Folia Biologica最新文献

{"title":"Semi-automated RNA Isolation from Tempus Blood RNA Tubes Using the Magcore Plus II Instrument.","authors":"Marta Černá, Barbora Šťastná, Pavel Pešek, Taťána Ptáčková, Markéta Janatová, Jana Soukupová, Klára Horáčková, Petra Kleiblová","doi":"10.14712/fb2025071020088","DOIUrl":"https://doi.org/10.14712/fb2025071020088","url":null,"abstract":"<p><p>High-throughput, precise and cost-effective isolation of high-quality RNA is essential for the growing number of RNA-based next-generation sequencing (NGS) analyses. Manual RNA isolation provides sufficient quality but requires significant hands-on time and carries an increased risk of contamination and sample misidentification. Here we describe a semi-automated protocol for the isolation of high-quality total RNA from 3 ml of peripheral blood collected in Tempus Blood RNA Tubes. The isolation can be performed either from the total volume of 9 ml of Tempus blood lysate or from smaller volumes (6 and 3 ml, respectively) using the MagCore triXact RNA Kit on the MagCore Plus II automated nucleic acid extractor, which allows RNA isolation in single tubes. The original isolation protocol (#631) for whole blood RNA isolation was customized by the manufacturer (#631T) by omitting the cell lysis step. After optimizing the process, we compared the yield and quality of 760 RNA samples isolated manually or by semi-automated methods. We conclude that RNA isolation using the semi-automated MagCore protocol yields 5-10 μg of total RNA from 6 ml of lysate (2 ml of peripheral blood), which is almost comparable in quantity and quality to manual isolation. In addition, we show that the remaining 3 ml of lysate is sufficient for backup re-isolation. Our semi-automated RNA protocol reduces hands-on time without increasing costs and yields bulky total RNA of a quali-ty suitable for subsequent RNA NGS applications.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"71 2","pages":"88-94"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Clinical Significance and Mechanistic Role of the LINC00487/hsa-miR-663b Axis in Cell Line Models of Acute Lung Injury.","authors":"Xixiang Yan, Ziqi Xie, Xiaoye Zheng, Qing Xie, Junle Yang, Xiaojuan Wu","doi":"10.14712/fb2025071020079","DOIUrl":"https://doi.org/10.14712/fb2025071020079","url":null,"abstract":"<p><p>Acute lung injury (ALI) is a serious lung disease that tends to progress to acute respiratory distress syndrome (ARDS). This study was aimed to seek new biomarkers of ALI to provide a basis for monitoring the progress of ALI in time. A human bronchial epithelial cell line (HBEC3-KT) was treated with 1 μg/ml lipopolysaccharide (LPS) to induce the ALI response. The expression of LINC00487 and hsa-miR-663b in LPS-treated HBEC3-KT cells was detected by RT-qPCR. The regulation of hsa-miR-663b by LINC00487 was investigated using a dual luciferase assay and an over-expression experiment. Cell proliferation and apoptosis were detected by the CCK-8 assay and annexin V-FITC kit. Serum levels of LINC00487 and hsa-miR-663b were detected by collecting blood samples from ALI patients (with or without ARDS), and the ROC curve was constructed to assess their clinical value in ALI. LPS inhibited proliferation of HBEC3-KT cells and promoted their apoptosis and inflammatory response, which were further enhanced by LINC00487 over-expression and reversed by an hsa-miR-663b mimic. The hsa-miR-663b mimic weakened the luciferase activity of HBEC3-KT cells transfected with the luciferase vector of wild-type LINC00487. The cellular level of hsa-miR-663b was down-regulated by LINC00487 over-expression and increased by LINC00487 knockdown. The ROC curve showed that LINC00487 combined with hsa-miR-663b effectively diagnosed ALI (AUC = 0.840) and was a classifier for ALI patients with or without ARDS (AUC = 0.822). Serum LINC00487 and hsa-miR-663b levels are valuable biomarkers of ALI and can monitor the ALI progress. LINC00487 may promote ALI progression by negatively regulating hsa-miR-663b.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"71 2","pages":"79-87"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selected Genetic Characteristics of the Vietnamese Minority Living in the Czech Republic.","authors":"Khanh Ha Pham, Jaroslav A Hubáček","doi":"10.14712/fb2025071010001","DOIUrl":"https://doi.org/10.14712/fb2025071010001","url":null,"abstract":"<p><p>The aim of this study was to analyse the allelic distribution of selected genes in the Czech and Vietnamese populations. We analysed samples from 94 Vietnamese volunteers and 2,859 Czech population-based subjects (2,559 from the Czechs post-MONICA and 300 volunteers from the South region of the Czech Republic). There were significant differences between the two populations for most, but