Frontiers in bioscience (Scholar edition)最新文献

{"title":"Evaluation of Reference Gene Stability for Investigations of Intracellular Signalling in Human Cancer and Non-Malignant Mesenchymal Stromal Cells.","authors":"Vera Kosheverova, Alexander Schwarz, Rimma Kamentseva, Marianna Kharchenko, Elena Kornilova","doi":"10.31083/j.fbs1604026","DOIUrl":"https://doi.org/10.31083/j.fbs1604026","url":null,"abstract":"<p><strong>Background: </strong>Real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a powerful tool for analysing target gene expression in biological samples. To achieve reliable results by RT-qPCR, the most stable reference genes must be selected for proper data normalisation, particularly when comparing cells of different types. We aimed to choose the least variable candidate reference genes among eight housekeeping genes tested within a set of human cancer cell lines (HeLa, MCF-7, SK-UT-1B, A549, A431, SK-BR-3), as well as four lines of normal, non-malignant mesenchymal stromal cells (MSCs) of different origins.</p><p><strong>Methods: </strong>The reference gene stability was evaluated using four algorithms (BestKeeper, NormFinder, geNorm and the comparative ΔCt method) and ranked with the RefFinder web-based tool.</p><p><strong>Results: </strong>We found increased variability in the housekeeping genes' expression in the cancer cell lines compared to that in normal MSCs. <i>POP4</i> and <i>GAPDH</i> were identified as the most suitable reference genes in cancer cells, while <i>18S</i> and <i>B2M</i> were the most suitable in MSCs. <i>POP4</i> and <i>EIF2B1</i> were shown to be the least variable genes when analysing normal and cancer cell lines together. Epidermal growth factor receptor (EGFR) mRNA relative expression was normalised by the three most stable or three least stable reference genes to demonstrate the reliability of reference genes validation.</p><p><strong>Conclusion: </strong>We analysed and selected stable reference genes for RT-qPCR analysis in the wide panel of cancer cell lines and MSCs. The study provides a reliable tool for future research concerning the expression of genes involved in various intracellular signalling pathways and emphasises the need for careful selection of suitable references before analysing target gene expression.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 4","pages":"26"},"PeriodicalIF":0.0,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Interferon Gamma</i> Gene Polymorphisms in Greek Primary Breast Cancer Patients.","authors":"Nyanbol Kuol, Xu Yan, Jimsheena Karakkat, Stamatis Vassilaros, Ioannis Fyssas, Anastasios Tsibanis, Sarah Fraser, Kulmira Nurgali, Vasso Apostolopoulos","doi":"10.31083/j.fbs1604025","DOIUrl":"https://doi.org/10.31083/j.fbs1604025","url":null,"abstract":"<p><strong>Background: </strong>Breast cancer is a heterogeneous disease with distinct clinical subtypes, categorized by hormone receptor status, which exhibits different prognoses and requires personalized treatment approaches. These subtypes included luminal A and luminal B, which have different prognoses. Breast cancer development and progression involve many factors, including interferon-gamma (<i>IFNG</i>). Moreover, single nucleotide polymorphisms (SNPs) in <i>IFNG</i> have been associated with cancer risk. However, the functional role of <i>IFNG</i> polymorphisms in primary breast cancer subtypes, luminal A and luminal B, is unclear.</p><p><strong>Methods: </strong>A total of 138 breast cancer tissues were acquired: 81 had luminal A, 42 had luminal B, 10 had triple-negative, and 3 had human epidermal growth factor receptor 2 (HER2) subtypes, while 2 had missing data. The tissues were evaluated in relation to luminal A and luminal B primary breast cancer subtypes. DNA was extracted from freshly frozen samples, and three SNPs (rs1861493 (chr12:68157416 (GRCh38.p13)), rs1861494 (chr12:68157629 (GRCh38.p13)) and rs2430561 (chr12:68158742 (GRCh38.p13))) in the <i>IFNG</i> gene were selected and evaluated based on previously published associations with cancer or other diseases.