Journal of Applied Genetics最新文献

{"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}

{"title":"Identification of variants from gene expression data of opioid-addicted patients.","authors":"Swati Ajmeriya, Biswadip Chatterjee, Subhradip Karmakar","doi":"10.1007/s13353-025-00989-x","DOIUrl":"https://doi.org/10.1007/s13353-025-00989-x","url":null,"abstract":"<p><p>NGS (next-generation sequencing) has become a rapid advance in discovering the variants in the genomic data for disease diagnosis, prognosis, and therapeutic decision. However, the scope of detecting single nucleotide polymorphisms (SNPs) becomes limited by the availability of reliable high-throughput data. OUD (opioid use disorder) is a chronic condition marked by prolonged opioid misuse, leading to cycles of relapse and remission. The discovery of genetic variants associated with OUD is constrained by limited genomic data, making it crucial to identify these variants and their genetic factors. The identification of variants from RNA-seq (RNA-sequencing) data can become the representative of the SNP analysis that is generally preferred from the whole genome or exome sequencing data. This study aimed to identify variants from gene expression data downloaded from NCBI GEO with accession PRJNA492904 in postmortem ventral midbrain specimens of chronic opioid users. We hypothesized that the NRXN3 gene would exhibit the highest number of variants due to its significant role in neuronal synapse function and its association with opioid addiction and impulsivity. We utilized RNA-Seq data from OUD patients (PRJNA492904, NCBI SRA) to detect variants in expressed RNA, which can indicate functional protein changes. Eight genes were analyzed: BDNF, DRD2, DRD3, NRXN3, OPRD1, OPRM1, and NGFB, with a primary focus on NRXN3. Our findings revealed the highest number of variants in NRXN3 compared to the other genes, highlighting its potential importance in OUD and the robustness of RNA-Seq in variant detection.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583916","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":"Genome-wide identification of genetic determinants for gall midge resistance in rice using genic markers.","authors":"Basana Gowda Gadratagi, Lopamudra Mandal, Rameswar Prasad Sah, Anilkumar C, Guru-Pirasanna-Pandi G, Naveenkumar B Patil, Nandini Sahu, Muhammed Azharudheen T P, Sasmita Behera, Prakash Chandra Rath, Shyamaranjan Das Mohapatra","doi":"10.1007/s13353-025-00985-1","DOIUrl":"https://doi.org/10.1007/s13353-025-00985-1","url":null,"abstract":"<p><p>The Asian rice gall midge poses a severe threat to rice yields, making the development of resistant rice cultivars the most cost-effective and efficient strategy to manage the gall midge. A diverse panel of 115 rice accessions was phenotyped, revealing varying resistance to the gall midge biotype 2. The panel's diversity and familial relatedness were assessed before conducting a genome-wide association study to identify marker-trait associations (MTAs) for gall midge resistance. Newly developed candidate gene-derived markers were used along with random microsatellite markers in genotyping. A total of 50 significant MTAs with P < 0.05 were found. Except for chromosome 11, all of the rice chromosomes had significant MTAs. The QTL identified on chromosomes 6, 8, and 9 has been associated with 66F 67R, 54F 55R, and RM107, explaining maximum phenotypic variation. The allele effects of the associated markers differentiated susceptible and highly resistant genotypes, confirming their association with gall midge resistance. Seven genes associated with the general response to stress tolerance were found in the gall midge resistance QTL region. On chromosome 9, one putative gene for gall midge resistance was identified, which is associated with marker RM23914. These candidate genes identified have a significant impact on the gall midge resistance response. This investigation contributes to a better understanding of the rice gall midge resistance mechanism and provides essential genetic information for the breeding and functional verification of resistant cultivars.