Biochemical Genetics[JOURNAL]
Sun
200 papers
Assembly and Characterization of the First Complete Mitochondrial Genome of Tussilago farfara L.: Insights into Biological Functions and Phylogenetic Relationships within the Asteraceae Family.
Zhang Y, Yan Y, Zhang G … +5 more , Chen Y, Li Y, Gao J, Yang B, Peng L
Biochem Genet · 2026 Feb · PMID 41746552 · Publisher ↗
Tussilago farfara L., a member of the Asteraceae family, is an economically valuable species due to its edible and medicinal properties. To elucidate the structural characteristics, genetic mechanisms, and evolutionary p...
Tussilago farfara L., a member of the Asteraceae family, is an economically valuable species due to its edible and medicinal properties. To elucidate the structural characteristics, genetic mechanisms, and evolutionary pathways of the organelle genomes of T. farfara, we sequenced, assembled, and annotated its mitochondrial genome for the first time. The complete mitochondrial genome of T. farfara spans 306,024 bp and contains 33 mitochondrial protein-coding genes (PCGs), 3 rRNAs, and 22 tRNAs. Analysis of the nucleotide substitution rate and genetic diversity revealed that most mitochondrial genome genes may have undergone purifying selection, indicating a slow evolutionary rate and a relatively conserved genomic structure. We further identified 13 fragments of chloroplast-derived DNA integrated into the mitochondrial genome, evidencing intracellular gene transfer. Collinearity analysis showed that Arctium lappa shares the most extensive mitochondrial homologous sequences and the highest sequence similarity with T. farfara. Phylogenetic analysis based on the mitochondrial genome helped to clarify the evolutionary and taxonomic position of T. farfara within the Asteraceae family. The mitochondrial genome sequence of T. farfara provides a valuable genomic resource for species identification and for evolutionary studies within the Asteraceae family.
Identification of Gene Signatures Differentiating Cancer from Normal Tissues Across Histological Classifications of Gastric Adenocarcinoma via Machine Learning Methods.
Ren J, Gao Q, Zhou X … +4 more , Feng K, Guo W, Huang T, Cai YD
Biochem Genet · 2026 Feb · PMID 41746551 · Publisher ↗
Gastric adenocarcinoma is a significant global health concern. Among the myriad histologic classification methods for this cancer, the Lauren classification stands out as a pivotal tool. Nonetheless, the precision and de...
Gastric adenocarcinoma is a significant global health concern. Among the myriad histologic classification methods for this cancer, the Lauren classification stands out as a pivotal tool. Nonetheless, the precision and detail of current histological staging techniques frequently face scrutiny. Utilizing high-resolution single-cell transcriptomic data, this research delves into the distinctive gene expression patterns in diffuse, intestinal, and mixed gastric cancers by deploying various machine learning algorithms. The main goal was to recognize important gene markers and establish efficient classification models. The data was derived from the tumor microenvironment, with cells categorized into six groups according to two locations: tumoral and normal, and three histology types: diffuse, intestinal, and mixed. Every cell describes the expression level of 56,265 genes. We integrated seven feature selection algorithms and four classification algorithms, which increased the accuracy of classification. Importantly, our approach detected intricate expression patterns realized for the first time-for example, high expression of CLDN4 in intestinal-type gastric cancers and CCL4 and CXCR4 in diffuse-type gastric cancers. The identified gene markers and gene expression patterns provide insights into subtype-specific molecular characteristics of gastric cancer. These candidate markers may serve as a foundation for future studies aimed at validating their utility in subtype classification and clinical stratification.
Unravelling Ovarian Cancer: an analysis of the Influence of LRP1 and PAI1 Genetic Variations.
Devi Krishna RB, Mathews SG, Agarwal P … +7 more , Rani CE, Krishnamurthy N, Murali S, Rani AL, Joseph LD, Rajasekaran B, Mary FA
Biochem Genet · 2026 Feb · PMID 41729408 · Publisher ↗
To assess the potential association between LRP1 (rs715948) and PAI1 (rs2227631, rs1799889) gene variation and ovarian cancer (OC) susceptibility. This study evaluated the genotypic and allelic distributions of LRP1 gene...
To assess the potential association between LRP1 (rs715948) and PAI1 (rs2227631, rs1799889) gene variation and ovarian cancer (OC) susceptibility. This study evaluated the genotypic and allelic distributions of LRP1 gene and PAI1 gene variants using Restriction Fragment Length Polymorphism (RFLP) analysis in 134 °C patients and 134 healthy controls. LRP1 (rs715948) showed a significant association with OC risk. The TC genotype was (OR = 3.7823, 95% CI: 2.1732-6.5825, p < 0.0001), and the CC genotype has (OR = 2.1613, 95% CI: 1.0054-4.6459, p = 0.0484). The C allele was significantly more frequent in cases (46%) than controls (32%) (OR = 1.7684, 95% CI: 1.2443-2.5133, p = 0.0015). For PAI1 (rs2227631), AG and GG genotypes showed no significant association (p = 0.3519 and p = 0.1165, respectively). PAI1 (rs1799889) AG genotype was (OR = 5.855, 95% CI: 2.4663-13.9027, p < 0.0001), while GG genotype showed no significance (p = 0.1025). The dominant model of LRP1, (TC + CC) and C alleles, were significantly more frequent in OC cases, indicating a potential risk factor. In contrast, the dominant models (AG + GG) and G alleles of PAI1 (rs2227631, rs1799889) showed no significance with OC susceptibility. Genetic variation in LRP1 (rs715948) significantly associated with increased OC risk, particularly the TC and CC genotypes and C allele. The C allele of this gene is key markers linked to higher OC susceptibility. Whereas in PAI1 (rs2227631, rs1799889), dominant models (AG + GG) show no significance, association suggesting a less prominent role in OC susceptibility. These findings highlight LRP1 as a potential genetic biomarker for OC risk assessment, while the role of PAI1 variants warrants further investigation in larger sample size.
