Genetics research最新文献

Sepsis is a severe disease with high mortality, and liver injury is an independent risk factor for sepsis morbidity and mortality. We analyzed co-differentially expressed genes (co-DEGs) to explore potential biomarkers and therapeutic targets for sepsis-related liver injury. Three gene expression datasets (GSE60088, GSE23767, and GSE71530) were downloaded from the Gene Expression Omnibus (GEO). DEGs were screened between sepsis and control samples using GEO2R. The association of these DEGs with infection and liver disease was analyzed by using the CTD database. GO functional analysis, KEGG pathway enrichment analysis, and protein-protein interaction (PPI) network analysis were performed to elucidate the potential molecular mechanism of DEGs. DEGs of different tissues in GSE60088 were analyzed again to obtain specific markers of septic liver injury. Mouse model of sepsis was also established by cecal ligation and puncture (CLP), and the expression of specific markers in liver, lung, and kidney tissues was analyzed using Western blot. Here, we identified 21 DEGs in three datasets with 8 hub genes, all of which showed higher inference scores in liver diseases than bacterial infections. Among them, only TNFRSF1A had a liver-specific differential expression. TNFRSF1A was also confirmed to be specifically reduced in septic liver tissues in mice. Therefore, TNFRSF1A may serve as a potential biomarker for septic liver injury.

Background: The most common site of prostate cancer metastasis is bone tissue with many recent studies having conducted genomic and clinical research regarding bone metastatic prostate cancer. However, further work is needed to better define those patients that are at an elevated risk of such metastasis.

Methods: SEER and TCGA databases were searched to develop a nomogram for predicting prostate cancer bone metastasis.

Results: Herein, we leveraged the Surveillance, Epidemiology, and End Results (SEER) database to construct a predictive nomogram capable of readily and accurately predicted the odds of bone metastasis in prostate cancer patients. This nomogram was utilized to assign patients with prostate cancer included in The Cancer Genome Atlas (TCGA) to cohorts at a high or low risk of bone metastasis (HRBM and LRBM, respectively). Comparisons of these LRBM and HRBM cohorts revealed marked differences in mutational landscapes between these patient cohorts, with increased frequencies of gene fusions, somatic copy number variations (CNVs), and single nucleotide variations (SNVs), particularly in the P53 gene, being evident in the HRBM cohort. We additionally identified lncRNAs, miRNAs, and mRNAs that were differentially expressed between these two patient cohorts and used them to construct a competing endogenous RNA (ceRNA) network. Moreover, three weighted gene co-expression network analysis (WGCNA) modules were constructed from the results of these analyses, with KIF14, MYH7, and COL10A1 being identified as hub genes within these modules. We further found immune response activity levels in the HRBM cohort to be elevated relative to that in the LRBM cohort, with single sample gene enrichment analysis (ssGSEA) scores for the immune checkpoint signature being increased in HRBM patient samples relative to those from LRBM patients.

Conclusion: We successfully developed a nomogram capable of readily detecting patients with prostate cancer at an elevated risk of bone metastasis.

Uterine Corpus Endometrial Carcinoma (UCEC), the most common gynecologic malignancy in developed countries, remains to be a major public health problem. Further studies are surely needed to elucidate the tumorigenesis of UCEC. Herein, intersecting 203 differentially expressed genes (DEGs) were identified with the GSE17025, GSE63678, and The Cancer Genome Atlas-UCEC datasets. The Gene Ontology/Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction (PPI) network were performed on those 203 DEGs. Intriguingly, 6 of the top 10 nodes in the PPI network were related to unfavorable prognosis, that is, ASPM, CDC20, DLGAP5, BUB1B, CDCA8, and NCAPG. The mRNA and protein expression levels of the 6 hub genes were elevated in UCEC tissues compared to normal tissues. Higher expression of the 6 hub genes was associated with poor prognostic clinicopathological characteristics. The receiver operating characteristic curve suggested the significant diagnostic ability of the 6 hub genes for UCEC. Then, underlying pathogeneses of UCEC including promoter methylation level, TP53 mutation status, genomic genetic variation, and immune cells infiltration were analyzed. The mRNA expression level of the 6 hub genes was also higher in cervical squamous cell carcinoma and endocervical adenocarcinoma, uterine carcinosarcoma, and ovarian serous cystadenocarcinoma tissues than in corresponding normal tissues. In conclusion, ASPM, CDC20, DLGAP5, BUB1B, CDCA8, and NCAPG may be considered diagnostic and prognostic biomarkers in UCEC.

Background: Glycogen storage disease type 1a (GSD1a) is a rare autosomal recessive metabolic disorder characterized by hypoglycaemia, growth retardation, lactic acidosis, hepatomegaly, hyperlipidemia, and nephromegaly. GSD1a is caused by a mutation in the G6PC gene encoding glucose-6-phosphatase (G6Pase); an enzyme that catalyses the hydrolysis of glucose-6-phosphate (G6P) to phosphate and glucose.

