Meta GenePub Date : 2021-12-01DOI: 10.1016/j.mgene.2021.100964
Sumita Dutta Gupta , Bishal Dhar , Sharbadeb Kundu , Nabarun Das , Arun Paul Choudhury , Monica Deb , Abhijit Das , Amrita Das , Nayanika Das , Biswadeep Choudhury , Alex C. Varghese , Kushal Kumar Kar , Yashmin Choudhury , Sankar Kumar Ghosh
{"title":"Association between gene expression levels of GDF9 and BMP15 and clinicopathological factors in the prognosis of female infertility in northeast Indian populations","authors":"Sumita Dutta Gupta , Bishal Dhar , Sharbadeb Kundu , Nabarun Das , Arun Paul Choudhury , Monica Deb , Abhijit Das , Amrita Das , Nayanika Das , Biswadeep Choudhury , Alex C. Varghese , Kushal Kumar Kar , Yashmin Choudhury , Sankar Kumar Ghosh","doi":"10.1016/j.mgene.2021.100964","DOIUrl":"10.1016/j.mgene.2021.100964","url":null,"abstract":"<div><p>Female Infertility is a serious health issue, and genetic factors plays crucial role in female infertility. To explore the molecular mechanism involved in female infertility, we had investigated demographic, clinicopathological factors and gene expression profile of <em>BMP15</em> and <em>GDF9</em> in primary and secondary female infertility patients. Present study comprised of 469 primary and 210 secondary infertile females, and 419 fertile females (controls). The expression level of <em>GDF9</em> and <em>BMP15</em> genes was studied using quantitative real-time PCR and multifactor dimensionality reduction tool (MDR) was used to detect high-risk interaction. Finding revealed that there was down-regulation of the <em>BMP15</em> and <em>GDF9</em> gene in both primary and secondary infertile women in comparison to fertile women. A significant difference in the expression level of <em>GDF9</em> gene among the study subjects for the various levels of TSH and RBS (<em>p</em> < 0.01) indicating that the level of gene expression was influenced by few hormonal factors. The best risk factor model predicted for female infertility was the five-factors model of TSH, LH, LH/FSH ratio, Hb, MCV with 100% CVC and maximum TBA = 0.921 and <em>p</em> < 0.01. Thus, down-regulation of <em>GDF9</em> and <em>BMP15</em> gene and interaction of clinicopathological factors significantly persuade female infertility, and these findings might be useful as possible biomarker for the estimation of primary and secondary female infertility.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100964"},"PeriodicalIF":0.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mgene.2021.100964","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43120331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meta GenePub Date : 2021-12-01DOI: 10.1016/j.mgene.2021.100947
Elham Nazari , Reza ArefNezhad , Mahla Tabadkani , Amir Hossein Farzin , Mahmood Tara , Seyed Mahdi Hassanian , Majid Khazaei , Gordon A. Ferns , Hamed Tabesh , Amir Avan
{"title":"Using correlation matrix for the investigation the interaction of genes and traditional risk factor in breast cancer","authors":"Elham Nazari , Reza ArefNezhad , Mahla Tabadkani , Amir Hossein Farzin , Mahmood Tara , Seyed Mahdi Hassanian , Majid Khazaei , Gordon A. Ferns , Hamed Tabesh , Amir Avan","doi":"10.1016/j.mgene.2021.100947","DOIUrl":"10.1016/j.mgene.2021.100947","url":null,"abstract":"<div><h3>Background</h3><p>Despite extensive effort<strong>,</strong> breast cancer (BC) is still among the most lethal cancer in women. Here we explored the interaction of traditional markers (including pathological, clinical and demographical parameters) associated with breast cancer and 5 genetic variants (e.g., connexin37-rs1764391; ABCB1-rs2032582; CYP1B1-rs1056836; CDKN2A/B-rsrs10811661; CDKN2A/B-rs1333049) in BC.</p></div><div><h3>Methods</h3><p>Forty variables from 115 patients and 230 healthy individuals (e.g., pathology [T, N, M], genes, biochemical parameters [e.g., CA153, ki_67, ER, CEA] were collected and then analyzed. For studying internal relationships of each variables and as a risk factor, the correlation matrix was used. For implementation, Python programming language 3.7.2 was utilized and the coefficient of correlation between 0.7 and 1 was considered.</p></div><div><h3>Results</h3><p>Our finding revealed that there is a correlation between Ki_67 and cancer_family, between PR and ER, as well as a correlation between T and P53, CA153, ER, PR and cancer_family. Moreover, our result showed a relationship between Stage with p53, PR, CA153, T and N. Similarly, there was also a correlation between the genetic variables ABCB1 and CYP1B1, CDKN2 and CYP1B1, CDKN2 and ABCB1, CYP1B1 and Connexin37, ABCB1 and Connexin37, CDKN2A and CYP1B1, CDKN2A and ABCB1. The strong correlation of variables was seen stage T N in BC. However,the good correlation of variables was seen rs1764391, Dominnt108, p53, CA153, ER and PR in BC.</p></div><div><h3>Conclusion</h3><p>Our data provide a novel inside on the potential values of emerging markers in combination with current traditional markers as an approach in identification of high risk breast cancer patients.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100947"},"PeriodicalIF":0.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mgene.2021.100947","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41820201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meta GenePub Date : 2021-12-01DOI: 10.1016/j.mgene.2021.100982
