Journal Of Applied Genetics[JOURNAL]
Sun
200 papers
Rare co-existence of 15q26 deletion syndrome and lymphangioleiomyomatosis: diagnostic and therapeutic challenge.
Buha I, Maric N, Bonaci-Nikolic B … +8 more , Stjepanovic M, Belic S, Milenkovic B, Savic M, Bogdanovic A, Zecevic A, Jankovic J, Spasovski V
J Appl Genet · 2025 Dec · PMID 41339980 · Publisher ↗
15q26 deletion syndrome is a rare genetic condition caused by the deletion of terminal end of the long arm of chromosome 15 (Drayer's syndrome). Clinical presentation usually implies intrauterine growth restriction, post...
15q26 deletion syndrome is a rare genetic condition caused by the deletion of terminal end of the long arm of chromosome 15 (Drayer's syndrome). Clinical presentation usually implies intrauterine growth restriction, postnatal growth failure, varying degrees of intellectual disability, developmental delay, typical facial appearance, brachydactyly and diaphragmatic hernia. Lymphangioleiomiomatosis (LAM) is a rare genetic disease affecting multiple organs, which almost exclusively afflicts women. Typical presentation of LAM disease is pulmonary LAM, characterized by cyst-like destruction of pulmonary tissue, which leads to loss of pulmonary function, and if progresses further can lead to recurring pneumothoraxes. Co-existence of these two rare diseases hasn't been reported so far. Here we report a case of the simultaneous presence of 15q26 deletion syndrome and LAM disease in a 38-year-old female. She presented with short statue, brachydactyly, pes equinovarus, microcephaly and signs of intellectual disability manifesting from birth and early childhood. At the age of 23 she starts to suffer of recurring pneumothoraxes with gradual loss of pulmonary function. CT and pathohistological findings revealed the presence of pulmonary LAM and genetic testing revealed 15q26.2 microdeletion characteristic for 15q26 deletion syndrome. Successful treatment of LAM using mTOR inhibitor Sirolimus resulted in clinical and functional improvement.
The role of the CEBPB gene in porcine adipogenesis: a study using CRISPR/Cas9-edited mesenchymal stem cells.
Aksoy MO, Rozynek J, Stachowiak M … +1 more , Szczerbal I
J Appl Genet · 2026 May · PMID 41296247 · Full text
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 is a powerful tool for gene editing and the regulation of gene expression. It enables the introduction of targeted mutations, thereby facilitating f...
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 is a powerful tool for gene editing and the regulation of gene expression. It enables the introduction of targeted mutations, thereby facilitating functional studies of specific genes in various cellular processes. In this study, we aimed to generate a deletion in the promoter region of the CEBPB gene, which encodes a transcription factor involved in adipogenesis, and to evaluate the impact of this modification on the adipogenic differentiation potential of porcine mesenchymal stem cells (MSCs). A 575-bp deletion was introduced in the target region, resulting in the generation of both homozygous and heterozygous mutant cells. Adipogenic differentiation was assessed by quantifying transcript levels of adipocyte marker genes (GATA2, CEBPA, PPARG, and FABP4) at days 0, 4, 6, 8, and 10 of the differentiation process. Disruption of CEBPB expression led to the downregulation of these adipogenic markers, indicating impaired adipocyte differentiation. Additionally, to assess the proliferative capacity of the edited cells, the expression levels of proliferation-associated genes (CCND1, MCM2, and PCNA) were measured. A reduction in their transcript levels was observed in both homozygous and heterozygous mutant cells. These findings indicate that both homozygous and heterozygous deletions in the CEBPB promoter completely block adipogenesis and alter MSC proliferation, highlighting the pivotal role of CEBPB not only in adipogenic differentiation but also in the regulation of cell proliferation in porcine mesenchymal stem cells. These results provide new insights into the molecular mechanisms underlying adipose tissue development and have implications for pig breeding strategies aimed at optimizing carcass composition, as well as for biomedical research focused on adipose tissue biology.
Genetic variations in NFKB1 signaling molecules: implications for acute lymphoblastic leukemia in Saudi Arabia.
Alkhulaifi FM, Alshammari J, Alobaid HM … +2 more , Alqarzae SA, Alomar S
J Appl Genet · 2025 Nov · PMID 41205109 · Publisher ↗
Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling regulates immune responses and tumorigenesis. Variations in NF-κB pathway genes may alter susceptibility to acute lymphoblastic leukemia (A...
Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling regulates immune responses and tumorigenesis. Variations in NF-κB pathway genes may alter susceptibility to acute lymphoblastic leukemia (ALL). To evaluate associations between selected NFKB1 and NFKBIA polymorphisms and ALL risk in a Saudi population. We genotyped NFKB1 (rs93059, rs1287, rs1801) and NFKBIA (rs1050851, rs1957106, rs3138054) in 150 ALL patients and 115 matched controls using TaqMan® assays. Associations were assessed under multiple genetic models, and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. The NFKB1 rs93059 A allele was associated with reduced ALL risk (OR = 0.68; 95% CI: 0.48-0.97; p = 0.03), with the AA genotype showing protection in codominant (p = 0.03) and recessive (p = 0.02) models. For NFKB1 rs1287, the AA genotype increased risk (OR = 2.75; 95% CI: 1.14-6.62; p = 0.02) in the codominant model. The NFKB1 rs1801 C allele was enriched in patients (OR = 1.54; 95% CI: 1.04-2.23; p = 0.01). No significant associations were observed for NFKBIA variants after multiple-testing correction. NFKB1 rs93059 and rs1801 may influence ALL susceptibility in the Saudi population, underscoring the potential contribution of NF-κB pathway variants to leukemia risk. Functional analyses are warranted to clarify underlying mechanisms.
Extricating the allelic variation, population structure and genetic potential in buckwheat genotypes and substantiation of high yielding and stable genotypes with superior biochemical quality.
Swain S, Laloo B, Dutta PP … +6 more , Kaur S, Touthang L, Verma VK, Chandora R, Yadav SK, Kumar A
J Appl Genet · 2025 Nov · PMID 41204046 · Publisher ↗
Buckwheat is an underutilized crop with high nutritional values and antioxidant properties. The study was conducted with an aim to assess the genetic variability of 37 Fagopyrum esculentum Moench. and 67 Fagopyrum tatari...
Buckwheat is an underutilized crop with high nutritional values and antioxidant properties. The study was conducted with an aim to assess the genetic variability of 37 Fagopyrum esculentum Moench. and 67 Fagopyrum tataricum Gaertn. accessions using agro-morphological, biochemical, and microsatellite markers. For yield per plant, accessions, namely, IC24297, IC26591, and IC13413, with superior performances were identified. Based on correlations and regression-based path analysis, the key component traits, namely, number of seeds per plant, 100-seed weight, leaf blade width, seed width, and cyme length, were identified. Among F. esculentum group, EC18771, IC107238, and IC107265 had the highest carbohydrate, protein, and the lowest phytic acid, respectively. Likewise, IC24297, EC18769, and IC26596, with the highest carbohydrate, protein, and lowest phytic acid content, respectively, were identified under the F. tataricum group. By analyzing 65 SSR markers, an average of 2.63 alleles per locus was detected, with an average PIC value of 0.431. The observed heterozygosity for the polymorphic markers varied from 0.019 (Fagopyrum tataricum) to 0.462 (Fagopyrum esculentum), with an average of 0.099, showing the lower level of expected heterozygosity in tartary buckwheat accessions. Based on Nei's genetic distances, the buckwheat accessions were grouped into three clusters. Clusters I and III included the tartary accessions, while Cluster II encompassed both species. The AMOVA, conducted by categorizing the accessions into 25 subpopulations, indicated that 80% of the observed variation was due to differences among individuals, whereas 19% was due to within individuals. Based on additive main effects and multiplicative interaction (AMMI) and multi-trait stability index (MTSI) analyses, accessions, namely, IC13141, IC49667, IC26587, IC107983, and IC107981, have been identified as the best accessions, exhibiting high mean yield and stability across all three environments, and could be utilized in augmenting the buckwheat cultivation.
Association of polymorphisms of antioxidants (GSTM1/T1) and inflammation-related genes (CXCL8, IL-33, and IL-6) with chronic obstructive pulmonary disease (COPD).
Masood O, Kumar S, Kant S … +1 more , Banerjee M
J Appl Genet · 2025 Nov · PMID 41193663 · Publisher ↗
Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality globally. COPD, within its context of disease etiology, is characterized by chronic inflammation of the lungs. It is distinguishe...
Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality globally. COPD, within its context of disease etiology, is characterized by chronic inflammation of the lungs. It is distinguished by the aberrant production of oxidants, inflammatory cytokines, dysregulated immune cell activity, and remodeling of the airways. In this study, we analyzed the polymorphic association of antioxidants (GSTM1/T1) and inflammation-related genes (CXCL8, IL-33, and IL-6) with COPD. A case-control study was conducted with 227 subjects (116 healthy controls and 111 COPD cases). GSTM1/T1 genes were amplified by multiplex PCR' and inflammatory genes (CXCL8, IL-33, and IL-6) were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. GSTM1/T1 gene deletion rates in the COPD group were significantly higher than those in the control group (GSTM1: OR = 11.85, CI = 4.033-34.79, P < 0.0001; GSTT1: OR = 2.303, CI = 1.206-4.399, P = 0.0113). In addition, our research revealed a significant association between the combined GSTM1/T1 null genotype and increased susceptibility to COPD (OR = 18.66, CI = 2.345-148.5, P = 0.0003). A significantly increased frequency of the "CC" genotype of the CXCL8 (rs2227532) gene variant (OR = 7.50, CI = 2.429-23.16, P < 0.0001) was observed in COPD patients compared to the control group. However, there was no significant association of the IL-33 (rs7044343) polymorphism between healthy controls and COPD patients. The IL-6 (rs2069860) gene variant was found to be monomorphic. As a result of the investigation, it was concluded that individuals with the null genotype of GSTM1/T1 combined and the presence of the CXCL8 (rs2227532) gene variant have a higher likelihood of developing COPD.
Familial hyponatremia conditioned by the R137C mutation with constitutive activation of the vasopressin receptor.
Szymanik-Grzelak H, Daniel M, Pańczyk-Tomaszewska M
J Appl Genet · 2025 Nov · PMID 41177862 · Publisher ↗
Hyponatremia can occur in endocrinological diseases, neoplasms, kidney diseases, and acquired or genetically conditioned disorders of antidiuretic hormone levels. Nephrogenic syndrome of inappropriate antidiuresis (NSIAD...
Hyponatremia can occur in endocrinological diseases, neoplasms, kidney diseases, and acquired or genetically conditioned disorders of antidiuretic hormone levels. Nephrogenic syndrome of inappropriate antidiuresis (NSIAD) is a rare X-linked disease caused by a point mutation of the type 2 vasopressin receptor (AVPR2) gene. This mutation results in constitutive activation of the AVPR2 and a low sodium level.We reported the first familial NSIAD in Poland in siblings with hyponatremia. Case 1. A 2.5-year-old boy, during a respiratory tract infection, showed the following laboratory test results: Na 125 mmol/L, serumosmolality 260 mOsm/kg H2O, low uric acid level, and increased fractional sodium and uric acid excretions. Thyroid, adrenal, and renal function were normal. Copeptin level was low. Case 2. A 7-month-old brother presented with reduced activity and muscle tone, a sodium level of 117 mmol/L, and a serum osmolality of 249 mOsm/kg H2O. They were both confirmed to be hemizygous for the R137C mutation on the AVPR2 gene. The boys were advised to restrict their oral fluid intake and supplement sodium orally, aiming for sodium levels of 133-140 mmol/L. Conclusions: Genetic testing for an AVPR2 mutation is crucial in patients with hyponatremia, normovolemia, hypoosmolality, and low copeptin level.
MicroRNA bioinformatics in precision oncology: an integrated pipeline from NGS to AI-based target discovery.
Dey M, Remiszewski P, Piątkowski J … +3 more , Golik P, Teterycz P, Czarnecka AM
J Appl Genet · 2025 Oct · PMID 41168533 · Publisher ↗
Despite the growing recognition of microRNAs (miRNAs) as critical biomarkers in cancer, current approaches to their analysis remain fragmented, disjointed, and poorly integrated with emerging computational advances. This...
Despite the growing recognition of microRNAs (miRNAs) as critical biomarkers in cancer, current approaches to their analysis remain fragmented, disjointed, and poorly integrated with emerging computational advances. This lack of cohesion limits progress toward reproducible and clinically actionable biomarker discovery. To address this unmet need, we present a review that unifies the latest findings and tools in bioinformatics, machine learning (ML), and large language models (LLMs) for miRNA analysis in oncology, thereby bridging a significant methodological gap in the field. We begin by critically synthesizing, benchmarking, and evaluating algorithms, including miRDeep2 and DIANA-miRPath, within a functional pipeline that spans next-generation sequencing (NGS) data processing to multi-omics integration. Building on this foundation, we review ML-augmented layers incorporating supervised and deep learning (DL) algorithms, specifically support vector machines (SVMs), convolutional neural networks (CNNs), and recurrent neural networks (RNNs), to enable robust miRNA signature identification, classification, and target prediction. Furthermore, we explore the integration of generative models and LLMs to support hypothesis generation and enhance reproducibility in biomarker discovery workflows. This comprehensive framework enhanced with artificial intelligence (AI) is contextualized through cancer-specific datasets, with particular emphasis on translational applications for early detection, prognosis, and therapy selection. By systematically organizing fragmented methodologies into a scalable and reproducible pipeline, our work provides a strategic roadmap to accelerate the development of miRNA-based precision cancer.
