Pub Date : 2024-03-27DOI: 10.1186/s43042-024-00474-w
Homa Akhavan Aghghaleh, Najmeh Ranji, Hadi Habibollahi
The age-standardized incidence rate for gastric cancer is estimated to be 11.1% worldwide and 39.1% for Ardabil province in northwest Iran. Single nucleotide polymorphisms (SNPs) occur in coding and non-coding regions, contributing to cancer susceptibility. To identify SNPs predisposing individuals to gastric cancer in this region, we compared 263 variants between the Ardabil population and other populations. Whole exome sequencing was used to determine the distribution of variants in the genomic DNA of 150 volunteers (aged < 35 years) from the general population of Ardabil. We compared allele frequencies with databases such as Iranome, Alfa, GnomAD, and 1000G, and statistically analyzed their correlation with age-standardized incidence rates (ASRs) for gastric cancer in related populations using the Pearson correlation test. Some findings were validated using Sanger-based PCR-Sequencing. We determined the frequency of seventeen variants among 150 individuals with gastric cancer and 150 healthy volunteers (matched for age and sex) as the control group. Nineteen variants, including rs10061133, rs1050631, rs12220909, rs12983273, rs1695, rs2274223, rs2292832, rs2294008, rs2505901, rs2976391, rs33927012, rs3744037, rs3745469, rs4789936, rs4986790, rs4986791, rs6194, rs63750447, and rs6505162, were found to be significantly different between the general population of Ardabil and other populations. Among them, the variants rs1050631, rs12983273, rs1695, rs2274223, rs2292832, rs2505901, rs33927012, rs374569, and rs6505162 showed significant differences between the cases and controls. In this study, 17 variants appeared to be involved in the etiology of the high frequency of gastric cancer in the Ardabil population. Some of the observed differences were consistent with previous case–control and meta-analysis reports from various parts of the world. These findings motivate further cohort investigations in this population. Ultimately, identifying prognostic factors can help diagnose individuals predisposed to gastric cancer in this population.
{"title":"Genomic susceptibility to gastric cancer in Northwest Iran: population-based and case–control studies","authors":"Homa Akhavan Aghghaleh, Najmeh Ranji, Hadi Habibollahi","doi":"10.1186/s43042-024-00474-w","DOIUrl":"https://doi.org/10.1186/s43042-024-00474-w","url":null,"abstract":"The age-standardized incidence rate for gastric cancer is estimated to be 11.1% worldwide and 39.1% for Ardabil province in northwest Iran. Single nucleotide polymorphisms (SNPs) occur in coding and non-coding regions, contributing to cancer susceptibility. To identify SNPs predisposing individuals to gastric cancer in this region, we compared 263 variants between the Ardabil population and other populations. Whole exome sequencing was used to determine the distribution of variants in the genomic DNA of 150 volunteers (aged < 35 years) from the general population of Ardabil. We compared allele frequencies with databases such as Iranome, Alfa, GnomAD, and 1000G, and statistically analyzed their correlation with age-standardized incidence rates (ASRs) for gastric cancer in related populations using the Pearson correlation test. Some findings were validated using Sanger-based PCR-Sequencing. We determined the frequency of seventeen variants among 150 individuals with gastric cancer and 150 healthy volunteers (matched for age and sex) as the control group. Nineteen variants, including rs10061133, rs1050631, rs12220909, rs12983273, rs1695, rs2274223, rs2292832, rs2294008, rs2505901, rs2976391, rs33927012, rs3744037, rs3745469, rs4789936, rs4986790, rs4986791, rs6194, rs63750447, and rs6505162, were found to be significantly different between the general population of Ardabil and other populations. Among them, the variants rs1050631, rs12983273, rs1695, rs2274223, rs2292832, rs2505901, rs33927012, rs374569, and rs6505162 showed significant differences between the cases and controls. In this study, 17 variants appeared to be involved in the etiology of the high frequency of gastric cancer in the Ardabil population. Some of the observed differences were consistent with previous case–control and meta-analysis reports from various parts of the world. These findings motivate further cohort investigations in this population. Ultimately, identifying prognostic factors can help diagnose individuals predisposed to gastric cancer in this population.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"20 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140312548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-27DOI: 10.1186/s43042-024-00517-2
Yalda Zhoulideh, Jamil Joolideh
Mowat-Wilson syndrome can be mentioned as one of the most severe and, at the same time, rare genetic abnormalities. The inheritance pattern of this disorder is an autosomal dominant pattern. In this disease, the ZEB2 gene becomes abnormal. The severity of the disease and associated signs and symptoms can vary widely but may include distinct facial features, developmental delay, intellectual disability, and Hirschsprung. MWS treatment may vary based on the specific symptoms that appear in each individual. This review will examine the gene involved in this disease, phenotype, clinical manifestations, ways of diagnosis, and treatment of this disease.
