Journal Of Applied Genetics[JOURNAL]
Sun
200 papers
Harnessing CRISPR-Cas technology to enhance rice resilience under abiotic and biotic stress.
Verupanda S, Chakraborty A, Shrivastava M … +2 more , Pati SK, Nandi D
J Appl Genet · 2026 Jul · PMID 42402524 · Publisher ↗
The CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats) genome-editing technology has become an effective and accurate tool for crop development, enabling targeted changes to genes linked to stress tol...
The CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats) genome-editing technology has become an effective and accurate tool for crop development, enabling targeted changes to genes linked to stress tolerance, agronomic performance, and yield. CRISPR-Cas-based technologies are increasingly used in rice (Oryza sativa L.), one of the world's most significant staple crops, to mitigate the negative impacts of disease stress and climate change on productivity. Abiotic factors, including drought, salinity, heat, and cold, as well as biotic challenges such as rice blast, bacterial blight, sheath blight, and insect pests, have a significant impact on rice cultivation and cause substantial yield losses globally. Recent advances in CRISPR/Cas9, base editing, and prime editing have enabled precise manipulation of stress-responsive genes, facilitating the development of climate-resilient and disease and pest-resistant rice varieties. This review summarizes the current progress in CRISPR-Cas-mediated rice improvement, highlighting key genes and molecular pathways involved in tolerance to abiotic and biotic stresses. It also discusses emerging approaches such as transgene-free editing via ribonucleoprotein (RNP) delivery, and high-fidelity Cas variants that enhance editing efficiency and minimize off-target effects. Overall, CRISPR-Cas-based genome editing represents a promising and efficient approach for accelerating the development of high-yielding, climate-resilient, and stress-tolerant rice cultivars, thereby contributing significantly to sustainable rice production and global food security under changing environmental conditions.
Estimation of genetic parameters for growth and shell color traits in the tetraploid 'Haida No. 3' line of Pacific oysters (Magallana gigas) in China.
Zhou J, Li Q, Xu C … +1 more , Liu H
J Appl Genet · 2026 Jul · PMID 42399511 · Publisher ↗
The Pacific oyster (Magallana gigas) is a widely cultivated species, and its commercial value has been significantly enhanced by the widespread adoption of triploid oysters. Since triploid offspring inherit two chromosom...
The Pacific oyster (Magallana gigas) is a widely cultivated species, and its commercial value has been significantly enhanced by the widespread adoption of triploid oysters. Since triploid offspring inherit two chromosome sets from tetraploid males, this suggests that genetic improvement of tetraploid oysters is essential. The induction of the dark-shelled tetraploid 'Haida No. 3' line from selected diploid lines of Pacific oysters has been achieved. However, the genetic parameters of growth and shell color traits in this line remain unclear. This study involved analyzing the genetic parameters of 42 tetraploid full-sibling families using the restricted maximum-likelihood (REML) method, with a tetraploid inverse additive relationship matrix constructed by the polyAinv package. These results indicated that the heritability of growth traits was moderate, with values ranging from 0.19 ± 0.05 for shell width to 0.45 ± 0.09 for whole weight. For shell color traits, the heritability values for color L*, color a*, color b*, and ΔE were 0.42 ± 0.09, 0.46 ± 0.09, 0.55 ± 0.10, and 0.63 ± 0.12, respectively. The genetic correlations ([Formula: see text]) between color L* and growth traits (excluding shell width) were moderate, ranging from 0.32 ± 0.15 to 0.42 ± 0.15. The low ΔE values observed across the tetraploid 'Haida No. 3' families indicate that the shell color purification has achieved the desired level of phenotypic consistency. Therefore, growth was identified as the primary breeding objective, with shell color regarded as secondary for the subsequent breeding program. The results provide useful information into selective breeding of fast-growing, black-shelled tetraploid oysters in aquaculture.
Molecular and bioinformatic analysis of apoptotic tumor suppressor genes in cervical cancer.
Yadav C, Nanda S, Sehrawat N … +1 more , Yadav R
J Appl Genet · 2026 Jul · PMID 42393365 · Publisher ↗
This study aims to investigate the methylation status and mRNA expression of key apoptotic genes, including death-associated protein kinase (DAPK 1), tumor necrosis factor receptor superfamily member 6 (FAS), SMAC, and t...