Effect of selection for growth on reproductive traits in Nellore females: Genetic parameters and genome-wide association studies.
Garcia IMC, Ligori VA, Malheiros JM … +6 more , Rodrigues GRD, Dominguez-Castaño P, Ii Vasconcelos Silva JA, Monteiro FM, Dos Santos Gonçalves Cyrillo JN, Mercadante MEZ
J Appl Genet · 2026 May · PMID 41139770 · Publisher ↗
This study aimed to evaluate the effects of selection for post-weaning weight on reproductive traits in Nellore cattle by (i) estimating genetic parameters and trends for birth weight (BIW), body weight at selection (BW)...
This study aimed to evaluate the effects of selection for post-weaning weight on reproductive traits in Nellore cattle by (i) estimating genetic parameters and trends for birth weight (BIW), body weight at selection (BW), days to calving (DC), and pregnancy rate (PR); and (ii) performing a genome-wide association study (GWAS), gene annotation, and functional enrichment analyses to uncover genomic regions, candidate genes, biological processes, and metabolic pathways underlying DC and PR. The dataset contained 12,865 Nellore animals from the experimental breeding program of the Institute of Animal Science (IZ, Sertãozinho, Brazil), including three selection lines: Nellore Control (NeC, stablishing selection for post-weaning weight), Nellore Selection (NeS, selected for higher post-weaning weight), and Nellore Traditional (NeT, selected for higher post-weaning weight and lower residual feed intake). Genomic data were available for 2,326 animals and 384,521 autosomal SNP markers after quality control. Genetic parameters were estimated using Bayesian inference under the ssGBLUP framework. Genetic trends from 1981 to 2021 were derived from linear regressions considering genomic estimated breeding values (GEBVs). The weighted single-step GWAS (WssGWAS) was used to identify genomic regions that explained more than 1.0% of the additive genetic variance for DC and PR, which were further analyzed for gene annotation and functional enrichment. Heritability estimates were high for BIW (0.46 ± 0.02) and BW (0.41 ± 0.02), and low for DC and PR (0.10 ± 0.02 for both). Moderate genetic correlations were observed between BIW and DC, especially in lines selected for higher growth (NeS: 0.38 ± 0.12; NeT: 0.56 ± 0.09), in contrast, BW showed weak genetic correlations with reproductive traits, with estimates for DC of - 0.11 ± 0.18 (NeC), 0.15 ± 0.15 (NeS), and 0.36 ± 0.14 (NeT), and for PR of 0.25 ± 0.22 (NeC), - 0.12 ± 0.17 (NeS), and - 0.44 ± 0.16 (NeT). Genetic trends indicated consistent increases in BW and BIW in NeS and NeT, while NeC showed more favorable trends for DC and PR. The GWAS identified 13 and 9 genomic windows associated with DC and PR, respectively, with pleiotropic regions on chromosome 14 influencing both traits. Key candidate genes annotated included PLAG1, MOS, MAPK13, MAPK14, and FKBP5. Functional enrichment revealed biological processes related to hormone metabolism, immune modulation, and oocyte development. Selection for increased growth does not directly impair reproductive traits; however, it indirectly influences fertility due to correlated response in BIW, which is genetically associated with DC.
Genetic variations and functions of KLF14 in gene expression and metabolic disease development.
Riaz Z, Saeed S, Riaz S
J Appl Genet · 2025 Oct · PMID 41136864 · Publisher ↗
Krüppel-like factor 14 (KLF14) is a pivotal trans-regulatory transcription factor that modulates diverse biological processes, including insulin sensitivity, glucose homeostasis, lipid metabolism, and potentially cancer...
Krüppel-like factor 14 (KLF14) is a pivotal trans-regulatory transcription factor that modulates diverse biological processes, including insulin sensitivity, glucose homeostasis, lipid metabolism, and potentially cancer suppression through its regulation of centrosome amplification and apoptosis in colorectal cancer cells. KLF14 has been associated with the pathogenesis of metabolic disorders, including obesity, insulin resistance, and type 2 diabetes (T2D), and contains CpG sites that exhibit age-associated methylation changes, which may serve as potential biomarkers for estimating an individual age. Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) that are significantly associated with KLF14 expression in adipose tissue. The functional impact of KLF14 is influenced by both physiological and environmental factors, underscoring its complex role in disease pathogenesis. Population-based genetic studies reveal significant interethnic variability in KLF14 polymorphisms, highlighting the necessity of incorporating ethnic diversity into genetic research. Moreover, a deeper understanding of the molecular regulatory mechanisms and disease associations of KLF14 could inform the development of targeted therapies and personalized medicine strategies. Thus, the current study underscores the significance of KLF14 as a trans-regulatory gene and a potential therapeutic target, emphasizing its intricate role in biological regulation and disease pathogenesis.
