Biochemical Genetics最新文献

{"title":"Haplotypes of Chloroquine Resistance Marker Genes Among Uncomplicated Malaria Cases in Lagos, Nigeria.","authors":"Uche Thecla Igbasi, Wellington Aghoghavia Oyibo, Jun-Hu Chen, Hong Quan, Sunday Aremu Omilabu, Shen-Bo Chen, Hai-Mo Shen, Xiao-Nong Zhou","doi":"10.1007/s10528-025-11022-5","DOIUrl":"https://doi.org/10.1007/s10528-025-11022-5","url":null,"abstract":"<p><p>Drug resistance resulting from mutations in Plasmodium falciparum, that caused the failure of previously effective malaria drugs, has continued to threaten the global malaria elimination goal. This study describes the profiles of P. falciparum chloroquine resistance transporter (Pfcrt) and P. falciparum multidrug resistance 1 (Pfmdr1), the genetic markers associated with 4-aminoquinoline resistance, among P. falciparum isolates from Lagos, Nigeria. Genomic DNA was extracted from the dried blood spot samples obtained from individuals with microscopically confirmed P. falciparum infection in health facilities and communities in Lagos State, Nigeria. The DNA was amplified using nested polymerase chain reaction, and sequence analysis was performed to identify single nucleotide polymorphisms in the pfcrt and pfmdr1 genes. The study showed that 82.4% (178) of the isolates had pfmdr1 wild-type, while mutations were observed at codons N86Y (11.6%) and D1246Y (3.2%). Other mutations seen were at codons Y23S (0.5%), E130K (2.3%), and S149P (0.5%). 30.8% (64) of the isolates had pfcrt wild-type (CVMNK), while 62.0% (129) had CVIET (mutant) haplotype. Other pfcrt haplotypes detected include; CVIDT (1.9%); CVMDT (1.4%); CVIKT (1.0%); CVINT (0.5%); CVMET (0.5%); CVMKT (0.5%); CVMNT (1.0%); and CVMEK (0.5%). The findings underscore the presence of uncommon pfcrt haplotypes and a high prevalence of drug-resistant pfcrt haplotypes (CVIET), alongside a high prevalence of wild-type pfmdr in Lagos. This study highlights the need for ongoing surveillance of these genetic markers to provide data that can inform decisions on malaria case management and preserve the efficacy of artemisinin combination therapies (ACTs) in Nigeria.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998118","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":"Correction: Curcumol Attenuates Portal Hypertension and Collateral Shunting Via Inhibition of Extrahepatic Angiogenesis in Cirrhotic Rats.","authors":"Xinyuan Wang, Juan Li, Jiao Nong, Xin Deng, Yiping Chen, Peibin Wu, Xiabing Huang","doi":"10.1007/s10528-025-11023-4","DOIUrl":"10.1007/s10528-025-11023-4","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998035","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":"Correction: Identification of Novel Genomic Variants in COVID-19 Patients Using Whole-Exome Sequencing: Exploring the Plausible Targets of Functional Genomics.","authors":"Rashid Mir, Faisal H Altemani, Naseh A Algehainy, Mohammad A Alanazi, Imadeldin Elfaki, Badr A Alsayed, Mohammad Muzaffar Mir, Syed Khalid Mustafa, Mamdoh S Moawadh, Faris J Tayeb, Jaber Alfaifi, Sael M Alatawi, Mohammed Saad Alhiwety, Mohammad Fahad Ullah","doi":"10.1007/s10528-025-11024-3","DOIUrl":"https://doi.org/10.1007/s10528-025-11024-3","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998115","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":"The Circadian Rhythm Regulates the Hepato-ovarian Axis Linking Polycystic Ovary Syndrome and Non-alcoholic Fatty Liver Disease.","authors":"Yibing Lan, Bihui Jin, Yuhang Fan, Yizhou Huang, Jianhong Zhou","doi":"10.1007/s10528-024-11010-1","DOIUrl":"https://doi.org/10.1007/s10528-024-11010-1","url":null,"abstract":"<p><p>This study aimed to identify shared gene expression related to circadian rhythm disruption in polycystic ovary syndrome (PCOS) and non-alcoholic fatty liver disease (NAFLD) to discover common diagnostic biomarkers. Visceral fat RNA samples were collected from 12 PCOS and 14 non-PCOS patients, a sample size representing the clinical situation and sufficient to capture PCOS gene expression profiles. Along with liver transcriptome profiles from NAFLD patients, these data were analyzed to identify crosstalk circadian rhythm-related genes (CRRGs) between the diseases. Single-sample and single-gene gene set enrichment analyses explored immune infiltration and pathways associated with CRRGs. Diagnostic biomarkers were