Journal of Applied Genetics最新文献

{"title":"An updated molecular toolkit for genomics-assisted breeding of waxy sorghum [Sorghum bicolor (L.) Moench].","authors":"Melinda K Yerka, Zhiyuan Liu, Scott Bean, Deepti Nigam, Chad Hayes, Diego Druetto, Gabriel Krishnamoorthy, Shelley Meiwes, Gonzalo Cucit, Gunvant B Patil, Yinping Jiao","doi":"10.1007/s13353-025-00993-1","DOIUrl":"https://doi.org/10.1007/s13353-025-00993-1","url":null,"abstract":"<p><p>Several mutations of the sorghum [Sorghum bicolor (L.) Moench] GRANULE-BOUND STARCH SYNTHASE (GBSS) gene [Sobic.010G022600; commonly known as Waxy (Wx)] result in a low amylose:amylopectin starch ratio. Recessive waxy (wx) alleles improve starch digestibility in ethanol production, human foods and beverages, and animal feed. However, breeding waxy sorghum is challenging due to reliance on traditional PCR markers for genotyping, which are not amenable to next-generation sequencing (NGS). Most commercial breeding programs use high-throughput genotyping and genomic selection in large, segregating populations prior to flowering. This study provides the first published NGS markers for the two most commonly used waxy (wx) alleles of sorghum and is the first to fully sequence the large insertion that is causal of the wx^a allele. In the absence of a pangenome including wx^a genotypes, we constructed an in silico B.Tx623 wx^a genome assembly from the B.Tx623 reference genome (v3.1.1) including the insertion, a ~ 5-kb-long terminal repeat (LTR) retrotransposon of the copia superfamily. The in silico wx^a assembly improved read mapping at Sobic.010G022600 in wx^a individuals, identified 78 new uniquely mapped reads, and made it possible to distinguish different Waxy genotypes using short-read sequencing data. Functional PACE-PCR markers, suitable for marker-assisted selection and multiplexed, low-to-mid-density genomic selection, were developed for Wx, wx^a, and wx^b alleles. The PACE markers were validated in segregating populations of three public and private breeding programs. These new molecular breeding resources comprise a toolkit that will improve the efficiency of developing commercial waxy sorghum hybrids using genomics-assisted approaches.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144816711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic background of Richter transformation of atypical chronic lymphocytic leukemia to diffuse large B-cell lymphoma - a case study.","authors":"Sandra Przybysz, Anna Łojko-Dankowska, Magdalena Rakoczy, Małgorzata Marcinkowska-Swojak, Michał Zeńczak, Kinga Gwóźdź-Bąk, Luiza Handschuh, Krzysztof Lewandowski","doi":"10.1007/s13353-025-00999-9","DOIUrl":"https://doi.org/10.1007/s13353-025-00999-9","url":null,"abstract":"<p><p>Atypical chronic lymphocytic leukemia (aCLL) is an indolent lymphoproliferative neoplasm derived from CD19-positive and CD5 or CD23-negative B cells. This paper presents the results of whole genome sequencing (WGS) of lymphoma cells collected from a 29-year-old woman initially diagnosed with aCLL and successfully treated with fludarabine, cyclophosphamide, and rituximab. Eight years later, due to disease progression, she was treated with ibrutinib. After 5 months, her status suddenly deteriorated. PET-CT results suggested Richter transformation (RT). Histopathological examination of nodal lesions confirmed the diagnosis of Diffuse Large B Cell Lymphoma (DLBCL). Finally, the patient was successfully treated with DHAP-R and alloHSCT. WGS of lymphoma cells revealed the presence of pathogenic (COL11A1, MGME1) and likely pathogenic variants (ZMYM3, ALG6, UBA5, and ATG7). Out of these genes, only ZMYM3 is recurrently mutated in B-cell chronic lymphocytic leukemia (B-CLL). The presence of the other lesions requires further studies and indicates the complex molecular background of aCLL transformation to DLBCL. Therefore, the whole-genome variant assessment is worth considering for introduction into a routine procedure at the time of B-CLL diagnosis, especially when RT is suspected.