Frontiers in bioscience (Scholar edition)最新文献

{"title":"Evaluation of Fish Species Detection in the Northwestern Pacific using eDNA Metabarcoding: A Mock Community Approach.","authors":"Sergei V Turanov, Olesia A Rutenko","doi":"10.31083/FBS26247","DOIUrl":"https://doi.org/10.31083/FBS26247","url":null,"abstract":"<p><strong>Background: </strong>Metabarcoding of environmental DNA (eDNA), a technique using high-throughput sequencing, has transformed biodiversity monitoring by identifying organisms from DNA fragments present in the environment. This method, particularly useful for aquatic ecosystems, allows for non-invasive species monitoring, helping to provide insight into ecosystem composition and taxonomic diversity. The objective of this study was to assess the efficacy of eDNA metabarcoding for fish species identification in a model community from the northeast Pacific Ocean using <i>12S</i> ribosomal RNA (<i>12S</i> rRNA) marker.</p><p><strong>Methods: </strong>Water samples were collected from the tank of the Primorsky Aquarium, which contains fish species from the Sea of Japan, Sea of Okhotsk, and Bering Sea. DNA was extracted using syringe filters and enriched with polymerase chain reaction (PCR) of mitochondrial <i>12S</i> rRNA fragment, followed by sequencing on Illumina platform. The resulting reads were processed using the bayesian generalized uncertainty modeling (BEGUM) pipeline and their taxonomic diversity was assessed by basic local alignment search tool (BLAST) search. Using <i>in silico</i> PCR, we also assessed the possible association of detection failures of some species with the presence of primer-to-target sequence mismatches.</p><p><strong>Results: </strong>From a fish community of only 20 species in the tank, we identified 56 operational taxonomic units (OTUs) corresponding to 28 genera. Among these OTUs, 20 species were unambiguously classified by BLAST-based analysis, though only 9 of them corresponded to the species actually present in the tank. Significant problems included inconsistent reference data and marker biases that affected the accuracy of species identification. In addition to DNA contamination from feed, contamination from the water source may have introduced extraneous DNA into the samples. Also, using <i>in silico</i> PCR analysis with a small number of available reference sequences, we demonstrated a significantly higher number of primer mismatches for species that were not identified.</p><p><strong>Conclusions: </strong>This study highlights the relative efficacy of eDNA metabarcoding for fish species identification, but also highlights the need to improve reference databases and minimise contamination, searching for references and primers to improve accuracy. Further research should focus on optimising marker selection and controlling methodological bias to ensure robust biodiversity estimates.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"26247"},"PeriodicalIF":0.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733443","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":"Genome-wide Identification, Characterization, and Expression Analysis of <i>NHX</i> Genes in <i>Phaseolus</i> <i>vulgaris</i> L. under Salt Stress: An <i>In Silico</i> Approach.","authors":"Edinara Maria Barbosa, Jardel de Oliveira, Tiago Benedito Dos Santos, Silvia Graciele Hülse de Souza","doi":"10.31083/FBS26725","DOIUrl":"https://doi.org/10.31083/FBS26725","url":null,"abstract":"<p><strong>Background: </strong>Climate change is among the major triggering agents of abiotic stresses (e.g., saline stress), culminating in a vulnerability of common bean production systems. In recent decades, important research has identified and characterized genes that can mitigate the adverse effects caused by salt stress; among them, the Na⁺/H⁺ antiporters (<i>NHXs</i>) gene stands out. The <i>NHX</i> genes are widely distributed in all organisms and play significant roles in osmotic regulation in plants under salt stress conditions. Genome-wide identification of <i>NHX</i> genes has been performed in several plant species but not in <i>Phaseolus vulgaris</i> L.</p><p><strong>Methods: </strong>This study aimed to identify and characterize <i>NHX</i> genes in <i>P. vulgaris</i> L. using a genome-wide analysis approach conducted <i>in silico</i>. The common bean genome revealed nine putative <i>PvNHX</i> genes, and their subcellular localization, phylogenetic relationship, cis-regulatory elements, conserved motifs identification, chromosomal location, expression patterns, and interaction networks were analyzed.</p><p><strong>Results: </strong>Promoter analysis suggested that <i>PvNHX</i> genes shared hormone-related elements and were light-responsive and stress-responsive. Seven <i>PvNHX</i> genes were under the regulation of five microRNA (miRNA) families. RNA-seq analysis revealed that most <i>PvNHX</i> genes were expressed in response to salt stress. Currently, the most assertive strategy to confront these adversities is to use the information generated by sequencing plants to identify candidate genes that can be introgressed to improve programs in producing resilient cultures.