identified using a random forest algorithm and validated through nomograms and a mouse model. Seven crosstalk CRRGs (FOS, ACHE, FOSB, EGR1, NR4A1, DUSP1, and EGR3) were associated with clinical features, immunoinflammatory microenvironment, and metabolic pathways in both diseases. EGR1, DUSP1, and NR4A1 were identified as diagnostic biomarkers, exhibiting robust diagnostic capacity (AUC = 0.7679 for PCOS, AUG = 0.9981 for NAFLD). Nomogram validation showed excellent calibration, and independent datasets confirmed their discriminatory ability (AUC = 0.6528 for PCOS, AUC = 0.8275 for NAFLD). Additionally, ceRNA networks and androgen receptor binding sites were identified, suggesting their regulatory roles. Mouse model validation confirmed significant downregulation of EGR1, DUSP1, and NR4A1 in liver tissues, consistent with sequencing data. This study identifies crosstalk CRRGs and diagnostic biomarkers shared between PCOS and NAFLD, highlighting their roles in immune and metabolic dysregulation. These biomarkers offer the potential for improving diagnosis and guiding targeted treatments for both diseases.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998143","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":"High Expression of GPR183 Predicts Poor Survival in Cytogenetically Normal Acute Myeloid Leukemia.","authors":"Haihui Zhuang, Fenglin Li, Renzhi Pei, Xia Jiang, Dong Chen, Shuangyue Li, Peipei Ye, Jiaojiao Yuan, Jiangyin Lian, Jie Jin, Ying Lu","doi":"10.1007/s10528-025-11026-1","DOIUrl":"https://doi.org/10.1007/s10528-025-11026-1","url":null,"abstract":"<p><p>Acute myeloid leukemia (AML) with a normal karyotype (CN-AML) constitutes approximately 50% of all AML cases, presenting significant prognostic variability, and highlighting the urgent need for the identification of novel molecular biomarkers. In this study, we systematically assessed GPR183 expression levels using qRT-PCR in our clinical follow-up study which included 283 CN-AML patients. Using Kaplan-Meier analysis, we found that patients with high GPR183 expression levels exhibited significantly worse overall survival (OS) (P = 0.046) and event-free survival (EFS) (P = 0.030) compared to those with low GPR183 expression. Comprehensive univariate and multivariate Cox regression analyses confirmed that GPR183 expression is a prognostic factor for OS and EFS (P < 0.05). To further validate these findings, we analyzed an independent cohort of 104 CN-AML patients from the GSE71014 dataset, corroborating our primary results, and indicating that high GPR183 expression is associated with poorer survival outcomes. Additionally, RNA-seq data from the GSE71014 dataset were analyzed by Gene Set Enrichment Analysis (GSEA). The results suggested that GPR183 may influence disease progression through the activation of the \"TNFa Signaling Via NF-κB\" pathway. Collectively, these findings suggested that GPR183 could serve as a valuable prognostic biomarker in CN-AML, offering insights into the underlying mechanisms of disease progression.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998132","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":"METTL14 Promotes the Osteogenic Differentiation of Human Bone Marrow Stromal Cells via m6A-Dependent Stabilization of USP7 mRNA.","authors":"Yu Leng, Zhiwen Liu, Jun Min, Qing Ke, Yiqing Shao, Junyan Lai, Jing Zhao","doi":"10.1007/s10528-024-10999-9","DOIUrl":"https://doi.org/10.1007/s10528-024-10999-9","url":null,"abstract":"<p><p>Osteoporosis (OP) is a common clinical bone disease that can cause a high incidence of non-stress fractures and is one of the main degenerative diseases that endangers the health and life of middle-aged and older women. The mechanism underlying the abnormal differentiation and function of human bone marrow stem cells (hBMSCs) remains to be elucidated. Cell proliferation and differentiation were determined using 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di-phenytetrazoliumromide (MTT) assay, alkaline phosphatase (ALP) staining, and Alizarin Red Staining. The interaction between insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and ubiquitin-specific protease 7 (USP7) was predicted and validated using bioinformatics approaches, luciferase assays, RNA immunoprecipitation (RIP), and immunoprecipitation (IP). Actinomycin D treatment was used