This study aims to investigate the methylation status and mRNA expression of key apoptotic genes, including death-associated protein kinase (DAPK 1), tumor necrosis factor receptor superfamily member 6 (FAS), SMAC, and tumor necrosis factor-related apoptosis-inducing ligand receptor 1 (TRAIL-R1) and its association with clinicopathological factors in cervical cancer cases. Methylation analysis was performed on 110 cervical cancer patients using qualitative methylation-specific polymerase chain reaction (MSP). Real-time PCR was used to analyze expression levels of selected genes. All samples were also analysed for the presence of high-risk HPV types (HPV 16 and 18) with specific primer. Additionally, association with clinicopathological and risk factors were evaluated. In-silico analysis was also done for further validation. The methylation status of DAPK, TRAIL R1, SMAC, and FAS was significantly different between cancer tissues and normal tissues. DAPK (0.001), FAS (0.001), and TRAIL R1 (0.02) were hypermethylated, and SMAC was found to be hypomethylated with the highest significance of < 0.0001. HPV 16 + samples were highly significant with DAPK (0.007) and FAS (0.013), and HPV 18 + samples were significant with DAPK (0.024), FAS (0.002) and TRAIL R1 (0.009). No HPV association was found with SMAC. Methylation was found to be inversely proportional to DAPK, TRAIL R1, and FAS expression. Aberrant promoter methylation of key apoptotic genes is significantly associated with cervical cancer and may contribute to its progression. Significant correlations with HPV infection and clinicopathological factors highlight their possible potential as predictive biomarkers. However, larger studies and functional validation are needed to confirm these findings and their clinical applicability.
Analysis of genetic risk factors for Leber hereditary optic neuropathy in the Polish population.
Sikorska J, Krawczyński MR, Korwin M … +4 more , Ołdak M, Bartnik E, Tońska K, Piotrowska-Nowak A
J Appl Genet · 2026 Jun · PMID 42362998 · Publisher ↗
Leber hereditary optic neuropathy (LHON) is primarily caused by pathogenic mitochondrial DNA (mtDNA) variants, most commonly the m.11778G>A variant in the MT-ND4 gene. The presence of this variant alone is insufficient t...
Leber hereditary optic neuropathy (LHON) is primarily caused by pathogenic mitochondrial DNA (mtDNA) variants, most commonly the m.11778G>A variant in the MT-ND4 gene. The presence of this variant alone is insufficient to trigger disease symptoms, of which vision loss is the hallmark. Given the incomplete penetrance and inter-population variability in modifying factors, this study aimed to investigate two previously proposed genetic risk factors for LHON in the Polish population. Using quantitative PCR, we measured the mtDNA copy number in peripheral blood of affected and unaffected carriers of the m.11778G>A variant. In addition, we assessed the frequency of the PRICKLE3 c.157C>T variant in symptomatic, asymptomatic and control individuals using PCR-RFLP. Our results indicate that mtDNA copy number was not associated with LHON symptom manifestation in the Polish cohort under conditions tested, in contrast to previously reported associations in other populations. In addition, the PRICKLE3 c.157C>T variant was absent in our cohort, indicating that it is not a common modifier of LHON penetrance in the Polish population. These findings suggest that the incomplete penetrance of LHON in the Polish population may involve other modifying factors, such as yet unidentified nuclear DNA variants.
DUS based morphological evaluation of bell pepper (Capsicum annuum L. var. grossum Sendt.) germplasm for identification of promising breeding lines in Himachal Pradesh, India.
Kaur G, Mehta DK, Sohi A … +2 more , Deep N, Meena TK
J Appl Genet · 2026 Jun · PMID 42340593 · Publisher ↗
Bell pepper (Capsicum annuum L. var. grossum Sendt.) is a major Solanaceous vegetable crop exhibiting wide variability in fruit size, shape and colour, which are critical market traits. The present study aimed to evaluat...
Bell pepper (Capsicum annuum L. var. grossum Sendt.) is a major Solanaceous vegetable crop exhibiting wide variability in fruit size, shape and colour, which are critical market traits. The present study aimed to evaluate genetic diversity among 34 advanced breeding lines of bell pepper along with two check varieties (California Wonder and Solan Bharpur) using 30 agro-morphological descriptors (13 qualitative and 17 quantitative) under DUS (Distinctness, Uniformity, Stability) guidelines. The experiment was conducted during 2022 and 2023 at Dr YS Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, in a randomized complete block design (RCBD) with three replications. Significant variation was observed across morphological traits, with highest diversity index (H = 1.01) recorded for fruit shape in longitudinal section. Analysis of variance revealed substantial genetic variability and several genotypes (UHF-CAP-108, UHF-CAP-119, IIHR-131, UHF-CAP-106, UHF-CAP-113) significantly outperformed the better check variety Solan Bharpur for fruit yield per plant, producing medium-sized, blocky, glossy, dark green fruits with 3-4 lobes. Principal component analysis (PCA) identified six components explaining 83.08% of total variance, with thousand seed weight, number of lobes per fruit, fruit diameter, fruit weight, internodal length and fruit length as major contributors. Cluster analysis grouped the genotypes into five distinct clusters, with maximum inter-cluster (D² = 9.74) distance observed between cluster III and cluster V, indicating broad genetic diversity. Overall, the study highlights the effectiveness of DUS-based characterization supported by multivariate analysis in identifying promising breeding lines and key traits for future bell pepper improvement programmes.
