Folia Biologica最新文献

CD8+ T-Cell Signatures as Prognostic and Immunotherapy Response Predictors in Non-Small Cell Lung Cancer. CD8+ t细胞特征作为非小细胞肺癌的预后和免疫治疗反应预测因子。

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070040196

Tienan Zhao, Sarinder Kaur Dhillon

{"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":"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.","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}

引用次数: 0

Heat Shock Protein Network: the Mode of Action, the Role in Protein Folding and Human Pathologies. 热休克蛋白网络：作用模式，在蛋白质折叠和人类病理中的作用。

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070030152

Aleksandr Melikov, Petr Novák

引用次数: 0

Dyslipidaemia in Liver Diseases.

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070050239

Jiří Hlušička, Aleš Žák

{"title":"Dyslipidaemia in Liver Diseases.","authors":"Jiří Hlušička, Aleš Žák","doi":"10.14712/fb2024070050239","DOIUrl":"https://doi.org/10.14712/fb2024070050239","url":null,"abstract":"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.","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}

引用次数: 0

Taurine Improved Autism-Like Behaviours and Defective Neurogenesis of the Hippocampus in BTBR Mice through the PTEN/mTOR/AKT Signalling Pathway. 牛磺酸可通过 PTEN/mTOR/AKT 信号通路改善 BTBR 小鼠的自闭症样行为和海马神经发生缺陷。

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070010045

Huang Xiaoyan, Yang Zhaoxi, Zhang Lingli, Chen Jinyuan, Qin Wen

{"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":"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.","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}

引用次数: 0

Effect of Cryoprotectants on Long-Term Storage of Oral Mucosal Epithelial Cells: Implications for Stem Cell Preservation and Proliferation Status. 冷冻保护剂对口腔黏膜上皮细胞长期保存的影响：对干细胞保存和增殖状态的影响。

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070040209

Joao Victor Cabral, Natálie Smorodinová, Eleni Voukali, Lukáš Balogh, Tomáš Kučera, Vojtěch Kolín, Pavel Studený, Tomáš Vacík, Kateřina Jirsová

{"title":"Effect of Cryoprotectants on Long-Term Storage of Oral Mucosal Epithelial Cells: Implications for Stem Cell Preservation and Proliferation Status.","authors":"Joao Victor Cabral, Natálie Smorodinová, Eleni Voukali, Lukáš Balogh, Tomáš Kučera, Vojtěch Kolín, Pavel Studený, Tomáš Vacík, Kateřina Jirsová","doi":"10.14712/fb2024070040209","DOIUrl":"https://doi.org/10.14712/fb2024070040209","url":null,"abstract":"In this study, we tested a method for long-term storage of oral mucosal epithelial cells (OMECs) so that the cells could be expanded in vitro after cryopreservation and used for the treatment of bilateral limbal stem cell deficiency. The ability of suspended primary OMECs to proliferate in vitro after cryopreservation was compared to that of OMEC cultures that had undergone the same process. Both were preserved in standard complex medium (COM) with or without cryoprotective agents (CPAs) (gly-cerol at 5 % or 10 % or dimethyl sulphoxide at 10 %). We found that after cryopreservation, primary OMECs could form a confluent cell sheet only in a few samples after 22 ± 2.9 (mean ± SD) days of cultivation with 72.4 % ± 12.9 % overall viability. Instead, all ex vivo OMEC cultures could re-expand after cryopreservation with a comparable viability of 78.6 ± 13.8 %, like primary OMECs, but with significantly faster growth rate (adj. P < 001), forming a confluent cell sheet at 13.7 ± 3.9 days. Gene expression analyses of the ex vivo expansion of OMEC cultures showed that the stemness, proliferation and differentiation-related gene expression was similar before and after cryopreservation, except for KRT13 expres-sion, which significantly decreased after the second passage (adj. P < 0.05). The addition of CPAs had no effect on these outcomes. In conclusion, the optimal strategy for OMEC preservation is to freeze the cells that have been previously cultured, in order to maintain cell viability and the capacity to create a sizable graft even without CPAs.","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 4","pages":"209-218"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846186","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}

引用次数: 0

Serum Biomarkers in Diagnosis and Clinical Management of Inflammatory Bowel Disease: Anything New on the Horizon?