not all, of the SNPs analysed. In particular, the prevalence of risk alleles in the analysed polymorphisms tended to be lower in the Vietnamese community compared to the Czech population, especially within the FTO (rs17817449; associated with obesity risk, P &lt; 0.0001), TCF7L2 (rs7903146; linked to type 2 dia-betes, P &lt; 0.0001) and ADH1B (rs1229984; related to alcohol consumption, P &lt; 0.0001) genes. The genotype within the MCM6/LCT cluster (rs4988235) associated with lactase persistence was not present in the Vietnamese population. Slight genotype differences were detected for one HFE polymorphism (rs1799945 with P = 0.005; but not for rs1800562). Only the genotype frequencies within the MC4R and APOE genes were almost identical in both populations. We conclude that the Vietnamese population may have a lower genetic predisposition to the non-communicable diseases such as obesity or diabetes mellitus.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"71 1","pages":"1-7"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and Technical Validation of the Clinical Lymphoma Exploration and Research Sequencing (CLEARS) Panel and Its Optimization for ctDNA Analysis.","authors":"Iva Hamová, Adriana Velasová, Petra Zemánková, Petr Nehasil, Kristýna Kupcová, Jana Soukupová, Markéta Janatová, Milena Hovhannisyan, Jana Seňavová, Anton Tkachenko, Marek Trněný, Ondřej Havránek","doi":"10.14712/fb2025.0009","DOIUrl":"https://doi.org/10.14712/fb2025.0009","url":null,"abstract":"<p><p>Circulating tumour DNA (ctDNA) is a potential biomarker for the assessment of prognosis and treatment response in lymphoma patients. However, there is still a lack of standardization of ctDNA analysis. Here, we present the development of our Clinical Lymphoma Exploration And Research Sequencing (CLEARS) panel for cancer personalized profiling by deep sequencing (CAPP-Seq), together with optimization of sequencing library preparation for ctDNA analysis. The CLEARS panel targets coding sequences of 521 genes most frequently altered in lymphomas, with its main purpose to analyse ctDNA. We tested its performance, determined the optimal workflow for cell‑free DNA (cfDNA) pre-capture sample library preparation, and confirmed our ability to achieve sufficient variant allele frequency detection limit for baseline ctDNA evaluation. Reported technical considerations and optimization results could further help standardize preparation of sequencing libraries from cfDNA samples.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"71 5-6","pages":"244-255"},"PeriodicalIF":0.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hsa_circ_0000977 Sponges miR-338-3p to Drive Cholangiocarcinoma Progression and Predict Poor Prognosis.","authors":"Shanshan Zhou, Chengcheng Ying, Guanbao Long, Zouxiao Hu, Jiangyang Sun","doi":"10.14712/fb2025.0002","DOIUrl":"https://doi.org/10.14712/fb2025.0002","url":null,"abstract":"<p><p>With a dismal prognosis, cholangiocarcinoma (CCA) is a highly invasive cancer and its global incidence is increasing. Non-coding RNAs, particularly circRNAs, are increasingly recognized as important regulators in tumorigenesis, yet the mechanistic details of hsa_circ_0000977-mediated miR-338-3p regulation in CCA remain incompletely understood. This study aimed to investigate the mechanism of the hsa_circ_0000977/miR-338-3p/ETS1 axis in CCA progression, evaluate its prognostic significance and investigate its functional role in CCA cells. Real-time quantitative PCR (RT-qPCR) was performed to quantify hsa_circ_0000977, miR-338-3p and ETS1 mRNA expression levels. Pearson correlation was used to assess their association. To confirm the molecular interactions between these molecules, dual-luciferase reporter assays were employed. Cell migration capacity was evaluated via Transwell migration assays, while CCK-8 tests analysed proliferation. Prognostic value was assessed through survival analysis and multi-variate regression. The study revealed significant up-regulation of hsa_circ_0000977 in CCA tumour tissues, with elevated expression levels associated with poorer 5-year survival outcomes. Multivariate analysis confirmed that hsa_circ_0000977 over-expression is an independent predictor of survival. Functional assays indicated that hsa_circ_0000977 negatively regulated miR-338-3p, which was down-regulated in CCA and exhibited tumour-suppressive effects. CCA cell proliferation and migration were suppressed following hsa_circ_0000977 knockdown, effects that were partially reversed by miR-338-3p inhibition. Further investigation demonstrated that miR-338-3p exerts its tumour-suppressive effects by directly targeting ETS1, and the hsa_circ_0000977/miR-338-3p/ETS1 axis regulates the proliferation and migration of CCA cells. We have concluded that hsa_circ_0000977 drives CCA progression by sponging miR-338-3p and modulating its target ETS1, suggesting its clinical value for predicting outcomes and developing targeted therapies.