Gastrointestinal tract (GIT) cancers are complex disorders affecting millions of people worldwide. The vascular endothelial growth factor (VEGF) helps in the development of different GIT cancers by promoting abnormal angiogenesis in cancer cells. The role of VEGF-2549I/D polymorphism in influencing GIT cancer susceptibility has been studied in different populations with inconclusive results. Therefore, the relationship between VEGF-2549I/D polymorphism with GIT susceptibility was studied by performing a meta-analysis study. Various online databases were used for identifying the articles. Based on study selection criteria, five studies on different GIT cancers including 1178 patients and 1520 controls were included in the meta-analysis. The accuracy of the study results was determined by performing a trial sequential analysis. In this study, the VEGF-2549I/D polymorphism did not influence the GIT cancer susceptibility in the overall analysis as well as when stratified according to ethnicity (p > 0.05). Stratification of all the studies based on the different GIT cancers reported an increased susceptibility to gastric cancer under different genetic models including allele contrast (OR = 1.67, CI = 1.294–2.157, p = 0.00008), recessive (OR = 1.68, CI = 1.056–2.660, p = 0.029), dominant (OR = 2.49, CI = 1.617–3.823, p = 0.00003), over-dominant (OR = 1.52, CI = 1.055–2.177, p = 0.025), II vs DD (OR = 2.97, CI = 1.692–5.208, p = 0.00015) and ID vs DD model (OR = 2.35, CI = 1.501–3.669, p = 0.00018). There was no relationship between VEGF-2549I/D promoter polymorphism and GIT cancer susceptibility in the overall population and also in different ethnic groups. Stratification analysis revealed higher susceptibility towards gastric cancer development with VEGF-2549I/D polymorphism.
{"title":"Association of VEGF-2549I/D promoter polymorphism with gastrointestinal tract cancer risk: a meta-analysis","authors":"Deepanshi Mahajan, Vasudha Sambyal, Kamlesh Guleria","doi":"10.1186/s43042-024-00535-0","DOIUrl":"https://doi.org/10.1186/s43042-024-00535-0","url":null,"abstract":"Gastrointestinal tract (GIT) cancers are complex disorders affecting millions of people worldwide. The vascular endothelial growth factor (VEGF) helps in the development of different GIT cancers by promoting abnormal angiogenesis in cancer cells. The role of VEGF-2549I/D polymorphism in influencing GIT cancer susceptibility has been studied in different populations with inconclusive results. Therefore, the relationship between VEGF-2549I/D polymorphism with GIT susceptibility was studied by performing a meta-analysis study. Various online databases were used for identifying the articles. Based on study selection criteria, five studies on different GIT cancers including 1178 patients and 1520 controls were included in the meta-analysis. The accuracy of the study results was determined by performing a trial sequential analysis. In this study, the VEGF-2549I/D polymorphism did not influence the GIT cancer susceptibility in the overall analysis as well as when stratified according to ethnicity (p > 0.05). Stratification of all the studies based on the different GIT cancers reported an increased susceptibility to gastric cancer under different genetic models including allele contrast (OR = 1.67, CI = 1.294–2.157, p = 0.00008), recessive (OR = 1.68, CI = 1.056–2.660, p = 0.029), dominant (OR = 2.49, CI = 1.617–3.823, p = 0.00003), over-dominant (OR = 1.52, CI = 1.055–2.177, p = 0.025), II vs DD (OR = 2.97, CI = 1.692–5.208, p = 0.00015) and ID vs DD model (OR = 2.35, CI = 1.501–3.669, p = 0.00018). There was no relationship between VEGF-2549I/D promoter polymorphism and GIT cancer susceptibility in the overall population and also in different ethnic groups. Stratification analysis revealed higher susceptibility towards gastric cancer development with VEGF-2549I/D polymorphism.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"15 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530521","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 : 2024-05-28DOI: 10.1186/s43042-024-00532-3
Yeting Li, Kai Ma, Chuanxin Zhao, Nannan Li, Shanshan Li, Man Zheng
Additional evidence has indicated a correlation between N6-methyladenosine (m6A) RNA methylation and cardiovascular disease. Nevertheless, the alterations in RNA methylation modification and the expression of numerous genes remains unclear. This study aimed to identify the role of m6A in ST-segment elevation myocardial infarction (STEMI). Two microarray datasets (GSE123342 and GSE59867) were downloaded from the GEO database. After merging the data and batch normalization, differentially expressed regulators were identified using the limma package. Subtyping consistency analysis was performed to group samples. The random forest algorithm and support vector machine were used to identify diagnostic biomarkers. Immune infiltration and inflammation levels among the subtypes were assessed using a single-sample gene set enrichment analysis. A total of 15 key differential m6A regulators (RBM15B, ELAVL1, ALKBH5, METTL16, ZC3H13, RBM15, YTHDC1, YTHDC2, YTHDF3, HNRNPC, FMR1, LRPPRC, HNRNPA2B1, RBMX, FTO) were identified using the random forest classifier and were found to be highly correlated by PPI analysis. Two distinct RNA modification patterns (cluster A and B) were validated based on the expression levels of the 15 key m6A regulators. GO and KEGG annotations showed that immunity and inflammation pathways were enriched. Immune infiltration analysis revealed that cluster 2 had higher immune activation than cluster 1. Further analysis showed that cluster 2 had a higher inflammation level, with IL-4 and IL-33 showing differential expression (p < 0.05). A set of 15 m6A RNA methylation regulators could alter the STEMI microenvironment to improve risk stratification and clinical treatment.