Non-coding RNAs in peripheral vascular diseases - a snRNA study.
Zalewski DP, Feldo M, Stępniewski A … +3 more , Łuszczak J, Kocki J, Bogucka-Kocka A
J Appl Genet · 2026 Jun · PMID 42319738 · Publisher ↗
Lower extremity artery disease (LEAD), abdominal aortic aneurysm (AAA), and chronic venous disease (CVD) are frequently underdiagnosed vascular conditions that contribute significantly to morbidity, mortality, and dimini...
Lower extremity artery disease (LEAD), abdominal aortic aneurysm (AAA), and chronic venous disease (CVD) are frequently underdiagnosed vascular conditions that contribute significantly to morbidity, mortality, and diminished quality of life, representing a considerable public health burden. The discovery of novel molecular biomarkers is crucial to improving early diagnosis, enabling accurate risk stratification, uncovering disease mechanisms, and facilitating the development of targeted therapies.This study aimed to investigate alterations in small nuclear RNAs (snRNAs) in peripheral blood mononuclear cells (PBMCs) of patients with LEAD, AAA, and CVD. The snRNA expression profiles were analyzed using snRNA-seq data and the DESeq2 package. In parallel, miRNA-seq data were used to identify differentially expressed microRNAs (miRNAs) associated with snRNA dysregulation.Using a strict selection criterion, we identified 4 (RNU6-4P, RNU6-18P, RNU6-36P, and RNU2-48P) and 2 (RNVU1-19 and RNU1-146P) dysregulated snRNAs in patients with LEAD and CVD, respectively. Three miRNA-snRNA interactions involving miRNAs differentially expressed in these diseases were identified and confirmed in silico using the IntaRNA platform. Genetic variants located within dysregulated snRNAs indicate a potential functional association between selected snRNAs and vascular biology, particularly in relation to platelet function, blood pressure regulation, and smoking.Obtained findings underscore the potential of snRNAs as novel biomarkers and offer insights into their possible involvement in the vascular pathophysiological mechanisms underlying LEAD and CVD.
Distribution of mrk genes among uopathogenic Klebsiella pneumoniae.
Fallah Vosoughi A, Foroohi F, Ahmadi S … +3 more , Shirzadian M, Golpasand T, Behzadi P
J Appl Genet · 2026 Jun · PMID 42313334 · Publisher ↗
The mrk operon gene clusters encode type 3 fimbriae, involving in biofilm formation. Hence, we aimed to find out the distribution of mrk genes among uropathogenic Klebsiella pneumoniae (UPKP) strains. Moreover, mrk genes...
The mrk operon gene clusters encode type 3 fimbriae, involving in biofilm formation. Hence, we aimed to find out the distribution of mrk genes among uropathogenic Klebsiella pneumoniae (UPKP) strains. Moreover, mrk genes, hypermucoviscosity (HMV) characteristic and antimicrobial resistance (AMR) patterns and profiles were successfully, provided. From August 2023 to January 2024, 104 positive urine samples were collected. Standard microbiological and biochemical tests were employed to confirm the UPKP strains. Kirby-Bauer disc diffusion method was recruited to conduct antimicrobial susceptibility test (AST). The HMV characteristic in UPKP isolates was assessed using the string test. Finally, multiplex polymerase chain reaction (mPCR) was used to identify mrk genes distribution. Chi-square (χ) and Fisher's exact tests were utilized for statistical analysis. The mrk gene distribution varied among the UPKP isolates comprising mrkA (1.92%), mrkB (0.00%), mrkC (5.77%), mrkD (23.08%), mrkE (37.50%), and mrkF (83.65%). No mrk genes were detected among 13.46% (14/104) of UPKP isolates. The most common mrk gene patterns involved mrkF (32.70%), mrkE-mrkF (25.00%), and mrkD-mrkF (11.54%). In addition, the isolates exhibited diverse AMR profiles and phenotypes including: 65 multi-drug resistant (MDR) strains (nine groups, 42 patterns), 13 extensively drug-resistant (XDR) strains (nine patterns), nine pan drug-resistant (PDR) strains, 23 ESBL producers, and nine HMV isolates. None of the HMV strains displayed XDR, PDR, or ESBL phenotypes, suggesting limited horizontal gene transfer (HGT). Detailed analysis of mrk genes and AMR characteristics in UPKP, provides essential information for selecting effective prevention protocols and treatments for urinary tract infections (UTIs) and combating AMR.
Maize chromatin introgression's effect in oat × maize addition lines.
Juzoń-Sikora K, Nowicka A, Said M … +5 more , Idziak-Helmcke D, Warzecha T, Warchoł M, Skrzypek E, Pecinka A
J Appl Genet · 2026 Jun · PMID 42310257 · Publisher ↗
The addition lines derived from oat (Avena sativa L.) × maize (Zea mays L.) crosses constitute a unique tool for studying gene expression and the structure of chromatin, as well as a source of agronomically desirable tra...