{"title":"Mowat-Wilson syndrome: unraveling the complexities of diagnosis, treatment, and symptom management","authors":"Yalda Zhoulideh, Jamil Joolideh","doi":"10.1186/s43042-024-00517-2","DOIUrl":"https://doi.org/10.1186/s43042-024-00517-2","url":null,"abstract":"Mowat-Wilson syndrome can be mentioned as one of the most severe and, at the same time, rare genetic abnormalities. The inheritance pattern of this disorder is an autosomal dominant pattern. In this disease, the ZEB2 gene becomes abnormal. The severity of the disease and associated signs and symptoms can vary widely but may include distinct facial features, developmental delay, intellectual disability, and Hirschsprung. MWS treatment may vary based on the specific symptoms that appear in each individual. This review will examine the gene involved in this disease, phenotype, clinical manifestations, ways of diagnosis, and treatment of this disease.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"47 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140312022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-26DOI: 10.1186/s43042-024-00512-7
Devalina Junahar, Rinesia Dwiputri, Wirawan Adikusuma, Darmawi Darmawi, Afdal Afdal, Lalu Muhammad Irham, Suyanto Suyanto
Studies have attributed 50% of infertility cases to male infertility, 15% of which is caused by idiopathic genetic factors. Currently, no specific biomarkers have been revealed for male infertility. Furthermore, research on genetic factors causing male infertility is still limited. As with other multifactorial genetic disorders, numerous risk loci for male infertility have been identified by genome-wide association studies (GWAS), although their clinical significance remains uncertain. Therefore, we utilized an integrative bioinformatics-based approach to identify biomarkers for male infertility. Bioinformatics analysis was performed using Open Targets Platform, DisGeNet, and GWAS Catalog. After that, the STRING database and the Cytoscape program were used to analyze protein–protein interaction. CytoHubba was used to determine the most significant gene candidates. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were used to assess biological functions that correspond to the male infertility disease pathway. We identified 305 genes associated with male infertility and highlighted 10 biological risk genes as potential biomarkers for male infertility such as TEX11, SPO11, SYCP3, HORMAD1, STAG3, MSH4, SYCP2, SYCE1, RAD21L1, and AMH. Of all the genes, we took the top three genes, namely, TEX11, SPO11, and SYCP3 as the genes that have the most potential as biomarkers. TEX11, SPO11, and SYCP3 are involved in meiosis and spermatogenesis. We propose that further research in regarding these genes in detecting male infertility.
{"title":"Potential biomarker signatures in male infertility: integrative genomic analysis","authors":"Devalina Junahar, Rinesia Dwiputri, Wirawan Adikusuma, Darmawi Darmawi, Afdal Afdal, Lalu Muhammad Irham, Suyanto Suyanto","doi":"10.1186/s43042-024-00512-7","DOIUrl":"https://doi.org/10.1186/s43042-024-00512-7","url":null,"abstract":"Studies have attributed 50% of infertility cases to male infertility, 15% of which is caused by idiopathic genetic factors. Currently, no specific biomarkers have been revealed for male infertility. Furthermore, research on genetic factors causing male infertility is still limited. As with other multifactorial genetic disorders, numerous risk loci for male infertility have been identified by genome-wide association studies (GWAS), although their clinical significance remains uncertain. Therefore, we utilized an integrative bioinformatics-based approach to identify biomarkers for male infertility. Bioinformatics analysis was performed using Open Targets Platform, DisGeNet, and GWAS Catalog. After that, the STRING database and the Cytoscape program were used to analyze protein–protein interaction. CytoHubba was used to determine the most significant gene candidates. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were used to assess biological functions that correspond to the male infertility disease pathway. We identified 305 genes associated with male infertility and highlighted 10 biological risk genes as potential biomarkers for male infertility such as TEX11, SPO11, SYCP3, HORMAD1, STAG3, MSH4, SYCP2, SYCE1, RAD21L1, and AMH. Of all the genes, we took the top three genes, namely, TEX11, SPO11, and SYCP3 as the genes that have the most potential as biomarkers. TEX11, SPO11, and SYCP3 are involved in meiosis and spermatogenesis. We propose that further research in regarding these genes in detecting male infertility.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"6 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140298515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hydrocephalus is one of the most common pathophysiological disabilities with a high mortality rate, which occurs both congenitally and acquired. It is estimated that genetic components are the etiology for up to 40% of hydrocephalus cases; however, causal mutations identified until now could only explain approximately 20% of congenital hydrocephalus (CH) patients, and most potential hydrocephalus-associated genes have yet to be determined. This study sought to find causal variations in a consanguineous family with four affected children diagnosed with hydrocephalus. In this study, we evaluated twenty-five members of an extended family consisting of a nuclear family with four affected children resulting from a consanguineous couple and eighteen of their relatives, including one hydrocephalus case. The mother of this family was experiencing her 15th week of pregnancy, and cytogenetic evaluation was performed using amniocentesis to identify fetal chromosomal abnormalities. We conducted whole-exome sequencing (WES) on the genomic DNA of the proband to detect the CH-causing variants, followed by confirmation and segregation analysis of the detected variant in the proband, fetus, and family members through Sanger sequencing. Following the bioinformatic analysis and data filtering, we found a homozygous variant [NM_001243766.2:c.74G>A:p.W25X] within the protein O-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (POMGNT1) gene confirmed by Sanger sequencing in the proband and segregated with the hydrocephalus in the family. The variant was described as pathogenic and regarded as a nonsense-mediated mRNA decay (NMD) due to the premature stop codon, which results in a truncated protein. The results of the current study broadened the mutational gene spectrum of CH and our knowledge of the hydrocephalus etiology by introducing a novel homozygous variant within the POMGNT1 gene, which had never been previously reported solitary in these patients.
