Genetic testing and molecular biomarkers最新文献

{"title":"Upregulation of Long Noncoding RNA PCAT1 in Iranian Patients with Colorectal Cancer and Its Performance as a Potential Diagnostic Biomarker.","authors":"Negin Sadi Khosroshahi, Shabnam Koulaeizadeh, Adel Abdi, Sama Akbarzadeh, Seyed Mehran Hashemi Aghdam, Ali Rajabi, Reza Safaralizadeh","doi":"10.1089/gtmb.2023.0676","DOIUrl":"10.1089/gtmb.2023.0676","url":null,"abstract":"<p><p><b><i>Background:</i></b> Long noncoding RNAs (lncRNAs) as critical molecules play an essential role in the development of cancers. In colorectal cancer (CRC), various lncRNAs are related to cell proliferation, apoptosis, migration, and invasion. <i>LncRNA</i> prostate cancer-associated transcript 1 (<i>PCAT-1</i>), as an oncogenic factor, is a diagnostic biomarker that regulates cell proliferation, migration, invasion, and apoptosis. <b><i>Methods:</i></b> This study evaluated the relationship between <i>PCAT-1</i>, CRC occurrence, and pathological features of Iranian patients. The studied samples included 100 colorectal tumor tissues and 100 adjacent healthy tissues of Iranian CRC patients. RNAs were extracted from cancerous and noncancerous tissues to synthesize complementary DNA. The expression level of <i>PCAT-1</i> was assessed using the real-time PCR method, and the data analysis was assessed using SPSS software. <b><i>Results:</i></b> In this study, expression level of <i>PCAT-1</i> in tumor tissue was significantly increased in Iranian patients, and pathological studies of the patients had no significant relationship with the <i>PCAT-1</i> expression profile. <b><i>Conclusion:</i></b> Our results suggested that the high expression of <i>PCAT-1</i> resulted in the occurrence of colorectal tumor tissues in Iranian patients, which can be considered a diagnostic biomarker in CRC.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 2","pages":"65-69"},"PeriodicalIF":1.4,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association of Interleukin-17A and Interleukin-17F Gene Polymorphisms with Atopic Dermatitis in Chinese Children.","authors":"Chen Shen, Yunling Li, Jian Huang, Jing Li, Guoqiang Qi, Zhu Zhu, Huiwen Zheng","doi":"10.1089/gtmb.2023.0379","DOIUrl":"10.1089/gtmb.2023.0379","url":null,"abstract":"<p><p><b><i>Background:</i></b> Atopic dermatitis (AD) is a chronic, recurrent inflammatory disease associated with an unbalanced immune response in the upper layers of the skin tissue, mostly starting in childhood. As important factors in gene expression regulation, polymorphisms in interleukin (IL)-17A and IL-17F may be associated with the susceptibility and severity of AD. <b><i>Methods:</i></b> Blood samples and clinical information were obtained from 132 patients with AD and 100 healthy children. Using multiplex polymerase chain reaction and next-generation sequencing, five potential single-nucleotide polymorphisms (SNPs) of IL-17A and IL-17F were genotyped in all participants. The relationship between SNPs and susceptibility to or severity of AD was examined by analyzing haplotypes and genetic models. <b><i>Results:</i></b> The IL-17A rs3819025 polymorphism was substantially associated with higher AD risk in both the allele model (<i>p</i> = 0.03; odds ratio [OR] = 1.76; confidence interval [CI]: 1.05-2.95) and the dominant model (<i>p</i> = 0.04, OR = 1.85; CI: 1.03-3.33). There was no correlation between AD susceptibility and the IL-17A (rs2275913 and rs4711998) or IL-17F (rs763780 and rs12203736) SNPs (all <i>p</i> > 0.05). Additionally, the five IL-17A and IL-17F SNPs did not significantly differ across the mild-to-moderate and severe subgroups (all <i>p</i> > 0.05). <b><i>Conclusions:</i></b> The IL-17A/rs3819025 polymorphism was linked to the development of AD, whereas the IL-17F polymorphism was unrelated to the susceptibility to and severity of AD. The IL-17A polymorphism may provide valuable information to speculate on the susceptibility to AD in Chinese Han children.