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540284","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":"Design principle of successful genome editing applications using CRISPR-based toolkits.","authors":"Juhi Sharma, Rajesh Biswas, Prashant Khare","doi":"10.1007/s13353-025-00979-z","DOIUrl":"https://doi.org/10.1007/s13353-025-00979-z","url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins are the most promising toolkit of synthetic biology for genetic engineering applications across species. Essentially, the Type II CRISPR system, featuring Cas9 nuclease from Streptococcus pyogenes complexed with sgRNA, introduces targeted DNA cleavage, enabling modifications with exceptional precision. This technology can be utilized for not only editing but also modulating gene expressions, thereby finding widespread utility in various biotechnological applications. Here we discuss strategies to construct a consolidated platform aiming at developing a CRISPR-based gene editing system in microbial hosts such as yeast. Employing the well-known gene editing enzymes, i.e., Cpf1 and dCas9, two independent strategies to develop a one-pot plasmid system have been proposed. Furthermore, approaches to reduce off-target cleavages introduced by non-specific targeting of CRISPR complex have been discussed. Finally, an overarching discussion on advanced strategies to design robust CRISPR components is provided for streamlining future genome editing applications.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540283","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":"Expanding the knowledge about Thauvin-Robinet-Faivre syndrome: a case report with novel clinical findings and review of the literature.","authors":"Andrea Cosentino, Flavia D'Orazio, Roberto Magnato, Wilhelm Berger","doi":"10.1007/s13353-025-00984-2","DOIUrl":"https://doi.org/10.1007/s13353-025-00984-2","url":null,"abstract":"<p><p>This case report expands the phenotypic spectrum of Thauvin-Robinet-Faivre syndrome (TROFAS, OMIM #617107), a rare autosomal recessive disorder caused by biallelic loss-of-function mutations in the FIBP gene. We describe a patient with genetically confirmed TROFAS who presented with novel clinical features, including non-ossifying fibromas, subglottic tracheal stenosis, intermediate uveitis, and complete atrioventricular block requiring pacemaker implantation. The findings significantly broaden the phenotypic landscape of TROFAS and underscore the need for multidisciplinary management and long-term follow-up.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325813","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":"Exploring the role of circRNA-miRNA-mRNA interactions in cervical cancer progression: insights into HPV status and potential therapeutic approaches.","authors":"K J Sindhu, Venkatesan Nalini, Sundaram Sandhya, Devarajan Karunagaran","doi":"10.1007/s13353-025-00982-4","DOIUrl":"https://doi.org/10.1007/s13353-025-00982-4","url":null,"abstract":"<p><p>Human papillomavirus (HPV) is the primary etiological factor in cervical cancer. Circular RNAs (circRNAs) contribute significantly to tumor progression, functioning as microRNA (miRNA) sponges and interacting with RNA-binding proteins (RBPs). While circRNA-miRNA-mRNA regulatory networks have been studied in cervical cancer, the lack of intermediate neoplastic samples has limited the understanding of circRNA-driven progression from HPV-positive (HPV ⁺) or HPV-negative (HPV ^-) normal cervical epithelium (NCE) to cervical squamous cell carcinoma (CSCC). This study addressed that gap by identifying differentially expressed (DE) circRNAs across four comparisons: high-grade squamous intraepithelial lesions (HSIL) vs. HPV ⁺ NCE, HSIL vs. HPV ^-NCE, CSCC vs. HPV ⁺NCE, and CSCC vs. HPV ^- NCE, using the limma R package. Commonly dysregulated circRNAs across comparisons were identified, revealing potential contributors to cancer progression regardless of HPV status. Of the 12 DE circRNAs identified, 11 had miRNA partners predicted via circAtlas, implicated in various oncogenic pathways. A protein-protein interaction (PPI) network of 30 hub genes was generated using STRING analysis. Among these, USP39, PQBP1, ANAPC5, STUB1, and UBE2D2 were significantly associated with overall survival in cervical cancer. Validation using qRT-PCR confirmed a competing endogenous RNA (ceRNA) network involving hsa-KIF4A_0022, hsa-miR-29b-2-5p, and UBE2D2 in cervical cancer of South Asian Indian origin. The study utilized CMAP2 and CTDBASE, identifying foretinib, TPCA-1, and dequalinium as promising drugs targeting key hub genes. Although limitations include a small sample size and ethnic heterogeneity in in vitro validation, this study advances our understanding of circRNA mechanisms in cervical cancer and identifies novel biomarkers and therapeutic targets.