Biochemical Genetics最新文献

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.

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.

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.

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.

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.

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.

IKZF1 deletions (ΔIKZF1) are common in precursor B-cell acute lymphoblastic leukemia (B-ALL) and are assumed to have a prognostic impact. We aimed to determine the prognostic implications of ΔIKZF1 and CRLF2 overexpression in pediatric B-ALL. Furthermore, we sought to compare the multiplex polymerase chain reaction (PCR) assay with standard multiplex ligand-dependent probe amplification (MLPA) methods to ascertain IKZF1 status in a clinical context. Seventy-nine diagnoses and 43 relapse B-ALL samples were evaluated for deletions of IKZF1 Δ2-7, Δ4-7, and Δ4-8 by conventional PCR and then sequenced by targeted sequencing. Subsequently, MLPA analysis was performed for ΔIKZF1 detection, and CRLF2 expression was evaluated in 42 diagnose time B-ALL patients by QRT-PCR. ΔIKZF1 was detected in 10 out of 79 diagnose samples (12.66%) and eight of the 43 first relapsed materials (18.60%). Our results revealed no association between survival outcomes with ΔIKZF1 or CRLF2 overexpression status in pediatric B-ALL patients. However, we found ΔIKZF1 was more frequent among relapsed samples, and the deletions showed consistency between diagnose-first/second relapse pairs of samples. These results suggest that ΔIKZF1 may contribute to the development of treatment failure in B-ALL. Furthermore, we demonstrated methodological adjustments in conventional PCR and MLPA for selected alterations in ΔIKZF1.

Single nucleotide polymorphisms (SNPs) have been reported to influence the activity of specific genes involved with the innate immune response to Mycobacterium; hence, they are crucial in tuberculosis (TB) susceptibility studies. The study aimed to investigate the polymorphism in the NOS2A (Nitric oxide synthase 2A) gene and its association with susceptibility to TB in the Manipuri population of northeast India. This case-control study includes 495 subjects- 220 TB patients and 275 control individuals. TaqMan allelic discrimination assay was used to study the gene polymorphism, and Griess's test was employed to determine the serum nitric oxide (NO) levels. Serum NO levels were analysed to correlate with the functional changes associated with the polymorphisms. Two SNPs of the gene, NOS2A (rs8078340 and rs2274894), were studied. For the SNP-rs8078340, a significant difference in the genotypic and allelic frequencies was observed between the cases and control groups (p = 0.001; AA genotype OR = 30.288, 95% CI: 1.703-538.44 and A allele OR = 2.937, 95% CI: 1.762-4.896). However, for the SNP-rs2274894, only the T allele (with OR = 1.464; 95% CI: 1.080-1.983, p = 0.014) was associated with susceptibility to TB. Serum levels of NO were significantly different between the cases and control groups (p < 0.05). Significant associations of both homozygous AA genotype and allele A of the NOS2A (rs8078340) and minor allele T of NOS2A (rs2274894) were observed with susceptibility to TB. Patients with the AA genotype of NOS2A show a higher NO level, suggesting its role in greater expression of the NOS2A gene.

To analyze whether the single-nucleotide polymorphisms (SNPs) in Matrix metalloproteinases 2, 3, and 9 (MMP2, MMP3, and MMP9), Tissue Inhibitor of Metalloproteinases 1 and 2 (TIMP1 and TIMP2), methionine synthase (MTR) and methionine synthase reductase (MTRR) influence delayed deciduous tooth eruption (DDTE). This cross-sectional study included 1060 biologic unrelated children (aged between 6 and 36 months) of both sexes, selected from 25 public schools in Nova Friburgo, Rio de Janeiro, Brazil. Oral examination was conducted and DDTE was defined by the absence of gingival eruption according to a chronology based on the Brazilian population. Genotyping of selected SNPs (rs243847, rs52261, rs17576, rs4898, rs7501477, rs1805087, and rs1801394) was performed using TaqMan real-time PCR with genomic DNA extracted from buccal cells. The association between genotypes and DDTE was evaluated using univariate and multivariate analyses (p < 0.05). A total of 224 children and caregivers were included after the eligibility criteria. The heterozygous genotype for the SNPs MTR (rs11805087) was associated with DDTE in both the univariate (p = 0.004) and multivariate (p < 0.001) codominant models, as well as in the univariate (p = 0.010) and multivariate (p = 0.001) recessive models. TIMP1 (rs4898) and MMP3 (rs522616) were associated with DDTE only in the univariate model (p < 0.05). The SNPs in MTR (rs11805087), MMP3 (rs522616) and TIMP (rs4898) genes are associated with DDTE. The factors affecting the chronology of deciduous tooth eruption has been insufficiently studied. This article brings novel knowledge regarding the role of genetics polymorphisms on timing variation of deciduous tooth eruption. Understanding the factors that impact tooth eruption is crucial for the fields of pediatric dentistry and orthodontics.

The tumor microenvironment has a significant input on prognosis and also for predicting clinical outcomes in various types of cancers. However, tumor tissue is not always available, thus, rendering peripheral blood a preferable alternative in the search for prognostic and predictive gene signatures. Head and neck squamous cell carcinoma (HNSCC) constitutes a quite heterogeneous disease characterized by poor prognosis. Therefore, the discovery of novel therapeutics based on prognostic gene signatures for effective disease governance is of paramount importance. In this study, we report for the first time an immune-gene signature identified in the peripheral blood of HNSCC patients comprising five genes (CLEC4C, IL23A, LCK, LY9, and CD19) which were more than threefold downregulated as compared to healthy individuals and were associated with poor prognosis. By performing analyses of HNSCC tumor samples from The Cancer Genome Atlas (TCGA) database, we discovered that decreased expression of these genes, both as single genes and as a 5-gene signature (5-GS), was significantly correlated with worse overall survival (OS). Our data show that the levels of expression of the 5-GS represent an immune profile predicting OS in patients with HNSCC.