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 2","pages":"43-49"},"PeriodicalIF":1.4,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and Analysis of Gene Biomarkers for Ovarian Cancer.","authors":"Xiaodan Wang, Chengmao Xie, Chang Lu","doi":"10.1089/gtmb.2023.0222","DOIUrl":"10.1089/gtmb.2023.0222","url":null,"abstract":"<p><p><b><i>Objective:</i></b> To identify potential diagnostic markers for ovarian cancer (OC) and explore the contribution of immune cells infiltration to the pathogenesis of OC. <b><i>Methods:</i></b> As the study cohort, two gene expression datasets of human OC (GSE27651 and GSE26712, taken as the metadata) taken from the Gene Expression Omnibus (GEO) database were combined, comprising 228 OC and 16 control samples. Analysis was performed to identify the differentially expressed genes between the OC and control samples, while support vector machine analysis using the recursive feature elimination algorithm and least absolute shrinkage and selection operator regression were performed to identify candidate biomarkers that could discriminate OC. In addition, immunohistochemistry staining was performed to verify the diagnostic value and protein expression levels of the candidate biomarkers. The GSE146553 dataset (OC <i>n</i> = 40, control <i>n</i> = 3) was used to further validate the diagnostic values of those biomarkers. Further, the proportions of various immune cells infiltration in the OC and control samples were evaluated using the CIBERSORT algorithm. <b><i>Results:</i></b> CLEC4M, PFKP, and SCRIB were identified as potential diagnostic markers for OC in both the metadata (area under the receiver operating characteristic curve [AUC] = 0.996, AUC = 1.000, AUC = 1.000) and GSE146553 dataset (AUC = 0.983, AUC = 0.975, AUC = 0.892). Regarding immune cell infiltration, there was an increase in the infiltration of follicular helper dendritic cells, and a decrease in the infiltration of M2 macrophages and neutrophils, as well as activated natural killer (NK) cells and T cells in OC. CLEC4M showed a significantly positive correlation with neutrophils (<i>r</i> = 0.57, <i>p</i> < 0.001) and resting NK cells (<i>r</i> = 0.42, <i>p</i> = 0.0047), but a negative correlation with activated dendritic cells (<i>r</i> = -0.33, <i>p</i> = 0.032). PFKP displayed a significantly positive correlation with activated NK cells (<i>r</i> = 0.36, <i>p</i> = 0.016) and follicular helper T cells (<i>r</i> = 0.32, <i>p</i> = 0.035), but a negative correlation with the naive B cells (<i>r</i> = -0.3, <i>p</i> = 0.049) and resting NK cells (<i>r</i> = -0.41, <i>p</i> = 0.007). SCRIB demonstrated a significantly positive correlation with plasma cells (<i>r</i> = 0.39, <i>p</i> = 0.01), memory B cells (<i>r</i> = 0.34, <i>p</i> = 0.025), and follicular helper T cells (<i>r</i> = 0.31, <i>p</i> = 0.04), but a negative correlation with neutrophils (<i>r</i> = -0.46, <i>p</i> = 0.002) and naive B cells (<i>r</i> = -0.48, <i>p</i> = 0.0012). <b><i>Conclusion:</i></b> CLEC4M, PFKP, and SCRIB were identified and verified as potential diagnostic biomarkers for OC. This work and identification of the three biomarkers may provide guidance for future studies into the mechanism and treatment of OC.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 2","pages":"70-81"},"PeriodicalIF":1.4,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A New Era for Genetic Testing and Molecular Biomarkers.","authors":"Sharon F Terry","doi":"10.1089/gtmb.2024.29084.persp","DOIUrl":"10.1089/gtmb.2024.29084.persp","url":null,"abstract":"","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":" ","pages":"41-42"},"PeriodicalIF":1.4,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139740892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vitamin D Receptor Polymorphisms in a Spanish Cohort of Parkinson's Disease Patients.","authors":"Saray Canales-Cortés, Mario Rodríguez-Arribas, María F Galindo, Joaquín Jordan, Ignacio Casado-Naranjo, José M Fuentes, Sokhna M S Yakhine-Diop","doi":"10.1089/gtmb.2023.0344","DOIUrl":"10.1089/gtmb.2023.0344","url":null,"abstract":"<p><p><b><i>Background:</i></b> Vitamin D receptor (VDR) is a nuclear hormone receptor widely expressed in the substantia nigra. Its association with an increased risk of Parkinson's disease (PD) is based on vitamin D deficiency and/or different polymorphisms