Journal Of Applied Genetics[JOURNAL]
Sun
200 papers
MiR-1976 affects lung squamous cell carcinoma development by targeting NCAPH.
Li Y, Zhou H, Yao Y … +1 more , Fan Z
J Appl Genet · 2025 Jul · PMID 40699282 · Publisher ↗
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...
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.
Genotype by environment interaction for productive and reproductive traits in beef cattle using imputed whole genome sequence.
Carvalho Filho I, Campos GS, Lourenco D … +8 more , Schenkel FS, da Silva DA, Lima Silva T, Souza Teixeira C, Fonseca LFS, Fernandes Júnior GA, de Albuquerque LG, Carvalheiro R
J Appl Genet · 2026 Feb · PMID 40689903 · Publisher ↗
Accounting for genotype by environment interaction (GxE) and using genomic information may enhance the prediction accuracy of breeding values. Hence, the objective of this study was to evaluate the gain in using single...
Accounting for genotype by environment interaction (GxE) and using genomic information may enhance the prediction accuracy of breeding values. Hence, the objective of this study was to evaluate the gain in 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 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 for genotyped young bulls increased as the EG increased. In conclusion, ssGBLUP_SEQ yielded higher 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.
Screening and investigating the regulatory mechanisms of oxidative stress-related biomarkers in thoracic aortic aneurysms.
Liu T, Wang P, Guo C … +2 more , Liang X, Zheng B
J Appl Genet · 2025 Jul · PMID 40643772 · Publisher ↗
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 ane...
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.
Identification of variants from gene expression data of opioid-addicted patients.
Ajmeriya S, Chatterjee B, Karmakar S
J Appl Genet · 2025 Jul · PMID 40627269 · Publisher ↗
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 po...
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.
Genome-wide identification of genetic determinants for gall midge resistance in rice using genic markers.
Gadratagi BG, Mandal L, Sah RP … +8 more , C A, G GP, Patil NB, Sahu N, P MAT, Behera S, Rath PC, Das Mohapatra S
J Appl Genet · 2026 May · PMID 40601239 · Publisher ↗
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 acce...
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.
Design principle of successful genome editing applications using CRISPR-based toolkits.
Sharma J, Biswas R, Khare P
J Appl Genet · 2025 Dec · PMID 40591237 · Publisher ↗
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...
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.
Masquerading as lymphoma: the accelerated phase of Chediak-Higashi syndrome and its novel mutation.
Aggarwal P, Agarwal A, Aggarwal S … +2 more , Rani D, Gupta V
J Appl Genet · 2025 Sep · PMID 40591236 · Publisher ↗
Chediak-Higashi syndrome (CHS) is a rare autosomal recessive disorder. The clinical presentation may be fatal if these patients develop the catastrophic accelerated phase, i.e., hemophagocytic lymphohistiocytosis (HLH)....
Chediak-Higashi syndrome (CHS) is a rare autosomal recessive disorder. The clinical presentation may be fatal if these patients develop the catastrophic accelerated phase, i.e., hemophagocytic lymphohistiocytosis (HLH). We report a 2.5-year boy that presented to us with complaints of fever, recurrent cough, glandular neck swelling, and abdominal distension for 6 months. He also had a history of female sibling death (age, 3 years) 3 years ago with similar complaints. On examination, he had light skin and silver hair along with severe pallor, generalized significant lymphadenopathy, severe acute malnutrition, and hepatosplenomegaly. Since the patient's peripheral blood smear and bone marrow showed giant primary azurophilic granules in lymphocytes and eosinophils and the presence of 5 out of 8 HLH 2004 criteria, i.e., fever, hepatosplenomegaly, pancytopenia, hyperferritinemia, and hypertriglyceridemia, a diagnosis of CHS with HLH was made. However, no hemophagocytosis was observed. A novel homozygous nonsense variant in exon 45 of the LYST gene (chr1:g.235702929G > A) similar to the one found in the elder female sibling and previously reported "likely pathogenic" was discovered, which was identified through genetic testing. This case highlights the importance of genetic testing in diagnosis as well as antenatal counselling.
Expanding the knowledge about Thauvin-Robinet-Faivre syndrome: a case report with novel clinical findings and review of the literature.
Cosentino A, D'Orazio F, Magnato R … +1 more , Berger W
J Appl Genet · 2026 May · PMID 40536757 · Full text
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...