</p><p><strong>Results: </strong>The data showed that <i>IFNG</i> polymorphisms rs1861493 and rs1861494 were associated with breast cancer risk, with the A allele of rs1861493 and T allele of rs1861494 being noted as the risk alleles. Furthermore, the <i>IFNG</i> polymorphism rs2430561 was associated with breast cancer risk, with the A allele being the risk allele. In addition, the risk alleles were more prevalent in the more aggressive subtype, luminal B breast cancer, compared to luminal A. Similarly, the rs2430561 AA genotype was associated with the breast cancer severity.</p><p><strong>Conclusion: </strong><i>IFNG</i> polymorphisms rs1861493, rs1861494, and rs2430561, with their respective risk alleles, are associated with increased breast cancer risk and severity. These risk alleles are more prevalent in the aggressive luminal B subtype compared to luminal A, indicating their role in both the prevalence and prognosis of breast cancer in a Greek population.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 4","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GWAS-Significant Loci and Uterine Fibroids Risk: Analysis of Associations, Gene-Gene and Gene-Environmental Interactions.","authors":"Liubov Ponomareva, Ksenia Kobzeva, Olga Bushueva","doi":"10.31083/j.fbs1604024","DOIUrl":"https://doi.org/10.31083/j.fbs1604024","url":null,"abstract":"<p><strong>Background: </strong>Uterine fibroids (UF) is the most common benign tumour of the female reproductive system. We investigated the joint contribution of genome-wide association studies (GWAS)-significant loci and environment-associated risk factors to the UF risk, along with epistatic interactions between single nucleotide polymorphisms (SNPs).</p><p><strong>Methods: </strong>DNA samples from 737 hospitalised patients with UF and 451 controls were genotyped using probe-based PCR for seven common GWAS SNPs: rs117245733 <i>LINC00598</i>, rs547025 <i>SIRT3,</i> rs2456181 <i>ZNF346</i>, rs7907606 <i>STN1</i>, <i>SLK</i>, rs58415480 <i>SYNE1</i>, rs7986407 <i>FOXO1</i>, and rs72709458 <i>TERT</i>.</p><p><strong>Results: </strong>We observed an association between rs547025 <i>SIRT3</i> and the decreased risk of UF in overall group (effect allele C, odds ratio (OR) = 0.61, 95% confidence interval (CI) = 0.43-0.866, <i>p</i> = 0.005). SNP rs547025 exhibits protective effects against UF exclusively in patients with normal fruit and vegetable intake (OR = 0.39, 95% CI = 0.21-0.75, <i>p</i> = 0.002), no history of spontaneous abortions (OR = 0.48, 95% CI = 0.33-0.70, <i>p</i> = 0.0001), no pelvic inflammatory diseases (PID) in anamnesis (OR = 0.55, 95% CI = 0.38-0.80, <i>p</i> = 0.0016), and in smokers (OR = 0.20, 95% CI = 0.06-0.65, <i>p</i> = 0.006). In addition, rs7907606 <i>STN1</i>, <i>SLK</i> was associated with the risk of UF in patients without a history of pelvic inflammatory diseases (PID) (OR = 1.34, 95% CI = 1.03-1.74, <i>p</i> = 0.028). SNPs rs547025 <i>SIRT3</i> and rs7907606 <i>STN1</i>, <i>SLK</i>, displayed the strongest mono-effects (0.71% and 0.52% contribution to UF entropy) and were characterized by the most pronounced gene-gene (G×G) effects when interacting with each other (0.60% contribution to entropy). The interaction Medical abortion×rs547025 <i>SIRT3</i> served as the base for all the best gene-environment (G×E) models. Medical abortions have the most pronounced mono-effect (1.15% contribution to the entropy of UF), exceeding the mono-effects of SNPs involved in the most significant G×E-models (0.01%-0.49% contribution to entropy) and spontaneous abortions (0.48% of UF entropy) and exceeding the effects of G×E interactions (0.05-0.46% of UF entropy).</p><p><strong>Conclusions: </strong>Bioinformatics analysis showed that GWAS SNPs are involved in the molecular mechanisms of UF mainly through the regulation of vasculogenesis, cell proliferation, apoptosis, DNA damage, inflammation, hypoxia, steroid hormone metabolism, cell signaling, organ formation.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 4","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conservation Genetics and Breeding using Molecular Genetic Markers in Japanese Quail (<i>Coturnix japonica</i>).","authors":"Michael N Romanov, Questan Ali Ameen, Ahmed Sami Shaker, Rana Mohammed Al-Obaidi, Darren K Griffin","doi":"10.31083/j.fbs1604023","DOIUrl":"https://doi.org/10.31083/j.fbs1604023","url":null,"abstract":"<p><strong>Background: </strong>The Japanese quail (<i>Coturnix japonica</i>) is a small migratory bird whose main habitats are located in East Asia, Russia, China, Japan, Korea, and India. The Japanese quail was first introduced into the Iraqi research sector in the early 1980s. This investigation aimed to identify the genetic divergence between the available genetic lines of the Japanese quail in Iraq as a first step to conducting further conservation and breeding, benefiting from studying the genetic diversity related to productivity, adaptation, and immune susceptibility.