similar to that reported in other studies. The analysis of these mutations may be important to establish prognostic factors and for the development of future therapeutic targets in gliomas.

Estudio de variantes de los genes BDNF, COMT, DAT1 y SERT en niños colombianos con déficit de atención / Study of genetic variants in the BDNF, COMT, DAT1 and SERT genes in Colombian children with attention deficit disorder

Resumen Introducción: El trastorno por déficit de atención e hiperactividad (TDAH) es una perturbación con elevada prevalencia en población infantil de Bogotá. Entre las causas de este trastorno se encuentran factores genéticos y ambientales, pero pocos estudios han tratado de abordar el componente genético en población colombiana. Objetivos: Realizar un estudio de asociación genética entre diferentes polimorfismos y el TDAH en la población de Bogotá. Métodos: Múltiples polimorfismos de los genes DAT1, SERT, COMT y BDNF fueron genotipificados empleando las técnicas de PCR convencional y RFLP en 97 tríos de Bogotá. El test de desequilibrio de trasmisión (TDT) se empleó para determinar la asociación entre las diferentes variantes y el TDAH. Resultados: El análisis de TDT no identificó una transmisión preferencial de alelos de ninguna de las variantes estudiadas. Conclusiones: Nuestros resultados indican que la etiología del TDAH es heterogénea e involucra diversos factores genéticos. Futuros estudios enfocados en otros polimorfismos candidatos en una muestra más grande ayudarán a comprender el TDAH en la población colombiana.

Abstract Background: Attention deficit and hyperactive disorder (ADHD) is highly prevalent among children in Bogota City. Both genetic and environmental factors play a very important role in the etiology of ADHD. However, to date few studies have addressed the association of genetic variants and ADHD in the Colombian population. Objectives: To test the genetic association between polymorphisms in the DAT1, HTTLPR, COMT and BDNF genes and ADHD in a sample from Bogota City. Methods: We genotyped the most common polymorphisms in DAT1, SERT, COMT and BDNF genes associated with ADHD using conventional PCR followed by restriction fragment length polymorphism (RFLP) in 97 trios recruited in a medical center in Bogota. The transmission disequilibrium test (TDT) was used to determine the association between such genetic variants and ADHD. Results: The TDT analysis showed that no individual allele of any variant studied has a preferential transmission. Conclusions: Our results suggest that the etiology of the ADHD maybe complex and involves several genetic factors. Further studies in other candidate polymorphisms in a larger sample size will improve our knowledge of the ADHD in Colombian population.

[Study of genetic variants in the BDNF, COMT, DAT1 and SERT genes in Colombian children with attention deficit disorder]. / Estudio de variantes de los genes BDNF, COMT, DAT1 y SERT en niños colombianos con déficit de atención.

BACKGROUND: Attention deficit and hyperactive disorder (ADHD) is highly prevalent among children in Bogota City. Both genetic and environmental factors play a very important role in the etiology of ADHD. However, to date few studies have addressed the association of genetic variants and ADHD in the Colombian population. OBJECTIVES: To test the genetic association between polymorphisms in the DAT1, HTTLPR, COMT and BDNF genes and ADHD in a sample from Bogota City. METHODS: We genotyped the most common polymorphisms in DAT1, SERT, COMT and BDNF genes associated with ADHD using conventional PCR followed by restriction fragment length polymorphism (RFLP) in 97 trios recruited in a medical center in Bogota. The transmission disequilibrium test (TDT) was used to determine the association between such genetic variants and ADHD. RESULTS: The TDT analysis showed that no individual allele of any variant studied has a preferential transmission. CONCLUSIONS: Our results suggest that the etiology of the ADHD may be complex and involves several genetic factors. Further studies in other candidate polymorphisms in a larger sample size will improve our knowledge of the ADHD in Colombian population.

Association Analysis of Polymorphisms in TOMM40, CR1, PVRL2, SORL1, PICALM, and 14q32.13 Regions in Colombian Alzheimer Disease Patients.