to test the stability of mRNA in the various groups. Methyltransferase-like 14 (METTL14) expression was increased in osteogenic differentiation medium-induced hBSMCs and was associated with enhanced osteogenic differentiation. METTL14 regulated the expression USP7 by modulating its N⁶-methyladenosine (m6A) level. IGF2BP2 exerted an m6A-dependent effect on USP7 mRNA stability and USP7 increased sirtuin 1 (SIRT1) expression in hBMSCs by enhancing SIRT1 deubiquitination. METTL14 stimulated the osteogenic differentiation of hBMSCs through the m6A-IGF2BP2-USP7 pathway and promoted hBMSCs osteogenic development via SIRT1-Bmi1 signaling. METTL14 stimulated the osteogenic differentiation of hBMSCs by stabilizing USP7 mRNA in an m6A-dependent manner. USP7 was also stabilized by IGF2BP2 and it regulated downstream SIRT1-Bmi1 signaling.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998135","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":"Study on Immune-Related Genes and Clinical Validation of Acute Myocardial Infarction Based on Bioinformatics.","authors":"Shuang Jin, Zhang Wu","doi":"10.1007/s10528-025-11029-y","DOIUrl":"https://doi.org/10.1007/s10528-025-11029-y","url":null,"abstract":"<p><p>Acute myocardial infarction (AMI) is a cardiovascular disease featuring the narrowing and hardening of coronary arteries triggered by a combination of factors, which ultimately leads to the death of heart muscle. We retrieved the GSE109048 and GSE123342 datasets from the Gene Expression Omnibus (GEO) database. After integrating these datasets, we selected 154 module key genes with the help of weighted correlation network analysis (WGCNA). After that, we used protein-protein interaction networks (PPI) analysis to screen out 18 core genes in the protein interaction network from 154 genes. Finally, we used three machine learning algorithms to jointly identify three genes (CLEC4D, CLEC4E and LY96) that may predict or influence the progression of AMI. In the dataset, CLEC4D, CLEC4E and LY96 were significantly overexpressed in AMI patients. Immune infiltration analysis revealed that CLEC4D, CLEC4E and LY96 could affect the extent of immune cell infiltration. For further verification, we found that the expression levels of CLEC4D, CLEC4E and LY96 in the AMI cohort were significantly higher than those in coronary heart disease (CAD) patients by qRT-PCR. This finding corroborated the results derived from bioinformatics analysis. In summary, CLEC4D, CLEC4E and LY96 can be used to predict the occurrence of AMI.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998141","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":"Spectrum of ARSA mutations in Iranian patients with metachromatic leukodystrophy.","authors":"Mohadeseh Fathi, Sheyda Khalilian, Mohammad Miryounesi, Soudeh Ghafouri-Fard","doi":"10.1007/s10528-025-11025-2","DOIUrl":"https://doi.org/10.1007/s10528-025-11025-2","url":null,"abstract":"<p><p>Metachromatic leukodystrophy (MLD) is an autosomal recessive disorder caused by mutations in the arylsulfatase A (ARSA) gene. Few studies have assessed the spectrum of ARSA mutations among Iranian patients. Here, we report eight Iranian patients with clinical features of MLD. Whole exome sequencing led to identification of the underlying mutation in ARSA gene in these patients. Among identified mutations was the recurrent c.938G > C (p.R313P) mutation in exon 5 of this gene, showing its relatively high frequency among Iranians. The results of this study helps in design of population-specific panels for screening purposes in order to decrease the burden of MLD.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976834","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":"SLC6A14 as a Key Diagnostic Biomarker for Ulcerative Colitis: An Integrative Bioinformatics and Machine Learning Approach.","authors":"Xiao-Jun Ren, Man-Ling Zhang, Zhao-Hong Shi, Pei-Pei Zhu","doi":"10.1007/s10528-025-11027-0","DOIUrl":"https://doi.org/10.1007/s10528-025-11027-0","url":null,"abstract":"<p><p>Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by intestinal inflammation and autoimmune responses. This study aimed to identify diagnostic biomarkers for UC through bioinformatics analysis and machine learning, and to validate these findings through immunofluorescence staining of clinical samples. Differential