{"title":"Diagnostic biomarkers for ST-segment elevation myocardial infarction using RNA methylation regulators","authors":"Yeting Li, Kai Ma, Chuanxin Zhao, Nannan Li, Shanshan Li, Man Zheng","doi":"10.1186/s43042-024-00532-3","DOIUrl":"https://doi.org/10.1186/s43042-024-00532-3","url":null,"abstract":"Additional evidence has indicated a correlation between N6-methyladenosine (m6A) RNA methylation and cardiovascular disease. Nevertheless, the alterations in RNA methylation modification and the expression of numerous genes remains unclear. This study aimed to identify the role of m6A in ST-segment elevation myocardial infarction (STEMI). Two microarray datasets (GSE123342 and GSE59867) were downloaded from the GEO database. After merging the data and batch normalization, differentially expressed regulators were identified using the limma package. Subtyping consistency analysis was performed to group samples. The random forest algorithm and support vector machine were used to identify diagnostic biomarkers. Immune infiltration and inflammation levels among the subtypes were assessed using a single-sample gene set enrichment analysis. A total of 15 key differential m6A regulators (RBM15B, ELAVL1, ALKBH5, METTL16, ZC3H13, RBM15, YTHDC1, YTHDC2, YTHDF3, HNRNPC, FMR1, LRPPRC, HNRNPA2B1, RBMX, FTO) were identified using the random forest classifier and were found to be highly correlated by PPI analysis. Two distinct RNA modification patterns (cluster A and B) were validated based on the expression levels of the 15 key m6A regulators. GO and KEGG annotations showed that immunity and inflammation pathways were enriched. Immune infiltration analysis revealed that cluster 2 had higher immune activation than cluster 1. Further analysis showed that cluster 2 had a higher inflammation level, with IL-4 and IL-33 showing differential expression (p < 0.05). A set of 15 m6A RNA methylation regulators could alter the STEMI microenvironment to improve risk stratification and clinical treatment.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"40 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141168822","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 : 2024-05-22DOI: 10.1186/s43042-024-00519-0
Yuanyuan Luo, Chunya Ma, Lihui Fu, Yang Yu
D–Phenotype is linked to abnormal expression of RHCE gene. Consequently, individuals with this condition may develop antibodies against high-prevalence Rh antigens when exposed to a normal Rh phenotype, leading to challenges in blood matching. A 90-year-old male was admitted to the hospital due to prostatitis and acute retention of urinary. Surgery was planned after evaluation by urologist. A request was made for 2 units of red blood cells (RBC). The result for unexpected antibody screening was positive, and the antibody was identified as anti-Hr0 alloantibody , a rare RHCE * CE-D (5) – CE was discovered by genetic testing. The patient has only one history of blood transfusion, which may result in the production of the anti-Hr0 antibody. Compatible blood donors for this patient were not found, even after extensive screening. This report records a rare case of a D-- phenotype individual who produced anti-Hr0 alloantibody. Subsequent analysis of RH gene sequencing revealed a genotype that has not been previously reported in Asia.