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"71 4","pages":"162-170"},"PeriodicalIF":0.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145862531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dyslipidaemia in Liver Diseases.","authors":"Jiří Hlušička, Aleš Žák","doi":"10.14712/fb2024070050239","DOIUrl":"https://doi.org/10.14712/fb2024070050239","url":null,"abstract":"<p><p>The liver is the central organ in lipid metabolism and plays a key role in a variety of biochemical processes. It is involved in lipoprotein synthesis, fatty acid beta oxidation, ketone body production, cholesterol synthesis, bile production, and storage and mobilization of lipids. Metabolic diseases such as obesity, type 2 diabetes mellitus and certain dyslipidaemias can lead to chronic liver conditions, especially non-alcoholic fatty liver disease. Conversely, chronic liver diseases such as liver cirrhosis and chronic cholestasis can induce dyslipidaemias. This review provides a comprehensive biochemical and clinical overview of the intricate relationship between the lipid-lipoprotein metabolism and chronic liver diseases, including non-alcoholic fatty liver disease, cholestasis, alcohol-related liver disease, viral hepatitis and cirrhosis, all of which have been selected due to their importance in current clinical practice. These conditions not only affect liver function but also have widespread metabolic implications critical for patient management and therapeutic strategies. In addition to discussing the clinical manifestations and pathophysiology of liver diseases, this review delves into the genetic and non-genetic factors that influence their development and progression. By bridging clinical observations with biochemical me-chanisms, this review aims to improve the understan-ding of how lipid metabolism disorders contribute to chronic liver diseases and to identify potential targets for therapeutic intervention.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 5-6","pages":"239-247"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CD8+ T-Cell Signatures as Prognostic and Immunotherapy Response Predictors in Non-Small Cell Lung Cancer.","authors":"Tienan Zhao, Sarinder Kaur Dhillon","doi":"10.14712/fb2024070040196","DOIUrl":"https://doi.org/10.14712/fb2024070040196","url":null,"abstract":"<p><p>Non-small cell lung carcinoma (NSCLC) represents the majority of lung cancer cases, comprising approximately 85 % of the total. The five-year survival rate for NSCLC patients remains discouragingly low. Recently, immunotherapy has emerged as a promising approach. Nevertheless, only a minority of patients experience considerable benefits from these treatments. This highlights the critical need for effective biomarkers that can predict both patient prognosis and response to immunotherapy. CD8+ T cells play a crucial role in cancer immunotherapy. Their presence within tumours is generally indicative of a favourable prognosis and increased efficacy of immunotherapy. This study was undertaken to identify and authenticate a novel biomarker signature based on CD8+ T-cell marker genes, to prognosticate therapeutic responses in individuals afflicted with NSCLC. This in-depth study was based on a total of 1,200 samples, which included four NSCLC specimens analysed through single-cell RNA sequencing (scRNA-seq), 1,000 NSCLC samples obtained from The Cancer Genome Atlas (TCGA) and 196 NSCLC specimens collected from the GSE37745 cohort. In patients with NSCLC, those presenting a favourable risk profile demonstrated notable elevations in specific immune cells while concurrently exhibiting reductions in other types. CD8+ T cells, with their established role in inducing apoptosis in cancer cells, have emerged as crucial predictors and modulators of treatment strategies for NSCLC patients. The combination of single-cell and bulk RNA sequencing has produced a biomarker signature, emphasizing the CD8+ T cells' crucial role in NSCLC prognosis and treatment.