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070050248

Juraj Ondriš, Rastislav Husťak, Juraj Ďurina, Eva Malicherová Jurková, Vladimír Bošák

{"title":"Serum Biomarkers in Diagnosis and Clinical Management of Inflammatory Bowel Disease: Anything New on the Horizon?","authors":"Juraj Ondriš, Rastislav Husťak, Juraj Ďurina, Eva Malicherová Jurková, Vladimír Bošák","doi":"10.14712/fb2024070050248","DOIUrl":"https://doi.org/10.14712/fb2024070050248","url":null,"abstract":"Persistent inflammation in inflammatory bowel disease (IBD) leads to progressive damage to the gastrointestinal tract, resulting in potentially severe sequelae. Diagnosis primarily relies on invasive endoscopy and monitoring of faecal calprotectin (FC), which has limitations, particularly regarding patient compliance. There is a pressing need for a new biomarker that is non-invasive, easily determinable, and possesses good diagnostic accuracy for both dia-gnosing and monitoring IBD. Our narrative review covers the latest developments in novel serum biomarkers, focusing on those with promising diagnostic accuracy and laboratory methods, and evaluates them in the context of established biomarkers such as FC and CRP. Serum calprotectin (SC) and leucine-rich alpha-2 glycoprotein (LRG) show the most extensive evidence and relatively good diagnostic accuracy but currently cannot replace FC due to insufficient evidence. Major limitations of the analysed studies include their monocentric nature, small sample sizes, lack of longitudinal monitoring and in some cases, missing assessments of endoscopic activity. ELISA holds a leading position among the laboratory methods; however, emerging evidence supports the potential use of point-of-care testing (POCT). Establishing these biomarkers for regular clinical application will require further validation through multicentric studies involving a larger number of patients with a longitudinal design, concurrent assessment of endoscopic activity and pro-active monitoring of the biomarker. However, based on the evidence accumulated so far, SC might potentially serve as a complementary biomarker and/or in assessing the activity of extraintestinal manifestations in IBD patients, while LRG appears to be effective in evaluating endoscopic activity, especially in small bowel CD.","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 5-6","pages":"248-261"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070839","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}

引用次数: 0

Down-regulation of lncRNA EMX2OS Is Associated with the Prognosis of Patients with Cervical Squamous Cell Carcinoma and Regulates Tumour Cell Progression via miR-574-5p.

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070050262

Quan Cheng, Ting Hu, Wenhui Zhang, Wei Shang, Jinwei Cao, Huijuan Zhao, Haiyan Wang

{"title":"Down-regulation of lncRNA EMX2OS Is Associated with the Prognosis of Patients with Cervical Squamous Cell Carcinoma and Regulates Tumour Cell Progression via miR-574-5p.","authors":"Quan Cheng, Ting Hu, Wenhui Zhang, Wei Shang, Jinwei Cao, Huijuan Zhao, Haiyan Wang","doi":"10.14712/fb2024070050262","DOIUrl":"https://doi.org/10.14712/fb2024070050262","url":null,"abstract":"Cervical squamous cell carcinoma (CSCC) represents a malignant subtype of cervical cancer. Identification of novel biomarkers for CSCC development could enhance therapeutic efficiency and improve the patients' outcomes. This study focused on lncRNA EMX2OS, evaluating its expression and significance in the progression of CSCC while exploring its potential as a therapeutic target. A cohort of 135 patients with CSCC were enrolled, and tissue samples were collected for analysis. The expression of EMX2OS in the tissues was quantified by PCR, with its correlation to the clinicopathological features, and prognosis was evaluated by χ2, Kaplan-Meier and Cox regression analyses. The regulatory effects of EMX2OS on CSCC cells were investigated by CCK8 and Transwell assays, while the underlying molecular mechanisms were elucidated by luciferase reporter assays. Significant down-regulation of EMX2OS was observed in CSCC, correlating with advanced FIGO stages, poor differentiation and adverse prognosis of patients. Over-expression of EMX2OS significantly suppressed cell growth and metastasis in CSCC. Negative regulation of miR-574-5p by EMX2OS was observed, and over-expression of miR-574-5p alleviated the inhibition of CSCC cells by EMX2OS. Down-regulated EMX2OS indicates severe disease progression and poor prognosis in CSCC. Over-expression of EMX2OS could inhibit CSCC cell growth and metastasis by negatively modulating miR-574-5p.","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 5-6","pages":"262-269"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070798","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}

引用次数: 0

circRACGAP1 Promotes Proliferation of Non-Small Cell Lung Cancer Cells through the miR-1296/CDK2 Pathway. circRACGAP1 通过 miR-1296/CDK2 通路促进非小细胞肺癌细胞增殖

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070020104

Yang Zhao, Liyong Deng, Yi Xie, Weiming Wang, Qin Chai, Guihua Wang

{"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":"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.","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}

引用次数: 0

Integrating Lysosomal Genes and Immune Infiltration for Multiple Myeloma Subtyping and Prognostic Stratification. 整合溶酶体基因和免疫渗透，进行多发性骨髓瘤亚型和预后分层。