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144804115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-trait stability index in the selection of high-yielding and stable barley genotypes.","authors":"Alireza Pour-Aboughadareh, Bita Jamshidi, Omid Jadidi, Jan Bocianowski, Janetta Niemann","doi":"10.1007/s13353-025-00998-w","DOIUrl":"https://doi.org/10.1007/s13353-025-00998-w","url":null,"abstract":"<p><p>The analysis of genotype-by-environment interaction (GEI) in multi-environmental trials (METs) represents a crucial component of breeding programs prior to the release of new commercial cultivars tailored for specific regions or diverse environmental conditions. Moreover, emphasizing individual traits during selection can yield misleading conclusions. Consequently, the implementation of robust selection models is essential for identifying superior genotypes based on multiple traits. The present dataset demonstrates the utility of the multi-trait stability index (MTSI) in identifying high-yielding and stable barley genotypes across ten diverse environments. The evaluated phenological and agronomic traits included days to heading, days to physiological maturity, grain-filling period, plant height, thousand-kernel weight, and grain yield. A combined analysis of variance (ANOVA) revealed significant effects attributable to environments (E), genotypes (G), and their interaction (GEI) across all assessed traits. Correlation analysis further indicated positive associations between all measured traits and grain yield. In the MTSI model, three first factors accounted for 75% of the total phenotypic variation observed across the test environments. The highest selection gain percentages were recorded for thousand-kernel weight and grain yield. Among the genotypes evaluated, G3, G10, and G14, characterized by the lowest values of the MTSI index, were identified as superior in terms of grain yield, stability, and desirable agronomic attributes. In conclusion, the findings highlight the efficacy of the MTSI in reliably identifying superior genotypes in METs. The results demonstrate that the MTSI index not only enhances the efficiency of the selection process but also improves the accuracy of genotype evaluation and ranking across heterogeneous environmental conditions. This underscores the potential of the MTSI index to support informed breeding decisions, ultimately facilitating the development of high-performing plant varieties that exhibit both yield stability and adaptability across diverse environments.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cellular and molecular changes in mucopolysaccharidosis-plus syndrome caused by a homozygous c.599G > C (p.Arg200Pro) variant of the VPS33A gene.","authors":"Zuzanna Cyske, Estera Rintz, Magdalena Narajczyk, Natalia Świątek, Lidia Gaffke, Karolina Pierzynowska, Grzegorz Węgrzyn","doi":"10.1007/s13353-025-00997-x","DOIUrl":"https://doi.org/10.1007/s13353-025-00997-x","url":null,"abstract":"<p><p>Mucopolysaccharidosis-plus syndrome (MPSPS) is an ultrarare inherited metabolic disease (a few dozen patients diagnosed to date) which is characterised by accumulation of undegraded glycosaminoglycans (GAGs). Despite GAG storage occurs also in the groups of diseases classified as mucopolysaccharidoses (MPS), contrary to MPS, no dysfunctions of lysosomal enzymes is detected in MPSPS which is caused by mutations in the VPS33A gene. The c.1492C > T (p.Arg498Trp) variant, associated with a severe course of the disease, was found in most MPSPS patients. There are only two patients described to date with a homozygous c.599G > C (p.Arg200Pro) variant and a milder (juvenile) form. Until now, the molecular mechanism of MPSPS remained largely unknown, especially for the juvenile form. Here, a battery of cellular and molecular assays, performed using fibroblasts derived from a patient bearing the c.599G > C (p.Arg200Pro) variant of the VPS33A gene, indicated specific changes in cellular vacuoles, elevated levels of the EEA1 protein (required at the stages of the fusions of early and late endosomes, and early endosome sorting), changes in Golgi apparatus morphology, decreased levels of F-actin, and increased levels of α- and β-tubulins, as well as elevated levels of the LC3-II and p62 proteins (autophagy markers). Results of experiments presented here might suggest that severely decreased levels the p.Arg200Pro variant of VSP33A could cause defective endosomal trafficking, possibly resulting in inefficient delivery of GAGs to lysosomes, and their subsequent accumulation in cells. This might induce a cascade of secondary and tertiary disorders, finally expressing as the disease symptoms.