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 4","pages":"196-208"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heat Shock Protein Network: the Mode of Action, the Role in Protein Folding and Human Pathologies.","authors":"Aleksandr Melikov, Petr Novák","doi":"10.14712/fb2024070030152","DOIUrl":"https://doi.org/10.14712/fb2024070030152","url":null,"abstract":"<p><p>Protein folding is an extremely complicated process, which has been extensively tackled during the last decades. In vivo, a certain molecular machinery is responsible for assisting the correct folding of proteins and maintaining protein homeostasis: the members of this machinery are the heat shock proteins (HSPs), which belong among molecular chaperones. Mutations in HSPs are associated with several inherited diseases, and members of this group were also proved to be involved in neurodegenerative pathologies (e.g., Alzheimer and Parkinson diseases), cancer, viral infections, and antibiotic resistance of bacteria. Therefore, it is critical to understand the principles of HSP functioning and their exact role in human physiology and pathology. This review attempts to briefly describe the main chaperone families and the interplay between individual chaperones, as well as their general and specific functions in the context of cell physiology and human diseases.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 3","pages":"152-165"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taurine Improved Autism-Like Behaviours and Defective Neurogenesis of the Hippocampus in BTBR Mice through the PTEN/mTOR/AKT Signalling Pathway.","authors":"Huang Xiaoyan, Yang Zhaoxi, Zhang Lingli, Chen Jinyuan, Qin Wen","doi":"10.14712/fb2024070010045","DOIUrl":"10.14712/fb2024070010045","url":null,"abstract":"<p><p>Effective treatment of patients with autism spectrum disorder (ASD) is still absent so far. Taurine exhibits therapeutic effects towards the autism-like behaviour in ASD model animals. Here, we determined the mechanism of taurine effect on hippocampal neurogenesis in genetically inbred BTBR T+ tf/J (BTBR) mice, a proposed model of ASD. In this ASD mouse model, we explored the effect of oral taurine supplementation on ASD-like behaviours in an open field test, elevated plus maze, marble burying test, self-grooming test, and three-chamber test. The mice were divided into four groups of normal controls (WT) and models (BTBR), who did or did not receive 6-week taurine supplementation in water (WT, WT+ Taurine, BTBR, and BTBR+Taurine). Neurogenesis-related effects were determined by Ki67 immunofluorescence staining. Western blot analysis was performed to detect the expression of phosphatase and tensin homologue deleted from chromosome 10 (PTEN)/mTOR/AKT pathway-associated proteins. Our results showed that taurine improved the autism-like behaviour, increased the proliferation of hippocampal cells, promoted PTEN expression, and reduced phosphorylation of mTOR and AKT in hippocampal tissue of the BTBR mice. In conclusion, taurine reduced the autism-like behaviour in partially inherited autism model mice, which may be associa-ted with improving the defective neural precursor cell proliferation and enhancing the PTEN-associated pathway in hippocampal tissue.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 1","pages":"45-52"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"circRACGAP1 Promotes Proliferation of Non-Small Cell Lung Cancer Cells through the miR-1296/CDK2 Pathway.","authors":"Yang Zhao, Liyong Deng, Yi Xie, Weiming Wang, Qin Chai, Guihua Wang","doi":"10.14712/fb2024070020104","DOIUrl":"10.14712/fb2024070020104","url":null,"abstract":"<p><p>Circular RNAs (circRNAs) have played an essential role in cancer development. This study aimed to illustrate the impact and potential mechanism of circRACGAP1 action in NSCLC development. The expression patterns of circRACGAP1, miR-1296, and CDK2 in NSCLC tissues and cell lines were analysed by RT-qPCR. The function of circRACGAP1 in NSCLC cell proliferation and apoptosis was investigated using the CCK-8 assay, flow cytometry, TUNEL staining, and Western blot. The interaction among circRACGAP1, miR-1296, and CDK2 was clarified by dual-luciferase reporter assay while the correlation was confirmed by the Pearson correlation coefficient. The expression of circRACGAP1 and CDK2 was up-regulated in NSCLC tissues, while the expression of miR-1296 was down-regulated. Cell function studies further revealed that circRACGAP1 could promote NSCLC cell proliferation, accelerate the cell cycle process, up-regulate B-cell lymphoma 2 (Bcl2) expression, and down-regulate Bcl2-associated X (Bax) expression. miR-1296 was identified as a downstream target to reverse circRACGAP1-mediated cell proliferation. miR-1296 directly targeted the 3'-UTR of CDK2 to regulate proliferation and apoptosis of NSCLC cells. Additionally, the dual-luciferase reporter assay and Pearson correlation coefficient analysis proved that circRACGAP1 acted in NSCLC cells by negatively regulating miR-1296 expression and positively regulating CDK2 expression. In summary, our study revealed that circRACGAP1 promoted NSCLC cell proliferation by regulating the miR-1296/CDK2 pathway, providing potential diagnostic and therapeutic targets for NSCLC.</p>","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 2","pages":"104-112"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}