IF 1.1 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070020085

Shu Deng, Jingjing Xiangang, Zhiyin Zheng, Jianping Shen

{"title":"Integrating Lysosomal Genes and Immune Infiltration for Multiple Myeloma Subtyping and Prognostic Stratification.","authors":"Shu Deng, Jingjing Xiangang, Zhiyin Zheng, Jianping Shen","doi":"10.14712/fb2024070020085","DOIUrl":"https://doi.org/10.14712/fb2024070020085","url":null,"abstract":"Lysosomes are crucial in the tumour immune microenvironment, which is essential for the survival and homeostasis in multiple myeloma (MM). Here, we aimed to identify lysosome-related genes for the prognosis of MM and predicted their regulatory mechanisms. Gene expression profiles of MM from the GSE2658 and GSE57317 datasets were analysed. Lysosome-related differentially expressed genes (DEGs) were identified and used for molecular subtyping of MM patients. A prognostic model was constructed using univariate Cox regression and LASSO regression analyses. The relationship between prognostic genes, immune cell types, and autophagy pathways was assessed through correlation analysis. RT-qPCR was performed to validate the expression of prognostic genes in MM cells. A total of 9,954 DEGs were identified between high and low immune score groups, with 213 intersecting with lysosomal genes. Molecular subtyping revealed two distinct MM subtypes with significant differences in immune cell types and autophagy pathway activities. Five lysosome-related DEGs (CORO1A, ELANE, PSAP, RNASE2, and SNAPIN) were identified as significant prognostic markers. The prognostic model showed moderate predictive accuracy with AUC values up to 0.723. Prognostic genes demonstrated significant correlations with various immune cell types and autophagy pathways. Additionally, CORO1A, PSAP and RNASE2 expression was up-regulated in MM cells, while ELANE and SNAPIN were down-regulated. Five lysosomal genes in MM were identified, and a new risk model for prognosis was developed using these genes. This research could lead to discovering important gene markers for the treatment and prognosis of MM.","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 2","pages":"85-94"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132186","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}

引用次数: 0

Parallel DNA/RNA NGS Using an Identical Target Enrichment Panel in the Analysis of Hereditary Cancer Predisposition. 在遗传性癌症易感性分析中使用同源靶标富集面板的平行 DNA/RNA NGS。

IF 0.6 4区医学

Folia Biologica Pub Date : 2024-01-01 DOI: 10.14712/fb2024070010062

Petra Kleiblová, Marta Černá, Petra Zemánková, Kateřina Matějková, Petr Nehasil, Jan Hojný, Klára Horáčková, Markéta Janatová, Jana Soukupová, Barbora Šťastná, Zdeněk Kleibl

{"title":"Parallel DNA/RNA NGS Using an Identical Target Enrichment Panel in the Analysis of Hereditary Cancer Predisposition.","authors":"Petra Kleiblová, Marta Černá, Petra Zemánková, Kateřina Matějková, Petr Nehasil, Jan Hojný, Klára Horáčková, Markéta Janatová, Jana Soukupová, Barbora Šťastná, Zdeněk Kleibl","doi":"10.14712/fb2024070010062","DOIUrl":"https://doi.org/10.14712/fb2024070010062","url":null,"abstract":"Germline DNA testing using the next-gene-ration sequencing (NGS) technology has become the analytical standard for the diagnostics of hereditary diseases, including cancer. Its increasing use places high demands on correct sample identification, independent confirmation of prioritized variants, and their functional and clinical interpretation. To streamline these processes, we introduced parallel DNA and RNA capture-based NGS using identical capture panel CZECANCA, which is routinely used for DNA analysis of hereditary cancer predisposition. Here, we present the analytical workflow for RNA sample processing and its analytical and diagnostic performance. Parallel DNA/RNA analysis allowed credible sample identification by calculating the kinship coefficient. The RNA capture-based approach enriched transcriptional targets for the majority of clinically relevant cancer predisposition genes to a degree that allowed analysis of the effect of identified DNA variants on mRNA processing. By comparing the panel and whole-exome RNA enrichment, we demonstrated that the tissue-specific gene expression pattern is independent of the capture panel. Moreover, technical replicates confirmed high reproducibility of the tested RNA analysis. We concluded that parallel DNA/RNA NGS using the identical gene panel is a robust and cost-effective diagnostic strategy. In our setting, it allows routine analysis of 48 DNA/RNA pairs using NextSeq 500/550 Mid Output Kit v2.5 (150 cycles) in a single run with sufficient coverage to analyse 226 cancer predisposition and candidate ge-nes. This approach can replace laborious Sanger confirmatory sequencing, increase testing turnaround, reduce analysis costs, and improve interpretation of the impact of variants by analysing their effect on mRNA processing.","PeriodicalId":12281,"journal":{"name":"Folia Biologica","volume":"70 1","pages":"62-73"},"PeriodicalIF":0.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237164","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}

引用次数: 0