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325814","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":"Overexpression of adenosine receptor (A1, A2a, A2b, A3) genes in esophageal tumor tissue: A2b adenosine receptor as a potential biomarker and anticancer target.","authors":"Mahmood Poorjam, Marie Saghaeian Jazi, Jahanbakhsh Asadi, Alireza Norouzi, Abdolsamad Gharavi, Seyyed Mehdi Jafari","doi":"10.1007/s13353-025-00981-5","DOIUrl":"https://doi.org/10.1007/s13353-025-00981-5","url":null,"abstract":"<p><p>Esophageal cancer is the eighth most common cancer, the third most common gastrointestinal cancer, and the leading cause of cancer death worldwide. Adenosine receptor signaling is one of the important pathways that have been recently found to be dysregulated in some cancers. Adenosine receptors are divided into four subgroups: A1, A2a, A2b, A3, and here in the current study, we aimed to investigate their association with esophageal cancer. The results showed that the expression level of adenosine receptor genes A1, A2a, A2b, and A3 in esophageal tumor tissue was increased 5.02, 4.22, 9.36, and 3.90 times compared to tumor margin tissue, respectively (p < 0.05). According to the comparison of these values, the A2b receptor gene has the highest overexpression in esophageal tumor samples. There was no significant relationship between adenosine receptor gene expression and age, grade, and tumor size of patients with esophageal cancer. Our data also indicated that adenosine-induced cell death was inhibited by the A2B adenosine receptor antagonist (PSB 603). Finally, our results showed an increase in the expression of all four adenosine receptors in tumor tissue relative to the tumor margin, and the pattern of adenosine receptor expression (A2b > A1 > A2a > A3) shows that the A2b receptor is probably more important than the other adenosine receptors regarding the overexpression level and adenosine-mediated cell death in esophageal cancer cells.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144274881","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":"Dynamics of accumulation of lysine and tryptophan, and kernel modification in opaque2, opaque16, and double mutant (opaque2/opaque16) genotypes during kernel development in maize.","authors":"Gulab Chand, Vignesh Muthusamy, Tanu Allen, Nisrita Gain, Bhavna Singh, Suman Dutta, Nitish R Prakash, Sohini Singh, Konsam Sarika, Gautam Chawla, Rajkumar U Zunjare, Firoz Hossain","doi":"10.1007/s13353-025-00983-3","DOIUrl":"https://doi.org/10.1007/s13353-025-00983-3","url":null,"abstract":"<p><p>Recessive opaque2 (o2) and opaque16 (o16) genes enhance lysine and tryptophan in maize kernels. Though few o2, o16-, and o2o16-based maize genotypes have been developed, the transition of quality attributes and seed morphology through different stages of kernel development has not been studied yet. To understand the role of o2 and o16 genes in the regulation of essential amino acids and kernel opaqueness in maize, we analyzed the accumulation pattern of lysine and tryptophan, and the occurrence of opaqueness in the developing kernels at 15, 30, and 45 days after pollination (DAP) among a set of o2-, o16-, and o2o16-based inbreds. Genotypes with o2o16 possessed significantly higher lysine (0.64%) and tryptophan (0.25%) over o2 (lysine, 0.48%; tryptophan, 0.18%) and o16 (lysine, 0.46%; tryptophan, 0.17%) alone across kernel development stages. A decreasing trend of amino acid accumulation in o2-, o16-, and o2o16-based genotypes was observed through 15-, 30-, and 45-DAP. Kernel opaqueness also showed a similar decreasing trend among o2-, o16-, and o2o16-based inbreds during kernel development. A positive association was observed between lysine and tryptophan (r = 0.95), tryptophan and opaqueness (r = 0.60), and lysine and opaqueness (r = 0.60) across DAPs. Hard endosperm in wild types and o16 genotypes was due to compact starch-granule structures packed with more proteinaceous matrix compared to o2 and o2o16. This is the first report on nutritional quality and opaqueness at different stages of kernel development in o2-, o16-, and o2o16-based genotypes.