Mohsen Saravani , Mahnaz Sandoughi , Zohreh Heidary , Ghasem Ebrahimi , Solmaz Mirzamohammadi , Mohammad Haddadi , Mohammad Hadi Nematollahi
{"title":"HIF-1α and VEGF polymorphisms and systemic lupus erythematosus susceptibility","authors":"Mohsen Saravani , Mahnaz Sandoughi , Zohreh Heidary , Ghasem Ebrahimi , Solmaz Mirzamohammadi , Mohammad Haddadi , Mohammad Hadi Nematollahi","doi":"10.1016/j.mgene.2021.100982","DOIUrl":"10.1016/j.mgene.2021.100982","url":null,"abstract":"<div><h3>Background</h3><p>Hypoxia-inducible factor-1α (HIF-1α) and its downstream gene, vascular endothelial factor (VEGF), play an important role in modulating the immune system function and consequently alternation the susceptibility to systemic lupus erythematosus (SLE) disease.</p></div><div><h3>Objective</h3><p>The present study aimed to investigate the effect of the HIF-1α and VEGF gene polymorphisms and the susceptibility to SLE.</p></div><div><h3>Methods</h3><p>The 140 patients and 150 healthy age and gender-matched people as a control group participated in the study. The PCR-RFLP method was used for genotyping.</p></div><div><h3>Results</h3><p>No remarkable differences in allele frequencies of HIF-1α (rs11549465) and VEGF (rs699947) were seen between the SLE and control groups. The frequencies of CT genotype of the HIF-1α (rs11549465) and CA genotype of VEGF (rs699947) in the control were significantly higher than SLE group (OR = 0.53; 95% CI = 0.32–0.53; <em>p</em> = 0.014; OR = 0.57;95% CI = 0.33–0.99; <em>p</em> = 0.046, resp.). In the case of HIF-1α (<em>C111A</em>) polymorphism, the CA and AA variants were not found.</p></div><div><h3>Conclusion</h3><p>HIF-1α (rs11549465) CT and VEGF (rs699947) CA genotypes were identified as protective factors for SLE. However, additional studies are required to confirm the association between HIF-1α and VEGF polymorphisms and SLE.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100982"},"PeriodicalIF":0.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S221454002100133X/pdfft?md5=abb894bfe601e6cac7ce4388e8f8dc74&pid=1-s2.0-S221454002100133X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42577461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meta GenePub Date : 2021-12-01DOI: 10.1016/j.mgene.2021.100974
K.G. Savikina , A.H. Abd Ali , T.P. Shkurat , S.V. Lomteva , G.V. Karantysh
{"title":"Association of CAT C262T (rs1001179) polymorphism with male infertility: Meta-analysis","authors":"K.G. Savikina , A.H. Abd Ali , T.P. Shkurat , S.V. Lomteva , G.V. Karantysh","doi":"10.1016/j.mgene.2021.100974","DOIUrl":"10.1016/j.mgene.2021.100974","url":null,"abstract":"<div><h3>Background</h3><p>In connection with the problems of infertility, one in four married couples in the world seek medical help because of the problems of the natural conception of a child. However, the biochemical and genetic mechanisms underlying male infertility are still poorly understood. This study aimed to identify a potential link between the –262C > T (rs1001179) polymorphism of the catalase (<em>CAT)</em> gene and pathospermia.</p></div><div><h3>Methods</h3><p>A total of 23 publications were analyzed up to July 2021, of which 5 case-control studies met all inclusion criteria. The analysis comprised a total of 1611 men: with pathospermia (<em>n</em> = 1082) and healthy donors (<em>n</em> = 529). Meta-analysis was performed using a “ fixed effects model” with a given OR and 95% confidence intervals for all models. The analysis of the “publication error” was carried out using the Begg and Egger tests. Then, the trial sequential analysis (TSA) was performed to assess association number of studies.</p></div><div><h3>Results</h3><p>Three studies have refer a correlation between the <em>CAT</em>-262C/C genotype and the risk of pathospermia. One study did not reveal a direct relationship between the rs1001179 polymorphism and pathospermia, and another study indicated an increased risk of pathospermia in carriers of the TT genotype. Based on the data of all analyzed studies, the odds ratio was calculated for the association of the rs1001179 polymorphism of the <em>CAT</em> gene with pathospermia; it was found that this value is 2.7 (OR = 0,73; 95% Cl = 0,57-0,92; <em>p</em> = 0.007).</p></div><div><h3>Conclusion</h3><p>Based on the results obtained, observed that the C-262 T locus of the <em>CAT</em> it is related with male infertility in various populations, but it requires more studies to confirm. As it can be assumed that the association of the <em>CAT</em> C262T (rs1001179) polymorphism with the development of pathospermia may vary depending on the ethnic group.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100974"},"PeriodicalIF":0.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mgene.2021.100974","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47857586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meta GenePub Date : 2021-12-01DOI: 10.1016/j.mgene.2021.100956