</p><p><strong>Methods: </strong>In this study, we harnessed the random amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR) protocol to investigate the genetic structure, diversity, and differentiation of seven distinct genetic lines of these birds with white, brown, wild grey, and yellow plumage guided by 20 molecular genetic markers.</p><p><strong>Results: </strong>Our findings showed a relatively high polymorphism level of these 20 markers, which was adequate for describing genetic variation within and between the quail lines under study. Overall, the pairs of the White male and Brown male, Brown female and Grey male, and Grey female and Grey male lines were the most genetically distant. Conversely, the White male and Grey male lines were the most similar.</p><p><strong>Conclusions: </strong>The genetic differences established between these lines can enable us to suggest recommendations for further conservation genetics and breeding of this species. In particular, we propose that choosing animals (lines) with the greatest genetic distances, i.e., the least genetic similarities, can help preserve the highest genetic variability within the population. This proposed approach mirrors many contemporary conservation strategies, and information derived directly from this study can potentially be used to improve breeder selection regimes for additional conservation initiatives <i>ex situ</i>.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 4","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gone with the Species: From Gene Loss to Gene Extinction.","authors":"Ammad Aslam Khan, Anees Fatima","doi":"10.31083/j.fbs1604022","DOIUrl":"https://doi.org/10.31083/j.fbs1604022","url":null,"abstract":"<p><strong>Background: </strong>Vertebrae protein-coding genes exhibit remarkable diversity and are organized into many gene families. These gene families have emerged through various gene duplication events, the most prominent being the two rounds of whole-genome duplication (WGD). The current research project analyzed a unique class of genes called \"singletons\". Notably, we introduce the concept of \"super-singletons\": genes that stand as the last representatives of their ancestral families and the sole representatives of their genetic makeup with no ortholog in any other species.</p><p><strong>Methods: </strong>We used the Ensembl/Biomart pipeline to identify duplicated and unduplicated protein-coding genes in different vertebrate species and found orthologs of human genes.</p><p><strong>Results: </strong>We showed the frequency of duplicated genes and singletons, demonstrating that singletons are more vulnerable to evolutionary loss than duplicated genes. Additionally, we found that contractions in vertebrate gene families are more prevalent than expansion.</p><p><strong>Conclusion: </strong>Our study provides insight into the evolution of gene families and presents a novel scenario where the extinction of species would lead to the extinction of a gene, ultimately shifting the narrative from the impact of genetics on species extinction to the extinction of genes.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 4","pages":"22"},"PeriodicalIF":0.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"InPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data.","authors":"Jianhong Ou, Haibo Liu, Sungmi Park, Michael R Green, Lihua Julie Zhu","doi":"10.31083/j.fbs1604021","DOIUrl":"https://doi.org/10.31083/j.fbs1604021","url":null,"abstract":"<p><strong>Background: </strong>Alternative cleavage and polyadenylation (APA) is a crucial post-transcriptional gene regulation mechanism that regulates gene expression in eukaryotes by increasing the diversity and complexity of both the transcriptome and proteome. Despite the development of more than a dozen experimental methods over the last decade to identify and quantify APA events, widespread adoption of these methods has been limited by technical, financial, and time constraints. Consequently, APA remains poorly understood in most eukaryotes. However, RNA sequencing (RNA-seq) technology has revolutionized transcriptome profiling and recent studies have shown that RNA-seq data can be leveraged to identify and quantify APA events.