in its gene receptor. This fact has been demonstrated by several case-control studies. <b><i>Materials and Methods:</i></b> Consequently, we investigated the association between VDR <i>Apa</i>I, <i>Bsm</i>I, <i>Fok</i>I, and <i>Taq</i>I gene polymorphisms and PD in a Spanish cohort that included 54 cases and 17 healthy controls. The detection of single nucleotide polymorphisms (SNPs) was performed using a polymerase chain reaction-restriction fragment length polymorphism. <b><i>Results:</i></b> Our data indicate that the SNPs were not associated with the age of onset of PD, nor with the occurrence of motor symptoms. However, only <i>Bsm</i>I polymorphism was significantly associated with PD in this Spanish cohort. In fact, <i>Bsm</i>I genotype was five times higher among PD patients than among controls, and the A allele was considered as a genetic risk for PD. Additionally, the combination of <i>Fok</i>I and <i>Bsm</i>I polymorphisms was significantly associated with PD and could represent a risk factor. <b><i>Conclusion:</i></b> We conclude that <i>Apa</i>I, <i>Taq</i>I, and <i>Fok</i>I polymorphisms were not associated with PD, but <i>Bsm</i>I could be a risk factor for PD in this randomized population.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 2","pages":"59-64"},"PeriodicalIF":1.4,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Determination of the Relationship Between the Development and Recurrence of Subacute Thyroiditis and Human Leukocyte Antigen Subtypes.","authors":"Fatma Nur Korkmaz, Asena Gökçay Canpolat, Klara Dalva, Atilla Halil Elhan, Mustafa Şahin, Demet Çorapçıoğlu, Özgür Demir","doi":"10.1089/gtmb.2023.0386","DOIUrl":"10.1089/gtmb.2023.0386","url":null,"abstract":"<p><p><b><i>Background:</i></b> There are several studies investigating the role of human leukocyte antigens (HLA) in the development and recurrence of subacute thyroiditis (SAT). The HLA subtypes associated with SAT were usually determined in a population-based manner and <i>HLA-B*35</i>, <i>HLA-B*18:01</i>, <i>HLA-C*04:01</i>, and <i>HLA-DRB1*01</i> were detected to play a role in the disease susceptibility and prognosis. The aim of this study was to determine HLA alleles associated with the tendency of recurrence and prevention of SAT within the Turkish population. <b><i>Methods:</i></b> This prospective study was conducted with 51 SAT patients and 720 healthy bone marrow donor volunteers. HLA-A, -B, -C, -DRB1, and -DQB1 were genotyped using next-generation sequencing. <b><i>Results:</i></b> The frequency of <i>HLA-A*02:09</i>, <i>HLA-B*35:01/35:02/35:03</i>, <i>HLA-C*04:01</i>, <i>HLA-DRB1*12:01</i>, <i>and DRB1*13:03</i> were associated with an increased risk of SAT development (Odds Ratio: 22.4, 9.5, 10.3, 4.2, and 3.5, respectively). While <i>HLA-A*02:09</i>, <i>HLA-B*35:01</i>, <i>HLA-B*44:02 HLA-C*07:18</i>, <i>and HLA-C*16:04</i> were associated with nonrelapsing SAT, <i>HLA-DR*12:01</i>was associated with relapsing SAT. <i>HLA-B*35:02</i>, <i>HLA-B*35:03</i>, and <i>HLA-C*04:01</i> were more frequent both in relapsing and nonrelapsing groups according to control group. The frequency of <i>HLA-B*18:01</i>, reported as a risk factor previously, was similar in the SAT and control groups (<i>p</i> = 0.959). <i>HLA-DRB1*11:01</i> was associated with a lower risk of SAT development. <b><i>Conclusions:</i></b> Along with -<i>B*358</i> and <i>-C*04</i>, <i>HLA-A*02:09</i> was detected as an important risk factor for SAT development in our population. <i>HLA-DRB1*11:01</i> appears to be the protective HLA subtype against SAT. <i>HLA-A*02:09</i>, <i>HLA-B*35:01</i>, <i>HLA-B*44:02</i>, <i>HLA-C*07:18</i>, <i>HLA-C*16:04</i>, <i>HLA-DQ*06:03</i>, and <i>HLA-DR*12:01</i> subtypes can establish a tendency to relapsing or nonrelapsing SAT.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 1","pages":"2-9"},"PeriodicalIF":1.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acknowledgment of Reviewers 2023.","authors":"","doi":"10.1089/gtmb.2023.29081.ack","DOIUrl":"https://doi.org/10.1089/gtmb.2023.29081.ack","url":null,"abstract":"","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 1","pages":"39"},"PeriodicalIF":1.