The addition lines derived from oat (Avena sativa L.) × maize (Zea mays L.) crosses constitute a unique tool for studying gene expression and the structure of chromatin, as well as a source of agronomically desirable traits in the context of new intergeneric hybrid cultivars. Therefore, for a better understanding of the introgression of maize chromatin into the oat genome, a comprehensive analysis of oat × maize lines was conducted. The presence of maize chromatin was confirmed in three tested lines by PCR-based amplification of the maize retrotransposon Grande-1, and verified by genomic in situ hybridization. Interestingly, the addition lines containing cytologically-detectable maize chromosomes showed a possible disturbance of the Rabl-like centromere-telomere polarization typical for oat. Moreover, the maize chromatin was consistently positioned near the nuclear periphery. The maize chromatin introgression caused a prolonged DNA replication phase, altering cell cycle dynamics, and may led to mitotic abnormalities, such as the formation of micronuclei and anaphase chromosome bridges. The introgression lines also showed morphological and physiological changes: smaller seeds, hampered seedlings' growth, and reduced yield parameters (number of flowers/seeds per plant/panicle and seed weight). These findings shed more light on the consequences of the maize chromatin introgression into the oat genome and the stability and utility of the obtained hybrids.
Unravelling obesity: from leptin to glucagon-like peptide-1 receptor agonists.
Idowu TO, Chmurzynska A
J Appl Genet · 2026 Jun · PMID 42298277 · Publisher ↗
The global obesity epidemic involves a multifaceted interplay between genetics, environment, and the interactions between them. The discovery of leptin in 1994 changed our understanding of body weight regulation and trig...
The global obesity epidemic involves a multifaceted interplay between genetics, environment, and the interactions between them. The discovery of leptin in 1994 changed our understanding of body weight regulation and triggered extensive genetic studies into monogenic and polygenic obesity. Despite initial therapeutic hopes, leptin's efficacy in obesity was limited by leptin resistance. However, glucagon-like peptide-1, an incretin hormone, has become an important tool for managing obesity. Glucagon-like peptide-1 receptor agonists aid in weight loss and glycemic control while also providing metabolic and cardiovascular benefits. This article presents the shift from leptin biology to the therapeutic application of glucagon-like peptide-1 receptor analogs, focusing on their unique mechanisms, gene polymorphisms, and the hormonal interactions that regulate energy homeostasis. It outlines the shift from leptin-based theories to therapies focused on glucagon-like peptide-1 as we have gained understanding of the gut-brain-adipose axis, paving the way for targeted therapies in obesity management.
The results of CNVs analysis in patients with neurodevelopmental delay, dysmorphic features and congenital defects.
Jakubiak A, Rowińska M, Gardas G … +10 more , Skiba P, Szmida E, Ślęzak R, Stembalska A, Śmigiel R, Pawelak A, Jabłońska I, Łaczmańska I, Gil J, Sąsiadek M
J Appl Genet · 2026 Jun · PMID 42298276 · Publisher ↗
Array Comparative Genomic Hybridization (aCGH) enables genome-wide detection of copy number variants (CNVs), representing a major advance in diagnosing neurodevelopmental disorders and congenital anomalies. We performed...
Array Comparative Genomic Hybridization (aCGH) enables genome-wide detection of copy number variants (CNVs), representing a major advance in diagnosing neurodevelopmental disorders and congenital anomalies. We performed aCGH in 1,468 patients referred for genetic evaluation due to neurodevelopmental delay, dysmorphic features, and congenital malformations. Pathogenic CNVs were detected in 24.5% of patients. The highest frequency of unbalanced aberrations occurred on chromosomes X, 15, 1, and 7. Most CNVs were small (< 10 Mbp), though entire-chromosome duplications (notably on 8, 9, and X) were also observed. The diagnostic yield and CNV distribution differed between prenatal and postnatal analyses, with deletions predominating in prenatal cases and a balanced ratio of deletions to duplications postnatally. The study confirms the high diagnostic utility of aCGH in patients with complex developmental phenotypes and highlights the importance of integrating cytogenetic analysis and periodic genomic data reinterpretation to refine diagnosis and counselling.
Novel genomic regions associated with adult-plant resistance to multiple fungal pathogens in wheat (Triticum aestivum L.) revealed by DArT marker sequencing.
Czembor E, Stępień Ł, Czembor JH
J Appl Genet · 2026 Jun · PMID 42295685 · Publisher ↗
Wheat is among the top three most important cereal crops globally and serves as a staple food for approximately 40% of the world's population. Fungal leaf diseases such as yellow and leaf rusts (YR, LR), septoria nodorum...