</p><p><strong>Conclusion: </strong>These results can provide valuable information for future studies on the functional mechanism of <i>PvNHX</i> genes in common beans in response to salt stress.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"26725"},"PeriodicalIF":0.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733407","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":"Aquaporins as Membrane Proteins: The Current Status.","authors":"Irena Roterman, Katarzyna Stapor, Dawid Dułak, Grzegorz Szoniec, Leszek Konieczny","doi":"10.31083/FBS27967","DOIUrl":"https://doi.org/10.31083/FBS27967","url":null,"abstract":"<p><strong>Background: </strong>The ambient conditions that ensure the expected protein folding activity are important in directing the protein folding process. Water favors the formation of a centrally located hydrophobic protein nucleus with exposed polar residues for preferable contact with polar water molecules. Different ambient conditions are created by the hydrophobic cell membrane, which also provides an environment for the activity of proteins, including channels responsible for transporting multiple molecules, the concentration of which is controlled as part of homeostasis. Aquaporins are transmembrane proteins responsible for primarily transporting water and low-molecular-weight compounds.</p><p><strong>Methods: </strong>The fuzzy oil drop (FOD) model was applied in its modified form, FOD-M, for the analysis. The FOD model allows quantitative assessment of protein structure adaptation to external conditions, ensuring its biological activity.</p><p><strong>Results: </strong>The aquaporins studied in this work revealed adaptations for stabilizing hydrophobic environments and transporting polar molecules.</p><p><strong>Conclusions: </strong>A significant degree of similarity was demonstrated in the structure of human aquaporins using FOD-M. This model enabled a quantitative assessment of the degree of adaptation to biological function achieved through an appropriate balance between micelle-like decomposition and appropriate modification due to the specificity of the environment that ensures adequate activity.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"27967"},"PeriodicalIF":0.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733436","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":"Genetic Diversity and Relationship Among Algerian, Nigerian, and Turkish Goat Breeds Using Microsatellite Markers.","authors":"Hakim Tefiel, Mohamed Chahbar, Khaled Fantazi, Onur Yilmaz, Ibrahim Cemal, Benali Kidoud, Kheira Setti Ahmed, Semir Bechir Suheil Gaouar","doi":"10.31083/FBS25866","DOIUrl":"https://doi.org/10.31083/FBS25866","url":null,"abstract":"<p><strong>Background: </strong>This study was conducted to identify genetic diversity among goat breeds in Algeria, Türkiye, and Nigeria, which is believed to have arisen due to historical influences, trade networks, and environmental adaptations, using 12 microsatellite markers. Additionally, the study provided insights into the population structure and kinship relationships among the breeds.</p><p><strong>Methods: </strong>The animal material of the study consisted of 514 goats from eight breeds: four Algerian (n = 224), two Turkish (n = 140), and two Nigerian (n = 150) native goat breeds. The quality and quantity control of DNA obtained from blood samples was determined using the Nanodrop 2000 device. In the study, 12 microsatellite markers were used. Capillary electrophoresis was used to separate polymerase chain reaction (PCR) fragments labeled with fluorescent dye in the Beckman Coulter GeXP Genetic Analyzer. Statistical analyses were used to calculate molecular genetic parameters, F-statistics, and genetic distances. Factorial correspondence analysis, structure analysis, and dendrogram construction were used to explore population structure.</p><p><strong>Results: </strong>The study used microsatellite markers to analyze genetic diversity in various breeds, revealing 149 alleles with a mean of 12.41 per locus. Positive inbreeding coefficient within subpopulations (F_IS) values indicated a heterozygote deficiency, suggesting potential breeding strategies. Population structure analyses revealed distinct genetic clusters and relationships, providing insights into genetic variation within populations.</p><p><strong>Conclusion: </strong>The study provides a detailed analysis of goat populations in Algeria, Türkiye, and Nigeria, revealing the presence of heterozygote deficiency and the need for strategic breeding interventions to preserve genetic diversity. The findings also reveal distinct genetic clusters and relationships with historical influences, particularly the role of the Mediterranean Sea, adding depth to our understanding. The research offers practical guidance for the sustainable management of these valuable genetic resources, emphasizing adaptive strategies to ensure the resilience and adaptability of goat populations. The findings are crucial for informed decision-making in conserving and utilizing diverse livestock breeds, urging further exploration of goat populations' genetic landscapes.