{"title":"Challenges in blood transfusion caused by anti-Hr0: A rare case of D-- Phenotype in Asia Abstract","authors":"Yuanyuan Luo, Chunya Ma, Lihui Fu, Yang Yu","doi":"10.1186/s43042-024-00519-0","DOIUrl":"https://doi.org/10.1186/s43042-024-00519-0","url":null,"abstract":" D–Phenotype is linked to abnormal expression of RHCE gene. Consequently, individuals with this condition may develop antibodies against high-prevalence Rh antigens when exposed to a normal Rh phenotype, leading to challenges in blood matching. A 90-year-old male was admitted to the hospital due to prostatitis and acute retention of urinary. Surgery was planned after evaluation by urologist. A request was made for 2 units of red blood cells (RBC). The result for unexpected antibody screening was positive, and the antibody was identified as anti-Hr0 alloantibody , a rare RHCE * CE-D (5) – CE was discovered by genetic testing. The patient has only one history of blood transfusion, which may result in the production of the anti-Hr0 antibody. Compatible blood donors for this patient were not found, even after extensive screening. This report records a rare case of a D-- phenotype individual who produced anti-Hr0 alloantibody. Subsequent analysis of RH gene sequencing revealed a genotype that has not been previously reported in Asia.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"11 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141153475","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}
Autism spectrum disorder (ASD) is a complex neurological disability with multifactorial etiology. ASD is described by behavior, speech, language, and communication defects. CircRNA is a type of ceRNA that plays an important role in modulating microRNAs (miRNA) in several disorders. However, the potential role of the circRNA/miRNA/mRNA regulatory network in the pathogenesis of ASD is not fully understood. Therefore, this study aimed to create a circRNA/miRNA/mRNA network associated with ASD to cast light on the pathogenesis of ASD. CircRNA expression profile data were recruited from Gene Expression Omnibus datasets, and the differentially expressed circRNAs (DEcircRNAs) were identified. Then, miRNAs modulated by these circRNAs were predicted and overlapped with differentially expressed miRNAs. Next, the potentially involved genes were identified by overlapping predicted targets, and differentially expressed genes. The enrichment analysis was performed, and a PPI network was projected. Subsequently, ten key genes were selected from the network. Furthermore, a circRNA/miRNA/mRNA regulatory network was constructed, and probable molecules and drugs with potential anti-ASD effects were predicted. 11 DEcircRNAs and 8 miRNAs regulated by 4 circRNAs were identified as being significantly involved. Subsequently, gene enrichment analysis of 71 overlapped mRNA regulated by these miRNAs showed that they are mostly associated with hippocampal synaptogenesis, neurogenesis, and axon guidance. Additionally, two high-score compounds, GSK3β inhibitor (SB216763) and dexamethasone, and three drugs (haloperidol, nystatin, paroxetine) were confirmed as potential therapeutic options for ASD. The results of this study may help gain deeper insight into the pathogenesis of the circRNA/miRNA/mRNA regulatory network in ASD, providing potential therapeutic management options.
{"title":"Identification of circRNA–miRNA–mRNA regulatory network associated to the autism spectrum disorder in children through integrated bioinformatics analysis","authors":"Somayeh Reiisi, Seyed Omar Ebrahimi, Kambiz Ahmadi, Najmeh Nezamabadi Pour, Abbas Jahanara","doi":"10.1186/s43042-024-00527-0","DOIUrl":"https://doi.org/10.1186/s43042-024-00527-0","url":null,"abstract":"Autism spectrum disorder (ASD) is a complex neurological disability with multifactorial etiology. ASD is described by behavior, speech, language, and communication defects. CircRNA is a type of ceRNA that plays an important role in modulating microRNAs (miRNA) in several disorders. However, the potential role of the circRNA/miRNA/mRNA regulatory network in the pathogenesis of ASD is not fully understood. Therefore, this study aimed to create a circRNA/miRNA/mRNA network associated with ASD to cast light on the pathogenesis of ASD. CircRNA expression profile data were recruited from Gene Expression Omnibus datasets, and the differentially expressed circRNAs (DEcircRNAs) were identified. Then, miRNAs modulated by these circRNAs were predicted and overlapped with differentially expressed miRNAs. Next, the potentially involved genes were identified by overlapping predicted targets, and differentially expressed genes. The enrichment analysis was performed, and a PPI network was projected. Subsequently, ten key genes were selected from the network. Furthermore, a circRNA/miRNA/mRNA regulatory network was constructed, and probable molecules and drugs with potential anti-ASD effects were predicted. 11 DEcircRNAs and 8 miRNAs regulated by 4 circRNAs were identified as being significantly involved. Subsequently, gene enrichment analysis of 71 overlapped mRNA regulated by these miRNAs showed that they are mostly associated with hippocampal synaptogenesis, neurogenesis, and axon guidance. Additionally, two high-score compounds, GSK3β inhibitor (SB216763) and dexamethasone, and three drugs (haloperidol, nystatin, paroxetine) were confirmed as potential therapeutic options for ASD. The results of this study may help gain deeper insight into the pathogenesis of the circRNA/miRNA/mRNA regulatory network in ASD, providing potential therapeutic management options.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"42 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140934623","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 : 2024-05-10DOI: 10.1186/s43042-024-00528-z
