Biochemical Genetics最新文献

{"title":"First Insight into the Phylogenetic Diversity of Bovicola caprae Infesting Goats of Different Agro-climatic Locations in India.","authors":"Aman D Moudgil, Anil K Nehra, Ankur Sharma, Santosh Patel, Sukhdeep Vohra","doi":"10.1007/s10528-024-10886-3","DOIUrl":"https://doi.org/10.1007/s10528-024-10886-3","url":null,"abstract":"<p><p>Bovicola caprae is an important obligate ectoparasite of goats worldwide including India. The present study aimed at the molecular confirmation, phylogenetics and population structure analyses of B. caprae infesting goats of three different agro-climatic locations in India, by targeting the mitochondrial cytochrome C oxidase subunit 1 (cox1) genetic marker. The phylogenetic tree exhibited the presence of two different lineages of B. caprae. The sequences generated herein clustered in lineage 2 along with the GenBank™ archived sequences from China and Iran. The sequences generated herein also showed the circulation of sub-lineages of B. caprae in India based on the analysis of pairwise genetic distances between sequences and median-joining haplotype network. The population structure analyses revealed low nucleotide (0.00353 ± 0.00291 and 0.02694 ± 0.00363) and high haplotype (0.667 ± 0.314 and 0.618 ± 0.104) diversities for the present study isolates as well as for the complete dataset, respectively, which evinced a recent demographic expansion. High genetic differentiation (F_ST value = 0.97826) and low gene flow (N_m = 0.00556) were also recorded in the different lineages/populations. In conclusion, the present study addressed the research gap and provided the first insight into the phylogenetics of the goat louse B. caprae and highlighted the circulation of sub-lineages of the ectoparasite in India.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603139","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 HOXC Gene Family as Prognostic and Immune-Related Biomarkers in Breast Cancer Through mRNA Transcriptional Profile and Experimental Validation.","authors":"Xiongtao Cheng, Jie Luo, Jianxiong Cao","doi":"10.1007/s10528-024-10884-5","DOIUrl":"https://doi.org/10.1007/s10528-024-10884-5","url":null,"abstract":"<p><p>Breast cancer (BC) is the most common malignancy in women worldwide, and more effective biomarkers are urgently needed for the prevention and treatment of BC. Our study aimed to investigate the role of the HOXC gene family (HOXCs) and its relationship with the immune response in BC. The differential expression of HOXCs and its clinical prognostic significance in BC were explored using bioinformatics analysis, and the cBioPortal database was used to evaluate the genetic mutation profile of the HOXCs in BC. The results indicated that the expression levels of HOXC4, 10, 11, 12, and 13 were significantly increased in BC tissues compared with the normal tissues, and expressions of these genes were closely associated with BC stage, among them, high expression levels of HOXC10 and HOXC13 predicted poor outcome in BC patients. In addition, to elucidate the essential role of HOXCs in the tumor microenvironment and immunotherapeutic response of BC, the impact of HOXCs on the regulation of immune infiltration in BC was comprehensively assessed. The result showed that HOXC10 and HOXC13 expressions were significantly positively linked with the infiltration levels of CD8+T cell and M1 macrophage, while they were negatively related to Mast and Natural killer cells, suggesting the important influence of HOXCs on regulating tumor immunity in BC patients. Lastly, the RT-qPCR assay was employed to validate HOXCs expression in samples of BC patients. In conclusion, HOXCs may be a promising prognostic indicator and could regulate the immune infiltration in BC patients, thus being a promising targeted immunotherapy for BC.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589314","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":"Optimization of Total DNA Extraction from Dried Blood Samples.","authors":"Jeanne V Samsonova, Nikolay Yu Saushkin, Valery N Voronkova, Yuri A Stolpovsky, Aleksei K Piskunov","doi":"10.1007/s10528-024-10882-7","DOIUrl":"https://doi.org/10.1007/s10528-024-10882-7","url":null,"abstract":"<p><p>While dried blood spots are a convenient source of genetic material, they are usually associated with a lower DNA yield than from a native sample. The study evaluated the DNA yield from dried blood samples prepared on glass fibre and cellulose membranes and investigated the reasons for the yield reduction. The extraction of total DNA from membrane-dried blood samples was optimized by spin-column extraction method. It was shown that preliminary short-term (20 min) solubilization of a dried matrix in an aqueous medium, followed by standard extraction protocols for the mixture of the eluate with membranes, provides the highest DNA yield. The yield of DNA from a glass fibre membrane was 40-50% lower compared to a native sample, but on average, two times higher than from a conventional cellulose membrane (filter paper). The reduction of DNA yield when using a dried sample was found to be due to partial retention of nucleic acids by the membrane material during the lysis stage.