Biochemical Genetics最新文献

Mounting evidence suggests that circulating microRNAs (miRNAs) hold diagnostic value in various malignancies. To identify circulating miRNAs for the early diagnosis of hepatocellular carcinoma (HCC), we conducted a meta-analysis to evaluate the diagnostic utility of miRNAs in HCC and further validated the results of the meta-analysis. English articles published prior to December 2023 were retrieved from databases including PubMed, Embase, and Web of Science. A random-effects or fixed-effects model was applied depending on the heterogeneity among studies. The pooled sensitivity, specificity, and the area under the summary receiver operating characteristic curve (AUC) were calculated to assess diagnostic accuracy. Additionally, RT-qPCR and receiver operating characteristic (ROC) analyses were employed to further validate the findings. A total of 36 studies were included, involving 3362 patients with HCC and 2150 patients with chronic hepatitis. The pooled sensitivity, specificity, and diagnostic odds ratio were 0.79 (95% CI 0.75-0.82), 0.79 (95% CI 0.73-0.84), and 14 (95% CI 9-22), respectively; the positive and negative likelihood ratios were 4.0 and 0.27, respectively; the area under the curve (AUC) in the summary receiver operating characteristic (ROC) was 0.85 (95% CI 0.82-0.88). Validation indicated a significant upregulation of miR-1246, miR-21, and miR-221 in HCC patients compared to those with chronic hepatitis (P < 0.01), while miR-122 and miR-26a were significantly downregulated (P < 0.01). Moreover, the validation results also demonstrated that serum levels of miR-21, miR-26a, miR-122, miR-221, and miR-1246 exhibit high sensitivity and specificity in the diagnosis of HCC. Circulating miRNAs may be promising biomarkers for HCC diagnosis.

Anoctamin 6 (ANO6) has been implicated in the oncogenicity of malignancies. However, pan-cancer analysis of ANO6 to fully explore its role in tumors has not been performed and little is reported on its role in melanoma. The ANO6 expression levels, clinical correlation, prognostic significance, mutational profiles, immune infiltration pattern, immune checkpoints, immunomodulatory genes, tumor heterogeneity, and molecular function were explored via systematic bioinformatics analysis and multiple public databases. Subsequently, the biological functions of ANO6 in the pulmonary metastasis of B16F10 melanoma cells in vivo were assessed by experimental validation. Our findings have demonstrated that ANO6 was highly expressed in most cancers and associated with poorer prognosis in cancer patients. A close relationship was observed between ANO6 expression level and clinicopathological characteristics, tumor immunity, and tumor heterogeneity. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that ANO6 was associated with immune response and regulated many cancer-related pathways. Furthermore, a melanoma pulmonary metastasis mice model showed that ANO6 was overexpressed in lung metastasis tissues compared with corresponding normal tissues. Collectively, ANO6 may serve as reliable biomarkers to predict the prognosis for diverse types of cancer and as a prospective marker for melanoma progression.

The variation of codon usage patterns in response to the evolution of organisms is an intriguing question to answer. This study investigated the relevance of the evolutionary events of vascularization and seed production with the codon usage patterns in different plant lineages. We found that the optimal codons of non-vascular lineages generally end with GC, whereas those of the vascular lineages end with AU. Correspondence analysis and model-based clustering showed that the evolution of the codon usage pattern follows the evolutionary event of the vascularization more precisely than that of the seed production. The dinucleotides CpG and TpA were under-represented in all the lineages, whereas the dinucleotide TpG was found over-represented in all the lineages, except algae. Evolutionary-related lineages showed similar codon pair bias. The dinucleotide CpA showed a similar representation as those of its parent codon pairs. Although natural selection predominates over mutational pressure in determining the codon usage bias, the relative influence of mutational pressure is higher in the non-vascular lineages than those in the vascular lineages.

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.

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.

In recent years, the BTB (Bric-a-brac/Tramtrack/Broad complex) gene family in plants has garnered widespread attention for its regulatory roles in plant growth and development. However, knowledge regarding BTBs in poplar trees remains limited. Here, we identified 94 BTB gene family members across the genome of Populus alba L. Through phylogenetic analysis, these members were classified into seven subfamilies and 16 branches, followed by comprehensive bioinformatics and biological analyses. Structural analysis revealed that poplar BTB gene family exhibits both high conservation and diversity, with distinct gene structures and protein features. Expression pattern analysis demonstrated differential expression of poplar BTB genes across various tissues, hormone treatments, and under drought stress, suggesting their potential roles in poplar growth and development and drought response. This study provides a vital foundation and reference for unraveling the BTB-involved regulatory mechanisms underlying poplar growth and development and drought response.