Quantitative trait loci for Globodera pallida resistance derived from wild potato species Solanum gourlayi.
Milczarek D, Śliwka J, Tatarowska B … +2 more , Podlewska-Przetakiewicz A, Plich J
J Appl Genet · 2025 Oct · PMID 41125880 · Publisher ↗
Globodera pallida is a major pest that is responsible for huge losses in potato yields worldwide. Expanding the gene pool of cultivated potatoes with clones resistant to this pest is made possible by searching for resist...
Globodera pallida is a major pest that is responsible for huge losses in potato yields worldwide. Expanding the gene pool of cultivated potatoes with clones resistant to this pest is made possible by searching for resistance genes in wild Solanum species. The aim of this study was to identify quantitative trait loci (QTLs) for potato resistance to Globodera pallida derived from Solanum gourlayi. A resistant diploid potato clone, Sg 2/7 (Solanum gourlayi, accession CGN17592), was crossed with a susceptible potato hybrid clone, DW 94-4235, to generate an F1 mapping population. All clones were tested for nematode resistance using G. pallida, pathotypes Pa2 and Pa3, in 2 or 3 years (2017-2019), respectively. Diversity Array Technology (DArTseq) was used for genotyping and genetic map construction. QTLs for nematode resistance were identified on potato chromosomes II, IV, V, VI, VII, X, XI, and XII, explaining from 10.1 to 21.5% of phenotypic variance. The most significant QTL for resistance to G. pallida pathotype Pa2 was identified on chromosome XII, explaining 20.9% of the phenotypic variance in the dataset from 2017. The most significant QTL for resistance to the G. pallida Pa3 pathotype was identified on chromosome VI, with a CAPS marker Exp928 in its peak, explaining 21.5% of the phenotypic variance in the dataset from 2017. The novel QTLs for resistance to S. gourlayi may be useful for breeding resistant potato cultivars, further studies of candidate genes, and host responses of potato to G. pallida infection.
The NANOS RNA-binding protein variants: a model for understanding human infertility.
Kunik A, Lakshmi B, Jaruzelska J … +1 more , Kusz-Zamelczyk K
J Appl Genet · 2025 Dec · PMID 41107697 · Full text
Infertility remains a significant global health challenge. With up to one in seven couples affected worldwide, the inability to conceive has become a major concern for reproductive health. Many causes of infertility are...
Infertility remains a significant global health challenge. With up to one in seven couples affected worldwide, the inability to conceive has become a major concern for reproductive health. Many causes of infertility are linked to genetic variants that are disruptive for germ cell homeostasis. Using causative variants to model human infertility can improve our understanding of the molecular pathways that regulate germ cell development. One notable example is the germ cell morphogen NANOS, which is highly conserved across species. Variants of NANOS are associated with infertility in various animal models, from Drosophila to humans. Here, we examine how modelling human infertility based on NANOS variants can offer insights into the molecular processes underlying germ cell development. Ultimately, uncovering the molecular basis of human infertility through this approach is vital for developing advanced diagnostic methods and therapeutic options in the future.
Recent advances in the diagnosis and molecular pathogenesis of holoprosencephaly: a review.
Glista F, Nienartowicz J, Bukowska-Olech E
J Appl Genet · 2025 Oct · PMID 41102431 · Publisher ↗
Holoprosencephaly (HPE) is the most common structural anomaly of developing forebrain, characterized by incomplete separation of the cerebral hemispheres. While mutations in the Sonic Hedgehog (SHH) signaling pathway rem...
Holoprosencephaly (HPE) is the most common structural anomaly of developing forebrain, characterized by incomplete separation of the cerebral hemispheres. While mutations in the Sonic Hedgehog (SHH) signaling pathway remain the most established genetic cause, recent studies have identified an expanding list of genes and molecular networks involved in the pathogenesis of HPE. These include modulators of the NODAL, NOTCH, WNT/PCP, FGF, and RAS/ERK1/2 pathways as well as components of ciliary structures and cohesin complexes. Incomplete penetrance, broad phenotypic heterogeneity, and gene-environment interactions complicate diagnostic and counselling efforts. This review summarizes recent insights into the molecular mechanisms of HPE, highlighting key signalling networks, gene candidates, and phenotypic correlations. We also discuss under-recognised contributors such as cohesin and ciliary gene defects, which may account for a significant subset of unresolved cases. Finally, we propose a diagnostic framework incorporating clinical stratification, extended gene panels, and consideration of syndromic features.