Ariza Julia Paulina, Y. Vitriyanna Mutiara, Lalu Muhammad Irham, Darmawi Darmawi, Nurul Qiyaam, Firdayani Firdayani, Dian Ayu Eka Pitaloka, Arfianti Arfianti, Wirawan Adikusuma
Liver fibrosis is a widespread chronic liver ailment linked to substantial mortality and limited therapeutic options. An in-depth comprehension of the genetic underpinnings of liver fibrogenesis is crucial for the development of effective management and treatment approaches. Using bioinformatics tools and the DisGeNET database, we pinpointed 105 genes significantly linked to liver fibrosis. Subsequently, we conducted functional assessments, incorporating gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and the STRING database, to construct protein–protein interaction networks (PPI) for these 105 liver fibrosis-associated genes. These analyses were executed via the WebGestalt 2019 online platform. We employed Cytoscape plugins, MCODE, and CytoHubba, to identify potential biomarker genes from these functional networks. Noteworthy hub genes encompassed TGF-β1, MMP2, CTNNB1, FGF2, IL6, LOX, CTGF, SMAD3, ALB, and VEGFA. TGF-β1 and MMP-2 exhibited substantial promise as liver fibrosis biomarkers, as denoted by their high systemic scores determined through the MCC algorithm in the CytoHubba methodology. In summary, this study presents a robust genetic biomarker strategy that may prove invaluable in the identification of potential liver fibrosis biomarkers.
{"title":"Genetic-driven biomarkers for liver fibrosis through bioinformatic approach","authors":"Ariza Julia Paulina, Y. Vitriyanna Mutiara, Lalu Muhammad Irham, Darmawi Darmawi, Nurul Qiyaam, Firdayani Firdayani, Dian Ayu Eka Pitaloka, Arfianti Arfianti, Wirawan Adikusuma","doi":"10.1186/s43042-024-00528-z","DOIUrl":"https://doi.org/10.1186/s43042-024-00528-z","url":null,"abstract":"Liver fibrosis is a widespread chronic liver ailment linked to substantial mortality and limited therapeutic options. An in-depth comprehension of the genetic underpinnings of liver fibrogenesis is crucial for the development of effective management and treatment approaches. Using bioinformatics tools and the DisGeNET database, we pinpointed 105 genes significantly linked to liver fibrosis. Subsequently, we conducted functional assessments, incorporating gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and the STRING database, to construct protein–protein interaction networks (PPI) for these 105 liver fibrosis-associated genes. These analyses were executed via the WebGestalt 2019 online platform. We employed Cytoscape plugins, MCODE, and CytoHubba, to identify potential biomarker genes from these functional networks. Noteworthy hub genes encompassed TGF-β1, MMP2, CTNNB1, FGF2, IL6, LOX, CTGF, SMAD3, ALB, and VEGFA. TGF-β1 and MMP-2 exhibited substantial promise as liver fibrosis biomarkers, as denoted by their high systemic scores determined through the MCC algorithm in the CytoHubba methodology. In summary, this study presents a robust genetic biomarker strategy that may prove invaluable in the identification of potential liver fibrosis biomarkers.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"23 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140934483","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}
Melanomas are highly aggressive in nature known for metastasis and death. Melanocytes that gave rise to melanomas are neural crest progenitor cells. Our research was primarily concerned with uveal melanoma (UM) and cutaneous melanoma (CM), respectively. Although they both have the same melanocytic origin, the biology of their respective is different. The aim of our study was to recognize the common differentially expressed genes (DEGs) between UM and CM. The gene expression profile was downloaded from the GEO and analyzed by GEO2R to recognize DEGs. By applying DAVID, GO, and KEGG, pathway enrichment analysis was performed. PPI of these DEGs was analyzed using STRING and visualized by Cytoscape and MCODE. Further, we utilized HPA and GEPIA to obtain Kaplan–Meier graph for survival analysis in order to assess the prognostic value of hub genes. We examined the UM and CM datasets and discovered three common upregulated and eight downregulated DEGs based on computational analysis. HMGCS1 and ELOVL5 were shown to be enriched in a variety of altered molecular pathways and pathways in cancer. Overexpression of HMGCS1 and ELOVL5 was linked to a poor prognosis in CM. Computational evaluation found that HMGCS1 and ELOVL5 were upregulated in both melanomas. Enrichment analysis showed that these genes are involved in cancer metabolism pathway and associated with poor prognosis in CM. However, the molecular study of these genes in UM is limited. Therefore, a better understanding of the cancer metabolism pathways should be carried to pave the way for clinical benefits.