TRIB3 Promotes Laryngeal Cancer Progression via Regulating Ubiquitination of PPARα.
Cheng Z, Yue K, Wang W … +4 more , Jiang C, Qiang H, Jiang Z, Huang L
Biochem Genet · 2026 Feb · PMID 41721959 · Publisher ↗
Laryngeal cancer is a prevalent malignancy within the head and neck region, and its incidence is progressively rising. This study aimed to examine the role of TRIB3 in laryngeal cancer. TU212 and TU686 cell lines were tr...
Laryngeal cancer is a prevalent malignancy within the head and neck region, and its incidence is progressively rising. This study aimed to examine the role of TRIB3 in laryngeal cancer. TU212 and TU686 cell lines were transfected with a TRIB3-targeting lentivirus. Colony formation, flow cytometry, and wound scratch healing assay were used to detect cell proliferation, apoptosis, and migration, respectively. TRIB3 expression levels were quantified using fluorescence real-time quantitative polymerase chain reaction (qRT-PCR). The protein expression levels of TRIB3 and PPARα were analyzed through Western blotting. The effect of TRIB3 knockdown on tumor growth was further examined using a nude mouse xenograft model. Cycloheximide (CHX) and MG-132 were used to treat cells, then co-immunoprecipitation (CO-IP) assays were employed to explore the interaction between TRIB3 and PPARα. Additionally, the effect of TRIB3 knockdown on PPARα ubiquitination was examined by CO-IP. Our results demonstrated that TRIB3 knockdown suppressed cell proliferation and migration while promoting cell apoptosis. In vivo experiment corroborated the suppressive effect of TRIB3 knockdown on cell proliferation, presented as suppressed tumor growth. Furthermore, CHX treatment suppressed the expression of PPARα while TRIB3 knockdown promoted PPARα expression in TU212 and TU686 cells. CO-IP assay and IF staining confirmed the interaction of TRIB3 and PPARα. MG-132 treatment promoted the expression of PPARα, and TRIB3 knockdown obviously promoted PPARα expression in TU212 and TU686 cells. CO-IP assay confirmed TRIB3 deubiquitinates and stabilizes PPARα. Our results suggest that TRIB3 knockdown inhibits the proliferation of laryngeal cancer cells. The mechanism of action is related to the regulation of ubiquitination of PPARα. Our research provide a novel insights into the treatment of laryngeal cancer.
Leish-F1 Multi-epitope Lentiviral Vaccine as a Novel Candidate Against Leishmania major in Balb/c Mice.
Daneshi R, Rabienia M, Roudbari Z … +4 more , Ghasemian A, Moulazadeh A, Mortazavidehkordi N, Farjadfar A
Biochem Genet · 2026 Feb · PMID 41706369 · Publisher ↗
The growing trend of Leishmania major (L. major) infections around the world has raised global concerns due to the lack of efficient vaccines and antiparasitic drugs. In addition, the drug resistance crisis and side effe...
The growing trend of Leishmania major (L. major) infections around the world has raised global concerns due to the lack of efficient vaccines and antiparasitic drugs. In addition, the drug resistance crisis and side effects of chemotherapy remain to be addressed. In the present study, the designed multi-epitope lentiviral vaccine from Leish-F1 (consisting of TSA, Leif, LmSTI1 proteins) was produced. For this purpose, multi-epitope construct was sub-cloned into the pCDH513 lentiviral vector, previously designed in silico. Subsequently, to produce a recombinant lentivirus, PCDH513B-Leish-F1 vector was co-transfected with packaging vectors into HEK293T cells. In order to confirm the gene expression, Western blot technique was performed. Finally, to evaluate the immune responses, the vaccine containing Leish-F1 selected epitopes, and two control groups, phosphate-buffered saline and lentivirus without multiepitope, were injected twice into the Balb/c mice. The enzyme linked immunosorbent assay method deciphered that the vaccinated group had a higher level of IFN (interferon)-γ and IL (interleukin)-4 levels compared to control groups (p < 0.05). Also, the IgG2a and IgG1 antibodies showed a significant increase in the main groups (p < 0.05). The results revealed that the immunization of the Balb/c mice using a multi-epitope lentiviral vaccine led to the stimulation of humoral and cellular responses.