Yuri Nishikawa, Takafumi Ishida
{"title":"Genetic lineage of the Amami islanders inferred from classical genetic markers","authors":"Yuri Nishikawa, Takafumi Ishida","doi":"10.1016/j.mgene.2021.100956","DOIUrl":"https://doi.org/10.1016/j.mgene.2021.100956","url":null,"abstract":"<div><p>The genetic structure of the people of mainland Japan and Okinawa has been gradually unveiled in recent years. However, previous anthropological studies dealing with people in the Amami islands, located between mainland Japan and Okinawa, were less informative because of the lack of genetic data. In this study, we collected DNAs from 104 subjects in two of the Amami islands, Amami-Oshima island and Kikai island. We analyzed the D-loop region of mtDNA, four Y-STRs, and four autosomal nonsynonymous SNPs to clarify the Amami islanders' genetic structure compared with peoples in Okinawa, mainland Japan, and other regions of East Asia. We found that the Amami islanders showed a genetically intermediate position between mainland Japan and Okinawa in mtDNA and Y-STR. However, the frequencies of several autosomal SNPs in the Amami islanders indicated a significant difference from mainland Japanese, which may be because of the gene flow from Okinawa but not natural selection. Moreover, extremely high or low frequencies of several alleles implied a founder effect in Kikai islanders. Note that there is room for the interpretation of the results because of the small sample size and number of alleles in the present study. Geographically broad and detailed samplings and genome-wide analyses are awaited.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100956"},"PeriodicalIF":0.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mgene.2021.100956","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"137299137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meta GenePub Date : 2021-12-01DOI: 10.1016/j.mgene.2021.100960
Mohd Murtaza , Mahrukh Hameed Zargar , Oliyath Ali , Ishfaq Shafi Khan , Md Niamat Ali
{"title":"Spectrum and frequency of connexin 26 & connexin 30 gene mutations in patients with congenital hearing loss from Ladakh India","authors":"Mohd Murtaza , Mahrukh Hameed Zargar , Oliyath Ali , Ishfaq Shafi Khan , Md Niamat Ali","doi":"10.1016/j.mgene.2021.100960","DOIUrl":"10.1016/j.mgene.2021.100960","url":null,"abstract":"<div><h3>Background</h3><p>Congenital hearing loss refers to prenatal hearing impairment, which is the commonly shared problem among sensory disorders that ranges from slight to profound. In this study, we screened the involvement of connexin 26 & connexin 30 gene in congenital hearing loss patients from the Kargil district of Ladakh, India by target gene sequencing.</p></div><div><h3>Materials and methods</h3><p>The peripheral blood sample of the patients was collected followed by DNA extraction and PCR of the target gene of interest. The amplified target gene was then sequenced and analysed for any changes in nucleotide sequence.</p></div><div><h3>Results</h3><p>In this study, the connexin 26 & connexin 30 are the target gene that are associated with hearing loss and in this study, we found mutations in the connexin 26 gene and none of the mutations were found in the connexin 30 gene. The mutations found in the connexin 26 gene are “NM_004004:c.71G>A, “NM_004004:c.223C>T, “NM_004004:c230G>A, “NM_004004:c.380G>A, and “NM_004004:c.439G>A which change the amino acids to W24X, R75W, W77X, R127H, and E147K respectively and the frequency of the connexin 26 mutations in patients was 23% and the overall mutations in the cohort were 14.5%. This study found that “NM_004004:c.71G>A (W24X) nucleotide variant as common mutation. Both homozygous as well as heterozygous variants were found. R127H was the only mutation observed in control samples. A significant association was seen between connexin 26 gene mutations and familial history of congenital hearing loss and consanguinity with the <em>p</em>-value <em>P</em><0.001.</p></div><div><h3>Conclusion and significance</h3><p>Although the etiology has been found to be multifactorial. However, the role of any nucleotide variant in the gene of interest needs to be thoroughly investigated to study the genetic etiology of the anomalies. The results of this study showed a positive association between congenital hearing loss and the connexin 26 gene. However, we did not find any role of the connexin 30 gene in congenital hearing loss.