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589315","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":"E2F1 Facilitates the Proliferation and Stemness of Gastric Cancer Cells by Activating CDC25B Transcription and Modulating the MAPK Pathway.","authors":"Ming Liu, Chaobo Xu, Guoxiong Cheng, Zhengwei Chen, Xiaoming Pan, Yijun Mei","doi":"10.1007/s10528-024-10864-9","DOIUrl":"https://doi.org/10.1007/s10528-024-10864-9","url":null,"abstract":"<p><p>Gastric cancer (GC) is a health problem that concerns people around the world. CDC25B is an essential cell cycle regulatory factor that is overexpressed in a variety of tumor cells. CDC25B plays a vital part in the progression and proliferation of malignant tumors. However, it is not yet clear that how CDC25B affects the stemness of GC cells. The study used bioinformatics to detect the expression of E2F1 and CDC25B in GC tissues and their correlation, as well as pathways enriched by CDC25B. We detected the expression of E2F1 and CDC25B in GC cell lines using quantitative reverse transcription polymerase chain reaction and tested the combination relationship between E2F1 and CDC25B using chromatin immunoprecipitation (ChIP) and dual-luciferase assays. We measured cell viability using CCK-8 assay, evaluated sphere-forming efficiency using sphere formation assay, and determined cell proliferation ability using colony formation assay. We also analyzed the expression of stemness markers and MAPK pathway-related proteins using western blot. In GC tissues and cells, CDC25B was upregulated. Silencing CDC25B could affect the MAPK pathway, thereby repressing the proliferation and stemness of GC cells. As predicted by bioinformatics, CDC25B had an upstream transcription factor, E2F1, which also had a high expression level in GC. Dual-luciferase and ChIP assays confirmed the combination relationship between the two. Rescue experiments uncovered that overexpression of CDC25B could reverse the impact induced by E2F1 knockdown on proliferation and stemness of cells. In conclusion, E2F1 could activate CDC25B transcription to regulate the MAPK pathway and enhance the proliferation and stemness of GC cells. We revealed a potential regulatory pathway of stemness of GC cells that was mediated by CDC25B, providing new ideas for improving and innovating GC treatment.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141562324","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":"New Variants Identified by Next-Generation Sequencing in Polycystic Kidney Disease Patients.","authors":"Pelin Ozyavuz Cubuk, Tugba Akin Duman","doi":"10.1007/s10528-024-10880-9","DOIUrl":"https://doi.org/10.1007/s10528-024-10880-9","url":null,"abstract":"<p><p>Polycystic kidney disease (PKD) is a common inherited disease characterized by multiple cysts in kidneys and various extra renal manifestations. Molecular diagnosis plays a crucial role in confirming both the clinical diagnosis and preimplantation genetic diagnosis furthermore, selecting appropriate treatment options. This study aimed to expand the understanding of genetic mutations in patients with polycystic kidney disease and to improve the management of patients. The study included 92 patients with a clinical diagnosis of PKD based on renal ultrasound criteria. Targeted next-generation sequencing was performed using a custom panel kit. Of the 92 patients included in the study, pathogenic/likely pathogenic variants of the PKD1, PKD2 genes were detected in 37 patients (40.2%), while 8 patients (8.6%) had variants with uncertain clinical significance. After the additional assessment of pathogenic/likely pathogenic variants, it was found that 15 of the variants in PKD1 and 2 of the variants in PKD2 have not been reported in the literature previously. Additionally, pathogenic variants, 5 of which were novel, have been identified in different genes in 8 patients. This study presented the largest patient cohort conducted in Turkey. These findings were significant in expanding our understanding of the genetic variations associated with polycystic kidney disease. The study contrıbuted the literature data on polycystic kidney disease by reporting important findings that could pave the way for further investigations in the diagnosis, treatment, and management of the affected patients.