Objective: To elaborate on the clinical findings, biochemical data, molecular genetic analysis, and short-term prognosis of 13 GSD1a patients in Malaysia.

Methods: The information about 13 clinically classified GSD1a patients was retrospectively studied. The G6PC mutation analysis was performed by PCR-DNA sequencing.

Results: Patients were presented with hepatomegaly (92%), hypoglycaemia (38%), poor weight gain (23%), and short stature (15%). Mutation analysis revealed nine heterozygous mutations; eight previously reported mutations (c.155 A > T, c.209 G > A, c.226 A > T, c.248 G > A, c.648 G > T, c.706 T > A, c.1022 T > A, c.262delG) and a novel mutation (c.325 T > C). The most common mutation found in Malaysian patients was c.648 G > T in ten patients (77%) of mostly Malay ethnicity, followed by c.248 G > A in 4 patients of Chinese ethnicity (30%). A novel missense mutation (c.325 T > C) was predicted to be disease-causing by various in silico software.

Conclusions: The establishment of G6PC molecular genetic testing will enable the detection of presymptomatic patients, assisting in genetic counselling while avoiding the invasive methods of liver biopsy.

Objective: The aim of the study is to investigate the potential role of keratoconus (KC) in the diagnosis of keratoconus (KC).

Methods: GSE151631 and GSE77938 were downloaded from the comprehensive gene expression database (GEO). By using the random forest model (RF), support vector machine model (SVM), and generalized linear model (GLM), important immune-related genes were identified as biomarkers for KC diagnosis.

Results: Through the LASSO, RFE, and RF algorithms and comparing the three sets of DEGs, a total of 8 overlapping DEGs were obtained. We took 8 DEGs as the final optimal combination of DEGs: AREG, BBC3, DUSP2, map3k8, Smad7, CDKN1A, JUN, and LIF.

Conclusion: Abnormal cell proliferation, apoptosis, and autophagy defects are related to KC, which may be the etiology and potential target of KC.

Background: Ultrafiltration failure remains one of the most severe complications of long-term peritoneal dialysis (PD), which results in death. This study aimed to characterize the circulating exosomal microRNA (miRNA) profiles associated with ultrafiltration failure and explore its underlying mechanisms.

Methods: Exosomes were isolated from the peritoneal dialysis effluent (PDE) of patients with ultrafiltration failure or success using the ultracentrifugation method, and then transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and western blot were used for exosome characterization. After that, the isolated exosomes were sent for small RNA sequencing, and eight differentially expressed miRNAs (DE-miRNAs) were chosen for RT-qPCR validation.

Results: TEM, NTA, and western blot revealed that exosomes were successfully isolated. After sequencing, 70 DE-miRNAs involved in ultrafiltration were identified, including 41 upregulated ones and 29 downregulated ones. Functional analyses revealed that these DE-miRNAs were significantly enriched in pathways of cancer, ubiquitin-mediated proteolysis, axon orientation, and the Rap1 and Ras signaling pathways. In addition, the consistency rate of RT-qPCR and sequencing results was 75%, which indicated the relatively high reliability of the sequencing data.

Conclusions: Our findings implied that these DE-miRNAs may be potential biomarkers of ultrafiltration failure, which would help us to discover novel therapeutic targets/pathways for ultrafiltration failure in patients with end-stage renal disease.

Objective: The purpose of this study is to screen for microRNAs (miRNAs) associated with the prognosis of lung adenocarcinoma (LUAD) and to explore its prognosis and effects on the tumor microenvironment in patients with LUAD.

Methods: Gene expression data, miRNA expression data, and clinical data for two different databases, TCGA-LUAD and CPTAC-3 LUAD, were downloaded from the GDC database. The miRNA prognosis of LUAD was filtered by the Cox proportional hazard model and the Least Absolute Shrinkage and Selection Operator (LASSO) regression model. The performance of the model was validated by time-dependent receiver operating characteristics (ROC) curves. Possible biological processes associated with the miRNAs target gene were analyzed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Finally, the prognostic model was scored by risk, divided into high- and low-risk groups by median, and the differences in the immersion level of 21 immune cells in the high- and low-risk groups were assessed. To gain a deeper understanding of the underlying mechanism behind the model, the two most important miRNAs in the model, miR-195-3p and miR-5571-5p, were selected for HPA database validation and ceRNA network construction.

Results: Of the 209 variance expressions identified in the screening analysis, 145 were upregulated and 64 were downregulated by miRNAs. The prognostic models of six miRNA genes were obtained: miR-195-3p, miR-5571-5p, miR-584-3p, miR-494-3p, miR-4664-3p, and miR-1293. These six genes were significantly associated with survival rates in LUAD patients. In particular, miR-1293, miR-195-3p, and miR-5571-5p are highly correlated with OS. The higher expression of miR-195-3p and miR-5571-5p, the better survival of LUAD OS is, and these two miRNA expressions contribute the most to the model. Finally, after sorting the risk scores calculated from low to high using the prognostic model, the patients with higher scores had shorter survival time and higher frequency of death, and there were significant differences in the immersion levels of 21 immune cells in the high- and low-risk groups. ceRNA network analysis found that TM9SF3 was regulated by miR-195-3p and was highly expressed in the tissues of LUAD patients, and the prognosis of the patients was poor.