Carfilzomib resistance in multiple myeloma: A comparative metabolomic analysis.
Żyłka K, Łuczak M, Kostrzewska-Poczekaj M … +6 more , Bednarek K, Bolomsky A, Kubicki T, Jarmuż-Szymczak M, Ludwig H, Dytfeld D
J Appl Genet · 2025 Oct · PMID 41102430 · Publisher ↗
Proteasome inhibitors are currently at the forefront of multiple myeloma (MM) treatment. Drug resistance in MM challenges treatment, causing relapses and making the disease incurable. Urgent strategies are needed to comb...
Proteasome inhibitors are currently at the forefront of multiple myeloma (MM) treatment. Drug resistance in MM challenges treatment, causing relapses and making the disease incurable. Urgent strategies are needed to combat resistance and understand its mechanisms. Targeting the metabolism of MM is a promising approach, as metabolic changes are associated with the disease and its adaptation to therapy. Metabolomics, the study of small molecule metabolites, is a powerful tool for identifying and analyzing a cell's metabolic phenotype. In this study, we aimed to investigate alterations in the metabolome of carfilzomib-resistant MM cells. We conducted global metabolomic comparative analyses of two carfilzomib-sensitive MM lines with their carfilzomib-resistant progenies. Additionally, we performed bioinformatic analysis to determine the top canonical pathways, biological functions, and upstream regulators linked to the differences in metabolomic profiles. Differential metabolite analysis showed increased amino acid and decreased fatty acid concentrations in carfilzomib-resistant cells. Functional analysis revealed increased glucose-6-phosphate oxidation and inhibited lipid accumulation in resistant lines. The bioinformatic analysis predicted PML, ARNT D-glucose, and UPC1 as upstream regulators of observed changes in carfilzomib-resistant cells. This study presents one of the first metabolomic profiles of two carfilzomib-resistant MM lines and the metabolome changes that may contribute to carfilzomib resistance.
Inheritance of physiological and biochemical attributes using numerical and graphical approaches of line × tester in Praecitrullus fistulosus.
Abbas A, Ejaz S, Malik W
J Appl Genet · 2025 Oct · PMID 41085940 · Publisher ↗
Praecitrullus fistulosus (Stocks) Pangalo is one of the nutrient-rich vegetables crops with proven therapeutic value. This study was designed to investigate the inheritance of important physiological and biochemical trai...
Praecitrullus fistulosus (Stocks) Pangalo is one of the nutrient-rich vegetables crops with proven therapeutic value. This study was designed to investigate the inheritance of important physiological and biochemical traits of Praecitrullus fistulosus. A set of 15 cross combinations were developed from five lines and three testers and evaluated for two years. The results depicted significant (p < 0.05) variation among the genotypes (parents and crosses) with respect to flavonoids, phenolic compounds, total carbohydrates, vitamin C, and carotenoids during both studied years. Data were analysed with traditional line × tester analysis for inheritance pattern, and the genotypes (parents and hybrids) were further analysed using polar plots for heterosis and gene action, and principal component biplot analysis for graphical explanation of combining abilities. The physiological traits, i.e., flavonoids, antioxidants, and total soluble proteins, showed significant means square values and general combining ability for genotypes, i.e., 20 and 47. The F1 hybrids 20 × 42, 8 × 63, and 20 × 40 showed high and significant specific combining ability for flavonoids, antioxidants, vitamin C, and carotenoids. GCA, SCA, and the PCA biplot also showed comparable results. The studies of heterosis using polar plots showed the preponderance of overdominance for the majority of traits. Conclusively, both conventional and graphical attribution of data using line × tester analysis could lead Praecitrullus fistulosus breeders to the selection of suitable breeding methods.
The molecular puzzle of autoinflammatory skin diseases-a review of chosen conditions.
Pieniawska M, Rassek K, Stein T … +3 more , Polańska A, Dańczak-Pazdrowska A, Iżykowska K
J Appl Genet · 2025 Oct · PMID 41085939 · Publisher ↗
The skin is one of the largest organs in humans and is formed by a layer (termed the epidermis) that enables the body to interact with the environment and protects it from various harmful agents. The epidermis includes a...