{"title":"The homozygous pathogenic variant of the POMGNT1 gene identified using whole-exome sequencing in Iranian family with congenital hydrocephalus","authors":"Masoud Sabzeghabaiean, Mohsen Maleknia, Javad Mohammadi-Asl, Hashem Kazemi, Fereshteh Golab, Zohreh Zargar, Maryam Naseroleslami","doi":"10.1186/s43042-024-00513-6","DOIUrl":"https://doi.org/10.1186/s43042-024-00513-6","url":null,"abstract":"Hydrocephalus is one of the most common pathophysiological disabilities with a high mortality rate, which occurs both congenitally and acquired. It is estimated that genetic components are the etiology for up to 40% of hydrocephalus cases; however, causal mutations identified until now could only explain approximately 20% of congenital hydrocephalus (CH) patients, and most potential hydrocephalus-associated genes have yet to be determined. This study sought to find causal variations in a consanguineous family with four affected children diagnosed with hydrocephalus. In this study, we evaluated twenty-five members of an extended family consisting of a nuclear family with four affected children resulting from a consanguineous couple and eighteen of their relatives, including one hydrocephalus case. The mother of this family was experiencing her 15th week of pregnancy, and cytogenetic evaluation was performed using amniocentesis to identify fetal chromosomal abnormalities. We conducted whole-exome sequencing (WES) on the genomic DNA of the proband to detect the CH-causing variants, followed by confirmation and segregation analysis of the detected variant in the proband, fetus, and family members through Sanger sequencing. Following the bioinformatic analysis and data filtering, we found a homozygous variant [NM_001243766.2:c.74G>A:p.W25X] within the protein O-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (POMGNT1) gene confirmed by Sanger sequencing in the proband and segregated with the hydrocephalus in the family. The variant was described as pathogenic and regarded as a nonsense-mediated mRNA decay (NMD) due to the premature stop codon, which results in a truncated protein. The results of the current study broadened the mutational gene spectrum of CH and our knowledge of the hydrocephalus etiology by introducing a novel homozygous variant within the POMGNT1 gene, which had never been previously reported solitary in these patients.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"5 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140298447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
WAGR syndrome is a rare genetic disorder characterized by a de novo deletion of 11p13 and is usually clinically associated with Wilms’ tumor, aniridia, genitourinary anomalies, and mental retardation (W-A-G-R). Although the genotypic defects in WAGR syndrome have been well established. The congenital aniridia is caused, in nearly 90% of cases by mutations in the gene PAX6. In the face of congenital aniridia, it is imperative to specify whether it falls within the scope of a WAGR syndrome or if it is an isolated congenital aniridia or inherited by performing karyotype, FISH (Fluorescence In Situ Hybridization) or a CGH array for genetic counseling. We report here a case of genetic testing for newborn with aniridia, to detect 11p13 rearrangements, using karyotyping and CGH array to complete picture of the chromosomal deletions and breakpoints in aniridia. Results show either a loss of 3811.196 kb on chromosome 11 delimited by the bands p14.1 and p13 with formula or a loss of a 1867.287 kb on chromosome 18 fragment delimited by q21.33 and q22.1 bands, that has not been detected by karyotype analysis. Cytogenetics screening is a good strategy for the genetic diagnosis of aniridia and associated syndromes, allowing for a better identification of breakpoints. Our results underline the clinical importance of performing exhaustive and accurate analysis of chromosomal rearrangements for patients with aniridia, especially newborns to improve survival and quality of life for affected individuals.