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.
Exploring the role of circRNA-miRNA-mRNA interactions in cervical cancer progression: insights into HPV status and potential therapeutic approaches.
Sindhu KJ, Nalini V, Sandhya S … +1 more , Karunagaran D
J Appl Genet · 2026 May · PMID 40531429 · Publisher ↗
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-bi...
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.
Overexpression of adenosine receptor (A1, A2a, A2b, A3) genes in esophageal tumor tissue: A2b adenosine receptor as a potential biomarker and anticancer target.
Poorjam M, Jazi MS, Asadi J … +3 more , Norouzi A, Gharavi A, Jafari SM
J Appl Genet · 2026 May · PMID 40504303 · Publisher ↗
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...
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.
Dynamics of accumulation of lysine and tryptophan, and kernel modification in opaque2, opaque16, and double mutant (opaque2/opaque16) genotypes during kernel development in maize.
Chand G, Muthusamy V, Allen T … +9 more , Gain N, Singh B, Dutta S, Prakash NR, Singh S, Sarika K, Chawla G, Zunjare RU, Hossain F
J Appl Genet · 2025 Dec · PMID 40484905 · Publisher ↗
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 morp...
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.
Genome-wide association study of seedling leaf rust resistance in European winter wheat cultivars.
Czembor PC, Piechota U, Song J … +5 more , Mańkowski D, Radecka-Janusik M, Piaskowska D, Słowacki P, Kilian A
J Appl Genet · 2025 Dec · PMID 40484904 · Full text
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 cultiv...
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.
Identification of subtropical breeding lines for ideal plant architecture in maize through multiple selection indices.
Sarma GR, Zunjare RU, Muthusamy V … +11 more , Kasana RK, Gopinath I, Singh B, Pawar GS, Sharma N, Duo H, Chhabra R, Devlash RK, Guleria SK, Chinnusamy V, Hossain F
J Appl Genet · 2026 Feb · PMID 40484903 · Publisher ↗
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. Her...
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 cm), 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.
Gene therapy strategies in ophthalmology-an overview of current developments and future prospects.
Krajewska JB, Waszczykowska A
J Appl Genet · 2026 May · PMID 40471435 · Full text
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 su...
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.
Endophytic fungal communities of Calicotome spinosa-an important medicinal plant of Tizi-Ouzou (Algeria).
Zareb A, Banachewicz P, Havrysh P … +4 more , Błaszczyk L, Hammad T, Meftah C, Salamon S
J Appl Genet · 2025 Sep · PMID 40459721 · Full text
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 tha...
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.
Haplotypes affecting stillbirth and fertility in Icelandic Dairy Cattle.
Gautason E, Þórarinsdóttir Þ, Sahana G
J Appl Genet · 2025 Dec · PMID 40451979 · Full text
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...
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.
Identification of a migracytosis and angiogenesis-associated lncRNAs signature in immunotherapy in breast cancer.
Qiu Y, Li M, Qiu Q … +1 more , Lu G
J Appl Genet · 2026 May · PMID 40445580 · Publisher ↗
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...
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.
Riboflavin treatment in L-2-hydroxyglutaric aciduria: report on a pediatric patient and literature review.
Lipiński P, Ciara E, Bogdańska A … +2 more , Jurkiewicz E, Tylki-Szymańska A
J Appl Genet · 2026 May · PMID 40380983 · Full text
L-2-hydroxyglutaric aciduria (L-2-HGA, #236,792) is an autosomal recessive neurodegenerative disorder caused by the deficiency of L-2-hydroxyglutarate dehydrogenase, a flavin adenine dinucleotide (FAD)-dependent enzyme,...
L-2-hydroxyglutaric aciduria (L-2-HGA, #236,792) is an autosomal recessive neurodegenerative disorder caused by the deficiency of L-2-hydroxyglutarate dehydrogenase, a flavin adenine dinucleotide (FAD)-dependent enzyme, due to biallelic pathogenic variants in the L2HGDH gene. The present study described the patient with L2HGA presenting with a slight psychomotor delay, epilepsy from 5 years of age, non-progressive cerebellar ataxia, and mild to moderate intellectual disability during 10 years of follow-up. Two different heterozygous variants in the L2HGDH gene were identified in the patient: a known substitution c.829C > T(p.Arg277*) and a novel substitution c.1196 + 1G > A corresponding with significantly increased urinary L-2-hydroxyglutarate (L2HG) excretion. A 6-month period of treatment with riboflavin (100 mg/day) was implemented with no clinical nor biochemical effect.