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144775392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of colorectal cancer molecular subtypes and prognostic features based on basement membrane-related genes.","authors":"Leilei Yang, Zhiqing Ji, Yufeng Ren, Chengfeng Fang, Jiaju Han, Dinghai Luo, Ruili Zhang, Shenkang Zhou","doi":"10.1007/s13353-025-00992-2","DOIUrl":"https://doi.org/10.1007/s13353-025-00992-2","url":null,"abstract":"<p><p>Recent evidence suggests that the basement membrane (BM) plays an important role in the progression of colorectal cancer (CRC). Here, we investigate the prognostic value of CRC based on BM-associated genes. BM-related differentially expressed genes (DEGs) in CRC were obtained through analysis of The Cancer Genome Atlas public database and literature. The DEGs were used to cluster tumor samples and perform survival analysis. A prognostic model was constructed based on the DEGs in CRC through regression analysis, and its predictive effect was evaluated and validated using the GEO dataset. The correlation between riskscore and tumor progression was evaluated, and Cox regression was used to verify the independence of riskscore by combining it with different clinical factors. A nomogram was drawn to predict the prognosis of CRC individuals. The differences in immune microenvironment between high-risk (H) and low-risk (L) groups were analyzed by ssGSEA and ESTIMATE. The tumor mutation burden (TMB) was calculated for the two groups. Drug sensitivity prediction was performed for the two groups. Finally, the expression levels of prognostic feature genes were validated through qPCR. Based on BM-related DEGs, CRC samples were classified into 2 clusters, with cluster 1 having significantly lower survival rates. A prognostic model was developed based on 7 genes (AGRN, TIMP1, UNC5A, SPARCL1, ADAMTS6, MMP1, and UNC5C). The model exhibited high predictive accuracy and demonstrated the potential to serve as an independent prognostic factor for predicting the prognosis of CRC individuals. A higher riskscore indicated a higher degree of tumor progression. Group H demonstrated higher levels of immune infiltration and TMB, suggesting that individuals in this group might be more suitable for immune therapy. Two first-line anti-tumor drugs, Gemcitabine and Cisplatin, with higher sensitivity to individuals in group L were obtained. The q-PCR results of the feature genes were consistent with the results of gene expression in the database. This study established a 7-gene BM-related prognostic model that could be used to analyze the immune landscape of CRC individuals and predict their sensitivity to immunotherapy and chemotherapy. This research provided a reference for the prognosis prediction and immunotherapy of CRC individuals.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are head and neck versus abdominal paragangliomas driven by different single nucleotide events?","authors":"Krzysztof Kotlarz, Katarzyna Ziemnicka, Bartłomiej Budny, Magda Mielczarek, Jakub Liu, Elżbieta Wrotkowska, Jarosław Kaznowski, Tomasz Suchocki, Jarosław Kałużny, Małgorzata Wierzbicka, Paula Dobosz, Marek Ruchała, Joanna Szyda","doi":"10.1007/s13353-025-00994-0","DOIUrl":"https://doi.org/10.1007/s13353-025-00994-0","url":null,"abstract":"<p><p>Paragangliomas (PGLs) are a heterogeneous group of tumours of the nonepithelial neuroendocrine type, with a significant percentage being genetically determined. They can develop from cells of the parasympathetic as well as the sympathetic nervous system. Tumours located in the head and neck usually have a parasympathetic origin, whereas those in the abdomen have a sympathetic origin. The aim of this study was to determine whether the development of PGLs at both locations is associated with specific variants of genes with proven relevance for the formation of these tumours. Thirty-one patients with abdominal PGL and 16 with head and neck PGLs were analysed at 12 genes whose defects are among the most common genetic determinants of PGLs. The impact of SNPs (single nucleotide polymorphisms) on differentiation between both tumour types was assessed by fitting a decision tree and quantifying genotype effects of SNPs by the Shapley Additive Explanation metric. The study demonstrated that SNPs rs3748576 within the KIF1B gene and rs10060259 within the SDHA gene increase the probability of abdominal tumour locations, while heterozygous GA genotypes of rs2435351 located within the RET gene increase the probability of head and neck locations. The SNPs marked genes involved in the formation and functioning of the nervous system, but are located in introns, and thus themselves do not contribute to protein diversity. Still, intronic SNPs can indirectly affect the transcriptome by influencing alternative splicing, mRNA stability, or overlap with non-coding genes and other regulatory elements that affect transcription. Given this, it seems important to consider variants from non-coding regions in genetic analyses.