</p><p><strong>Results: </strong>To fully capitalize on the exponentially growing RNA-seq data, we developed InPAS (Identification of Novel alternative PolyAdenylation Sites), an R/Bioconductor package for accurate identification of novel and known cleavage and polyadenylation sites (CPSs), as well as quantification of APA from RNA-seq data of various experimental designs. Compared to other APA analysis tools, InPAS offers several important advantages, including the ability to detect both novel proximal and distal CPSs, to fine tune positions of CPSs using a naïve Bayes classifier based on flanking sequence features, and to identify APA events from RNA-seq data of complex experimental designs using linear models. We benchmarked the performance of InPAS and other leading tools using simulated and experimental RNA-seq data with matched 3'-end RNA-seq data. Our results reveal that InPAS frequently outperforms existing tools in terms of precision, sensitivity, and specificity. Furthermore, we demonstrate its scalability and versatility by applying it to large, diverse RNA-seq datasets.</p><p><strong>Conclusions: </strong>InPAS is an efficient and robust tool for identifying and quantifying APA events using readily accessible conventional RNA-seq data. Its versatility opens doors to explore APA regulation across diverse eukaryotic systems with various experimental designs. We believe that InPAS will drive APA research forward, deepening our understanding of its role in regulating gene expression, and potentially leading to the discovery of biomarkers or therapeutics for diseases.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 4","pages":"21"},"PeriodicalIF":0.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Relative Frequency of Metachromatic Leukodystrophy in Egypt: A Reference Laboratory Report.","authors":"Ekram Fateen, Zeinab Y Abdallah","doi":"10.31083/j.fbs1604020","DOIUrl":"https://doi.org/10.31083/j.fbs1604020","url":null,"abstract":"<p><strong>Background: </strong>Metachromatic leukodystrophy (MLD) is an autosomal recessive hereditary neurodegenerative disease caused by a deficiency in arylsulfatase A (ARSA) activity and belongs to the group of lysosomal storage diseases. A biochemical diagnosis of MLD is based on determining the residual ARSA activity in leukocytes, skin fibroblasts, and urine. This study documents our biochemical experience and estimates the relative frequency of MLD over 21 years (2001-2022).</p><p><strong>Methods: </strong>This study analyzed 4357 suspected cases of MLD in Egypt. The ARSA activity was spectrophotometrically determined in leukocytes in all the referred cases.</p><p><strong>Results: </strong>Of these 4357 referred cases, 577 (13%) possessed decreased ARSA activity, less than 10% of the low normal range (50-200 micromole/gram protein/hour (μmol/g protein/h), and 104 cases were diagnosed as having a pseudodeficiency in enzyme activity (<20-50% of low-normal ARSA activity). The prevalence of MLD was 1.6/100,000.</p><p><strong>Conclusions: </strong>A diagnosis of MLD in Egypt is based on enzyme activity levels and clinical suspicion; molecular analysis was performed in a few cases.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 4","pages":"20"},"PeriodicalIF":0.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HSP90 Family Members, Their Regulators and Ischemic Stroke Risk: A Comprehensive Molecular-Genetics and Bioinformatics Analysis.","authors":"Ksenia Kobzeva, Maxim Ivenkov, Rostislav Gromov, Olga Bushueva","doi":"10.31083/j.fbs1604019","DOIUrl":"https://doi.org/10.31083/j.fbs1604019","url":null,"abstract":"<p><strong>Background: </strong>Disruptions in proteostasis are recognized as key drivers in cerebro- and cardiovascular disease progression. Heat shock proteins (HSPs), essential for maintaining protein stability and cellular homeostasis, are pivotal in neuroperotection. Consequently, deepening the understanding the role of HSPs in ischemic stroke (IS) risk is crucial for identifying novel therapeutic targets and advancing neuroprotective strategies.