Journal of Applied Genetics最新文献

{"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}

{"title":"Gene therapy strategies in ophthalmology-an overview of current developments and future prospects.","authors":"Julia B Krajewska, Arleta Waszczykowska","doi":"10.1007/s13353-025-00973-5","DOIUrl":"https://doi.org/10.1007/s13353-025-00973-5","url":null,"abstract":"<p><p>Gene therapies have recently emerged as promising strategies for treatment of previously incurable or poorly managed diseases. These hopes are particularly high in ophthalmology, as the eye is considered exceptionally suited for gene therapy. Expansion of gene therapy products may change the clinical course of treatment and give new chances to many patients. In this review, we address treatment possibilities and delivery methods as well as challenges and uncertainties related to gene therapy. We present inherited and acquired diseases which are subject to studies within this area, summarize current trends in ocular gene therapy, and indicate the future directions.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144225556","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":"Endophytic fungal communities of Calicotome spinosa-an important medicinal plant of Tizi-Ouzou (Algeria).","authors":"Amina Zareb, Piotr Banachewicz, Polina Havrysh, Lidia Błaszczyk, Tinhinane Hammad, Cylia Meftah, Sylwia Salamon","doi":"10.1007/s13353-025-00980-6","DOIUrl":"https://doi.org/10.1007/s13353-025-00980-6","url":null,"abstract":"<p><p>Endophytic fungi enhance plant growth and improve tolerance to abiotic and biotic stress. Calicotome spinosa is an important medicinal plant that occupies the area of Tizi-Ouzou and is considered a nonflammable plant that maintains this ecosystem and regenerates degraded substrates. However, the knowledge about the endogenous fungal assembly of C. spinosa remains underexplored. Therefore, this study aimed to isolate and determine the fungal communities inhabiting the C. spinosa leaves endosphere using morphological and molecular identification methods. Morphological identification revealed the presence of Alternaria, Cladosporium, Mucor, Neoscytalidium, Rhizoctonia, Rhodotorula, Phoma, Penicillium, and Trichophyton genera. Molecular analysis of the selected phylogenetic markers' nucleotide sequences detailed the previous one and discovered the following: Biscogniauxia mediterranea, Schizophyllum commune, Penicillium polonicum, Athelia bombacina, Chaetomium globosum, Penicillium brevicompactum, Coriolopsis sp., Coprinellus sp., Aspergillus chevalieri, Aspergillus wentii, Canariomyces microspores, Alternaria alternata, Canariomyces notabilis, Rosellinia sp., Penicillium sp., and Alternaria sp. The taxonomic knowledge gained here for the first time about the group of endophytic fungi associated with the ethnomedicinal plant growing in Algeria, and the disposition of these fungi isolates provides a basis for further research into understanding the functions they may have in the plant. These isolates are therefore a source of potential candidates for further research into their possible applications as beneficial microorganisms in ecology, environmental and plant protection, and sustainable agriculture.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208610","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":"Haplotypes affecting stillbirth and fertility in Icelandic Dairy Cattle.","authors":"Egill Gautason, Þórdís Þórarinsdóttir, Goutam Sahana","doi":"10.1007/s13353-025-00978-0","DOIUrl":"https://doi.org/10.1007/s13353-025-00978-0","url":null,"abstract":"<p><p>In the last decades, the rate of stillbirths in the Icelandic Dairy Cattle population has increased. Some of these stillbirths may be caused by recessive lethal mutations segregating in the population. These alleles can be identified by detecting homozygous haplotype deficiency (HHD) in genotyped animals. The aim of this study was to find genomic regions affecting stillbirth and fertility in the Icelandic Dairy Cattle population. We analysed genotypes from 20,557 animals with 35,481 autosomal markers. We identified HHD segments and estimated their effects on stillbirths and insemination failure, measured as non-return rates. We conducted genome-wide association studies (GWAS) for stillbirth and five fertility traits: interval from first to last inseminations, conception rate, number of inseminations, calving interval and infertility. While no GWAS association reached the genome-wide significance threshold, some of the top signals co-located with HHD haplotypes. A total of 19 haplotypes significantly either decreased fertility, or increased incidence of stillbirths, or both. Two HHD regions on BTA13: 43,577,221-59,026,521 and BTA8: 83,276,598-84,472,391 were associated with both lower fertility and higher incidence of stillbirths. We found no evidence of large structural variations in or around the HHD regions, suggesting that these signals are likely due to single loss-of-function mutation or small structural variations. Further research should focus on exploring these regions using whole genome sequence data.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144199161","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 a migracytosis and angiogenesis-associated lncRNAs signature in immunotherapy in breast cancer.","authors":"Yier Qiu, Mengting Li, Qianhui Qiu, Guowen Lu","doi":"10.1007/s13353-025-00977-1","DOIUrl":"https://doi.org/10.1007/s13353-025-00977-1","url":null,"abstract":"<p><p>Migracytosis and angiogenesis were crucial in breast cancer (BRCA) progression. This study aimed to develop a prognostic signature based on migracytosis- and angiogenesis-related lncRNAs. All genetic and clinical data of BRCA were acquired from The Cancer Genome Atlas (TCGA) database. A prognostic signature consisting of six lncRNAs (YTHDF3-AS1, AC018445.5, AP005131.1, AC010531.3, MIR200CHG, and AC000067.1) was established through correlation and Cox regression analysis, as well as the least absolute shrinkage and selection operator (LASSO) test. The BRCA patients from TCGA were categorized into high-risk and low-risk subgroups. Nomograms, calibration plots, Kaplan-Meier survival curves, and receiver operating characteristic (ROC) curves were used to evaluate the overall survival (OS) and predictive value of the signature. To explore the biological functions of migracytosis- and angiogenesis-related lncRNAs, enrichment analysis, tumor mutation burden (TMB), and the ESTIMATE algorithm were performed. Additionally, consensus clustering was applied to categorize tumor subtypes, and the disparity among all clusters was assessed, including drug sensitivity and immunotherapeutic efficacy. The expression levels of prognostic lncRNAs were validated using RT-PCR, while their functional impact on cell proliferation was assessed via the Cell Counting Kit-8 (CCK-8) assay in vitro. The results indicated that patients in the high-risk subgroup had a worse prognosis, higher TMB, stronger immune response, and greater sensitivity to immunotherapy. In summary, the prognostic risk signature based on migracytosis- and angiogenesis-related lncRNAs was associated with the clinical prognosis of BRCA patients. The signature's risk score could potentially be used to predict clinical classification and therapeutic efficacy.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187030","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}