Genetic Variability and Diversity Analysis for Nutritional and Anti-nutritional Traits in Pearl Millet [Pennisetum glaucum (L.) R.Br].
Singhal T, Singh SP, Yadav S … +4 more , Aavula N, Kapoor C, Singh N, Satyavathi CT
Biochem Genet · 2026 Feb · PMID 41706368 · Publisher ↗
Addressing micronutrient malnutrition requires targeted biofortification of staple crops such as pearl millet [Pennisetum glaucum (L.) R.Br.], which is widely consumed in arid and semi-arid regions. This study assessed 4...
Addressing micronutrient malnutrition requires targeted biofortification of staple crops such as pearl millet [Pennisetum glaucum (L.) R.Br.], which is widely consumed in arid and semi-arid regions. This study assessed 47 advanced breeding lines developed at ICAR-IARI, New Delhi, to evaluate genetic variability, heritability, and diversity for nutritional (iron, zinc, protein, starch, oil, amylose) and anti-nutritional (phytate and phenol) traits. Substantial variation was observed for grain iron (33.9-121.4 mg/kg), zinc (27.4-90.0 mg/kg), and protein (7.99-15.56%). High genotypic and phenotypic coefficients of variation, coupled with high heritability and genetic advance for iron, zinc, and protein, indicated the predominance of additive gene action, suggesting that simple phenotypic selection can be effectively employed for trait improvement. Correlation analysis revealed strong positive associations between iron, zinc, and protein, enabling simultaneous enhancement of these key traits. Multivariate analyses (PCA and hierarchical clustering) identified three distinct genetic clusters, with one group (Cluster II) exhibiting superior iron and zinc profiles. The presence of broad genetic diversity and favourable trait combinations underscore the potential of these genotypes as donors in breeding programs aimed at developing nutrient-dense pearl millet varieties/ hybrids. This work contributes critical insights toward the genetic enhancement of pearl millet to alleviate hidden hunger and improve dietary quality in vulnerable populations.
Exploring the Clinical Landscape of Long Non-coding RNAs in Cancer Diagnosis and Therapy.
Bhattacharyya R, Basu S, Gupta S … +1 more , Sur S
Biochem Genet · 2026 Feb · PMID 41706367 · Publisher ↗
Cancer remains a major global health challenge. Current diagnostic and therapeutic strategies are often limited by the complexity and heterogeneity of the disease. Long non-coding RNAs (lncRNAs) have recently emerged as...
Cancer remains a major global health challenge. Current diagnostic and therapeutic strategies are often limited by the complexity and heterogeneity of the disease. Long non-coding RNAs (lncRNAs) have recently emerged as important regulators of cancer. They influence tumor initiation, progression, metastasis, immune evasion, and therapy resistance. This review summarizes the clinical significance of lncRNAs and their potential as tools for cancer diagnosis, prognosis, and treatment. We describe their molecular functions, including interactions with DNA, RNA, and proteins, and explain how they regulate oncogenic pathways, contribute to drug resistance, and modulate immune responses. We also highlight the translational potential of lncRNAs as diagnostic and prognostic biomarkers, as well as therapeutic targets in multiple cancer types. Completed and ongoing clinical trials further support their relevance, particularly in cancer immunotherapy and lncRNA-based vaccine development. Despite these advances, important challenges remain. Efficient delivery, target specificity, and robust clinical validation are still major hurdles. Emerging strategies aim to address these issues and improve the clinical feasibility of lncRNA-based approaches. By integrating current molecular insights with clinical progress, this review underscores the promise of lncRNAs in oncology. They hold significant potential to advance precision medicine and shape future directions in cancer management.
hsa_circ_0006156 Suppresses Malignant Progression by Inducing Ferroptosis in Gastric Cancer Via miR-942-5p/NCOA4 Axis.
Niu S, Xie W, Zhan X … +3 more , Xu Q, Fang M, Zhang D
Biochem Genet · 2026 Feb · PMID 41701407 · Publisher ↗
Stomach carcinoma represents a malignancy with high prevalence and poor prognosis. hsa_circ_0006156’s expression level, a specific circular RNA (circRNA), shows a significant reduction in gastric carcinoma tissues when c...
Stomach carcinoma represents a malignancy with high prevalence and poor prognosis. hsa_circ_0006156’s expression level, a specific circular RNA (circRNA), shows a significant reduction in gastric carcinoma tissues when contrasted with normal tissues. The variations in the expression of hsa_circ_0006156correlates with gastric cancer differentiation, lymph node metastasis, and patient prognosis, although the underlying mechanisms remain elusive. In our study, cells were engineered to overexpress hsa_circ_0006156, while nude mice bearing HGC-27 tumor xenografts were established. Cell viability was assessed via CCK-8 assays, RNA levels were quantified using qRT-PCR, migration capabilities utilized wound healing assays and transwell assays, ferroptosis levels were determined by assessing reactive oxygen species (ROS), Fe2+, malondialdehyde (MDA), and glutathione (GSH) levels. Furthermore, RNA binding levels were investigated using dual-luciferase reporter assays. Our experimental outcomes revealed that in gastric carcinoma cells where founded a diminished expression of hsa_circ_0006156, while upregulation of hsa_circ_0006156 discovered restrain the growth, mobility, and spread of stomach cancer cells. Additionally, overexpression of hsa_circ_0006156 induced ferroptosis and concurrently suppressed tumor growth in gastric cancer cells. Mediated by the interaction with hsa_circ_0006156 and NCOA4, miR-942-5p reduces ferroptosis activation in stomach cancer cells. In gastric cancer cells, our current findings suggest that via the hsa_circ_0006156/miR-942-5p/NCOA4 axis hsa_circ_0006156 induces ferroptosis.