{"title":"Conventional and molecular cytogenetic characterization of a Moroccan patient with WAGR syndrome","authors":"Faiza Chbel, Hasna Hamdaoui, Houssein Mossafa, Karim Ouldim, Houda Benrahma","doi":"10.1186/s43042-024-00514-5","DOIUrl":"https://doi.org/10.1186/s43042-024-00514-5","url":null,"abstract":"WAGR syndrome is a rare genetic disorder characterized by a de novo deletion of 11p13 and is usually clinically associated with Wilms’ tumor, aniridia, genitourinary anomalies, and mental retardation (W-A-G-R). Although the genotypic defects in WAGR syndrome have been well established. The congenital aniridia is caused, in nearly 90% of cases by mutations in the gene PAX6. In the face of congenital aniridia, it is imperative to specify whether it falls within the scope of a WAGR syndrome or if it is an isolated congenital aniridia or inherited by performing karyotype, FISH (Fluorescence In Situ Hybridization) or a CGH array for genetic counseling. We report here a case of genetic testing for newborn with aniridia, to detect 11p13 rearrangements, using karyotyping and CGH array to complete picture of the chromosomal deletions and breakpoints in aniridia. Results show either a loss of 3811.196 kb on chromosome 11 delimited by the bands p14.1 and p13 with formula or a loss of a 1867.287 kb on chromosome 18 fragment delimited by q21.33 and q22.1 bands, that has not been detected by karyotype analysis. Cytogenetics screening is a good strategy for the genetic diagnosis of aniridia and associated syndromes, allowing for a better identification of breakpoints. Our results underline the clinical importance of performing exhaustive and accurate analysis of chromosomal rearrangements for patients with aniridia, especially newborns to improve survival and quality of life for affected individuals.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"65 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140201010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-21DOI: 10.1186/s43042-024-00503-8
Rawan A. Nijeeb, Adnan A. Aljber, Ali H. Ad’hiah
Interleukin-38 (IL-38), an inflammatory cytokine discovered in recent years, has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). IL-38 is encoded by the IL1F10 (interleukin 1 family member 10) gene. Genetic variants of this gene have been associated with susceptibility to a number of autoimmune and inflammatory diseases, while their association with SLE risk has not been explored. In this case–control study, two novel variants of the 5 prime untranslated region (5′UTR) of the IL1F10 gene, rs3811050 C/T and rs3811051 T/G, were investigated in 120 women with SLE and 120 age-matched control women. The TaqMan allelic discrimination assay was used for genotyping of rs3811050 and rs3811051. The frequency of the rs3811050 CT genotype was significantly lower in SLE patients compared to controls (30.8 vs. 50.0%; odds ratio = 0.49; 95% confidence interval = 0.28–0.86; corrected probability = 0.045). The rs3811051 genotype frequencies did not show significant differences between patients and controls. Rs3811050 and rs3811051 showed weak linkage disequilibrium (LD) as indicated by the estimated LD coefficient and correlation coefficient values (0.32 and 0.05, respectively), and two-locus haplotype analysis revealed no significant differences between patients and controls. The frequencies of the rs3811050 T allele (38.8 vs. 20.6%; probability = 0.029) and the rs3811051 G allele (56.3 vs. 38.2%; probability = 0.038) were significantly higher in patients with mild/moderate disease activity than in patients with high disease activity, but significance was not maintained after applying Bonferroni correction (corrected probability = 0.058 and 0.076, respectively). Serum IL-38 concentrations (median and interquartile range) were significantly decreased in patients compared with controls (69.5 [64.1–74.8] vs. 73.5 [66.1–82.9] pg/mL; probability = 0.03), but were not influenced by SNP genotypes. The heterozygous genotype of rs3811050, a 5'UTR variant, of the IL-38 encoding gene, IL1F10, is associated with a reduced risk of SLE among women. Furthermore, the rs3811050 T and rs3811051 G alleles may influence disease activity. In addition, serum IL-38 concentrations were down-regulated in SLE patients but were not affected by the rs3811050 and rs3811051 genotypes.
白细胞介素-38（IL-38）是近年来发现的一种炎性细胞因子，与系统性红斑狼疮（SLE）的发病机制有关。IL-38 由 IL1F10（白细胞介素 1 家族成员 10）基因编码。该基因的遗传变异与多种自身免疫性疾病和炎症性疾病的易感性有关，但它们与系统性红斑狼疮风险的关系尚未得到探讨。在这项病例对照研究中，研究人员在 120 名系统性红斑狼疮女性患者和 120 名年龄匹配的对照组女性患者中调查了 IL1F10 基因 5 prime 非翻译区（5′UTR）的两个新型变异，即 rs3811050 C/T 和 rs3811051 T/G。对 rs3811050 和 rs3811051 的基因分型采用了 TaqMan 等位基因鉴别测定法。与对照组相比，系统性红斑狼疮患者的rs3811050 CT基因型频率明显较低（30.8%对50.0%；几率比=0.49；95%置信区间=0.28-0.86；校正概率=0.045）。患者与对照组之间的 rs3811051 基因型频率没有显著差异。Rs3811050和rs3811051的估计LD系数和相关系数值（分别为0.32和0.05）显示出弱的连锁不平衡（LD），双病灶单倍型分析显示患者和对照组之间没有显著差异。轻度/中度疾病活动患者的rs3811050 T等位基因频率（38.8% vs. 20.6%；概率=0.029）和rs3811051 G等位基因频率（56.3% vs. 38.2%；概率=0.038）显著高于高度疾病活动患者，但在应用Bonferroni校正后，显著性并未保持（校正概率分别为0.058和0.076）。与对照组相比，患者的血清IL-38浓度（中位数和四分位间范围）显著降低（69.5 [64.1-74.8] vs. 73.5 [66.1-82.9] pg/mL；概率 = 0.03），但不受SNP基因型的影响。IL-38编码基因IL1F10的5'UTR变异rs3811050的杂合基因型与女性患系统性红斑狼疮的风险降低有关。此外，rs3811050 T 和 rs3811051 G 等位基因可能会影响疾病的活动性。此外，系统性红斑狼疮患者血清中的IL-38浓度下调，但不受rs3811050和rs3811051基因型的影响。