The skin is one of the largest organs in humans and is formed by a layer (termed the epidermis) that enables the body to interact with the environment and protects it from various harmful agents. The epidermis includes a physical, biochemical, and adaptive immune barrier. The immune system in the human body is responsible for protecting organisms from potentially infectious microorganisms, allergens, and toxins, maintaining homeostasis, controlling inflammation processes, and tissue repair. Autoimmune and autoinflammatory diseases are of the immune system manifesting as aberrations in adaptive and innate immunity that lead to an inflammatory state and self-attack damage, also in the skin. The commonness of cutaneous autoinflammations has increased over the past decades, and the occurrence of the disease can have a crucial impact on a patient's quality of life due to their visible nature, discomfort caused by somatic symptoms, and emotional and social challenges. In this review, we summarize the current knowledge of four common autoinflammatory skin diseases-vitiligo, alopecia areata, systemic lupus erythematosus, and psoriasis-with particular emphasis on their molecular background, including the role of genetic susceptibility, epigenetic regulation, and immunological pathways.
Potential biomarkers for early detection of endometriosis: current state of art (what we know so far).
Kliber-Gałuszka M, Kulczyńska-Figurny K, Jagodziński PP … +1 more , Pławski A
J Appl Genet · 2025 Oct · PMID 41081983 · Publisher ↗
Endometriosis is a chronic gynecological condition characterized by the presence of endometrial-like tissue outside the uterine cavity. Its diagnosis remains a significant clinical challenge, often delayed by 7 to 12 yea...
Endometriosis is a chronic gynecological condition characterized by the presence of endometrial-like tissue outside the uterine cavity. Its diagnosis remains a significant clinical challenge, often delayed by 7 to 12 years, leading to considerable socio-economic burden and a substantial decline in patients' quality of life, including potential infertility. Consequently, there is an urgent need to identify reliable biomarkers that would allow for earlier and more accurate detection. This review provides a comprehensive and up-to-date analysis of potential biomarkers for the diagnosis of endometriosis, including hormonal, inflammatory, genetic, epigenetic, immunological, metabolic, and imaging-based markers. Their diagnostic value and limitations are critically assessed, with particular emphasis on the advantages of multimarker and integrated diagnostic approaches to enhance early detection. The findings of this review offer valuable insights for clinicians, researchers, and healthcare professionals working to develop better diagnostic methods and improve patient outcomes. Moreover, the integration of emerging technologies, such as artificial intelligence, offers promising opportunities to revolutionize endometriosis diagnostics through personalized and precise medical care.
Genetic analysis of common bean (Phaseolus vulgaris L.) genotypes for root traits, yield components and seed yield.
Ibram AAMM, Constant LLB, Fort MNL
J Appl Genet · 2025 Oct · PMID 41073653 · Publisher ↗
Screening genotypes with robust root architecture is preeminent to increase considerably bean (Phaseolus vulgaris L.) seed yield. The survey consisted to evaluate the genetic variability, estimate broad sense heritabili...
Screening genotypes with robust root architecture is preeminent to increase considerably bean (Phaseolus vulgaris L.) seed yield. The survey consisted to evaluate the genetic variability, estimate broad sense heritability, genetic advance, and determine the correlations for root traits, seed yield, and its components for ten bean lines. The field trial was laid out in a randomized complete block design with three replications. Data were submitted to the analysis of variance (ANOVA) and multivariate analyses using STATGRAPHICS PLUS version 16.1 and R version 3.5.1 statistical package programmes, respectively. ANOVA showed that the results revealed significant differences among the bean lines denoting a wider genetic variability for root traits, seed yield and its components. Principal component analysis displayed the relationship between traits and genotypes, indicating a substantial level of variability among the genotypes for root traits, yield components and seed yield; hence, it could be exploited for more improvement bean yield. Cluster analysis confirmed a sufficient genetic variability; thereby, the distal clusters could be used for further improvement bean yield and root traits. All traits exhibited high values of broad sense heritability suggesting these characters could be improved by selection. High broad sense heritability associated to high genetic advance was observed for root growth angle and 100-seeds weight. This attests that additive gene effects were involved in the heredity of these traits, and they can be readily fixed in the genotypes by selection in the early generations. The number of basal roots exhibited significant and positive correlation with the number of adventitious roots; hence, these traits could be considered the main components and selection may be effective in improving the bean root system. The bean lines Bigarré, FEB192, GLP190 S, ECA-PAN021, Gros Rouge and Petit Rouge could be used as elite material in breeding programmes for seed yield and root traits.