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100960"},"PeriodicalIF":0.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mgene.2021.100960","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41437664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dysregulation of immune gene expression profiles during HTLV-1 infection","authors":"Masoud Keikha , Mohammad Ali-Hassanzadeh , Ramin Bagheri , Mohsen Karbalaei","doi":"10.1016/j.mgene.2021.100944","DOIUrl":"10.1016/j.mgene.2021.100944","url":null,"abstract":"<div><h3>Background</h3><p>Human T-lymphotropic virus type 1 (HTLV-1) is the main cause of adult T cell leukemia/lymphoma (ATLL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The aim of this study was to evaluate the dysregulation of immune genes that may be involved in the pathogenesis of ATLL using microarray datasets.</p></div><div><h3>Method</h3><p>The gene expression profiles of ATLL cases (GSE19080) were obtained from GEO database. Next, the quality and reliability of data were evaluated by MetaQC, and the expression data in each group were normalized by affy package. Subsequently, the R package MetaDE was applied for the analysis of differentially expressed genes (DEGs). Using STRING database, protein-protein interaction network (PPIN) was constructed for hub DEGs. Finally, online servers including STRING, Enrichr, and KEGG pathway were applied for gene enrichment and interpretation of the results.</p></div><div><h3>Results</h3><p>65 significant hub DEGs were divided in three groups, normal health, asymptomatic carrier and ATLL patients. The PPIN analysis between hub DEGs was carried out by STRING. Enrichment analysis revealed that the hub DEGs were involved in various pathways such as apoptosis, proliferation of T cell, Ras signaling, MAPK signaling, NF-κB signaling, integrin signaling, P53 signaling, angiogenesis, tissue invasion, and DNA damage process.</p></div><div><h3>Conclusion</h3><p>According to the present study, HTLV-1 appears to cause inflammation by enhancing cell proliferation. During the HTLV-1 infection, dysregulation of immune genes such as IL-10, TGF-β, JAK, BCL2, etc. result in immortalization of HTLV-1-infected CD4+ T cells, and eventually progression to ATLL.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100944"},"PeriodicalIF":0.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mgene.2021.100944","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48479701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Sirtuin1 and Sirtuin3 gene polymorphisms and acute myocardial infarction susceptibility","authors":"Mona Salah El-Din Habieb , Walaa Farid Abdel-Aziz , Abdel Hamid Abdo Ismail , Khadija Metwali Ahmed Sallam , Maathir Kamel El-Shafie","doi":"10.1016/j.mgene.2021.100965","DOIUrl":"10.1016/j.mgene.2021.100965","url":null,"abstract":"<div><h3>Objective</h3><p>Acute myocardial infarction is one of the leading causes of death in the developed countries. This study aimed to study the association between sirtuin1 (<em>SIRT1</em>) gene polymorphism rs7069102 and promoter variant rs12293349 of sirtuin3 (<em>SIRT3</em>) gene and MI.</p></div><div><h3>Patients and methods</h3><p>150 subjects were enrolled: 100 myocardial infarction (MI) patients and 50 healthy individuals. All subjects were investigated for blood glucose, lipid profile, cardiac markers (creatine kinase (CK-MB) and troponin I (TnI) by ELISA and genotyping of <em>SIRT1</em> rs7069102 and <em>SIRT3</em> rs12293349 by real time PCR.</p></div><div><h3>Results</h3><p>MI cases had significantly higher prevalence of <em>SIRT1</em> rs7069102 GG genotype and G allele when compared to controls. GG genotype and G allele elevated the risk of MI. The dominant (CG + GG versus CC) and recessive (GG versus CC + CG) models both showed a significant difference in the distribution of rs7069102 genotypes. Under the dominant model, total cholesterol, LDLc and CK-MB levels were significantly higher in CG + GG patients. While under the recessive model, GG patients showed significantly increased FBG, 2 h PPG, HbA1c, total cholesterol, and LDLc (<em>p</em> = 0.001). By univariate and multivariate logistic regression analysis, LDLc and total cholesterol were the only independent determining variables. Considering the <em>SIRT3</em> rs12293349, there is no significant differences between patients and controls.</p></div><div><h3>Conclusion</h3><p>According to the findings, carrying the variant-type G allele of the <em>SIRT1</em> rs7069102 was linked to an elevated risk of MI suggesting that this genetic variation could be a promising MI marker in an Egyptian population.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100965"},"PeriodicalIF":0.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.mgene.2021.100965","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45806962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}