{"title":"Low heterozygosity for rs3811050, a 5 prime untranslated region variant of the gene encoding interleukin-38 (IL1F10), is associated with a reduced risk of systemic lupus erythematosus","authors":"Rawan A. Nijeeb, Adnan A. Aljber, Ali H. Ad’hiah","doi":"10.1186/s43042-024-00503-8","DOIUrl":"https://doi.org/10.1186/s43042-024-00503-8","url":null,"abstract":"Interleukin-38 (IL-38), an inflammatory cytokine discovered in recent years, has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). IL-38 is encoded by the IL1F10 (interleukin 1 family member 10) gene. Genetic variants of this gene have been associated with susceptibility to a number of autoimmune and inflammatory diseases, while their association with SLE risk has not been explored. In this case–control study, two novel variants of the 5 prime untranslated region (5′UTR) of the IL1F10 gene, rs3811050 C/T and rs3811051 T/G, were investigated in 120 women with SLE and 120 age-matched control women. The TaqMan allelic discrimination assay was used for genotyping of rs3811050 and rs3811051. The frequency of the rs3811050 CT genotype was significantly lower in SLE patients compared to controls (30.8 vs. 50.0%; odds ratio = 0.49; 95% confidence interval = 0.28–0.86; corrected probability = 0.045). The rs3811051 genotype frequencies did not show significant differences between patients and controls. Rs3811050 and rs3811051 showed weak linkage disequilibrium (LD) as indicated by the estimated LD coefficient and correlation coefficient values (0.32 and 0.05, respectively), and two-locus haplotype analysis revealed no significant differences between patients and controls. The frequencies of the rs3811050 T allele (38.8 vs. 20.6%; probability = 0.029) and the rs3811051 G allele (56.3 vs. 38.2%; probability = 0.038) were significantly higher in patients with mild/moderate disease activity than in patients with high disease activity, but significance was not maintained after applying Bonferroni correction (corrected probability = 0.058 and 0.076, respectively). Serum IL-38 concentrations (median and interquartile range) were significantly decreased in patients compared with controls (69.5 [64.1–74.8] vs. 73.5 [66.1–82.9] pg/mL; probability = 0.03), but were not influenced by SNP genotypes. The heterozygous genotype of rs3811050, a 5'UTR variant, of the IL-38 encoding gene, IL1F10, is associated with a reduced risk of SLE among women. Furthermore, the rs3811050 T and rs3811051 G alleles may influence disease activity. In addition, serum IL-38 concentrations were down-regulated in SLE patients but were not affected by the rs3811050 and rs3811051 genotypes.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"43 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140201089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-20DOI: 10.1186/s43042-024-00506-5
Antonio Alejandro Esperón Álvarez, Inés Virginia Noa Hechavarría, Ixchel López Reyes, Teresa Collazo Mesa
Von Hippel-Lindau (VHL) syndrome is an autosomal dominantly inherited disorder that predisposes to multiple neoplasms. Patients may develop hemangioblastomas of the central nervous system and retina, multiple cysts in the pancreas and kidneys, renal carcinoma, and pheochromocytomas, among other lesions. This disease is caused by germline genetic variants in the VHL gene. The regulation of the alpha subunit of hypoxia-inducible factor-1 is the key tumor suppressor function of the VHL protein. To date, more than seven hundred variants have been reported in VHL gene. This study aimed to investigate the molecular etiology of VHL syndrome in Cuban patients. DNA samples from twenty-two individuals were analyzed by Sanger sequencing or enzymatic restriction. The analysis identified four novel pathogenic variants for the Cuban population: c.463 + 2T > C, C162W, R167W, and S183X, in addition to D121G and R161X, previously described in another work. The diagnosis was confirmed in seven patients with clinical manifestations and family history. Two at-risk family members without clinical signs were positive for presymptomatic diagnosis. The spectrum of germinal point mutations of VHL gene in Cuban patients was updated. The presence of genetic variants was ruled out in eight asymptomatic relatives, which is a psychological relief for these individuals. The results allow for offering other at-risk relatives the presymptomatic diagnosis and the possibility of receiving genetic counseling.