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144731059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Different mRNAs encoding identical proteins: how and why?","authors":"Yuange Duan, Qi Cao","doi":"10.1007/s13353-025-00995-z","DOIUrl":"https://doi.org/10.1007/s13353-025-00995-z","url":null,"abstract":"<p><p>Alternative splicing (AS) produces various forms of mRNAs and protein isoforms and contributes to biodiversity. However, different mRNAs might have identical CDS and encode the same protein sequence. It is unclear why organisms need these distinct mRNAs if they encode the same protein? We propose two complementary hypotheses, namely adaptive hypothesis and error hypothesis, and tested these ideas using genomes of four representative organisms, human, mouse, fruitfly, and Arabidopsis. We found that only the fruitfly meets most predictions made by the adaptive hypothesis, while the other species generally align with the error hypothesis. Fruitfly exhibits a surprisingly high fraction (> 70%) of protein-coding genes (PCGs) having multiple mRNAs encoding identical proteins. These mRNAs have long CDS, variable UTR lengths, and highly conserved protein sequences. In contrast, opposite or insignificant trends are observed in human, mouse, and Arabidopsis. While molecular errors are common in cell systems, in species like the fruitfly with large effective population size, the strong natural selection might maintain those mRNAs with potentially adaptive regulatory roles. Although encoding identical proteins, different mRNAs can be regulated in a condition-specific manner, facilitating adaptive evolution. Our work provides novel perspectives in genomics and evolutionary biology.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MiR-1976 affects lung squamous cell carcinoma development by targeting NCAPH.","authors":"Yan Li, Hongwei Zhou, Yibing Yao, Zaiwen Fan","doi":"10.1007/s13353-025-00990-4","DOIUrl":"https://doi.org/10.1007/s13353-025-00990-4","url":null,"abstract":"<p><p>Lung squamous cell carcinoma (LUSC) is one of the major subtypes of lung cancer. Non-SMC condensin I complex subunit H (NCAPH) is highly regarded as a valuable biomarker in certain malignant tumors. However, the specific roles of NCAPH in LUSC are not well understood. The objective of this work was to determine the effect of NCAPH on the progression of LUSC and to identify the microRNAs (miRNAs) located upstream of NCAPH that regulate its function. MicroRNA and mRNA expression profiles, as well as clinical data of LUSC (Normal: 49, LUSC: 502), were obtained from the TCGA database for the purpose of differential analysis and survival analysis. The expression of NCAPH and miR-1976 in LUSC cell lines was detected using Quantitative reverse transcription PCR (qRT-PCR) and western blot techniques. In this study, the impact of NCAPH on the proliferation of LUSC cells was assessed using CCK-8 and colony formation assay. Additionally, the effects of NCAPH on the migration and invasion of LUSC cells were evaluated using the Transwell assay. Furthermore, the effects of NCAPH on the apoptosis of LUSC cells were evaluated using flow cytometry. The target miRNAs of NCAPH were predicted using bioinformatics, and the targeting link between miR-1976 and NCAPH was confirmed using a dual-luciferase reporter gene experiment. The findings indicated that the expression of NCAPH was notably elevated in LUSC tissues (P < 0.05), while the expression of its upstream miRNA (miR-1976) was notably reduced (P < 0.05). The dual-luciferase test results indicated that miR-1976 functions as an upstream target miRNA of NCAPH. Low expression of NCAPH may inhibit the proliferation (P < 0.05), migration (P < 0.05), invasion (P < 0.05), and promote apoptosis (P < 0.05) in LUSC cells. However, the suppression of miR-1976 may reverse this inhibitory effect by specifically targeting NCAPH. This study showed that NCAPH can serves as a novel potential oncogenic biomarker for LUSC and its regulation is controlled by upstream miR-1976. miR-1976 can directly targets NCAPH to affect the proliferation, migration, invasion, and apoptosis of LUSC cell.