</p><p><strong>Aim: </strong>Our objective was to examine the potential correlation between single nucleotide polymorphisms (SNPs) in genes that encode members of the Heat shock protein 90 (HSP90), small heat shock proteins (HSPB), and heat shock factors (HSF) families, and the risk and clinical characteristics of IS.</p><p><strong>Methods: </strong>953 IS patients and 1265 controls from Central Russia were genotyped for nine SNPs in genes encoding <i>HSP90AA1</i>, <i>HSFs</i>, and <i>HSPBs</i> using the MassArray-4 system and probe-based polymerase chain reaction (PCR).</p><p><strong>Results: </strong>In smokers, SNP rs1133026 <i>HSPB8</i> increased the risk of IS (risk allele A, odds ratio (OR) = 1.43, 95% Confidence Interval (CI) 1.02-2.02, <i>p</i> = 0.035), and rs556439 <i>HSF2</i> increased the brain infarct size (risk allele A, <i>p</i> = 0.02). In non-smokers, SNPs rs4279640 <i>HSF1</i> (protective allele T, OR = 0.58, 95% CI 0.37-0.92, <i>p</i> = 0.02) and rs4264324 <i>HSP90AA1</i> (protective allele C, OR = 0.11, 95% CI 0.01-0.78, <i>p</i> = 0.001) lowered the risk of recurrent stroke; SNP rs7303637 <i>HSPB8</i> increased the age of onset of IS (protective allele T, <i>p</i> = 0.04). In patients with body mass index (BMI) ≥25, SNPs rs556439 <i>HSF2</i> (risk allele A, OR = 1.33, 95% CI 1.04-1.69, <i>p</i> = 0.02) and rs549302 <i>HSF2</i> (risk allele G, OR = 1.34, 95% CI 1.02-1.75, <i>p</i> = 0.03) were linked to a higher risk of IS.</p><p><strong>Conclusions: </strong>The primary molecular mechanisms through which the studied SNPs contribute to IS pathogenesis were found to be the regulation of cell death, inflammatory and oxidative stress responses.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 4","pages":"19"},"PeriodicalIF":0.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SRPK Inhibitors Reduce the Phosphorylation and Translocation of SR Protein Splicing Factors, thereby Correcting <i>BIN1</i>, <i>MCL-1</i> and <i>BCL2</i> Splicing Errors and Enabling Apoptosis of Cholangiocarcinoma Cells.","authors":"Preenapan Changphasuk, Chaturong Inpad, Sukanya Horpaopan, Sasiprapa Khunchai, Suchada Phimsen, Damratsamon Surangkul, Tavan Janvilisri, Atit Silsirivanit, Worasak Kaewkong","doi":"10.31083/j.fbs1603017","DOIUrl":"https://doi.org/10.31083/j.fbs1603017","url":null,"abstract":"<p><strong>Background: </strong>Cholangiocarcinoma (CCA) is a malignancy of the bile duct epithelium that is commonly found in the Thai population. CCA has poor prognosis and a low survival rate due to the lack of early diagnosis methods and the limited effectiveness of current treatments. A number of oncogenic spliced-transcripts resulting from mRNA splicing errors have been reported in CCA, and aberrant mRNA splicing is suspected to be a key driver of this cancer type. The hyperphosphorylation of serine/arginine rich-splicing factors (SRSFs) by serine/arginine protein kinases (SRPKs) causes them to translocate to the nucleus where they facilitate gene splicing errors that generate cancer-related mRNA/protein isoforms.</p><p><strong>Methods: </strong>The correlation between SRPK expression and the survival of CCA patients was analyzed using data from The Cancer Genome Atlas (TCGA) dataset. The effect of SRPK inhibitors (SRPIN340 and SPHINX31) on two CCA cell lines (KKU-213A and TFK-1) was also investigated. The induction of cell death was studied by Calcein-AM/PI staining, AnnexinV/7AAD staining, immunofluorescence (IF), and Western blotting (WB). The phosphorylation and nuclear translocation of SRSFs was tracked by WB and IF, and the repair of splicing errors was examined by Reverse Transcription-Polymerase Chain Reaction (RT-PCR).</p><p><strong>Results: </strong>High levels of SRPK1 and SRPK2 transcripts, and in particular SRPK1, correlated with shorter survival in CCA patients. SRPIN340 and SPHINX31 increased the number of dead and apoptotic cells in a dose-dependent manner. CCA also showed diffuse expression of cytoplasmic cytochrome C and upregulation of cleaved caspase-3. Moreover, SRSFs showed low levels of phosphorylation, resulting in the accumulation of cytoplasmic SRSF1. To link these phenotypes with aberrant gene splicing, the apoptosis-associated genes Bridging Integrator 1 (<i>BIN1</i>), Myeloid cell leukemia factor 1 (<i>MCL-1</i>) and B-cell lymphoma 2 (<i>BCL2</i>) were selected for further investigation. Treatment with SRPIN340 and SPHINX31 decreased anti-apoptotic <i>BIN1+12A</i> and increased pro-apoptotic <i>MCL-1S</i> and <i>BCL-xS</i>.