{"title":"Germline variants in the Von Hippel-Lindau tumor suppressor gene in Cuban patients","authors":"Antonio Alejandro Esperón Álvarez, Inés Virginia Noa Hechavarría, Ixchel López Reyes, Teresa Collazo Mesa","doi":"10.1186/s43042-024-00506-5","DOIUrl":"https://doi.org/10.1186/s43042-024-00506-5","url":null,"abstract":"Von Hippel-Lindau (VHL) syndrome is an autosomal dominantly inherited disorder that predisposes to multiple neoplasms. Patients may develop hemangioblastomas of the central nervous system and retina, multiple cysts in the pancreas and kidneys, renal carcinoma, and pheochromocytomas, among other lesions. This disease is caused by germline genetic variants in the VHL gene. The regulation of the alpha subunit of hypoxia-inducible factor-1 is the key tumor suppressor function of the VHL protein. To date, more than seven hundred variants have been reported in VHL gene. This study aimed to investigate the molecular etiology of VHL syndrome in Cuban patients. DNA samples from twenty-two individuals were analyzed by Sanger sequencing or enzymatic restriction. The analysis identified four novel pathogenic variants for the Cuban population: c.463 + 2T > C, C162W, R167W, and S183X, in addition to D121G and R161X, previously described in another work. The diagnosis was confirmed in seven patients with clinical manifestations and family history. Two at-risk family members without clinical signs were positive for presymptomatic diagnosis. The spectrum of germinal point mutations of VHL gene in Cuban patients was updated. The presence of genetic variants was ruled out in eight asymptomatic relatives, which is a psychological relief for these individuals. The results allow for offering other at-risk relatives the presymptomatic diagnosis and the possibility of receiving genetic counseling.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"136 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140166452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-14DOI: 10.1186/s43042-024-00507-4
Gloria Garavito De Egea, Alex Domínguez-Vargas, Luis Fang, Nicole Pereira-Sanandrés, Jonathan Rodríguez, Gustavo Aroca-Martinez, Zilac Espítatela, Clara Malagón, Antonio Iglesias-Gamarra, Ana Moreno-Woo, Guillermo López-Lluch, Eduardo Egea
Adiponectin and leptin are pivotal in the regulation of metabolism. Pediatric lupus nephritis (pLN), a manifestation of childhood systemic lupus erythematosus (SLE) affecting the kidneys, is associated with impaired adipokine levels, suggesting a role in pLN pathogenesis. The aim of this study was to explore the potential relationship between specific single-nucleotide polymorphisms (SNPs)—methylenetetrahydrofolate reductase (MTHFR) rs1801131 and fibrinogen gamma chain (FGG) rs2066865—and the serum levels of leptin and adiponectin in patients with pLN. Ninety-eight pLN patients and one hundred controls were enrolled in the study. Serum leptin and adiponectin levels were measured using ELISA. DNA extraction and real-time PCR genotyping were performed for MTHFR rs1801131 and FGG rs2066865 SNPs. Compared to healthy controls, pLN patients exhibited significantly greater serum leptin (11.3 vs. 18.2 ng/mL, p < 0.001) and adiponectin (18.2 vs. 2.7 ug/mL, p < 0.001). Adiponectin levels were positively correlated with proteinuria (p < 0.05), while leptin levels positively correlated with proteinuria, SLE disease activity index-2000 (SLEDAI-2K), and cyclophosphamide usage (all p < 0.05). There was no significant association between MTHFR rs1801131 or FGG rs2066865 SNPs and pLN in either codominant or allelic models (all p > 0.05). However, the AG genotype of FGG gene rs2066865 SNP was significantly associated with high leptin levels (> 15 ng/mL) (p = 0.01). Serum adiponectin and leptin levels are associated with pathological manifestations of pLN. High leptin levels are associated with the AG genotype of FGG rs2066865 SNP in pLN patients, suggesting direct involvement in disease progression and potential utility as a disease biomarker.