Wheat is among the top three most important cereal crops globally and serves as a staple food for approximately 40% of the world's population. Fungal leaf diseases such as yellow and leaf rusts (YR, LR), septoria nodorum blotch (SNB), septoria tritici blotch (STB), and powdery mildew (PM) have a major effect on yield loss in wheat, and resistance breeding is so far the most effective strategy to minimize those losses. Adult plant resistance (APR) is a crucial component of durable disease resistance; it reduces the pathogen's infection rate, keeping disease levels below the damage threshold, even in the absence of complete immunity. Therefore, this study aimed to identify sources of resistance in a collection of 411 accessions from diverse global origins. These accessions were phenotyped across 2018-2019. DArTseq technology and Genome-wide association studies (GWAS) analysis were conducted to identify single-nucleotide polymorphisms (SNPs) associated with APR for evaluated pathogens. DArT analysis showed that wheat chromosome 2B contains genomic regions associated with resistance to SNB, and that SNPs on chromosome 3B are associated with resistance to YR. On chromosome 6 A, there is a strong potential to explore, as a shared resistance locus for YR and SNB was found. SNPs: 3,937,236, 1,056,817 were consistent in both years, meaning their association with disease resistance is reliable and repeatable. Chromosome 7D is a strong region for SNPs significantly associated with both LR and SNB resistance. While multiple disease resistance genes are present on 7D, the 610 Mb LR locus is distinct from known LR, PM, and SNB loci, making it a strong candidate for functional validation. These findings highlight the value of historical resistance sources and uncover novel genomic regions for breeding a broad-spectrum APR-based resistance. Dual-trait loci, especially those effective against both biotrophic and necrotrophic pathogens, represent a promising material for achieving durable resistance in elite wheat cultivars.
Egyptian MASLD genetic map; between the leading TM6SF2 gene and role of epigenetic.
Hegazy MA, Fathy M, Abdelghani A … +7 more , Hassan SM, Abdelfatah D, Lithy R, Saad S, Hussein SM, Radwan NA, Ashoush O
J Appl Genet · 2026 Jun · PMID 42287598 · Publisher ↗
Metabolic dysfunction-associated steatotic liver disease (MASLD) is influenced by genetic variants, but population-specific data from Egypt are limited. This study investigated GCKR (rs1260326), PNPLA3 (rs738409), and TM...
Metabolic dysfunction-associated steatotic liver disease (MASLD) is influenced by genetic variants, but population-specific data from Egypt are limited. This study investigated GCKR (rs1260326), PNPLA3 (rs738409), and TM6SF2 (rs58542926) variants impact on MASLD severity and their association with cardiometabolic risk factors in an Egyptian cohort. This prospective case-control study included 476 adults (244 MASLD patients, 232 healthy controls). All participants underwent anthropometric assessment, liver ultrasound, and vibration-controlled transient elastography (VCTE) with controlled attenuation parameter (CAP) to quantify steatosis and fibrosis. Laboratory analysis included lipid profile, liver enzymes, fasting glucose, insulin, HbA1c, and HOMA-IR. Genotyping was performed using real-time PCR. TM6SF2 T variant allele was the strongest predictor of MASLD (16% vs. 9% in controls, p < 0.001), associated with higher CAP (P = 0.03) and elevated liver enzymes. PNPLA3showed no association with MASLD (24% allele frequency in both groups). Unexpectedly, GCKR wild-type C allele was associated with higher insulin levels and HOMA-IR. Haplotype analysis revealed a synergistic effect between GCKR wild-type C allele and TM6SF2 variant T allele, conferring a 2.81-fold increased MASLD risk (95% CI: 1.63-4.84). HDL < 40 mg/dL (OR = 2.7), BMI, and HOMA-IR were the strongest independent predictors. None of the variants significantly impacted fibrosis severity. The Egyptian MASLD genetic landscape features a dominant role for TM6SF2, a negligible role for PNPLA3, and paradoxical GCKR wild-type associations, implicating epigenetic factors or nutrigenomic interactions likely reflecting Egypt's unique nutritional transition and high consanguinity rates and that may modulate the expression and phenotypic penetrance of these established genetic variants.
Prognostic alternative mRNA splicing signature and immune infiltration in prostate cancer.
Wang Z, Tu J, Yin R … +6 more , Shang P, Zhang C, Zhou Y, Xu L, Zhu J, Zang Y
J Appl Genet · 2026 Jun · PMID 42286404 · Publisher ↗
Prostate cancer (PCa) is among the most prevalent malignancies in males across the globe. Alternative splicing (AS), a post-transcriptional modification, has been associated with several malignancies. This research focus...