ERBB2 as a Prognostic Biomarker in Prostate Cancer: Integration of Single-Cell Transcriptomics, Deep Learning, and Immunohistochemical Validation.
Wang C, Zhu LJ, Mao WB … +7 more , Chen T, Gu TF, Hu SP, Pan YT, Yan GL, Dong YP, Li J
Biochem Genet · 2026 Feb · PMID 41701406 · Publisher ↗
Biochemical recurrence (BCR) is a critical factor affecting the prognosis of prostate cancer (PCa) patients, while T cell exhaustion and metastatic prostate cancer (mPC)-related genes play significant roles in tumor prog...
Biochemical recurrence (BCR) is a critical factor affecting the prognosis of prostate cancer (PCa) patients, while T cell exhaustion and metastatic prostate cancer (mPC)-related genes play significant roles in tumor progression. This study aims to identify key genes associated with BCR by integrating single-cell transcriptomics and deep learning techniques, and to validate their clinical significance. First, we identified highly expressed genes in CD8 T cell exhaustion clusters from single-cell RNA sequencing data (scRNA-seq) of PCa and intersected them with mPC-related genes. Based on these genes, significant prognostic factors were screened using Cox regression analysis, and a deep learning neural network model was constructed to predict the risk of biochemical recurrence in prostate cancer patients. The tumor-infiltrating lymphocyte (TILs) infiltration was predicted by stratifying patients into high- and low-risk groups. ERBB2 was identified as the most predictive gene through model analysis. Subsequently, ERBB2 expression was validated in an independent PCa cohort using immunohistochemistry (IHC), and its association with biochemical recurrence and clinicopathological features was evaluated through survival analysis and statistical methods. The deep learning model demonstrated excellent performance in predicting BCR, with ERBB2 identified as the most important predictive factor. IHC results revealed that patients with high ERBB2 expression had significantly shorter biochemical recurrence-free survival (bRFS) (P < 0.05). Moreover, high ERBB2 expression was significantly associated with higher prostate-specific antigen (PSA) levels, Node-Metastasis (NM) stage, and International Society of Urological Pathology (ISUP) grade (P < 0.05). This study, for the first time, integrates single-cell transcriptomics, deep learning, and IHC to reveal the critical role of ERBB2 in biochemical recurrence of PCa. High ERBB2 expression is not only a potential biomarker for poor prognosis in PCa patients but may also provide a novel target for personalized therapy.
Clinico-Morphological and Genetic Features of Colorectal Cancer in Multiple Primary Cancers Cases.
Timoshkina NN, Gvaldin DY, Alset D … +2 more , Novikova IA, Kit OI
Biochem Genet · 2026 Feb · PMID 41697498 · Publisher ↗
Colorectal cancer (CRC) is a high-incidence malignancy that could be found a as a part of multiple primary cancers (MPCs). Although molecular mechanisms of MPCs have been widely discussed, they are not fully understood....
Colorectal cancer (CRC) is a high-incidence malignancy that could be found a as a part of multiple primary cancers (MPCs). Although molecular mechanisms of MPCs have been widely discussed, they are not fully understood. The aim of this study was to investigate clinical and genetic characteristics of MPCs colorectal component in Russian cohort patients. 512 CRC patients were included (62 with synchronous and/or metachronous MPCs). DNA was isolated from paraffin-embedded tissues, KRAS, NRAS, BRAF mutations and MSI status were analyzed, and targeted high-throughput sequencing was performed. Results were analyzed using bioinformatics tools to detect different genetic changes. No significant differences were observed between MPCs and single CRC (sCRC) in terms of gender, age, and histological type. Mucinous adenocarcinoma was more frequent in MPCs patients younger than 45 years, but in elderly sCRC patients. Neoplasms in the transverse colon were significantly higher in MPCs (p = 0.004) and rectum malignancies were mainly registered in sCRC (p = 0.005). The frequency of KRAS (G12A) and MSI-H were significantly higher in MPCs compared to sCRC group (p < 0.0001 and p = 0.04, respectively). CRC samples of MPCs showed predominantly missense mutations (51.9%) and nonsense mutations (42.3%) in 16 out of 32 analyzed genes, mainly TP53, KRAS, PIK3CA, APC and BRAF. Mutational profile of these samples identified alterations in RTK-RAS, WNT, TP53 and PI3K signaling pathways. Studying CRC morphological and genetic features in MPCs patients will expand the understanding of molecular genetic mechanisms of multiple cancers to improve treatment strategies and prognosis.