Reevaluating the total genotype score: a practical perspective from applied sport science.
Bottura RM, Dentillo DB
J Appl Genet · 2025 Oct · PMID 41032208 · Publisher ↗
Over the last few years, the number of publications regarding genetics and sports has notably increased. However, the way this information is actually used is often misinterpreted by those who do not apply genetics in th...
Over the last few years, the number of publications regarding genetics and sports has notably increased. However, the way this information is actually used is often misinterpreted by those who do not apply genetics in their day-to-day training. Therefore, the purpose of this short communication is to exemplify, using the real cases of identical twin athletes, how genetic information must be applied in sports. Additionally, we present data on performance tests and individual preferences for training and competitions between the athletes. Accordingly, the study concludes with a distinction between genetic profile studies and genetic application studies, emphasizing the importance of further research in this area, especially case reports.
Bioinformatics and machine learning reveal novel prognostic biomarkers in head and neck squamous cell carcinoma.
Judaki AA, Shirinpoor M, Farahani M … +3 more , Aldaghi T, Arefi-Oskouie A, Nazari E
J Appl Genet · 2025 Oct · PMID 41028529 · Publisher ↗
Head and neck squamous cell carcinoma (HNSCC), the seventh most common cancer worldwide, has become more closely linked to poor lifestyle habits. Despite improvements in cancer treatment approaches, patients with stage I...
Head and neck squamous cell carcinoma (HNSCC), the seventh most common cancer worldwide, has become more closely linked to poor lifestyle habits. Despite improvements in cancer treatment approaches, patients with stage I-II HNSCC have a 70-90% 5-year survival rate, and for patients with advanced stages III-IV, this rate falls to about 40%. This controversy is all about the heterogeneity of HNSCC. Finding diagnosis and prognosis biomarkers has the potential to make significant improvements in the life expectancy and overall health of these patients. The combination of bioinformatics and machine learning has facilitated the finding of the best markers for HNSCC. In this regard, RNA expression data were obtained to identify genes that were expressed differently (DEGs) and utilize a deep learning algorithm to identify genes that exhibited significant variability. In addition, correlations between clinical data and DEGs, the building of a Receiver Operating Characteristic (ROC) curve, and the prediction of tumor-infiltrating immune cells were analyzed. Deep learning analysis identified diagnostic and prognostic biomarkers strongly associated with carcinogenesis, such as KRT33B, KRTAP3-3, C14orf34, and ACADM. In addition, after analyzing the ROC curve, it was found that the combination of ACADM, KRT33B, and C14orf34 is the most practical combination of diagnostic markers. This combination achieved sensitivity, specificity, and Area Under the Curve (AUC) values of 0.92, 0.86, and 0.93, respectively.
Interfungal antagonism between Trichoderma and Fusarium proliferatum - metabolomic and DNA-based analyses.
Marta M, Dominik P, Lidia B … +4 more , Łukasz S, Agnieszka W, Moniak U, Marcin B
J Appl Genet · 2025 Dec · PMID 40999249 · Full text
This study evaluated the antagonistic capacity of eight Trichoderma isolates against two Fusarium proliferatum isolates that differed in their toxigenic potential. Using co-cultures on solid and liquid media, significant...
This study evaluated the antagonistic capacity of eight Trichoderma isolates against two Fusarium proliferatum isolates that differed in their toxigenic potential. Using co-cultures on solid and liquid media, significant variability in antifungal efficacy was observed among Trichoderma species. T. atroviride and T. viridescens isolates demonstrated the highest antagonistic activity, with markedly stronger inhibition of the less toxigenic F. proliferatum isolate. Quantitative PCR analysis confirmed a reduction in Fusarium biomass, which closely correlated with decreased levels of fumonisins (FB1, FB2, FB3) and beauvericin, as determined by UHPLC-HRMS. Notably, the most effective Trichoderma isolates (AN153, AN215, AN523) consistently suppressed both fungal growth and mycotoxin biosynthesis. Although fumonisin levels were reduced in co-cultures, independent assays in FB1-supplemented liquid media indicated that Trichoderma did not directly degrade mycotoxin. The presence of selected secondary metabolites, including 6-pentyl-2H-pyrone and phenolic acids, was confirmed in co-culture extracts. These findings highlight the isolate-specific nature of Trichoderma-Fusarium interactions and emphasise the potential of selected Trichoderma isolates as biocontrol agents capable of simultaneously limiting pathogen growth and mycotoxin accumulation. Further mechanistic studies are warranted to identify the molecular basis of these antagonistic effects.
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