Prostate cancer (PCa) is among the most prevalent malignancies in males across the globe. Alternative splicing (AS), a post-transcriptional modification, has been associated with several malignancies. This research focused on genome-wide analyses of AS events in PCa. Using gap analysis, we detected remarkable differential AS events (DASEs) related to PCa. Cox analysis was conducted to identify DASEs that prognostically affect the disease-free interval (DFI) and overall survival (OS) in PCa patients. Unsupervised cluster analysis was utilized to identify differential AS clusters and AS networks. We investigated whether patients with PCa who had a higher or lower risk of OS responded to chemotherapeutic and immunotherapeutic treatments. In the analysis of PCa, 296 DASEs were identified as clinically significant. The prognostic values for DFI and OS were used to construct a prognostic model. Using unsupervised cluster analysis, we determined the AS clusters related to OS. According to our findings, high- and low-risk groups have different outcomes for cisplatin and docetaxel chemotherapy. We conducted a detailed investigation of AS events in PCa by performing a genome-wide analysis. According to the data presented here, DASEs and splicing factors tend to influence the survival rates of PCa patients as well as their susceptibility to chemotherapeutic medications. This could offer innovative perspectives for the treatment of PCa.
Deciphering programmed cell death for gastric cancer prognosis: AKR1B1 as a key player.
Liu SP, Li X, Liu Q … +1 more , Xie S
J Appl Genet · 2026 May · PMID 42268527 · Publisher ↗
Gastric cancer (GC) has poor survival due to late diagnosis, heterogeneity, and limited treatment options. Understanding cell death pathways is crucial for developing effective therapies. This study aimed to investigate...
Gastric cancer (GC) has poor survival due to late diagnosis, heterogeneity, and limited treatment options. Understanding cell death pathways is crucial for developing effective therapies. This study aimed to investigate the prognostic value of multiple Programmed cell death (PCD) in GC, identify key genes associated with PCD. Bioinformatics methods including Cox regression and machine learning algorithms identified key genes. Evaluation of key gene by immune infiltration, single-cell analysis, drug sensitivity. In vitro experiments using siRNA knockdown of hub gene in GC cell lines confirmed the findings. The study developed prognostic models for 12 PCD pathways, finding extrinsic apoptosis and immunogenic cell death were most predictive of patient survival. A comprehensive risk model was built integrating 22 hub genes across 12 PCD pathways. Machine learning identified Aldo-keto reductase 1 member B1 (AKR1B1) as a key prognostic gene, which was validated to promote proliferation and migration in gastric cancer cells. AKR1B1 expression correlated with immune infiltration and drug sensitivity, suggesting a role in shaping the tumor microenvironment. This study reveals complex cell death mechanisms in GC, identifying key genes for targeted therapies. Further research on AKR1B1 and other genes holds promise for novel therapeutic strategies to combat GC and improve outcomes.
Genomic data security in the era of data capitalism: systematic threat or unwarranted alarm.
Madej M, Sąsiadek MM, Witt M
J Appl Genet · 2026 Jun · PMID 42258114 · Publisher ↗
The paper explores the question of threats related to commercial processing of genetic data putting the analysis in the context of data capitalism. Modern technological, social and economic changes translate to developme...
The paper explores the question of threats related to commercial processing of genetic data putting the analysis in the context of data capitalism. Modern technological, social and economic changes translate to development of huge databases and their commercial application. These phenomena concern processing of medical data and medical services too. The authors review the literature on risks associated with unauthorized use of personal data and present also some of the relevant legal acts. The focus is on problems arising from data subjects' decisions to provide their data to commercial controllers for lifestyle or genealogy testing purposes. While data subjects are in full right to consent to such processing, there are serious questions about further security of the data and control over their processing, which is especially problematic with genetic data, considering their unique nature. The paper illustrates this concern with the case of 23andMe and bankruptcy of this medical service provider, presenting the challenges of executing effective control over such actors, either by data subjects themselves or authorities. The paper highlights the need to update legal provisions to accommodate the processes occurring in the social environment.
Genomic diversity, inbreeding, and selection signatures in duroc, landrace, and yorkshire pigs from a long-term closed breeding system.
Tang H, Mulim HA, Chen SY … +5 more , Schinckel AP, Hongfeng-Xue, Dingjie-Qiu, Yizhan-Liu, de Oliveira HR
J Appl Genet · 2026 Jun · PMID 42234283 · Publisher ↗
Duroc (DD), Landrace (LL), and Yorkshire (YY) are among the most widely used commercial pig breeds, having undergone intense long-term selection within closed breeding systems. This study presents a comprehensive genomic...