脂联素和瘦素是调节新陈代谢的关键因素。小儿狼疮肾炎（pLN）是影响肾脏的儿童系统性红斑狼疮（SLE）的一种表现形式，与脂肪因子水平受损有关，这表明脂肪因子在小儿狼疮肾炎的发病机制中发挥作用。本研究旨在探讨特定单核苷酸多态性（SNPs）--亚甲基四氢叶酸还原酶（MTHFR）rs1801131和纤维蛋白原γ链（FGG）rs2066865--与pLN患者血清中瘦素和脂肪连素水平之间的潜在关系。研究共纳入了 98 名 pLN 患者和 100 名对照组。采用酶联免疫吸附法测定血清瘦素和脂肪连素水平。对 MTHFR rs1801131 和 FGG rs2066865 SNPs 进行了 DNA 提取和实时 PCR 基因分型。与健康对照组相比，pLN 患者的血清瘦素明显增加（11.3 vs. 18.2 ng/mL，P 0.05）。然而，FGG 基因 rs2066865 SNP 的 AG 基因型与高瘦素水平（> 15 ng/mL）明显相关（p = 0.01）。血清脂肪连接蛋白和瘦素水平与 pLN 的病理表现相关。高瘦素水平与pLN患者FGG rs2066865 SNP的AG基因型相关，这表明瘦素直接参与了疾病的进展，并有可能成为一种疾病生物标志物。
{"title":"Exploring the interplay of MTHFR and FGG polymorphisms with serum levels of adiponectin and leptin in pediatric lupus nephritis: a pilot study","authors":"Gloria Garavito De Egea, Alex Domínguez-Vargas, Luis Fang, Nicole Pereira-Sanandrés, Jonathan Rodríguez, Gustavo Aroca-Martinez, Zilac Espítatela, Clara Malagón, Antonio Iglesias-Gamarra, Ana Moreno-Woo, Guillermo López-Lluch, Eduardo Egea","doi":"10.1186/s43042-024-00507-4","DOIUrl":"https://doi.org/10.1186/s43042-024-00507-4","url":null,"abstract":"Adiponectin and leptin are pivotal in the regulation of metabolism. Pediatric lupus nephritis (pLN), a manifestation of childhood systemic lupus erythematosus (SLE) affecting the kidneys, is associated with impaired adipokine levels, suggesting a role in pLN pathogenesis. The aim of this study was to explore the potential relationship between specific single-nucleotide polymorphisms (SNPs)—methylenetetrahydrofolate reductase (MTHFR) rs1801131 and fibrinogen gamma chain (FGG) rs2066865—and the serum levels of leptin and adiponectin in patients with pLN. Ninety-eight pLN patients and one hundred controls were enrolled in the study. Serum leptin and adiponectin levels were measured using ELISA. DNA extraction and real-time PCR genotyping were performed for MTHFR rs1801131 and FGG rs2066865 SNPs. Compared to healthy controls, pLN patients exhibited significantly greater serum leptin (11.3 vs. 18.2 ng/mL, p < 0.001) and adiponectin (18.2 vs. 2.7 ug/mL, p < 0.001). Adiponectin levels were positively correlated with proteinuria (p < 0.05), while leptin levels positively correlated with proteinuria, SLE disease activity index-2000 (SLEDAI-2K), and cyclophosphamide usage (all p < 0.05). There was no significant association between MTHFR rs1801131 or FGG rs2066865 SNPs and pLN in either codominant or allelic models (all p > 0.05). However, the AG genotype of FGG gene rs2066865 SNP was significantly associated with high leptin levels (> 15 ng/mL) (p = 0.01). Serum adiponectin and leptin levels are associated with pathological manifestations of pLN. High leptin levels are associated with the AG genotype of FGG rs2066865 SNP in pLN patients, suggesting direct involvement in disease progression and potential utility as a disease biomarker.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"27 17 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140153887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-13DOI: 10.1186/s43042-024-00505-6
Mutiat A. Abdulkareem, Bunmi A. Owolabi, Emmanuel S. Saheed, Remilekun F. Aromolaran, Rukayat M. Bashiru, Toheeb A. Jumah, Doris U. Chijioke, Onyinyechi J. Amaechi, Fehintoluwa C. Adeleke, Omiyale O. Charles, Tunde S. Oluokun
This review article gives an insight into the genetic factors and the role of pancreatic amylase in type 2 diabetes (T2D). Diabetes is a non-communicable, multifactorial, heritable, complex, and irreversible disease of public health burden with a global prevalence rate of 6.28%, about 6% in sub-Saharan Africa, and 1.7% in Nigeria. T2D is recognized as the ninth leading cause of mortality worldwide. This disease is yet to be diagnosed in a significant number of people who live with it in underdeveloped and developing countries like Nigeria due to the lack of free or subsidized access to health care, especially medical checkups, inadequate health facilities, government policies, and negligence. Consequently, undiagnosed cases of T2D have contributed to the prevalence of this disease and its comorbidities -hypertension and chronic kidney disease. Obesity, age, race and ethnicity, inactivity, family history, underlying illness, and unhealthy diets are prominent undisputable predisposing factors of T2D. Pancreatic amylase is a type of amylase produced in the pancreas, known to hydrolyze starch and prone to mutations, but most of the genetic components, causative polymorphisms, and affected genes are yet unknown. Even as insulin secretion is found to be influenced by the loci, the causation of T2D cannot be inferred. Pancreatic amylase was observed to be the most relevant digestive enzyme, whose role is to bind to glycoprotein N-glycan to activate starch digestion. In a malfunctioning pancreas, little or no insulin is generated to keep the blood glucose at an appropriate level, thereby resulting in T2D.