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"25866"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733447","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":"Role of Polyadenylation in mRNA Genome Integration via LINE-1 Retrotransposons: An Opinion on mRNA Vaccine Safety.","authors":"Isidoro Feliciello","doi":"10.31083/FBS26335","DOIUrl":"https://doi.org/10.31083/FBS26335","url":null,"abstract":"<p><p>The polyadenylated (polyA) tail of mRNA plays a crucial role in regulating mRNA stability and translation, and it may also contribute to genome integration through interactions with long interspersed nuclear element-1 (LINE-1, L1) retrotransposons. This interaction is particularly relevant for mRNA vaccines. Understanding how the polyA tail interacts with L1 proteins, especially open reading frame 2 protein (ORF2p), is critical for assessing these risks and developing strategies to enhance the safety of mRNA vaccines. We suggest conducting in vitro experiments to explore polyA tail modifications and their effects on L1 binding.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"26335"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733494","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":"Can Individuals with 47,XYY Karyotypes Exist without Male Phenotype? A Narrative Literature Review and Case Report.","authors":"Marcelo Jones Pires, Laura Coimbra Teixeira, Luise Longo Angeloni, Julia Londero Heleno, Mariana Romano, Marcio Lopes Miranda, Tarsis Paiva Vieira, Mara Sanches Guaragna, Beatriz Amstaldem Barros, Andréa Trevas Maciel-Guerra, Gil Guerra-Junior","doi":"10.31083/FBS25251","DOIUrl":"https://doi.org/10.31083/FBS25251","url":null,"abstract":"<p><strong>Background: </strong>The 47,XYY syndrome is a genetic condition found in about 1 in 1000 male children. The expected phenotype is male but could vary greatly. Those with genitourinary abnormalities may also present with microphallus, hypoplastic scrotum, cryptorchidism, hypospadias and macroorchidism. This study reports a child with sex ambiguity who possesses an initial 47,XYY karyotype. We also conducted a narrative literature review of 47,XYY individuals and their respective genital phenotype and/or gender identity.</p><p><strong>Methods: </strong>The narrative literature review was performed by searching for \"47,XYY\" in the PubMed database. All studies published in English, Spanish or Portuguese from January 1960 to January 2024 that contained the term \"47,XYY\" in the title or abstract were included. Studies that did not describe the genital phenotype and/or gender identity of cases were excluded. We also described the case of a 2-month-old patient with the 47,XYY karyotype and sex ambiguity.</p><p><strong>Results: </strong>Our patient underwent additional karyotype testing, resulting in 47,XYY [30] and another 45,X [2]/47,XYY [98] with mosaicism being confirmed by fluorescent <i>in situ</i> hybridization (FISH) on buccal smears (nuc ish (DXZ1 × 1, DYZ3 × 2)[64/100]/(DXZ1 × 1, DYZ3 × 0)[36/100]. A gonadal biopsy revealed an atrophic testis on the left and a streak gonad on the right, with a final diagnosis of mixed gonadal dysgenesis determined. The narrative review revealed 643 articles, of which 350 met the inclusion criteria. However, we excluded 132 articles because they presented no new cases. We included 138 articles, which presented a series containing less than 10 new cases with the 47,XYY karyotype (total of 327 cases), 58 articles presented 4001 cases and 22 articles presented 75 patients with the 47,XYY karyotype in mosaic with 45,X. For all 4403 analyzed cases, 4354 (98.90%) presented a male phenotype, of which 4322 had the 47,XYY karyotype and 32 had mosaicism with 45,X lineage. A further 23 (0.52%) presented a female phenotype, of which four had the 47,XYY karyotype and 19 had mosaicism with 45,X lineage. In addition, 23 (0.52%) cases presented ambiguous genitalia, of which two had the 47,XYY karyotype and 21 had mosaicism with 45,X lineage. Finally, three (0.06%) cases had undefined phenotypes, all with mosaicism with 45,X lineage. Of the six cases with the 47,XYY karyotype and no male phenotype, one had complete androgen insensitivity syndrome (CAIS), one had lipoid congenital adrenal hyperplasia, two had probable CAIS, and two presented an incomplete diagnostic investigation.</p><p><strong>Conclusions: </strong>A female or ambiguous genital phenotype in an individual with 47,XYY karyotype is uncommon and should alert to the presence of the 45,X lineage or association with other causes of disorder/difference of sex development.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"25251"},"PeriodicalIF":0.