Duroc (DD), Landrace (LL), and Yorkshire (YY) are among the most widely used commercial pig breeds, having undergone intense long-term selection within closed breeding systems. This study presents a comprehensive genomic analysis of genetic diversity, inbreeding patterns, and selection signatures in DD, LL, and YY populations that have been subject to close breeding for over 15 years. Genomic and pedigree data were available for 1,088 animals (DD = 348, LL = 276, YY = 464), genotyped using the GenoBaits Porcine 100 K SNP panel. Principal component analysis and genetic diversity metrics revealed distinct population structures among the three breeds. Pairwise genetic differentiation supported this pattern, with DD showing the greatest divergence from LL (0.34 ± 0.24) and YY (0.33 ± 0.24), while LL and YY were more closely related (FST = 0.22 ± 0.19). Linkage disequilibrium (LD) analysis further confirmed these differences, as DD exhibited the highest average r² (0.34), followed by LL (0.28) and YY (0.25). Within-breed genetic diversity metrics, including observed heterozygosity (HO: 0.37 in DD, 0.39 in LL, 0.38 in YY), expected heterozygosity (HE: 0.36 in DD, 0.37 in LL, 0.38 in YY), and minor allele frequency (MAF: 0.27 in DD, 0.28 in LL, 0.29 in YY), indicated greater genetic variability in LL and YY compared to DD. Runs of homozygosity (ROH) analyses revealed different patterns of autozygosity, with DD exhibiting more long ROH indicative of recent inbreeding, while YY harbored a higher number of short ROH, suggestive of more ancient demographic events. ROH-based inbreeding coefficients (FROH) consistently exceeded pedigree-based estimates (FPED) across all breeds, highlighting the presence of recent or unrecorded inbreeding that pedigree data may not fully capture. According to Generation Proxy Selection Mapping (GPSM), 17, 1, and 12 significant SNPs were detected in DD, LL, and YY, respectively. Functional annotation of ROH islands and GPSM-significant loci revealed both breed-specific and overlapping QTLs related to traits such as growth, reproduction, and carcass. In general, the findings of this study contribute to a deeper understanding of the genomic consequences of long-term closed breeding and provide reference information to support consideration of breeding strategies that balance continued selection for productivity with the maintenance of genetic diversity in modern commercial pig populations.
Transcriptomic and proteomic analysis of MVK variant sites in two subtypes of porokeratosis.
Lai S, Zhu W, Lin C … +7 more , Guo Z, Chen S, Xie L, Liu J, Zeng Z, You C, Li L
J Appl Genet · 2026 Jun · PMID 42234282 · Publisher ↗
Porokeratosis (PK) encompasses genetically heterogeneous keratinization disorders, with disseminated superficial actinic porokeratosis (DSAP) and porokeratosis ptychotropica (PPt) as distinct subtypes. Although MVK is a...
Porokeratosis (PK) encompasses genetically heterogeneous keratinization disorders, with disseminated superficial actinic porokeratosis (DSAP) and porokeratosis ptychotropica (PPt) as distinct subtypes. Although MVK is a known causative gene, how different variants drive distinct phenotypes remains unclear. Through whole-exome sequencing of two DSAP patients, we identified an MVK variant (c.439G > A, p.Ala147Thr) cataloged as likely pathogenic in ClinVar yet uncharacterized functionally in DSAP keratinocytes. A previously reported PPt-associated variant (c.64G > A) was included for comparison. We established HaCaT cells stably overexpressing each mutant via lentiviral transduction and validated expression by qPCR and Western blot. Integrated transcriptomic and proteomic analyses identified differentially expressed genes (DEGs) and proteins (DEPs) across MVK439 versus control, MVK64 versus control, and MVK439 versus MVK64 groups, followed by GO and KEGG enrichment. Transcriptomic profiling revealed 231, 1,849, and 2,329 DEGs in the respective comparisons. Proteomic screening identified 2,673 DEPs, with 42 shared across all groups, 77 specifically associated with c.439G > A, and 832 linked to c.64G > A. Integrated analysis suggested IL12A and pIgR as potential contributors to c.439G > A-driven DSAP, while CXCL11, CXCL9, and TNFRSF12A may mediate c.64G > A-induced PPt. These findings offer new insights into MVK function and PK pathogenesis, warranting validation in larger cohorts.
Extracellular matrix gene variants and susceptibility to sport-related musculoskeletal injuries.
Kabelis P, Rzeszutko-Bełzowska A, Leońska-Duniec A
J Appl Genet · 2026 May · PMID 42209954 · Publisher ↗
The extracellular matrix (ECM) plays a fundamental role in maintaining skeletal muscle structure and facilitating tissue repair following injury. Alterations in its composition can disrupt regeneration, promote fibrosis,...