{"title":"A bioinformatics approach to reveal common genes and molecular pathways shared by cutaneous melanoma and uveal melanoma","authors":"Perumal Jayaraj, Tanisha Bhimwal, Khushneet Kaur, Kritika Gupta, Shreya Taluja, Anjali Priyadarshani","doi":"10.1186/s43042-024-00526-1","DOIUrl":"https://doi.org/10.1186/s43042-024-00526-1","url":null,"abstract":"Melanomas are highly aggressive in nature known for metastasis and death. Melanocytes that gave rise to melanomas are neural crest progenitor cells. Our research was primarily concerned with uveal melanoma (UM) and cutaneous melanoma (CM), respectively. Although they both have the same melanocytic origin, the biology of their respective is different. The aim of our study was to recognize the common differentially expressed genes (DEGs) between UM and CM. The gene expression profile was downloaded from the GEO and analyzed by GEO2R to recognize DEGs. By applying DAVID, GO, and KEGG, pathway enrichment analysis was performed. PPI of these DEGs was analyzed using STRING and visualized by Cytoscape and MCODE. Further, we utilized HPA and GEPIA to obtain Kaplan–Meier graph for survival analysis in order to assess the prognostic value of hub genes. We examined the UM and CM datasets and discovered three common upregulated and eight downregulated DEGs based on computational analysis. HMGCS1 and ELOVL5 were shown to be enriched in a variety of altered molecular pathways and pathways in cancer. Overexpression of HMGCS1 and ELOVL5 was linked to a poor prognosis in CM. Computational evaluation found that HMGCS1 and ELOVL5 were upregulated in both melanomas. Enrichment analysis showed that these genes are involved in cancer metabolism pathway and associated with poor prognosis in CM. However, the molecular study of these genes in UM is limited. Therefore, a better understanding of the cancer metabolism pathways should be carried to pave the way for clinical benefits.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"157 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140932828","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 : 2024-05-09DOI: 10.1186/s43042-024-00529-y
Tanmayi Sharma, Badaruddoza Badaruddoza
Obesity, a multifaceted endocrine issue, is adversely affecting all age groups and is posing a significant public health challenge. The genetic polymorphisms of the melanocortin 4 receptor (MC4R) and leptin (LEP) genes likely contribute to the development of obesity. The present study aimed to explore the effects of MC4R and LEP gene polymorphisms on obesity among the northwest Indian population. The present study was conducted among 333 obese cases and 338 non-obese controls (aged 18–50 years). All subjects underwent measurements for anthropometric, physiometric, as well as biochemical parameters. Genotyping for MC4R and LEP gene variants was performed using the polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method. However, 10% of the samples for each variant were confirmed using the Sanger sequencing method. The polymorphisms of leptin–melanocortin pathway genes (MC4R-LEP) were found to be significantly associated with various obesity-related parameters like waist circumference: p = 0.017, waist-to-height ratio: p = 0.009, total cholesterol: p = 0.0001 and triglycerides: p = 0.0001. Both the LEP gene variants rs2167270 and rs7799039 conferred 2.4- and 2.2-fold risk toward obesity under the recessive genetic model [OR (95% CI) 2.42 (1.44–4.07), p = 0.001; OR (95% CI) 2.26 (1.41–3.60), p = 0.0001, respectively]. All four polymorphisms of the MC4R and LEP genes demonstrated a strong interaction of 82.1% with the lifestyle factor (p = 0.001). The haplotype combinations A–A for rs571312 and rs12970134 conferred twofold risk [OR (95% CI) 2.61 (1.10–6.20), p = 0.028]. However, the combination A–G for rs2167270 and rs7799039 predicted sixfold risk [OR (95% CI) 6.02 (3.39–10.68), p = 0.0001] toward the obesity development in this population. Our study revealed a connection between MC4R (rs571312, rs12970134) and LEP (rs2167270, rs7799039) gene variants with obesity, highlighting their prominent role in assessing the risk of obesity among the northwest Indian population.