</p><p><strong>Conclusions: </strong>The SRPK inhibitors SRPIN340 and SPHINX31 can suppress the phosphorylation of SRSFs and their nuclear translocation, thereby producing <i>BIN1</i>, <i>MCL-1</i> and <i>BCL2</i> isoforms that favor apoptosis and facilitate CCA cell death.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 3","pages":"17"},"PeriodicalIF":0.0,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SNP Markers: Analysis of Genetic Diversity and Identification of Genomic Regions in Pantaneiro Sheep and Texel Sheep Under Natural Selection.","authors":"Layonel Alves de Sousa, Adriana Mello de Araujo, Francisco de Assis Diniz Sobrinho, Miklos Maximiliano Bajay, Raquel Soares Juliano, Fernando Alvarenga Reis, Marcos Barbosa Ferreira, Gustavo Daniel Vega-Britez, Fernando Miranda de Vargas Junior","doi":"10.31083/j.fbs1603018","DOIUrl":"https://doi.org/10.31083/j.fbs1603018","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Sheep farming is growing substantially in Brazil, driven by the increasing demand for sheep meat. This rising demand has heightened the focus on sheep, making them the subject of numerous studies, including those centered on genetic analysis. A notable research area involves Pantaneiro sheep, which are indigenous to the Pantanal region of Mato Grosso do Sul and other locations. These sheep are of particular interest due to their adaptation to the unique environmental conditions of the Pantanal, a floodplain characterized by its distinctive climatic and ecological features. This study primarily aimed to conduct a comprehensive genomic analysis of Pantanal sheep subjected to natural selection within the Pantanal region and compare different sample herds using methodological approaches.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Genomic analysis was performed to examine genetic diversity and structure via GGP50K single nucleotide polymorphism (SNP) analysis. A sample of 192 adult sheep over 4 years old was categorized into seven populations based on location: Six populations comprised Pantaneiro sheep with one Texel sheep population. Outlier SNPs were assessed to pinpoint regions under natural selection, with comparisons between the Pantaneiro and the commercial Texel breeds. All data analyses were conducted using the R programming language, employing specialized genetic analysis packages. These outlier SNPs were detected using three methodologies, PCAdapt, OutFLANK, and FDIST2/fsthet, with false discovery rate (FDR) corrections applied to ensure result accuracy. Each method was evaluated, and the genes associated with the identified SNPs were cross-referenced with the most recent sheep genome database, focusing specifically on genes with known phenotypic traits.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Analysis of a sample comprising 192 adult individuals revealed greater genetic variability within the Pantaneiro breed than the Texel breed, highlighting the adaptation of the Pantaneiro breed to the unique Pantanal environment. Conversely, the Texel breed exhibited significantly higher levels of inbreeding, attributed to its controlled breeding practices. Outlier SNPs were detected with notable variation across different methodologies, underscoring the importance of FDR correction in ensuring the reliability and concentration of identified outliers. These outlier SNPs facilitated the identification of genes associated with key phenotypic traits, including hair growth, tissue regeneration, pigmentation regulation, and muscle capacity.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;The integrated analysis of methodologies demonstrated significant efficiency in elucidating the genomic landscape of Pantanal sheep, highlighting the genetic richness inherent in sheep from the Pantanal region of Mato Grosso do Sul. The techniques employed effectively identified outlier SNPs associated with phenotypically relevant genes. These findings, which reveal greater","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"16 3","pages":"18"},"PeriodicalIF":0.0,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}