The Impact of NEAT1 on Inflammatory Responses and Processes in Arthropathic Diseases: Latest Findings and Perspectives.
Mohammad SI, Saleh RO, Owida HA … +7 more , Al-Khafaji ZA, Varma P, Vasudevan A, Kadhum WR, Al-Tameemi AR, Mustafa YF, Ansari SA
Biochem Genet · 2026 Feb · PMID 41670787 · Publisher ↗
Arthropathies are joint-related disorders with diverse etiologies but standard clinical and radiographic features. There is growing evidence that long non-coding RNAs (lncRNAs) play a crucial role in regulating the devel...
Arthropathies are joint-related disorders with diverse etiologies but standard clinical and radiographic features. There is growing evidence that long non-coding RNAs (lncRNAs) play a crucial role in regulating the development and progression of certain diseases. Nuclear-enriched abundant transcript 1 (NEAT1) is one of these lncRNAs. It is common and helps control transcription and epigenetics, especially during inflammation. This narrative review presents current data on NEAT1's role in inflammation and its contribution to the development of arthropathies, including psoriasis, rheumatoid arthritis, osteoarthritis, SLE, Behçet's disease, and hemophilic arthropathy. The research demonstrated that NEAT1 regulates immune cell activity, inflammasome formation, and inflammatory signaling pathways through interactions with miRNAs and transcriptional regulators. The activity, progression, and response to treatment of the disease are all linked to its dysregulated expression. In conclusion, NEAT1 appears to be a significant regulator of inflammation and joint disease, potentially serving as both a therapeutic target and a biomarker for joint-related disorders. More mechanistic and translational studies are needed to better understand how it works and how it might be used in medicine.
GLP-1 Mitigated Inflammation and Oxidative Stress in Oral Lichen Planus Via JAK-STAT3 Pathway.
Liu Y, Liu N, Wang W … +4 more , Zhang R, Liu X, Wu L, Li C
Biochem Genet · 2026 Feb · PMID 41653275 · Publisher ↗
Oral lichen planus (OLP) is a chronic inflammatory oral mucosal disease with immune-mediated pathogenesis and potential for malignant transformation. Elevated inflammatory cytokines and oxidative stress contribute to its...
Oral lichen planus (OLP) is a chronic inflammatory oral mucosal disease with immune-mediated pathogenesis and potential for malignant transformation. Elevated inflammatory cytokines and oxidative stress contribute to its progression. This study explored the therapeutic potential of glucagon-like peptide-1 (GLP-1) in modulating inflammation and oxidative stress in OLP. To establish an in vitro OLP model, human oral keratinocytes (HOK) were treated with lipopolysaccharide (LPS) at varying concentrations, and 5 µg/ml was selected as the optimal concentration based on CCK-8 assay results. The inflammatory response was assessed using qRT-PCR and ELISA to measure IL-6, TNF-α, and IL-1β expression. Oxidative stress levels were determined using DCF-DA fluorescence staining for ROS detection and SOD activity assays. The involvement of the JAK/STAT3 pathway was evaluated using western blot analysis of JAK, p-JAK, STAT3, and p-STAT3 protein expression. The OLP model was successfully established in HOK cells using LPS, with significant morphological changes and reduced cell viability observed at 10 µg/ml and higher concentrations. LPS stimulation induced inflammation and oxidative stress, marked by elevated IL-6, TNF-α, IL-1β mRNA and protein levels, increased ROS production, and reduced SOD activity. GLP-1 treatment (10 nM to 100 nM) significantly reduced inflammation and oxidative stress in a dose-dependent manner. GLP-1 inhibited the expression of pro-inflammatory cytokines and decreased ROS levels while enhancing SOD activity. Further analysis revealed that GLP-1’s effects were mediated through the JAK/STAT3 pathway, as demonstrated by the suppression of JAK and STAT3 phosphorylation, which was comparable to the effects of the JAK/STAT3 inhibitor Stattic. This study elucidated that GLP-1 mitigated inflammation and oxidative stress in an in vitro model of OLP via JAK/STAT3 signaling pathway, demonstrating its potential as a therapeutic agent in OLP. Glucagon-like peptide-1 (GLP-1) treatment inhibited activation of JAK/STAT3 signaling pathway, which in turn prevent oxidative stress and inflammation, thereby alleviating oral lichen planus (OLP).
Transcriptional Reprogramming of Lifespan-Associated Genes in Yeast Lacking TOR1.
Turgut Genç T, Günay M
Biochem Genet · 2026 Feb · PMID 41653274 · Publisher ↗
The Target of Rapamycin (TOR) signaling pathway is a central regulator of cell growth, metabolism, and aging across eukaryotes. In Saccharomyces cerevisiae, TOR1 deletion extends lifespan, yet the underlying transcriptio...