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544333","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":"CircFAM114A2 Suppresses Cell Proliferation, Migration, and Invasion of Colorectal Cancer Through Sponging miR-647 to Upregulate DAB2IP Expression.","authors":"Guanghao Huang, Dahua Sun, Xiaoli Hu, Qiushuang Wang","doi":"10.1007/s10528-024-10870-x","DOIUrl":"https://doi.org/10.1007/s10528-024-10870-x","url":null,"abstract":"<p><strong>Background: </strong>Increasing evidence had proved that some circular RNA (circRNA) exerted critical roles in tumors progression by functioning as \"microRNAs (miRNAs) sponges\" to regulate their targeted genes.</p><p><strong>Methods: </strong>circFAM114A2 and miR-647 expression was measured in CRC tissues and cells by quantitative real-time polymerase chain reaction (qRT-PCR), and the prognostic value of circFAM114A2 evaluated by Kaplan-Meier survival curve. Subsequently, wounding healing and transwell assays were performed to assess cell proliferation, migration, and invasion. RNA pull-down and dual-luciferase reporter assays were used to confirm the interactions between circFAM114A2, miR-647, and DAB2IP.</p><p><strong>Results: </strong>CircFAM114A2 was notably downregulated in CRC tissues and cells, and low circFAM114A2 expression indicated the poor prognosis of CRC patients. Next, overexpression of circFAM114A2 suppressed CRC cells proliferation, migration, and invasion in vitro and impede CRC tumor growth in vivo. Mechanically, circFAM114A2 competitively bound to miR-647 and upregulated its target gene DAB2IP expression in CRC cells.</p><p><strong>Conclusion: </strong>Our results indicated that circFAM114A2/miR-647/DAP2IP axis played an important role in CRC progression, suggesting that circFAM114A2 might be a novel therapeutic target in patients with CRC.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544332","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 Relationship Between GAPDH Gene Polymorphism and Risk of Acute Coronary Syndrome in South Indians with Type 2 Diabetes Mellitus.","authors":"Sushmita Bora, Prashant Shankarrao Adole, Kolar Vishwanath Vinod, Ajith Ananthakrishna Pillai, Shaheer Ahmed","doi":"10.1007/s10528-024-10881-8","DOIUrl":"https://doi.org/10.1007/s10528-024-10881-8","url":null,"abstract":"<p><p>As glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the regulators of carbonyl stress, a pathogenic mechanism for diabetic complications like acute coronary syndrome (ACS), the study aimed to investigate the relationship between GAPDH gene polymorphism, GAPDH activity in red blood cell (RBC), methylglyoxal (MG) levels in plasma and ACS risk in South Indians with type 2 diabetes mellitus (T2DM). This study comprised 150 T2DM with ACS as cases and 150 T2DM without ACS as controls. The GAPDH rs1136666, rs1060620 and rs1060619 gene polymorphisms were identified by TaqMan probe assays. The RBC GAPDH activity and plasma MG levels were estimated. Cases had significantly higher plasma MG levels and lower RBC GAPDH activity than controls (P < 0.001). The distribution of rs1060620 or rs1060619 alleles and genotypes significantly differed between groups. The rs1060620 AG (OR 0.55; 95% CI 0.33-0.92; P = 0.022) or rs1060619 CT (OR 0.51; 95% CI 0.31-0.83; P = 0.007) genotype was associated with reduced ACS risk, confirmed in the over-dominant genetic model. Haplotype analyses revealed that the GAT and CGC haplotypes were associated with increased (OR 28.37; 95% CI 3.82-210.49; P = 8.51 × 10^-7) and decreased (OR 0.45; 95% CI 0.24-0.86; P = 0.014) ACS risk in T2DM patients, respectively. Lower GAPDH activity was observed in the TT and CT genotypes compared to the CC genotype of rs1060619 (P < 0.001). This work established that the GAPDH rs1060620 or rs1060619 gene polymorphisms are associated with ACS risk in South Indians with T2DM.