OBJECTIVE: We evaluated the association of several single-nucleotide polymorphisms in different genes including APOE, TOMM40, CR1, PVRL2, SORL1, PICALM, and GWA_14q32.13 in a Colombian sample of Late-Onset Alzheimer disease (LOAD) patients. METHODS: A case-control study was conducted in 362 individuals (181 LOADs and 181 controls) to determine the association of single-nucleotide polymorphisms in APOE (e2, e3, and e4), TOMM40 (rs2075650), CR1 (rs665640), PVRL2 (rs6859), SORL1 (rs11218304), PICALM (rs3851179), and GWA_14q32.13 (rs11622883) with LOAD in a sample from Colombia. RESULTS: We were able to confirm the previously reported association of the APOE4 allele with AD. In addition, we report a new significant association with rs2075650 of TOMM40 for LOAD in our sample. We did not detect any significant interaction between TOMM40 and APOE4 carriers (heterozygous or homozygous) for disease risk development. However, Kaplan-Meier survival analyses suggest that AD patients with TOMM40 allele rs2075650-G have an average age of disease onset of 6 years earlier compared with carriers of the A allele. In addition, the age of disease onset is earlier if APOE4/4 is present. CONCLUSION: Our findings suggest that rs2075650 of TOMM40 could be involved in earlier presentation of LOAD in the Colombian population.

Análisis de mutaciones en los genes PINK1 Y PARKIN en pacientes colombianos con enfermedad de Parkinson / Analysis of mutations in the genes pink1 and parkin in Colombian patients with Parkinson's disease

La enfermedad de Parkinson es un desorden neurodegenerativo complejo, caracterizado por la pérdida progresiva de las neuronas dopaminérgicas de la sustancia nigra pars compacta. Factores tanto ambientales como genéticos se ha determinado que contribuyen a su desarrollo. Mutaciones en los genes PINK1 y PARKIN han sido asociadas con la enfermedad de inicio temprano e historia familiar. El objetivo del presente estudio fue identificar mutaciones en los genes PINK1 (exones 4 y 6) y PARKIN (exones 2 y 7) en 22 pacientes colombianos con EP de inicio temprano y/o antecedentes familiares, mediante amplificación por PCR y secuenciamiento. Las secuencias se compararon con la secuencia consenso de referencia. Se detectó una mutación homocigota de cambio en el marco de lectura ( frameshift) c.155 delA en el exón 2 del gen PARKIN en una paciente con inicio temprano de la enfermedad e historia familiar. Además se identificó la presencia de un polimorfismo en el intrón 2 del gen PARKIN en siete pacientes, uno de ellos en estado homocigoto. No se encontraron mutaciones en los exones 4 y 6 del gen PINK1. Se encontró una mutación homocigota c.155 delA en el exón 2 de PARKIN de una paciente con la enfermedad de Parkinson de inicio temprano con historia familiar. No se encontraron cambios el gen PINK1.

Parkinson's disease is a complex neurodegenerative disorder, characterized by the progressive loss of dopaminergic neurons of the substance nigra pars compacta. It has been determined that factors both environmental and genetic contribute to its development. Mutations in the genes PINK1 and PARKIN have been associated with the early onset of disease and family history. The goal of this study was to identify mutations in the PINK1 genes (exons 4 and 6) and PARKIN (exons 2 and 7) in 22 Colombian patients with EP of early onset and/or family history, by PCR amplification and sequencing. The sequences were compared with the reference consensus sequence. A homozygous change mutation was detected in the reading frame (frame shift) c.155 de la in exon 2 of the PAR-KIN gene in a patient with early onset of the disease and family history. In addition, the presence of a polymorphism in intron 2 of the PARKIN gene was identified in seven patients, one of them in homozygous state. Mutations were not found in exons 4 and 6 of the gene PINK1. A homozygous mutation c.155 de la in exon 2 of PARKIN was found in a female patient with Parkinson's disease early onset with family history. No changes to the gene PINK1 were found.