The Target of Rapamycin (TOR) signaling pathway is a central regulator of cell growth, metabolism, and aging across eukaryotes. In Saccharomyces cerevisiae, TOR1 deletion extends lifespan, yet the underlying transcriptional architecture remains incompletely characterized. RNA-seq analysis was performed on wild-type and tor1Δ mutant cells during exponential growth in glucose-rich conditions to identify key longevity-associated gene expression changes. Differential expression analysis revealed 3091 genes altered by TOR1 deletion, including 736 annotated as lifespan-related in the Saccharomyces Genome Database. TOR1 deletion triggered broad transcriptional reprogramming, including suppression of ribosome biogenesis and translation machinery, alongside induction of pathways supporting energy conservation, reserve carbohydrate metabolism, and stress resistance. These expression changes reflect a shift toward a metabolically reprogrammed state characterized by enhanced mitochondrial function and cellular redox balance. Promoter motif analysis implicated nutrient- and stress-responsive transcription factors such as Adr1 with its paralog YGR067C, Hap4, Mig1, and Msn4 in regulating these changes. Notably, HXK1 was among the most highly upregulated genes suggesting a potential regulatory role beyond its catalytic function, possibly contributing to transcriptional reprogramming under TOR1-deficient conditions. These findings demonstrate that TOR1 deletion coordinates a survival-oriented transcriptional program through lifespan-associated regulatory circuits. This study supports TORC1 as a central hub linking nutrient sensing to lifespan-related transcriptional networks. These findings provide novel insights into the transcriptional basis of yeast longevity and suggest that targeting TOR-regulated metabolic nodes may represent a promising strategy for modulating aging.
Genome Wide Association Study Reveals Novel Loci Controlling Agronomic Traits in Tomato (Solanum lycopersicum L.).
Tiwari JK, Rai N, Singh MK … +5 more , Singh R, Kant T, Yerasu SR, Singh AK, Kumar R
Biochem Genet · 2026 Feb · PMID 41653273 · Publisher ↗
The genetic basis of agronomic traits is critical for enhancing yield, quality, and disease resistance in tomato. In this study, genome-wide association study (GWAS) was performed on a diverse panel of 72 tomato accessio...
The genetic basis of agronomic traits is critical for enhancing yield, quality, and disease resistance in tomato. In this study, genome-wide association study (GWAS) was performed on a diverse panel of 72 tomato accessions to identify genomic regions linked to 18 agronomic, processing, and disease resistance traits. Phenotypic data were collected over two growing seasons, and genotyping was conducted using genotyping-by-sequencing (GBS) on the Illumina platform. A total of 78,828 high-quality single nucleotide polymorphisms (SNPs) were identified, primarily located in intergenic (54.66%), upstream (15.46%), downstream (14.35%), intronic (10.73%), and exonic (2.90%) regions. After stringent filtering, 7751 SNPs were retained for GWAS, leading to the identification of 47 significant quantitative trait loci (QTLs) associated with 13 traits. Fruit length exhibited the highest number of QTLs (23), while chromosomes 1 and 4 contained the most QTLs (9 each). Several candidate genes were identified for key traits, including F-box protein CPR1-like and transcription factor bHLH162-like for fruit weight, F-box protein At5g49610 for fruit length, transcription factor TGA9 for fruit diameter, F-box protein CPR1-like and Beta-D-xylosidase 2 for fruit yield, Cinnamoyl-CoA reductase-like SNL6 and UDP-glucosyltransferase, as well as stress-induced protein KIN2-like and serine/threonine-protein kinase BLUS1 for ToLCV resistance. Population structure and phylogenetic analyses indicated variation among ancestral populations (K = 3). These findings provide valuable genomic resources and identify candidate genes for key traits, supporting genomics-driven breeding in tomato.
Voltage-Gated Sodium Channel Na1.2: Structural Perspective of the Genetic Variability.
Oliveira-Madureira T, Leal B, Azevedo L
Biochem Genet · 2026 Feb · PMID 41632366 · Publisher ↗
The SCN2A gene encodes the alpha subunit of a voltage-gated sodium channel which is necessary for creating and propagating action potentials in neurons. Impairment of the Na1.2 function is associated with neurodevelopmen...
The SCN2A gene encodes the alpha subunit of a voltage-gated sodium channel which is necessary for creating and propagating action potentials in neurons. Impairment of the Na1.2 function is associated with neurodevelopmental disorders such as Developmental and Epileptic Encephalopathy, Self-limited Neonatal/Infantile Seizures, and Autism Spectrum Disorder. In this study, we used orthologous sequence comparisons, as well as disease associated variants to analyze their location in the structure of Na1.2, with the aim of understanding the impact of genetic variants in the structure of this protein at an evolutionary and clinical level. Our analyses reveal different spatial distribution of interspecific variation where different residues locate preferentially in the first cytoplasmic linker, while disease-associated variants tend to cluster in the voltage-sensing segments of the protein domains. Altogether, these discoveries point to structurally important segments in the Na1.2 structure that have been conserved through evolution due to their role in maintaining the function of the channel.
pCancer and FOXK2 (Forkhead Box K2): Oncogenic and Tumor-Suppressive Roles of FOXK2 in Cancer.
Akin S, Ozturk İ, Hepokur C
Biochem Genet · 2026 Feb · PMID 41632365 · Publisher ↗
Cancer is the second leading cause of death in both developed and developing countries. In cancer cells, hemostasis is disrupted, a process that is maintained under normal conditions in healthy cells. Transcription facto...
