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ABSTRACT Background: Early-onset diffuse gastric cancer (EODGC) occurs at or before 50 years of age. Pathogenic mutations and germline deletions in the CDH1 gene (E-cadherin) are well-documented genetic factors associated with the causes of EODGC. Objective: The objective of the study was to study CDH1 germline variants and their potential functional impact in patients with EODGC in a Mexican population. Methods: We studied seven EODGC patients from a biomedical research center in western Mexico. Variants were identified by Sanger sequencing and multiplex ligation-dependent probe amplification. The DeepSEA and SNPClinic v.1.0 software and the Ensembl (1000 Genomes Project, 1kGP) and ClinVar databases were used to predict functional single-nucleotide polymorphisms (SNPs). The genetic admixture of the Mexican patients was corroborated by 22 short tandem repeat loci genotyping and structure analysis. Results: We found 12 germline CDH1 variants in all EODGC patients, and all of them are considered as polymorphisms: rs34561447, rs5030625, rs16260, rs1330727101, rs28372783, rs942269593, rs3743674, rs1801552, rs34939176, rs33964119, rs3556654, and rs1801026. The prediction of regulatory SNPs in the promoter suggests a role for a retrovirus in EODGC that induces the transcription of interferon-related genes through toll-like receptor-interferon response factor 3 signaling, as three SNPs in the CDH1 promoter alter three binding sites for this transcription factor. In addition, SNPs rs28372783 and rs1801026 could alter upstream stimulatory factors 1 (USF1)/USF2-mediated telomerase-dependent lymphocyte activation in EODGC. Other interesting result is a CTCF-dependent shorter CDH1 isoform lacking exon 14, probably due to exon-skipping mediated by rs33964119. Conclusions: Classical pathogenic germline mutations in the CDH1 gene were not found in these 7 EODGC patients. However, the in silico approaches revealed the possible involvement of a retrovirus and a shorter E-cadherin isoform in EODGC. Nevertheless, further in vitro and in vivo assays are needed to confirm these predictions.
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BACKGROUND: Early-onset diffuse gastric cancer (EODGC) occurs at or before 50 years of age. Pathogenic mutations and germline deletions in the CDH1 gene (E-cadherin) are well-documented genetic factors associated with the causes of EODGC. OBJECTIVE: The objective of the study was to study CDH1 germline variants and their potential functional impact in patients with EODGC in a Mexican population. METHODS: We studied seven EODGC patients from a biomedical research center in western Mexico. Variants were identified by Sanger sequencing and multiplex ligation-dependent probe amplification. The DeepSEA and SNPClinic v.1.0 software and the Ensembl (1000 Genomes Project, 1kGP) and ClinVar databases were used to predict functional single-nucleotide polymorphisms (SNPs). The genetic admixture of the Mexican patients was corroborated by 22 short tandem repeat loci genotyping and structure analysis. RESULTS: We found 12 germline CDH1 variants in all EODGC patients, and all of them are considered as polymorphisms: rs34561447, rs5030625, rs16260, rs1330727101, rs28372783, rs942269593, rs3743674, rs1801552, rs34939176, rs33964119, rs3556654, and rs1801026. The prediction of regulatory SNPs in the promoter suggests a role for a retrovirus in EODGC that induces the transcription of interferon-related genes through toll-like receptor-interferon response factor 3 signaling, as three SNPs in the CDH1 promoter alter three binding sites for this transcription factor. In addition, SNPs rs28372783 and rs1801026 could alter upstream stimulatory factors 1 (USF1)/USF2-mediated telomerase-dependent lymphocyte activation in EODGC. Other interesting result is a CTCF-dependent shorter CDH1 isoform lacking exon 14, probably due to exon-skipping mediated by rs33964119. CONCLUSIONS: Classical pathogenic germline mutations in the CDH1 gene were not found in these 7 EODGC patients. However, the in silico approaches revealed the possible involvement of a retrovirus and a shorter E-cadherin isoform in EODGC. Nevertheless, further in vitro and in vivo assays are needed to confirm these predictions.
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Introducción. Los microsatélites o short tandem repeats son los marcadores de elección en identificación humana, para lo cual se deben analizar en las poblaciones. Esta tarea se ha realizado escasamente con los sistemas genéticos de nueva generación, lo cual es crítico en las poblaciones mestizas de México, ya que se ha demostrado una subestructura genética significativa por diferencias en sus componentes de mezcla. Objetivo. Hacer la validación poblacional del sistema de análisis genético Powerplex® 21 en mestizos de la región occidente de México. Material y métodos. Se analizaron 374 individuos no emparentados residentes de la región occidente de México con el sistema Powerplex® 21. Los datos genéticos se analizaron con diversos programas estadísticos y se compararon con poblaciones de referencia. Resultados y conclusiones. Se determinaron las frecuencias alélicas y la distribución de genotipos de todos los marcadores estuvieron en equilibrio Hardy-Weinberg; la prueba de desequilibrio de ligamiento descartó asociaciones entre pares de loci. Se estimaron los siguientes parámetros de interés forense para el sistema PowerPlex® 21: poder ddee discriminación (PD), poder de exclusión (PE), (heterocigosidad (Het), (contenido de información polimórfica (PIC) e índice de paternidad (IP) típico, cuyo poder de discriminación y exclusión combinado fue -100% y 99,999999473%, respectivamente. Esto constituye un incremento importante respecto a lo ofrecido por sistemas tradicionales con 15 short tandem repeats para la misma población/región. La información reportada valida el uso del sistema PowerPlex® 21 en mestizos del occidente de México para interpretar de forma confiable perfiles de ADN en pruebas de paternidad y casos forenses (AU)
Introduction. Microsatellites or short tandem repeats (STR) are the markers of choice in human identification. For this purpose, they must be analyzed in populations. This task has been scarcely performed for new generation human identification systems, which is critical in Mexican mestizo populations, because a significant genetic structure has been demonstrated due to admixture differences. Objective. To validate the System in mestizo populations from the west region of Mexico. Methods. A total of 374 unrelated Mexican-mestizos from the west region were analyzed with the Powerplex® 21 system. Genetic data were analyzed using different softwares and including additional related populations for comparison purposes. Results and conclusions. We estimated allele frequencies, and genotype distribution of all markers was in agreement with Hardy-Weinberg expectations; the linkage disequilibrium test discarded association between all pair of loci. The following forensic parameters were estimated: power of discrimination (PD), power of exclusion (PE), heterozygosity (Het), polymorphism information content (PIC), and typical paternity index (PI); its combined power of discrimination and exclusion was -100% and 99.999999473%, respectively. This constitutes an important increment with respect to typical 15 STR systems for the same population/region. This report validates the PowerPlex® 21 system in western Mexican-mestizos for confident interpretation of DNA profiles in forensic cases and paternity testing. Sistema Powerplex® 21; México; Identificación humana; Poblaciones (AU)
