Biochemical Genetics最新文献

{"title":"Associations between VMAT1 Polymorphisms and Obesity.","authors":"Shahryar Azizi, Maryam Dadyar, Solat Eslami, Bashdar Mahmud Hussen, Arezou Sayad, Soudeh Ghafouri-Fard","doi":"10.1007/s10528-025-11250-9","DOIUrl":"10.1007/s10528-025-11250-9","url":null,"abstract":"<p><p>Obesity is a multifactorial disorder with a significant genetic component. Variants within the VMAT1 gene have been proposed to influence susceptibility to obesity. This study aimed to assess the association of two single-nucleotide polymorphisms (SNPs), rs2270637 and rs1390938, within VMAT1 with obesity risk in an Iranian population undergoing sleeve gastrectomy. A number of obese patients selected for sleeve gastrectomy were genotyped for rs2270637 and rs1390938. Genotype and allele frequencies were compared using logistic regression under different genetic models (allelic, co-dominant, and recessive). Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the strength of associations. The rs1390938 SNP showed a significant association with obesity in the allelic model, with the A allele conferring protection against obesity (OR = 0.70, 95% CI 0.55-0.88, P = 0.003). In the co-dominant model, individuals with the AA genotype had a significantly reduced risk of obesity compared to those with the GG genotype (OR = 0.20, 95% CI 0.092-0.43, P = 0.000058). Similarly, in the recessive model, the AA genotype remained protective (OR = 0.21, 95% CI 0.099-0.46, P = 0.000087). The rs2270637 SNP also showed significant associations with obesity in co-dominant and recessive models. The GG genotype was protective compared to the CC genotype (OR = 0.11, 95% CI 0.034-0.41, P = 0.001) and compared to the combined GC + CC genotypes (OR = 0.11, 95% CI 0.034-0.40, P = 0.001). Both rs1390938 and rs2270637 polymorphisms in the VMAT1 gene are significantly associated with obesity risk in the studied Iranian cohort. The findings support the role of VMAT1 as a potential genetic susceptibility locus for obesity.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6163-6172"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical and Molecular Characterization of Five Additional Individuals With SATB2-Associated Syndrome in Guangxi.","authors":"Sheng Yi, Qinle Zhang, Fei Chen, Xunzhao Zhou, Qiang Zhang, Shang Yi, Xiaofei Zhang, Jiale Qian, Linlin Wang, Shujie Zhang, Biyan Chen, Zailong Qin, Jingsi Luo","doi":"10.1007/s10528-026-11323-3","DOIUrl":"10.1007/s10528-026-11323-3","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5868-5886"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146040176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Methodology for the Analysis of Odorant-Binding Proteins in Asiatic Genetic Groups of Bemisia tabaci.","authors":"M N Rudra Gouda, Sabtharishi Subramanian","doi":"10.1007/s10528-025-11294-x","DOIUrl":"10.1007/s10528-025-11294-x","url":null,"abstract":"<p><p>Insects rely heavily on their olfactory system for crucial behaviours like finding mates, locating food, and avoiding predators. Odorant binding proteins (OBPs) bind to odorant molecules, facilitating their transport to olfactory receptors. Understanding OBP diversity and the genomic landscape is vital for elucidating insect olfaction. Bemisia tabaci, a global invasive pest with significant economic impact, has limited OBP diversity studies across its genetic groups. This research investigates OBPs in B. tabaci Asiatic groups, a major invasive genetic group in Asia, to enhance our knowledge of their olfactory mechanisms and inform targeted pest control strategies. A computational pipeline identified OBPs in B. tabaci Asiatic groups using TBLASTN analysis of annotated genomes and whole-genome data. Unique OBP sequences were verified with BLASTX. Bioinformatics tools analysed gene structure, domain prediction, chromosomal localization, scaffold-wise arrangement, and protein structure. Phylogenetic analyses characterised OBPs and explored evolutionary relationships. We identified 9-10 OBPs in B. tabaci Asiatic groups, expanding our knowledge beyond previously studied genetic groups. Comparative analyses with other Hemipteran species showed similarities and differences in OBP diversity. Functional domain analysis highlighted conserved domains associated with odorant binding and membrane interactions. Variations in signal peptide presence suggested differences in protein stability and ligand-binding capabilities. Genomic organisation analysis revealed non-random OBP gene clustering on specific chromosomes, indicating potential co-regulation and functional relationships. The findings enhance understanding of B. tabaci olfaction and provide insights for targeted pest control strategies.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6125-6142"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145601613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating RNA-seq and Single-Cell RNA-seq to Uncover Transcriptional Signature of Fibroblasts in Oral Squamous Cell Carcinoma.","authors":"Ning Wen, Liting Gai, Yi Tao, Zhengxuan Shen","doi":"10.1007/s10528-025-11310-0","DOIUrl":"10.1007/s10528-025-11310-0","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5685-5700"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145766659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics Analysis Reveals the Prognostic and Therapeutic Value of TGF-β Signaling-related Genes in Idiopathic Pulmonary Fibrosis.","authors":"Chenkun Fu, Xiaoting Jing, Menglin Zhang, Yiju Cheng, Wenting Yang, Xiao Wu, Xiaojuan Chu, Xiaofeng Lu","doi":"10.1007/s10528-026-11325-1","DOIUrl":"10.1007/s10528-026-11325-1","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5927-5958"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146111729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanisms of DDR1 in Reinforcing the Resistance to Radiotherapy in Breast Cancer Through the AMPK/SIRT1/PGC-1α Pathway.","authors":"Shuai Wang, Yongjie Chen, Jie Wei, Haixia Wu, Jing Li","doi":"10.1007/s10528-025-11314-w","DOIUrl":"10.1007/s10528-025-11314-w","url":null,"abstract":"<p><p>Breast cancer (BC) is the leading cause of cancer mortality in women. The emergence of resistance to radiotherapy (RT) is a great challenge for BC