expression analysis was conducted on expression profile datasets from 4 UC samples. Key biomarkers were selected using LASSO logistic regression, SVM-RFE, and Random Forest algorithms. The diagnostic performance of these biomarkers was evaluated using receiver operating characteristic (ROC) curves. Functional enrichment analysis assessed the biological functions of these biomarkers. The CIBERSORT algorithm was used to analyze immune cell infiltration. Regulatory networks for diagnostic markers were constructed. Additionally, immunofluorescence staining was performed on clinical samples to validate the expression levels of key biomarkers. Differential analysis identified 199 significantly differentially expressed genes. SLC6A14 was selected as a key diagnostic biomarker, demonstrating excellent diagnostic performance in training and validation sets (AUC values: 0.973, 0.984, and 0.970). Immune cell infiltration analysis revealed significant increases in Neutrophils and activated Mast cells in UC samples, whereas resting Mast cells were relatively downregulated. Furthermore, SLC6A14 showed strong correlations with various immune cells. The ceRNA network identified 22 lncRNAs and 10 miRNAs associated with SLC6A14. Immunofluorescence staining of clinical samples confirmed that SLC6A14 expression is significantly higher in UC patients compared to normal intestinal mucosa, and its expression increases with UC activity. SLC6A14 has been confirmed as a key diagnostic marker for UC, validated both through bioinformatics analysis and immunofluorescence staining of clinical samples. It maintains regulatory relationships with various non-coding RNAs and plays a significant role in the pathogenesis of UC through its interactions with immune cells.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976796","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":"Molecular Taxonomy Suggests Presence of Two Distinct Lineages of Blue Sheep (Pseudois nayaur) in Indian Himalayan Region.","authors":"Deepesh Saini, Gaurav Sonker, Tushar Parab, Vishnupriya Kolipakam, Sambandam Sathyakumar, Salvador Lyngdoh, Sandeep Kumar Gupta","doi":"10.1007/s10528-024-11014-x","DOIUrl":"https://doi.org/10.1007/s10528-024-11014-x","url":null,"abstract":"<p><p>Indian Himalayan Region (IHR) supports a plethora of biodiversity with a unique assemblage of many charismatic and endemic species. We assessed the genetic diversity, demographic history, and habitat suitability of blue sheep (Pseudois nayaur) in the IHR through the analysis of the mitochondrial DNA (mtDNA) control region (CR) and Cytochrome b gene, and 14 ecological predictor variables. We observed high genetic divergence and designated them into two genetic lineage groups, i.e., the Himalayan blue sheep (P. n. nayaur) in the western part, and the Chinese blue sheep (P. n. szechuanensis) in the eastern part. They exhibited poor connectivity due to landscape resistance. The genetic distance value suggested substantial genetic differentiation between them. The habitat selection by blue sheep indicated the disparity between the residence preferences in the western and eastern Himalayas. In both the regions, the habitat suitability was mostly influenced by the minimum temperature of the coldest month. However, in the eastern Himalayas, precipitation seasonality emerged as a significant variable influencing habitat suitability. These findings provided strong support for the presumption that the habitats preferred by blue sheep in the western Himalayas are dryer, compared with the preferred habitats in the eastern region, which were moister. The identification of two separate lineages of P. nayaur in the IHR has significant conservation implications as it underlines the necessity for a unique management approach for each lineage. In order to preserve genetic integrity, conservation efforts must make sure that each population is maintained and monitored separately, as genetic divergence across the lineages that might indicate reproductive isolation. This study has potential conservation implications as it provides insights on the crucial ecological information of a relatively lesser-known ungulates species of Himalaya essential for effective conservation planning.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963495","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}