{"title":"Association of leptin–melanocortin gene polymorphisms with the risk of obesity in northwest Indian population","authors":"Tanmayi Sharma, Badaruddoza Badaruddoza","doi":"10.1186/s43042-024-00529-y","DOIUrl":"https://doi.org/10.1186/s43042-024-00529-y","url":null,"abstract":"Obesity, a multifaceted endocrine issue, is adversely affecting all age groups and is posing a significant public health challenge. The genetic polymorphisms of the melanocortin 4 receptor (MC4R) and leptin (LEP) genes likely contribute to the development of obesity. The present study aimed to explore the effects of MC4R and LEP gene polymorphisms on obesity among the northwest Indian population. The present study was conducted among 333 obese cases and 338 non-obese controls (aged 18–50 years). All subjects underwent measurements for anthropometric, physiometric, as well as biochemical parameters. Genotyping for MC4R and LEP gene variants was performed using the polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method. However, 10% of the samples for each variant were confirmed using the Sanger sequencing method. The polymorphisms of leptin–melanocortin pathway genes (MC4R-LEP) were found to be significantly associated with various obesity-related parameters like waist circumference: p = 0.017, waist-to-height ratio: p = 0.009, total cholesterol: p = 0.0001 and triglycerides: p = 0.0001. Both the LEP gene variants rs2167270 and rs7799039 conferred 2.4- and 2.2-fold risk toward obesity under the recessive genetic model [OR (95% CI) 2.42 (1.44–4.07), p = 0.001; OR (95% CI) 2.26 (1.41–3.60), p = 0.0001, respectively]. All four polymorphisms of the MC4R and LEP genes demonstrated a strong interaction of 82.1% with the lifestyle factor (p = 0.001). The haplotype combinations A–A for rs571312 and rs12970134 conferred twofold risk [OR (95% CI) 2.61 (1.10–6.20), p = 0.028]. However, the combination A–G for rs2167270 and rs7799039 predicted sixfold risk [OR (95% CI) 6.02 (3.39–10.68), p = 0.0001] toward the obesity development in this population. Our study revealed a connection between MC4R (rs571312, rs12970134) and LEP (rs2167270, rs7799039) gene variants with obesity, highlighting their prominent role in assessing the risk of obesity among the northwest Indian population.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"1 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140932760","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 : 2024-05-03DOI: 10.1186/s43042-024-00508-3
Sandra Paulina Smieszek
This study aimed to characterize the frequency of RAI1 genetic aberrations associated with Smith–Magenis syndrome (SMS), in a large cohort of autism spectrum disorder (ASD) whole-genome sequencing samples. We aimed to determine the frequencies of RAI1 single-nucleotide variants (SNVs) and copy number variants (CNVs). We report a 2.5 × enrichment of the major deletion and a > 5 × enrichment of the frameshift variants as compared to the known prevalence of SMS 1/15,000. Additionally, we report a significant enrichment of RAI1 rare missense variants in ASD subjects with respect to controls (54 variants/6080 ASD subjects and 6 variants/2541 controls, p-value < 0.002, OR 3.78, CI 1.62–8–81). The SMS phenotype including circadian dysregulation and associated sleep disturbances is mainly caused by RAI1 haploinsufficiency. Sleep disturbances as seen in SMS may overlap in ASD, especially in patients with consequential variants in RAI1 gene.