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733440","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":"Role of Retroelements in Frontotemporal Dementia Development.","authors":"Rustam Nailevich Mustafin","doi":"10.31083/FBS25922","DOIUrl":"https://doi.org/10.31083/FBS25922","url":null,"abstract":"<p><p>Frontotemporal dementia (FTD) develops in proteinopathies involving TDP-43 (transactive response DNA-binding protein 43 kDa), tau, and FUS (fused in sarcoma) proteins, which possess antiviral properties and exert inhibitory effects on human transposable elements. Viruses and aging have been suggested to trigger FTD by activating specific retroelements. FTD is associated with multiple single nucleotide polymorphisms (SNPs), most located in intergenic and regulatory regions where many transposable element genes are found. Therefore, genetic predisposition to FTD may influence the interaction between retroelements and the TDP-43, tau, and FUS proteins, causing pathological conformation changes and aggregate formation. Subsequently, these aggregates lose their ability to inhibit retroelements, leading to the activation of transposable elements. This creates a harmful negative feedback loop in which TDP-43, tau, and FUS protein expressions are further enhanced by retroelement transcripts and proteins, resulting in protein aggregate accumulation and pathological disease progression. Hence, epigenetic inhibition of pathologically activated retroelements using micro-ribonucleic acids (microRNAs) derived from transposable elements has been proposed as a potential treatment for FTD. Finally, a review of the current scientific literature identified 13 appropriate microRNAs (miR-1246, -181c, -330, -345-5p, -361, -548a-3p, -548b-5p, -548c-5p, -571, -588, -659-3p, -708-3p, -887).</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"25922"},"PeriodicalIF":0.0,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733497","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":"Genome-Wide Analysis of Genetic Predispositions Linked to Damaged Membranes and Impaired Fertility as Indicators of Compromised Sperm-Egg Interaction Mechanisms in Frozen-Thawed Rooster Semen.","authors":"Natalia V Dementieva, Elena V Nikitkina, Yuri S Shcherbakov, Nikolai V Pleshanov, Anna E Ryabova, Anastasiia I Azovtseva, Yulia L Silyukova, Artem A Musidray, Darren K Griffin, Michael N Romanov","doi":"10.31083/FBS26022","DOIUrl":"https://doi.org/10.31083/FBS26022","url":null,"abstract":"<p><strong>Background: </strong>Cryopreservation cannot be widely used for rooster sperm due to high incidences of cryoinjury, including damage to sperm membranes. Thus, cryopreserved rooster sperm has limited use due to low sperm motility and reduced fertilizing ability, which disrupts the mechanisms involved in sperm-egg interactions. Previously, we used an Illumina 60K single-nucleotide polymorphism (SNP) array to search for genes associated with rooster sperm quality, before and after freeze-thawing. As a continuation of these genome-wide association studies (GWAS), the present investigation used a denser 600K SNP chip. Consequently, the screen depth was expanded by many markers for cryo-resistance in rooster sperm while more candidate genes were identified. Thus, our study aimed to identify genome-wide associations with ejaculate quality indicators, including those concerning sperm membrane damage.</p><p><strong>Methods: </strong>We selected sperm quality indicators after freezing-thawing using samples from a proprietary cryobank collection created to preserve generative and germ cells of rare and endangered breeds of chickens and other animal species. A total of 258 ejaculates from 96 roosters of 16 different breeds were analyzed. Moreover, 96 respective DNA samples were isolated for genotyping using a 600K Affymetrix® Axiom® high-density genotyping array.</p><p><strong>Results: </strong>In total, 31 SNPs and 26 candidate genes were associated with characteristics of sperm membrane damage, progressive motility, and sperm cell respiration induction using 2,4-dinitrophenol. In particular, we identified the <i>ENSGALG00000029931</i> gene as a candidate for progressive motility, <i>PHF14</i> and <i>ARID1B</i> for damaged sperm membranes, and <i>KDELR3</i>, <i>DDX17</i>, <i>DMD</i>, <i>CDKL5</i>, <i>DGAT2</i>, <i>ST18</i>, <i>FAM150A</i>, <i>DIAPH2</i>, <i>MTMR7</i>, <i>NAV2</i>, <i>RAG2</i>, <i>PDE11A</i>, <i>IFT70A</i>, <i>AGPS</i>, <i>WDFY1</i>, <i>DEPDC5</i>, <i>TSC1</i>, <i>CASZ1</i>, and <i>PLEKHM2</i> for sperm cell respiration induction.</p><p><strong>Conclusions: </strong>Our findings provide important information for understanding the genetic basis of sperm membrane integrity and other traits that can potentially compromise the mechanisms involved in sperm-egg interactions. These findings are relevant to the persistence of fertility after thawing previously frozen rooster semen.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"26022"},"PeriodicalIF":0.0,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733451","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":"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}