Genetic testing and molecular biomarkers最新文献

{"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}

{"title":"<i>EGLN1:</i> A Biomarker of Poor Prognosis of Cervical Cancer and a Target of Treatment.","authors":"Yi-Ting Zhang, Lin-Jing Xu, Ling Li","doi":"10.1089/gtmb.2023.0024","DOIUrl":"10.1089/gtmb.2023.0024","url":null,"abstract":"<p><p><b><i>Objective:</i></b> To conduct bioinformatics analysis on the prognostic effect, mechanism of action, and drug sensitivity of Egl-9 family hypoxia-inducible factor 1 (<i>EGLN1</i>) expression on cervical cancer. <b><i>Methods:</i></b> Bioinformatics were obtained from Gene Expression Profiling Interactive Analysis (GEPIA), Tumor Immune Estimation Resource (TIMER), and the human cancer metastasis database (HCMDB), and the effect of <i>EGLN1</i> expression level on the prognosis of cervical cancer was comprehensively analyzed. The protein-protein interaction network was constructed by Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), and the possible mechanism of <i>EGLN1</i> affecting the prognosis of cervical cancer was discussed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. In addition, Gene Set Cancer Analysis (GSCALite) was used to predict sensitive drugs online. <b><i>Results:</i></b> The higher the expression level of <i>EGLN1</i>, the shorter the tumor-free survival time and overall survival time of cervical cancer. The higher the stage of cervical cancer, the higher the expression level of <i>EGLN1</i>. The expression of <i>EGLN1</i> affects the degree of immune infiltration, the variation of somatic copy number, and the level of N⁶-methyladenosine (m⁶A) modification in cervical cancer. COX regression model suggested that <i>EGLN1</i> was an independent prognostic factor of cervical cancer. <b><i>Conclusions:</i></b> The high expression of <i>EGLN1</i> in cervical cancer is an independent risk factor for the prognosis of cervical cancer, which affects the prognosis of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) through different signal pathways. It is expected to be used to predict the sensitive anticancer drugs for the treatment of cervical cancer.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"28 1","pages":"10-21"},"PeriodicalIF":1.4,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642023","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 of <i>IRF1</i> as a Novel Pyroptosis-Related Prognostic Biomarker of Atopic Dermatitis.","authors":"Xin Liu, Yi Wang, Ruofan Xi, Dongjie Guo, Wanjun Guo, Linyan Cheng, Ting Du, Hanzhi Lu, Peiyao Wang, Yanjuan Duan, Jianyong Zhu, Fulun Li","doi":"10.1089/gtmb.2023.0264","DOIUrl":"10.1089/gtmb.2023.0264","url":null,"abstract":"<p><p><b><i>Purpose:</i></b> The aim of this study was to characterize key biomarkers associated with pyroptosis in atopic dermatitis (AD). <b><i>Materials and methods:</i></b> To identify the differentially expressed pyroptosis-related genes (DEPRGs), the gene expression profiles GSE16161 and GSE32924 from the Gene Expression Omnibus (GEO) database were utilized. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to determine the potential biological functions and involved pathways. Furthermore, protein-protein interaction network analyses were performed to identify hub genes. The types and proportions of infiltrating immune cells were detected by immune filtration analysis using CIBERSORT. A 12-axis competing endogenous RNA (ceRNA) network was constructed utilizing the miRNet database. Immunohistochemistry (IHC) further validated the differential expression of a key gene <i>IRF1</i> in the skin tissues collected from AD patients. The collection of skin tissue from human subjects in this study were reviewed and approved by the IRB of Yueyang Integrated Chinese and Western Medicine Hospital (KYSKSB2020-125). <b><i>Results:</i></b> The study identified a total of 76 DEPRGs, which were enriched in genes associated with the inflammatory response and immune regulation. There was a higher percentage of activated dendritic cells and a lower percentage of resting mast cells in AD samples. <i>PVT1</i> expression was associated with upregulation of hub genes including <i>CXCL8, IRF1, MKI67,</i> and <i>TP53</i> in the ceRNA network and was correlated with activated dendritic cells in AD. As a transcription factor, <i>IRF1</i> could regulate the production of downstream inflammatory factors. The IHC study revealed that <i>IRF1</i> was overexpressed in the skin tissues of AD patients, which were consistent with the results of the bioinformatic study. <b><i>Conclusions:</i></b> IRF1 and its related genes were identified as key pyroptosis-related biomarkers in AD, which is a crucial pathway in the pathogenesis of AD.</p>","PeriodicalId":12603,"journal":{"name":"Genetic testing and molecular biomarkers","volume":"27 12","pages":"370-383"},"PeriodicalIF":1.4,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139073847","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}