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247976","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 subtropical breeding lines for ideal plant architecture in maize through multiple selection indices.","authors":"Govinda Rai Sarma, Rajkumar U Zunjare, Vignesh Muthusamy, Ravindra K Kasana, Ikkurti Gopinath, Bhavna Singh, Godawari S Pawar, Neha Sharma, Hriipulou Duo, Rashmi Chhabra, Rakesh K Devlash, Satish K Guleria, Viswanathan Chinnusamy, Firoz Hossain","doi":"10.1007/s13353-025-00975-3","DOIUrl":"https://doi.org/10.1007/s13353-025-00975-3","url":null,"abstract":"<p><p>High plant density assumes significance for higher yield per unit area. However, reports on breeding for ideal plant architecture (IPA) in maize are limited due to lack of comprehensive characterization of germplasm. Here, we assessed genetic variation and identified inbreds for 14 plant architectural traits among 48 subtropical maize inbreds through multi-location analysis. Wide genetic variation for (i) stalk-related traits, viz., plant height (100.5-209.8 cm), ear height (26.4-106.3 cm), internode number (3.8-10.9), and internode length (8.1-15 cm); (ii) leaf-related traits, viz., leaf length (39.7-77.1 cm), leaf width (5.2-10.5 cm), leaf area (158.6-568.4 cm²), leaf angle (18.4-84.6°), leaf orientation value (2.2-71.3), number of leaves above-ear (3.2-7.2), and husk number (5.7-14.4); and (iii) tassel-related traits, viz., tassel height (21.8-34.9 cm), number of tassel branches (3.9-16.6), and tassel branching angle (10.2-78.4°) were observed. All traits showed significant variation due to environment and genotype × environment interactions. Correlation analysis implied that narrow leaf angle would produce compact tassel as well (r = 0.53, p < 0.001). Internode number and leaf width (r = - 0.33, p = 0.031), number of leaves and leaf length (r = 0.42, p = 0.004), plant height and leaf length (r = 0.39, p = 0.005), and leaf length and tassel height (r = 0.44, p = 0.003) were also associated. HKI-1105, CML-568, BAUIM-4, and BAUIM-2 were the most stable and promising inbreds with IPA using three popular selection indices (AMMI-TGSI, WAASBY-I, and MTSI). These promising inbreds could serve as suitable donors for germplasm diversification, besides generating hybrid combinations for high plant density. This is the first comprehensive analysis to characterize sub-tropically adapted maize inbreds for plant architectural traits.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247989","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":"Genome-wide association study of seedling leaf rust resistance in European winter wheat cultivars.","authors":"Paweł Cz Czembor, Urszula Piechota, Jie Song, Dariusz Mańkowski, Magdalena Radecka-Janusik, Dominika Piaskowska, Piotr Słowacki, Andrzej Kilian","doi":"10.1007/s13353-025-00976-2","DOIUrl":"https://doi.org/10.1007/s13353-025-00976-2","url":null,"abstract":"<p><p>Leaf rust, caused by Puccinia triticina, is a major wheat disease that impacts yield and quality. This study aimed to identify genetic loci associated with seedling resistance to leaf rust in European winter wheat cultivars. A genome-wide association study was conducted on a panel of 181 wheat genotypes, including 143 modern cultivars and 38 lines with known leaf rust resistance genes. Pathogen evaluation involved 18 P. triticina isolates, which revealed diverse virulence levels and allowed resistant cultivars to be identified. The study identified 88 marker-trait associations clustered into 23 quantitative trait loci (QTL) across 13 chromosomes. Three QTL-QLr.ihar-1B.1, QLr.ihar-3D.1, and QLr.ihar-4 A.1-correspond to the major resistance genes Lr26, Lr24, and Lr28. Several QTL appear novel, with six (QLr.ihar-2B.2, QLr.ihar-3 A.1, QLr.ihar-3B.2, QLr.ihar-7 A.1, QLr.ihar-7D.1, and QLr.ihar-7D.2) explaining over 20% of phenotypic variance that could be considered for breeding purposes. Among 113 resistant cultivars, only 23 QTL were present in 51 genotypes, suggesting that resistance in the remaining 62 cultivars is under control of unidentified loci. The findings highlight the complex and diverse resistance patterns in European wheat, offering significant insights for breeding programs targeting enhanced leaf rust resistance.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247988","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}