treatment. Discoidin domain receptor 1 (DDR1) can modulate the proliferation, migration, and apoptosis of cancer cells, but its role in RT of BC has not been illuminated. This project evaluated the expression of DDR1 in BC based on single-cell RNA sequencing data. We established RT-resistant strains through radiation and detected the expression of DDR1 using qPCR. The proliferation and apoptosis abilities of BC cells were evaluated using CCK-8, colony formation assay, and flow cytometry. Western blot and IHC were applied to detect the levels of proteins related to the AMPK/SIRT1/PGC-1α pathway. The effect of the DDR1-mediated pathway on resistance to RT in BC was explored in combination with an AMPK inhibitor. DDR1 was highly expressed in BC. In vitro experiments demonstrated that knocking down DDR1 repressed the viability of BC cells during RT, curbed cell proliferation, facilitated apoptosis, and elevated the levels of p-AMPK, SIRT1, and PGC-1α proteins. The addition of an AMPK inhibitor reversed the effects of DDR1 knockdown on cell proliferation and apoptosis. In vivo experiments showed that knocking down DDR1 inhibited tumor growth, and the inhibitory effect was stronger when combined with radiation therapy. This study revealed that the upregulation of DDR1 in BC may reinforce RT resistance by modulating the AMPK/SIRT1/PGC-1α pathway, thus providing a new therapeutic target for improving the sensitivity of BC to RT.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5826-5842"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146008143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA Methylation-Guided Prediction and Validation of TAAD Molecular Targets.","authors":"Mengyao Sha, Qianying Wang, Qiwen Hu, Danlingyi Liu, Chang Liu","doi":"10.1007/s10528-026-11324-2","DOIUrl":"10.1007/s10528-026-11324-2","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6143-6162"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146111671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Translation Initiation Fidelity Defective Mutations in eIF5 and eIF2β Show Distinct Sensitivity to the Sequence Context for Recognition of the UUG Start Codon.","authors":"Anup Kumar Ram, Tanaya Kole, Pankaj V Alone","doi":"10.1007/s10528-025-11312-y","DOIUrl":"10.1007/s10528-025-11312-y","url":null,"abstract":"<p><p>In Saccharomyces cerevisiae, the AUG codon typically signals translation initiation to set an open reading frame, with a preference for the A^- 3AA/U^- 1(AUG)U^+ 4 sequence context. The mutant eIF5^G31R or eIF2β^S264Y proteins cause translation initiation fidelity defect by initiating translation at a near cognate UUG codon, in addition to the AUG start codon (suppressor of initiation codon; Sui¯ phenotype). However, the critical role of the - 3 to - 1 sequences in selecting the UUG start codon by these Sui¯ mutants is not fully explored. Different HIS4^UUG-LacZ reporter constructs were made with UUG as the start codon and varied nucleotides at the - 3 and - 2 positions or individually at -1 positions. These constructs were transformed to yeast cells having eIF5^G31R or eIF2β^S264Y mutation, and the β-galactosidase activity was measured. The HIS4^UUG-LacZ transcripts carrying a purine (A/G) at the - 3 position showed higher reporter activity than those with a pyrimidine (U/C). Additionally, purines were favored at the - 1 position within an AA (- 3 and - 2) context for efficient UUG start codon selection. Our findings demonstrate that UUG start codon recognition by Sui¯ mutants eIF5^G31R and eIF2β^S264Y is greatly influenced by the surrounding nucleotide context, each showing distinct context preferences. This highlights the nuanced role of sequence context in the near-cognate UUG codon initiation by the Sui¯ mutants.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5718-5730"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13388412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145848654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Boruta-SMOTE Integrated Approach for Rapid Donkey Breed Classification Using SNP Data: Addressing High-Dimensionality and Small Sample Challenges.","authors":"Chengyou Li, Shixin Xu, Dekui Li, Xiaolong Hu, Baoxian Jia","doi":"10.1007/s10528-025-11316-8","DOIUrl":"10.1007/s10528-025-11316-8","url":null,"abstract":"<p><p>With the increasing complexity of genomic data, traditional classification methods face dual challenges of the \"curse of dimensionality\" and class imbalance when processing multiple single nucleotide polymorphism (SNP) markers. To address these challenges, this study proposes an innovative approach integrating the Boruta dimensionality reduction algorithm with the Synthetic Minority Over-sampling Technique (SMOTE). The methodology involves two key steps: Feature optimization using the Boruta algorithm to identify the most representative genetic markers, thereby significantly reducing the complexity of high-dimensional data. Application of SMOTE technology to generate synthetic samples, balancing minority class distributions and alleviating data imbalance issues. Experimental results demonstrate that the proposed method outperforms traditional classifiers (Random Forest [RF], K-Nearest Neighbors [KNN], Extreme Gradient Boosting [XGBoost] and Convolutional Neural Network [CNN]) without Boruta-SMOTE integration across multiple metrics including accuracy, precision, recall, and F1-score. This study provides new insights for the conservation of donkey genetic resources, breed improvement, and commercial applications, while offering an effective solution for genomic data classification challenges.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5807-5825"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145964685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"hsa_circ_0006156 Suppresses Malignant Progression by Inducing Ferroptosis in Gastric Cancer Via miR-942-5p/NCOA4 Axis.","authors":"Sensen Niu, Weiwei Xie, Xiang Zhan, Qianru Xu, Min Fang, Daoquan Zhang","doi":"10.1007/s10528-026-11326-0","DOIUrl":"10.1007/s10528-026-11326-0","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6061-6076"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146211761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}