Genetic mapping of the Fusarium head blight resistance gene in wheat Guixie 3.
Luo Y, Cheng B, Chen T … +4 more , Sui J, Wu W, Xu Q, Wang W
J Appl Genet · 2025 Dec · PMID 40372629 · Full text
Fusarium head blight (FHB) is a global detrimental disease affecting wheat production. While Guixie 3 shows strong resistance to FHB, its resistance mechanism is not well understood. Hence, this study aims to elucidate t...
Fusarium head blight (FHB) is a global detrimental disease affecting wheat production. While Guixie 3 shows strong resistance to FHB, its resistance mechanism is not well understood. Hence, this study aims to elucidate the genetic basis of disease resistance in Guixie 3 and identify new genetic resources for FHB resistance in wheat. The study used an F recombinant inbred line population developed by crossing Avocet S with Guixie 3. FHB resistance was phenotypically evaluated across 2 years and two locations (i.e., four environments) after single-floret inoculation, and it was genetically mapped using the wheat 55 K single-nucleotide polymorphism array. A total of 15 quantitative trait loci (QTLs) for FHB resistance were detected on chromosomes 1D (2), 2A (2), 2B (3), 2D.1 (2), 3B (1), 4A (1), 4B (1), 4D (1), 5A (1), and 5B.2 (1). Notably, a QTL on chromosome 2D.1, designated as Qfhb.gaas.2D.1-1, was consistently detected in two environments. This QTL spanned the interval AX-86163393 to AX-110072786, with a genetic interval of 45.12-46.51 cM and a physical interval of 35.68-37.04 Mb (1.36 Mb). It explained 14.07-33.00% of the phenotypic variation. Furthermore, 39 candidate genes were identified in this target region, of which eight were predicted to be associated with FHB resistance. These candidate genes will be further analyzed and validated for FHB resistance in future studies.
Elucidating the transcriptomic response of adult-derived mHypoA-2/12 mouse hypothalamic neuron cell line to cannabidiol (CBD) exposure.
Gurgul A, Jasielczuk I, Szmatoła T … +4 more , Semik-Gurgul E, Kucharski M, Mizera-Szpilka K, Ocłoń E
J Appl Genet · 2025 Dec · PMID 40335839 · Full text
Cannabidiol (CBD) is a compound found in Cannabis sativa that is known for its neuroprotective, anti-inflammatory, analgesic, and anxiolytic properties. These properties make it a promising treatment for various neurolog...
Cannabidiol (CBD) is a compound found in Cannabis sativa that is known for its neuroprotective, anti-inflammatory, analgesic, and anxiolytic properties. These properties make it a promising treatment for various neurological conditions. This study aimed to examine the effects of CBD on hypothalamic neurons at the transcriptome level using the adult-derived mHypoA-2/12 mouse cell line. The cells were exposed to four different CBD concentrations (ranging from 0.325 to 3 µM) for 6 and 24 h. Apart from the transcriptome analysis, apoptosis (caspase 3/7 activity) and viability (MTT) assays were performed. The obtained results showed that CBD enhanced cell viability, especially after 24 h of treatment and at lower or intermediate concentrations, and reduced apoptosis, with significant effects at the highest concentration. CBD caused moderate transcriptome profile changes (13 to 69 genes per treatment), with more genes affected at higher concentrations and shorter exposure times, indicating a stronger initial cellular response. Further analysis revealed that CBD affects several biological processes, including: intrinsic apoptosis suppression via p53 modulation, impacting genes like Bbc3, Mdm2, Cdkn1a, and Smad3. Additionally, CBD influenced genes involved in extracellular matrix organization, including metalloproteinases (Mmp-3, Mmp-13) and their inhibitors (Timp1), as well as collagen components (Col11a1) and mitochondrial respiratory chain complexes (mt-Nd5, mt-Nd4). Genes related to serotonin and dopamine biosynthesis, as well as Aldh2, were also impacted, linking CBD's effects in hypothalamic neurons to potential benefits in managing alcohol use disorders. These findings suggest the hypothalamus is a significant target for CBD, warranting further investigation.
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