Cancer is the second leading cause of death in both developed and developing countries. In cancer cells, hemostasis is disrupted, a process that is maintained under normal conditions in healthy cells. Transcription factors that play a crucial role in preserving this hemostasis have been linked to cancer. In recent years, the involvement of proteins from the FOX transcription factor family in cancer development has been extensively studied, highlighting their potential relevance for therapeutic research. Although one of these proteins, Forkhead Box K2 (FOXK2), was identified in the early 1990s, its biological functions in cellular processes remain incompletely understood. Research has highlighted the roles of FOXK2 in critical molecular processes, including de novo nucleotide synthesis, the expression of metabolic-related enzymes, DNA mismatch repair, cell proliferation, differentiation, apoptosis, and autophagy. Furthermore, it has been shown that FOXK2 mediates the binding of transcription factors that do not directly interact with methylated DNA to methylated regions, and also influences the DNA methylation process. Studies investigating its role in cancer indicate that FOXK2 functions as an oncogenic in certain tissues while acting as a tumor suppressor in others. The role of FOXK2 is particularly controversial, especially in hormone-dependent diseases. In this review, the roles of FOXK2 in various cancer cell types were analysed. Additionally, Gene Ontology (GO) enrichment analyses of miRNAs targeting FOXK2 were conducted, highlighting aspects of FOXK2 that have yet to be explored. GO analysis revealed that miRNAs targeting FOXK2 are particularly involved in regulatory processes. In conclusion, FOXK2 may represent a potential therapeutic target in certain cancer types, although its context-dependent roles require further investigation.
DNA Methylation-Guided Prediction and Validation of TAAD Molecular Targets.
Sha M, Wang Q, Hu Q … +2 more , Liu D, Liu C
Biochem Genet · 2026 Feb · PMID 41632364 · Publisher ↗
Thoracic aortic aneurysms and dissection are pivotal cardiovascular conditions necessitating accurate diagnostics. DNA methylation, a crucial epigenetic mediator, is implicated in early disease biomarkers. Our analysis o...
Thoracic aortic aneurysms and dissection are pivotal cardiovascular conditions necessitating accurate diagnostics. DNA methylation, a crucial epigenetic mediator, is implicated in early disease biomarkers. Our analysis of GSE84274 and GSE202047 datasets pinpointed 498 DEGs with promoter DMPs and DMRs. Outliers were detected via DIvisive ANAlysis (DIANA) and Orthogonal Projection to Latent Structures-Discriminant Analysis (OPLS-DA) (P < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses emphasized vascular and TNF signaling. Utilizing the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, Nuclear Receptor Subfamily 2 Group F Member 2 (NR2F2) and GATA-Binding Protein 2 (GATA2) were identified as core differentially expressed genes (DEGs). Transcriptomic validation confirmed that promoter methylation modulates transcriptional activity (P < 0.05). Enzyme-Linked Immunosorbent Assay (ELISA) indicated heightened 5-mC levels in β-aminopropionitrile (BAPN)-challenged mice (P < 0.05), and Reverse Transcription-Polymerase Chain Reaction (RT-PCR) confirmed the modulation of DNA Methyltransferase 3 Alpha (DNMT3A), DNMT3B, NR2F2, and GATA2. Methylation-Specific PCR (MSP) and Bisulfite Sequencing PCR (BSP) substantiated the hypermethylation of NR2F2 and GATA2 promoters in TAAD (P < 0.05). Our study correlates heightened promoter methylation of NR2F2 and GATA2 with TAAD, proposing them as novel diagnostic biomarkers.
Multi-omics Analysis Reveals the Prognostic and Therapeutic Value of TGF-β Signaling-related Genes in Idiopathic Pulmonary Fibrosis.
Fu C, Jing X, Zhang M … +5 more , Cheng Y, Yang W, Wu X, Chu X, Lu X
Biochem Genet · 2026 Feb · PMID 41632363 · Publisher ↗
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease with a survival rate comparable to or worse than that of many cancers. Proper TGF-β signaling is essential for normal lung function, but its disr...
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease with a survival rate comparable to or worse than that of many cancers. Proper TGF-β signaling is essential for normal lung function, but its disruption plays a key role in pulmonary fibrosis and cancer progression. This study aims to elucidate the role of TGF-β signaling-related genes in the prognosis and treatment of IPF through multi-omics analysis. We obtained datasets from the GEO database and identified differentially expressed genes, followed by enrichment analyses. Core genes were identified using machine learning algorithms. Next, we evaluated the expression of core genes and their predictive ability for IPF, as well as their relationship with lung function and survival time. Then, mendelian randomization revealed core genes causally associated with IPF. Subsequently, pseudotime analysis, cell communication analysis and metabolic analysis were performed using single-cell data. Furthermore, we performed immune infiltration analysis to reveal the immune microenvironment of IPF. Finally, in vivo experiments validated the mRNA expression of the core genes. Two core genes (ACVRL1 and LTBP1) were identified through differential expression analysis and machine learning algorithms. Validation using multiple external datasets confirmed that these core genes exhibit stable expression patterns and have strong predictive ability for IPF patients. Further analysis revealed that the expression of these core genes correlates with lung function and survival time in IPF patients. Mendelian randomization analysis provided evidence of a causal link between ACVRL1 and IPF. Using eQTLGen data, our summary data-based mendelian randomization (SMR) analysis revealed a possible causal link between ACVRL1 and IPF. Similarly, using GTEx eQTL data, our SMR analysis revealed a potential causal link between ACVRL1 and IPF. Furthermore, single-cell data analysis highlighted differences in cell communication and metabolism between ACVRL1 + endothelial cell (EC) and ACVRL1-EC. Finally, RT-qPCR results support the potential role of core genes in IPF. This study provides new perspectives on the development of IPF and may help identify novel therapeutic targets. Further research may reveal how core genes influence cellular function and disease progression, providing novel insights into the intricate mechanisms underlying IPF.