{"title":"Genetic factors and the role of pancreatic amylase in the pathogenesis of type 2 diabetes","authors":"Mutiat A. Abdulkareem, Bunmi A. Owolabi, Emmanuel S. Saheed, Remilekun F. Aromolaran, Rukayat M. Bashiru, Toheeb A. Jumah, Doris U. Chijioke, Onyinyechi J. Amaechi, Fehintoluwa C. Adeleke, Omiyale O. Charles, Tunde S. Oluokun","doi":"10.1186/s43042-024-00505-6","DOIUrl":"https://doi.org/10.1186/s43042-024-00505-6","url":null,"abstract":"This review article gives an insight into the genetic factors and the role of pancreatic amylase in type 2 diabetes (T2D). Diabetes is a non-communicable, multifactorial, heritable, complex, and irreversible disease of public health burden with a global prevalence rate of 6.28%, about 6% in sub-Saharan Africa, and 1.7% in Nigeria. T2D is recognized as the ninth leading cause of mortality worldwide. This disease is yet to be diagnosed in a significant number of people who live with it in underdeveloped and developing countries like Nigeria due to the lack of free or subsidized access to health care, especially medical checkups, inadequate health facilities, government policies, and negligence. Consequently, undiagnosed cases of T2D have contributed to the prevalence of this disease and its comorbidities -hypertension and chronic kidney disease. Obesity, age, race and ethnicity, inactivity, family history, underlying illness, and unhealthy diets are prominent undisputable predisposing factors of T2D. Pancreatic amylase is a type of amylase produced in the pancreas, known to hydrolyze starch and prone to mutations, but most of the genetic components, causative polymorphisms, and affected genes are yet unknown. Even as insulin secretion is found to be influenced by the loci, the causation of T2D cannot be inferred. Pancreatic amylase was observed to be the most relevant digestive enzyme, whose role is to bind to glycoprotein N-glycan to activate starch digestion. In a malfunctioning pancreas, little or no insulin is generated to keep the blood glucose at an appropriate level, thereby resulting in T2D.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"135 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140129668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-12DOI: 10.1186/s43042-024-00504-7
Khyber Saify, Mostafa Saadat
Methadone has been reported to downregulate the expression of glutathione S-transferase P1 (GSTP1) among nine antioxidant genes in SH-SY5Y cells after both short- and long-term treatment. GSTP1 plays a key role in the detoxification of many xenobiotics and is frequently associated with various diseases, especially tumors. The objective of this study is to determine whether this change is reversible. Two different treatment protocols were used. The first protocol evaluated the reversibility of the GSTP1 mRNA change, while the second protocol evaluated the methylation status of the GSTP1 promoter site. To investigate the reversibility of the GSTP1 mRNA change, SH-SY5Y cells were treated with methadone. The drug was then removed from the medium and the cells were cultured in methadone-free medium for a period of time. GSTP1 mRNA levels were expressed as cycle threshold (Ct) values using TATA box-binding protein as a calibrator gene. Methylation at the promoter site was detected by bisulfite treatment. The analysis of variance revealed no significant change in GSTP1 mRNA levels in the cells after methadone was removed from the medium of methadone-treated cells. The study also examined the methylation status of a CpG island in the promoter of GSTP1 in the treated cells. The results demonstrate that although methadone downregulates the mRNA level of GSTP1 in treated cells, it does not induce methylation in the GSTP1 promoter region. The expression of the GSTP1 remains downregulated even after methadone removal from SH-SY5Y cell culture medium; however, methylation of the GSTP1 promoter site does not play a role in this process.
{"title":"Irreversible methadone-induced GSTP1 downregulation in SH-SY5Y cells","authors":"Khyber Saify, Mostafa Saadat","doi":"10.1186/s43042-024-00504-7","DOIUrl":"https://doi.org/10.1186/s43042-024-00504-7","url":null,"abstract":"Methadone has been reported to downregulate the expression of glutathione S-transferase P1 (GSTP1) among nine antioxidant genes in SH-SY5Y cells after both short- and long-term treatment. GSTP1 plays a key role in the detoxification of many xenobiotics and is frequently associated with various diseases, especially tumors. The objective of this study is to determine whether this change is reversible. Two different treatment protocols were used. The first protocol evaluated the reversibility of the GSTP1 mRNA change, while the second protocol evaluated the methylation status of the GSTP1 promoter site. To investigate the reversibility of the GSTP1 mRNA change, SH-SY5Y cells were treated with methadone. The drug was then removed from the medium and the cells were cultured in methadone-free medium for a period of time. GSTP1 mRNA levels were expressed as cycle threshold (Ct) values using TATA box-binding protein as a calibrator gene. Methylation at the promoter site was detected by bisulfite treatment. The analysis of variance revealed no significant change in GSTP1 mRNA levels in the cells after methadone was removed from the medium of methadone-treated cells. The study also examined the methylation status of a CpG island in the promoter of GSTP1 in the treated cells. The results demonstrate that although methadone downregulates the mRNA level of GSTP1 in treated cells, it does not induce methylation in the GSTP1 promoter region. The expression of the GSTP1 remains downregulated even after methadone removal from SH-SY5Y cell culture medium; however, methylation of the GSTP1 promoter site does not play a role in this process.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"16 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140128454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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