{"title":"Retinoic Acid-Induced 1 gene variants associated with Smith–Magenis syndrome circadian phenotypes enriched in autism spectrum disorder: whole-genome sequencing study","authors":"Sandra Paulina Smieszek","doi":"10.1186/s43042-024-00508-3","DOIUrl":"https://doi.org/10.1186/s43042-024-00508-3","url":null,"abstract":"This study aimed to characterize the frequency of RAI1 genetic aberrations associated with Smith–Magenis syndrome (SMS), in a large cohort of autism spectrum disorder (ASD) whole-genome sequencing samples. We aimed to determine the frequencies of RAI1 single-nucleotide variants (SNVs) and copy number variants (CNVs). We report a 2.5 × enrichment of the major deletion and a > 5 × enrichment of the frameshift variants as compared to the known prevalence of SMS 1/15,000. Additionally, we report a significant enrichment of RAI1 rare missense variants in ASD subjects with respect to controls (54 variants/6080 ASD subjects and 6 variants/2541 controls, p-value < 0.002, OR 3.78, CI 1.62–8–81). The SMS phenotype including circadian dysregulation and associated sleep disturbances is mainly caused by RAI1 haploinsufficiency. Sleep disturbances as seen in SMS may overlap in ASD, especially in patients with consequential variants in RAI1 gene.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"28 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140835738","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 : 2024-04-26DOI: 10.1186/s43042-024-00499-1
Dalida El Khatib, Moussa Hojeij, Sandra Sabbagh, Cybel Mehawej, Eliane Chouery, Seung Woo Ryu, JiHye Kim, Andre Mégarbané
Polymicrogyria is a spectrum of complex cortical malformations encompassing multiple subtypes. Of these, bilateral frontoparietal polymicrogyria (BFPP) has been associated with pathogenic variants in the ADGRG1 gene, formerly known as GPR56. BFPP is characterized by cognitive impairment, motor delay, seizures, oculomotor findings, cerebellar, pyramidal signs, and brain malformations that consist of abnormal changes in the cortex, white matter, brainstem, and cerebellum. A large consanguineous Syrian family with five affected individuals exhibiting features of BFPP, is included in this study. These patients presented with cognitive impairment, psychomotor delay, epileptic episodes, cerebellar signs, oculomotor findings, and brain malformations. Through whole exome sequencing, a novel homozygous pathogenic variant in the ADGRG1 gene (NM_201525.4: c.308T > C; p.Leu103Pro) was identified. Here, we report a thorough literature review of cases with BFPP, and we discuss the importance of genetic counseling in families with genetic disorders, especially in underdeveloped countries.
{"title":"ADGRG1-related polymicrogyria syndrome: report on a large consanguineous family with a novel variant and review","authors":"Dalida El Khatib, Moussa Hojeij, Sandra Sabbagh, Cybel Mehawej, Eliane Chouery, Seung Woo Ryu, JiHye Kim, Andre Mégarbané","doi":"10.1186/s43042-024-00499-1","DOIUrl":"https://doi.org/10.1186/s43042-024-00499-1","url":null,"abstract":"Polymicrogyria is a spectrum of complex cortical malformations encompassing multiple subtypes. Of these, bilateral frontoparietal polymicrogyria (BFPP) has been associated with pathogenic variants in the ADGRG1 gene, formerly known as GPR56. BFPP is characterized by cognitive impairment, motor delay, seizures, oculomotor findings, cerebellar, pyramidal signs, and brain malformations that consist of abnormal changes in the cortex, white matter, brainstem, and cerebellum. A large consanguineous Syrian family with five affected individuals exhibiting features of BFPP, is included in this study. These patients presented with cognitive impairment, psychomotor delay, epileptic episodes, cerebellar signs, oculomotor findings, and brain malformations. Through whole exome sequencing, a novel homozygous pathogenic variant in the ADGRG1 gene (NM_201525.4: c.308T > C; p.Leu103Pro) was identified. Here, we report a thorough literature review of cases with BFPP, and we discuss the importance of genetic counseling in families with genetic disorders, especially in underdeveloped countries.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"55 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140800585","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 : 2024-04-16DOI: 10.1186/s43042-024-00523-4
Amirul Faez Shamsudin, Sarina Sulong, Imran Ahmad, Nur Salwani Bakar