Potential Targets in Nonalcoholic Steatohepatitis Based on Bioinformatics Analysis and Machine Learning Strategies.
Lv T, Zhu L, Han Y … +9 more , Cheng Z, Cao Y, Zhang W, Huai J, Ma W, He Y, Zhu Y, Yan Q, Zhou X
Biochem Genet · 2026 Jan · PMID 41591694 · Publisher ↗
NASH poses a significant threat to human health and is recognized as the leading contributor to HCC. In this study, we leveraged publicly accessible datasets to identify novel differentially expressed genes that may serv...
NASH poses a significant threat to human health and is recognized as the leading contributor to HCC. In this study, we leveraged publicly accessible datasets to identify novel differentially expressed genes that may serve as potential targets in NASH or potentially NASH-induced HCC. The publicly available datasets were obtained from the GEO. Differential gene expression analysis and enrichment analysis was performed. Subsequently, WGCNA and PPI network were constructed. Lastly, machine learning was employed to identify key feature genes. Utilizing the integrated GEO database, we identified 446 genes exhibiting differential expression. Enrichment analysis indicated that these genes are predominantly associated with glucose and lipid metabolism and inflammatory processes. Through WGCNA, three modules were identified that demonstrated a significant correlation with NASH. Furthermore, core genes among the differentially expressed genes were extracted via protein and protein interaction analysis. Ultimately, machine learning techniques were employed, leading to the identification of three genes: FosB, Fos, and SOCS3. Notably, FosB exhibited consistent expression across various datasets, demonstrated strong predictive capabilities for NASH, and was associated with improved prognostic outcomes in hepatocellular carcinoma by data from TCGA. Additionally, in vitro immunohistochemistry experiments revealed significant reduction of FosB expression in NASH. Bioinformatics analyses conducted on various datasets, along with in vitro immunohistochemistry experiments, revealed significant downregulation of FosB in NASH. It indicates that FosB plays a critical role in the pathogenesis of NASH, and its expression is associated with the prognosis of patients with HCC. Further experimental studies are required to investigate the potential targeting of FosB in NASH and NASH-induced HCC.
Clinical and Molecular Characterization of Five Additional Individuals With SATB2-Associated Syndrome in Guangxi.
Yi S, Zhang Q, Chen F … +10 more , Zhou X, Zhang Q, Yi S, Zhang X, Qian J, Wang L, Zhang S, Chen B, Qin Z, Luo J
Biochem Genet · 2026 Jan · PMID 41579226 · Publisher ↗
SATB2-associated syndrome (SAS) is a multisystemic disorder characterized by developmental delay, moderate to profound intellectual disability, speech delay and/or absent speech, behavioral issues such as autistic tenden...
SATB2-associated syndrome (SAS) is a multisystemic disorder characterized by developmental delay, moderate to profound intellectual disability, speech delay and/or absent speech, behavioral issues such as autistic tendencies, agitation or aggressive outbursts, self-injury, impulsivity, hyperactivity, anxiety and sleeping difficulties. Alterations in the SATB2 gene have been identified as pathogenic causes of SAS. No formal clinical diagnostic criteria have been established for SAS, and molecular disruption of SATB2 is necessary to confirm the diagnosis. To investigate the molecular pathogenesis of five sporadic patients with intellectual disability, and to delineate the comprehensive clinical characteristics of SAS patients. Whole-exome sequencing analysis was performed in five unrelated patients, and RNA analysis was employed to validate the impact of genetic variation on aberrant splicing. Five SATB2 variants were identified, three of which were novel, including three frameshift variants, one nonsense variant, and a missense variant resulting in aberrant splicing was verified by RNA analysis. A comparative analysis was conducted between the clinical features of our patients and those reported in the literature. In addition to intellectual disability and impaired speech, abnormalities in palmar creases and postnatal growth delay were highlighted as clinically significant features for the diagnosis of SAS. Language regression, as well as joints and fingers abnormalities were also observed in our cohort. Our findings demonstrate that effective mRNA analysis is helpful for understanding the pathogenic mechanisms of novel variants. This study broadens the genetic and phenotypic spectrum of SAS and enhances our knowledge to facilitate accurate genetic counseling and appropriate treatment options.
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