The extracellular matrix (ECM) plays a fundamental role in maintaining skeletal muscle structure and facilitating tissue repair following injury. Alterations in its composition can disrupt regeneration, promote fibrosis, and increase susceptibility to musculoskeletal injury. The aim of this study was to investigate whether the BGN (rs1042103), DCN (rs13312816 and rs516115), ELN (rs2071307), FBN2 (rs331079), MMP1 (rs1799750), MMP10 (rs486055), and MMP12 (rs2276109) polymorphisms, either individually or in combination, are associated with susceptibility to musculoskeletal injury. This study included 142 physically active Caucasian participants with a self-reported history of non-contact musculoskeletal injury and 133 participants without such a history. All the samples were genotyped using real-time polymerase chain reaction (real-time PCR). Associations between genotypes, haplotypes, epistatic interactions, and musculoskeletal injury risk were analysed. A nominally increased risk of musculoskeletal injury was observed in individuals carrying:(i) FBN2 rs331079: GC and CC genotypes(ii) MMP12 rs2276109: GG genotype(iii) BGN rs1042103: AG and AA genotypes(iv) DCN rs516115: AG genotypeConversely, the GG genotype of DCN rs516115 appeared protective compared to AA. No significant associations were found for the remaining polymorphisms or for DCN and MMP haplotypes. An epistatic interaction between DCN (rs13312816) and BGN (rs1042103) was detected. Participants with AG/TT and AA/AT genotype combinations had a higher probability of belonging to the injury group. However, across all analyses, no associations remained statistically significant after Bonferroni correction. Specific genotypes of FBN2, MMP12, BGN, and DCN genotypes showed nominal associations with susceptibility to musculoskeletal injury in a physically active Caucasian population; therefore, these findings should be regarded as exploratory.
Genome-wide association in quality protein maize: identifying key loci for yield enhancement.
Rainy R, Sandhu SS, Kumar S … +3 more , Kumar R, Vikal Y, Sharma P
J Appl Genet · 2026 May · PMID 42204050 · Publisher ↗
Grain yield in maize (Zea mays L.) is a complex quantitative trait influenced by multiple component traits. Achieving sustainable yield improvement in nutritionally enhanced Quality Protein Maize (QPM) lines under growin...
Grain yield in maize (Zea mays L.) is a complex quantitative trait influenced by multiple component traits. Achieving sustainable yield improvement in nutritionally enhanced Quality Protein Maize (QPM) lines under growing population pressure and changing climate requires enhanced genetic gain. This study aimed to dissect the genetic basis of key yield components in 149 QPM inbred lines using five genome-wide association study (GWAS) models. Multi-environment phenotypic evaluation revealed moderate to high heritability and significant genotypic and environmental effects for most traits. GWAS identified a total of 27 stable marker-trait associations (MTAs) distributed across all chromosomes except chromosome 6, including nine pleiotropic loci. Novel genomic bins 3.03-3.04 and 5.01 were associated with kernel length. Functional annotation of potential candidate genes revealed enrichment for processes related to cell elongation, seed development, and sugar transport, with predominant expression in reproductive tissues during early kernel development. The gene Zm00001d039637 encoding GLK14 exhibited pleiotropic effects on kernel length and cob diameter, whereas MADS-box and AP2/EREBP transcription factors were linked to kernel number. Collectively, these results refine the current understanding of kernel development and identify promising genomic regions and functional candidates for deployment in genomics-assisted breeding for yield improvement in maize.
Liver response to early embryonic stimulation with xylo-and mannooligosaccharides in broiler chickens.
Bełdowska A, Barszcz M, Tuśnio A … +5 more , Konopka A, Gawin K, Święch E, Siwek M, Dunisławska A
J Appl Genet · 2026 May · PMID 42204049 · Publisher ↗
The gut microbiota plays an important role in signaling between the intestines and the liver. These two organs are connected by a bidirectional relationship known as the gut-liver axis. The aim of this study was to deter...
The gut microbiota plays an important role in signaling between the intestines and the liver. These two organs are connected by a bidirectional relationship known as the gut-liver axis. The aim of this study was to determine the impact of oligosaccharides delivered in ovo on liver physiology in broiler chickens. On the 12th day of incubation, the following substances were injected into the eggs of ROSS 308 broiler chickens: saline (control), xylotriose (XOS3), xylotetrose (XOS4), mannotriose (MOS3) or mannotetrose (MOS4). The dose of oligosaccharides was 0.5 mg/0.2 ml saline. Blood, bile and liver samples were collected post-mortem on day 42. Compared to the other groups, the MOS3 significantly increased the level of uric acid in the blood, while the XOS3, XOS4 and MOS3 groups had a higher magnesium concentration than the control group. All oligosaccharides decreased catalase and total superoxide dismutase activity. Compared to the other groups, the administration of MOS3 and MOS4 increased the content of oxidants in the liver of chickens. XOS4 increased the expression of the ANGPTL4, CYR61, KLHL6, NR4A3 and SYK genes compared to the control group, while MOS3 increased the expression of ANGPTL4, KLHL6 and NR4A3 genes. MOS3 increased and MOS4 decreased the level of DNA methylation for the ANGPTL4 gene. XOS4 and both MOS3 and MOS4 increased the methylation of NR4A3 gene. Therefore, it can be concluded that XOS and MOS decrease antioxidant status of the liver but increased the expression of genes related to the immunity and metabolism.
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