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Correlation Between Clinical Phenotype and Genotype of Hereditary Spherocytosis.","authors":"Hao Shen, Zhigang Gao, Qing Ye","doi":"10.1089/gtmb.2023.0307","DOIUrl":"10.1089/gtmb.2023.0307","url":null,"abstract":"<p><p><b><i>Objective:</i></b> Hereditary spherocytosis (HS) is a common hereditary hemolytic disease. This study aimed to explore the correlation between the phenotype and mutant genotype of HS to improve the clinical understanding of HS. <b><i>Methods:</i></b> This study reported a case of spontaneous mutation of the ANK1 gene in HS, reviewed previous studies on the genotype-phenotype correlation of HS, statistically analyzed the main types of gene mutations in HS, and summarized the clinical data of patients. <b><i>Results:</i></b> This patient had clinical manifestations of anemia, splenomegaly, peripheral blood smear with increased spherocytosis, and bilirubin, confirmed as ANK1 gene mutant HS by gene detection. In addition, this study included 14 previous studies on genotype-phenotype correlation, collected data, and determined that the ANK1 and SPTB genes were the most common types of gene mutations in HS patients. The mutant HS of the ANK1 gene would lead to lower hemoglobin levels. <b><i>Conclusion:</i></b> The results of this study showed that ANK1 and SPTB were the most common types of gene mutations in HS patients. Compared with patients with the SPTB genotype HS, patients with ANK1 mutant HS had more severe extravascular hemolysis, and a higher proportion needed splenectomy in early childhood.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 1","pages":"33-38"},"PeriodicalIF":1.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139641951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of Prognostic Apoptosis-Related Gene Signature to Evaluate Glioma Immune Microenvironment and Experimental Verification.","authors":"Hao Yu, Jiapeng Yu, Minjie Wang, Xiaobing Jiang","doi":"10.1089/gtmb.2023.0483","DOIUrl":"10.1089/gtmb.2023.0483","url":null,"abstract":"<p><p><b><i>Purpose:</i></b> Recently, apoptosis-related genes were shown to modulate cancer immunity. However, the role of apoptosis-related genes in the glioma immune microenvironment (GIME) remains unknown. This study aimed to explore the prognostic value of apoptosis-related genes in glioma. <b><i>Methods:</i></b> Doxorubicin was used to induce glioma cell apoptosis, and four differentially expressed apoptosis-related genes were identified: <i>CREM</i>, <i>TNFSF12</i>, <i>PEA15</i>, and <i>PRKCD</i>. Kaplan-Meier analyses, receiver operating characteristic curve analyses, and nomograms were established to determine the relationship between risk markers and the prognosis of patients with glioma. <b><i>Results:</i></b> Risk biomarkers were significantly associated with overall survival, immune cell infiltration, and immune checkpoints in patients with glioma. Somatic mutations and anti-PD-1/L1 immunotherapy were associated with worse prognosis in the high-risk group receiving anti-PD-1/L1 therapy. The expression of these four apoptosis-related genes was verified using quantitative polymerase chain reaction and immunohistochemistry, and the relationship between these four genes and apoptosis was examined using flow cytometry. <b><i>Conclusions:</i></b> This study suggests that apoptosis-related genes play a critical role in shaping the GIME. Assessing the apoptotic patterns of individual tumors will enhance our understanding of GIME infiltration features and lead to improved strategies for immunotherapy.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 1","pages":"22-32"},"PeriodicalIF":1.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward the Future: Perspectives on the Impacts of Genetic Testing and Biomarkers on Advancing Health Care.","authors":"Jane Gibson","doi":"10.1089/gtmb.2024.29083.editorial","DOIUrl":"10.1089/gtmb.2024.29083.editorial","url":null,"abstract":"","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 1","pages":"1"},"PeriodicalIF":1.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139643842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}