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144690295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotype by environment interaction for productive and reproductive traits in beef cattle using imputed whole genome sequence.","authors":"Ivan Carvalho Filho, Gabriel Soares Campos, Daniela Lourenco, Flavio Schram Schenkel, Delvan Alves da Silva, Thales Lima Silva, Caio Souza Teixeira, Larissa Fernanda Simielli Fonseca, Gerardo Alves Fernandes Júnior, Lucia Galvão de Albuquerque, Roberto Carvalheiro","doi":"10.1007/s13353-025-00987-z","DOIUrl":"https://doi.org/10.1007/s13353-025-00987-z","url":null,"abstract":"<p><p>Accounting for genotype by environment interaction (GxE) and using genomic information may enhance the prediction accuracy <math><mrow><mo>(</mo> <mover><mtext>ACC</mtext> <mo>^</mo></mover> <mo>)</mo></mrow> </math> of breeding values. Hence, the objective of this study was to evaluate the gain in <math><mover><mtext>ACC</mtext> <mo>^</mo></mover> </math> using single-step genomic BLUP using high-density SNP chip (ssGBLUP_HD) or whole genome imputed sequence (ssGBLUP_SEQ) compared to pedigree BLUP in the presence of GxE. Phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW) were obtained from commercial breeding programs of Nellore cattle. There were 1,578,591 animals in the pedigree, from which 51,485 had genotypes with high-density SNP chip (HD) and whol- genome imputed sequence (WGS), totaling 460,578 and 2,437,948 SNPs, respectively, after quality control. Contemporary group effects, estimated with a regular animal model (without modeling GxE), were used to define the environmental gradients (EG) for the reaction norm model (RNM). Genetic sensitivity to environmental variation was assessed by fitting three different linear RNM: the first considering only pedigree (BLUP), the second also considering the genomic information from HD, and the third considering the genomic information from WGS. The validation was carried out for genotyped young bulls, with no progeny records in the reduced data and at least one in the complete data. Models were compared using prediction accuracy, dispersion, correlation between the breeding values from reduced data and complete data, and bias from the linear regression method. Re-ranking between animals and heterogeneity of genetic variance in different EG were observed, suggesting the presence of GxE. The results for the regression coefficients of the RNM showed, in general, that the inclusion of genomic information increased the <math><mover><mtext>ACC</mtext> <mo>^</mo></mover> </math> for the RNM regression coefficients for all traits. For SC, PWG, and YW, the highest accuracies were obtained with ssGBLUP_SEQ. Conversely, AFC had higher accuracy with ssGBLUP_HD. In addition, the <math><mover><mtext>ACC</mtext> <mo>^</mo></mover> </math> for genotyped young bulls increased as the EG increased. In conclusion, ssGBLUP_SEQ yielded higher <math><mover><mtext>ACC</mtext> <mo>^</mo></mover> </math> and correlation and a lower bias than the BLUP across all EG, indicating that the implementation of genomic selection using the whole genome sequence and accounting for GxE benefits this Nellore beef cattle population.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144674828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening and investigating the regulatory mechanisms of oxidative stress-related biomarkers in thoracic aortic aneurysms.","authors":"Tao Liu, Pandeng Wang, Chenfan Guo, Xiangsen Liang, Baoshi Zheng","doi":"10.1007/s13353-025-00988-y","DOIUrl":"https://doi.org/10.1007/s13353-025-00988-y","url":null,"abstract":"<p><p>Excess reactive oxygen species leading to oxidative stress has been identified as a significant factor in cardiovascular disease. However, the molecular mechanisms of oxidative stress-related genes in thoracic aortic aneurysm have not been thoroughly explored. An analysis of the GSE9106 dataset, using a geneset related to oxidative stress, revealed important links to purine metabolism pathways through functional enrichment analysis. A systematic investigation identified seven candidate genes, resulting in the identification of four potential biomarkers (IL10, SNCA, MAP1LC3A, and EPX) that show strong diagnostic promise for thoracic aortic aneurysm. These biomarkers were associated with critical pathways, including neuroactive ligand-receptor interaction and olfactory transduction. Correlation analysis also highlighted their relationships with specific immune cell types. The study not only examined biomarker-drug interactions but also performed experimental validations using qRT-PCR and immunohistochemistry. While the expression patterns of IL10 aligned with existing databases, some inconsistencies were observed in the validation of the other three biomarkers. Overall, these findings provide important insights into the diagnosis and treatment of thoracic aortic aneurysm, underscoring the significant role of oxidative stress-related biomarkers in this condition.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144608405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}