COVID-19, caused by SARS-CoV-2 infection, frequently induces thrombotic complications in affected individuals. P-selectin, a pivotal platelet marker, plays a central role in platelet-leukocyte aggregation, contributing to hemostasis and thrombosis. Additionally, D-dimer serves as an indicator of coagulation system activity, while miR-17-5p exhibits antiviral properties in respiratory infections. This study aimed to evaluate and compare the expression levels of D-dimer, P-selectin, and miR-17-5p in COVID-19 patients hospitalized in intensive care units (ICUs) and those in non-ICU wards. This cross-sectional study included 50 COVID-19 patients, divided into ICU and non-ICU groups. P-selectin expression was assessed using Flow cytometry, D-dimer levels were measured via chemiluminescence, and miR-17-5p expression was analyzed using quantitative real-time polymerase chain reaction (qRT-PCR). Our analysis revealed no significant difference in P-selectin expression levels between ICU and non-ICU patients (p = 0.1068). However, the expression levels of D-dimer and miR-17-5p were significantly elevated in ICU patients compared to non-ICU patients, with corresponding p-values of 0.032 and 0.0176, respectively. The heightened expression of D-dimer and miR-17-5p in ICU patients suggests their potential utility as predictive biomarkers for assessing the hemostatic status of COVID-19 patients.

Mentha piperita L. commonly known as peppermint, is valued for its essential oil, which is rich in menthol and has various applications. However, challenges such as low oil yield and poor oil quality have limited the potential of peppermint cultivation. This study aimed to develop a noble mutant of Mentha piperita that complements US-type peppermint oil, characterized by higher oil yield and improved oil quality, specifically targeting a menthol content of 36-46% and less than 5% menthofuran. Induced mutagenesis was achieved through gamma radiation, with seeds from a menthofuran-rich variety CIM-Indus of Mentha piperita subjected to varying doses (10 Gy, 20 Gy, 30 Gy, 40 Gy, 50 Gy, 70 Gy, 90 Gy, and 110 Gy). A broad range of diversity was observed among the resulting mutant lines, leading to the selection of improved lines. Notably, CIM-I452 exhibited the highest oil yield along with substantial herb yield, followed by CIM-I332 and CIM-I324. Lines CIM-I43, CIM-I44, CIM-I451, CIM-I32, CIM-I34, CIM-I332, and CIM-I452 were identified as menthol-rich, while CIM-I311 and CIM-I431 were menthofuran-rich. Additionally, CIM-I322 and CIM-I331 were recognized as limonene-rich lines. Because of the high menthol content and low amount of menthofuran, the mutant lines CIM-I452, CIM-I332, and CIM-I324 showed widely acceptance peppermint oil quality. These selected mutant lines exhibit promising mutant lines that may be utilised as parent lines for upcoming recombinant breeding or hybridization initiatives.

This study employs a comprehensive multi-omics approach to investigate the regulatory roles of specific microRNAs (miRNAs) in Congenital Tooth Agenesis (CTA). A total of 58 miRNAs associated with tooth diseases, cancer, and bone development were initially identified through a literature review and analyzed using bioinformatics. Based on target prediction and network analysis, eight miRNAs with strong connectivity and common target genes were shortlisted for further investigation. Blood samples from 10 CTA patients and 5 healthy controls were analyzed for miRNA expression using stem-loop RT-PCR. Four miRNAs-hsa-miR-218-5p, hsa-miR-15b-5p, hsa-miR-200b-3p, and hsa-let-7a-3p-were identified as significantly differentially expressed, marking their first reported involvement in CTA. Notably, hsa-miR-218-5p and hsa-let-7a-3p emerged as novel regulators with no prior associations with CTA or tooth development. To address the limitations of a small sample size, a multi-omics strategy was employed to validate these findings, integrating miRNA expression data with whole exome sequencing (WES), gene expression panels, and metabolomic profiling. The analysis confirmed the association of these four miRNAs with CTA and highlighted their involvement in critical biological pathways such as Wnt signaling, FGF signaling, and PI3 kinase pathways, which are essential for cellular proliferation, differentiation, and tissue morphogenesis. Importantly, the identification of these miRNAs in blood samples, rather than traditional dental tissues, highlights a minimally invasive approach that could aid in the early detection, therapeutic targeting, and personalized management of dental anomalies.