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141537355","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":"LncRNA BBOX1-AS1 Contributes to Laryngeal Carcinoma Progression by Recruiting SRSF1 to Maintain EFNB2 mRNA Stability.","authors":"Xiaowen Zhu, Xuan Li, MeiJia Zhang, Jian Ni","doi":"10.1007/s10528-024-10879-2","DOIUrl":"https://doi.org/10.1007/s10528-024-10879-2","url":null,"abstract":"<p><p>Laryngeal cancer is a common malignancy of the larynx with a generally poor prognosis. This study systematically assessed the functional role of lncRNA BBOX1-AS1 in laryngeal carcinoma progression and associated molecular regulatory mechanisms. The proliferation, migration, and invasion of laryngeal carcinoma cells were detected by Cell Counting Kit-8, wound healing, clonal formation, and transwell assays. In addition, the interaction between BBOX1-AS1, Serine/Arginine Splicing Factor 1 (SRSF1), and Ephrin-B2 (EFNB2) mRNA was examined employing RNA immunoprecipitation and RNA pull-down experiments. Furthermore, western blotting, and RT-qPCR assays were adopted to detect the expression levels of BBOX1-AS1, SRSF1, and EFNB2. The impact of BBOX1-AS1 and SRSF1 on EFNB2 mRNA stability was examined using the RNA stability assay. BBOX1-AS1 was highly expressed in human laryngeal carcinoma tissues and cell lines. BBOX1-AS1 knockdown suppressed the growth, proliferation, migration, and invasion of laryngeal carcinoma cells. BBOX1-AS1 maintained the stability of EFNB2 mRNA in laryngeal carcinoma cells by recruiting SRSF1. EFNB2 knockdown inhibited the growth and metastatic function of laryngeal carcinoma cells in vitro. EFNB2 overexpression reversed the influence of BBOX1-AS1 knockdown on laryngeal cancer tumorigenesis. BBOX1-AS1 maintained EFNB2 mRNA stability by recruiting SRSF1, thereby aggravating laryngeal carcinoma malignant phenotypes. BBOX1-AS1 might be a new theoretical target for the treatment of laryngeal carcinoma.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533194","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":"Exosomal miR-17-92 Cluster from BMSCs Alleviates Apoptosis and Inflammation in Spinal Cord Injury.","authors":"Wei Wang, Fei Yao, Haiyuan Xing, Fan Yang, Li Yan","doi":"10.1007/s10528-024-10876-5","DOIUrl":"https://doi.org/10.1007/s10528-024-10876-5","url":null,"abstract":"<p><p>Spinal cord injury (SCI) involves neuronal apoptosis and axonal disruption, leading to severe motor dysfunction. Studies indicate that exosomes transport microRNAs (miRNAs) and play a crucial role in intercellular communication. This study aimed to explore whether the bone marrow mesenchymal stem cell (BMSCs)-exosomal miR-17-92 cluster can protect against SCI and to explain the underlying mechanisms. In vivo and in vitro SCI models were established and treated with control exosomes (con-exo) or exosomes derived from BMSCs transfected with miR-17-92 cluster plasmid (miR-17-92-exo). Rat BMSCs were isolated and positive markers were identified by flow cytometry. BMSC-derived exosomes were extracted and verified using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and western blotting. The expression of the miR-17-92 cluster was validated by quantitative reverse transcription PCR (qRT-PCR). Spinal cord function, histopathological changes, apoptotic cells, and inflammatory cytokines release in spinal cord tissues were assessed using the Basso-Beattie-Bresnahan (BBB) score, hematoxylin and eosin (HE) staining, terminal deoxynucleotide transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) staining, enzyme-linked immunosorbent assay (ELISA), and qRT-PCR. In PC12 cells, cell proliferation, apoptosis, apoptosis-related proteins cleaved-Caspase3 expression, and inflammatory factors secretion were analyzed using a cell counting kit-8 (CCK8) assay, flow cytometry, western blotting, and ELISA. Our data revealed that the exosomes were successfully isolated from rat BMSCs. The BMSC-exosomal miR-17-92 cluster improved neural functional recovery after SCI, as evidenced by an increased BBB score, improved pathological damage, reduced neuronal apoptosis, and decreased inflammatory factors release. Additionally, miR-17-92-exo treatment significantly inhibited lipopolysaccharide (LPS)-induced reduction in cell viability, increase in cell apoptosis, and upregulation of inflammatory factors in PC12 cells. The exosomal miR-17-92 cluster derived from BMSCs improved functional recovery and exhibited neuroprotective effects in SCI by alleviating apoptosis and inflammation.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141496703","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":"Correction: Hypermethylation of BMPR2 and TGF-β Promoter Regions in Tibetan Patients with High-Altitude Polycythemia at Extreme Altitude.","authors":"Quzong Zhaxi, Luobu Gesang, Ju Huang, Yangzong Suona, Bai Ci, Zhuoga Danzeng, Rui Zhang, Binyun Liu","doi":"10.1007/s10528-024-10877-4","DOIUrl":"https://doi.org/10.1007/s10528-024-10877-4","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490366","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}