Statins are well known for their efficacy to improve lipid profiles. Their efficacy varies between individuals and can be modified by patient factors such as genetic polymorphisms. This study used a cross-sectional retrospective design to assess the effect of selected single nucleotide polymorphisms (SNPs) and other patient-specific clinical variables on statin-related lipid profile changes in a subgroup of Malaysians. The impact of low and moderate intensity of statin doses (10–40 mg/day for at least six weeks), regardless of statin types, was assessed between SNPs of previously identified genes with clinical relation to statin efficacy and lipid profile changes before (baseline) and after statin treatment; two ranges of treatment durations, i.e. ≤ 6 months and 7–12 months. DNA was extracted from patient's venous blood (3 mL), and SNP genotyping was performed using PCR–RFLP method. Using a dominant genetic model, the association between selected SNPs from six genes of interest (ABCG2, ABCC2, APOE, APOA5, GATM and COQ2) and the patients' lipid profiles was investigated. A total of 229 statin-treated patients were included. The mean age of the patients was 53 ± 7.16 years, and they were mostly females (53.3%), Malay (96.1%), and were taking atorvastatin and simvastatin (90.4%). Seven SNPs genotyped from six genes investigated were related to different lipid profile before and after statin treatment. At baseline, ABCG2 rs2231142 (P = 0.035) and APOA5 rs662799 (P = 0.007) variants had higher HDL-c levels, while ABCC2 rs717620 variants had higher TC (P = 0.040) and LDL-c levels (P = 0.022). Following statin treatment, ABCC2 rs717620 (lower TG, P = 0.009) and APOA5 rs662799 (higher HDL, P = 0.031; lower TG, P = 0.037) were associated with improved lipid profiles, with the association being substantially related to males carrying minor alleles of the SNPs. None of the investigated SNPs were related to significant statin-related LDL-c lowering effects during statin therapy. To better understand inter-individual heterogeneity in lipid profiles during statin therapy, it would be helpful to take patient genetics and gender into consideration before and after administering statins.
{"title":"Association between genetic polymorphisms and other attributing factors with lipid profiles among statin users: a cross-sectional retrospective study","authors":"Amirul Faez Shamsudin, Sarina Sulong, Imran Ahmad, Nur Salwani Bakar","doi":"10.1186/s43042-024-00523-4","DOIUrl":"https://doi.org/10.1186/s43042-024-00523-4","url":null,"abstract":"Statins are well known for their efficacy to improve lipid profiles. Their efficacy varies between individuals and can be modified by patient factors such as genetic polymorphisms. This study used a cross-sectional retrospective design to assess the effect of selected single nucleotide polymorphisms (SNPs) and other patient-specific clinical variables on statin-related lipid profile changes in a subgroup of Malaysians. The impact of low and moderate intensity of statin doses (10–40 mg/day for at least six weeks), regardless of statin types, was assessed between SNPs of previously identified genes with clinical relation to statin efficacy and lipid profile changes before (baseline) and after statin treatment; two ranges of treatment durations, i.e. ≤ 6 months and 7–12 months. DNA was extracted from patient's venous blood (3 mL), and SNP genotyping was performed using PCR–RFLP method. Using a dominant genetic model, the association between selected SNPs from six genes of interest (ABCG2, ABCC2, APOE, APOA5, GATM and COQ2) and the patients' lipid profiles was investigated. A total of 229 statin-treated patients were included. The mean age of the patients was 53 ± 7.16 years, and they were mostly females (53.3%), Malay (96.1%), and were taking atorvastatin and simvastatin (90.4%). Seven SNPs genotyped from six genes investigated were related to different lipid profile before and after statin treatment. At baseline, ABCG2 rs2231142 (P = 0.035) and APOA5 rs662799 (P = 0.007) variants had higher HDL-c levels, while ABCC2 rs717620 variants had higher TC (P = 0.040) and LDL-c levels (P = 0.022). Following statin treatment, ABCC2 rs717620 (lower TG, P = 0.009) and APOA5 rs662799 (higher HDL, P = 0.031; lower TG, P = 0.037) were associated with improved lipid profiles, with the association being substantially related to males carrying minor alleles of the SNPs. None of the investigated SNPs were related to significant statin-related LDL-c lowering effects during statin therapy. To better understand inter-individual heterogeneity in lipid profiles during statin therapy, it would be helpful to take patient genetics and gender into consideration before and after administering statins.","PeriodicalId":39112,"journal":{"name":"Egyptian Journal of Medical Human Genetics","volume":"23 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140612897","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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