Conclusions: miR-195-3p, miR-5571-5p, miR-584-3p, miR-494-3p, miR-4664-3p, and miR-1293 may be used as new biomarkers for prognosis prediction of LUAD. Our results also identified a lncRNA MEG3/miR-195-3p/RAB1A/TM9SF3 regulatory axis, which may also play an important role in the progression of LUAD. Further study needs to be conducted to verify this result.

Objective: To screen the cell differentiation trajectory-related genes and build a cell differentiation trajectory-related signature for predicting the prognosis of lung adenocarcinoma (LUAD).

Methods: LUAD single cell mRNA expression profile, TCGA-LUAD transcriptome data were obtained from GEO and TCGA databases. Single-cell RNA-seq data were used for cell clustering and pseudotime analysis after dimensionality reduction analysis, and the cell differentiation trajectory-related genes were acquired after differential expression analysis conducted between the main branches. Then, the consensus clustering analysis was carried out on TCGA-LUAD samples, and the GSEA analysis was performed, then the differences on the expression levels of immune checkpoint genes and immunotherapy response were compared among clusters. The prognostic model was constructed, and the GSE42127 dataset was used to validate. A nomogram evaluation model was used to predict prognosis.

Results: Two subsets with distinct differentiation states were found after cell differentiation trajectory analysis. TCGA-LUAD samples were divided into two cell differentiation trajectory-related gene-based clusters, GSEA found that cluster 1 was significantly related to 20 pathways, cluster 2 was significantly enriched in three pathways, and it was also shown that clusters could better predict immune checkpoint gene expression and immunotherapy response. A six cell differentiation-related genes-based prognostic signature was constructed, and the patients in the high-risk group had poorer prognosis than those in the low-risk group. Moreover, a nomogram was constructed based on the prognostic signature and clinicopathological features, and this nomogram had strong predictive performance and high accuracy.

Conclusion: The cell differentiation-related signature and the prognostic nomogram could accurately predict survival.

Background: Assays of transposase accessible chromatin sequencing (ATAC-seq) is an efficient assay to investigate chromatin accessibility, which depends on the activity of a robust Tn5 transposase to fragment the genome while cutting in the sequencing adapters.

Methods: We propose reliable approaches for purifying hyperactive Tn5 transposase by chitin magnetic bead sorting. Double-stranded DNA of J76 cells and 293T cells were digested and subjected to tagmentation as test samples with Tn5 transposase, and libraries were established and sequenced. Sequencing data was then analyzed for peak calling, GO enrichment, and motif analysis.

Results: We report a set of rapid, efficient, and low-cost methods for ATAC-seq library construction and data analysis, through large-scale and rapid sequencing. These methods can provide a reference for the study of epigenetic regulation of gene expression.

Background: Liver hepatocellular carcinoma (LIHC) is the predominant type of liver cancer, and its treatment still faces great challenges presently. Mitochondrial inner membrane protein MPV17 is reported to be involved in multiple biological activities of cancers. Here, we seek to investigate the specific role and functions of MPV17 in LIHC progression.

Methods: Firstly, MPV17 expressions in various tumors and corresponding normal samples and LIHC groups with various clinical features were analyzed, respectively. Next, the relationship between MPV17 expression and LIHC survival was analyzed and verified by AUC curves. Besides, differentially expressed genes (DEGs) for LIHC were screened from TCGA and then analyzed by GO and KEGG. Then, MPV17 was analyzed by prognostic model, Cox analysis, predictive nomogram, pathway correlation, and immunoassay. Finally, the functions of MPV17 were determined by CCK-8 and Tranwell assays.

Results: In most tumors, MPV17 expression was higher than that in the normal group, and it was related to LIHC clinical features. In the LIHC survival analysis, highly expressed MPV17 was associated with a poor prognosis. Besides, 314 upregulated and 193 downregulated DEGs are mainly involved in the TNF signaling pathway and tyrosine metabolism. Through prognostic model, Cox analysis, and predictive nomogram, MPV17 had the prognostic value for LIHC. Gene-pathway correlation analysis showed that MPV17 had the strongest correlation with the G2M_checkpoint pathway. In an immunoassay, MPV17 had a strong correlation with many immune cells. Functional assays showed that MPV17 reduction in LIHC cells could inhibit cell invasion, migration, and proliferation.

Conclusion: MPV17, as a tumor promoter, could be a new biomarker for LIHC diagnosis and prognosis and probably shed new light on the exploration of LIHC therapies.