Genetic Screening of Deaf Mutation for 2545 Newborn / 中国康复理论与实践

Objective:To investigate the mutative rate and spectrum of common hereditary deafness genes in Chinese. Methods:Heel blood samples from 2545 infants born from January to October, 2018, were collected, and screened with microarray chip. Results:There were 119 children with mutation of deafness gene, including 60 cases (2.36%) with GJB2 mutation, male/female = 1∶1 (30/30); 48 (1.88%) with SLC26A4 mutation, male/female nearly 1∶1 (26/22); five (0.20%) with mutation of mitochondrial 12S rRNA gene; five (0.20%) with GJB3 mutation; one (0.04%) with heterozygosis in GJB2 235 and SLC26A4 IVS7-2 mutation. Other more, mutations of 1174A > T, 1229C > T and 15+5G>A of SLC26A4 were found in one child, respectively. Conclusion:The distribution of deafness gene loci has been investigated, which can be reference for prevention and control of hereditary deafness in Chinese.

Bioinformatics analysis of genes related to endometrial cancer with lymph nodes metastasis / 中国肿瘤生物治疗杂志

@#Objective: To investigate the potential genes associated with lymph nodes metastasis in endometrial cancer (EC) through microarray data analysis and bioinformatics methods. Methods: We screened mRNA expression profiling chip data related to lymph node metastasis of EC from the GEO database and analyzed mRNAexpression profile to screen the differentially expressed genes; with the integrated bioinformatics approach, such as biological process annotation, biological signaling pathway enrichment, text mining and protein/gene interactions, we further explored the signaling pathways and genes associated with lymph node metastasis in endometrial cancer. Results: GSE2109 and GSE39099 accessions were obtained in the GEO database, and 8 signaling pathways related to lymph node metastasis in EC (type I interferon, interferon-gamma-mediated, PI3K-Akt, Rap1, TGF-beta, cGMP-PKG, Wnt and Ras) and 14 differentially expressed genes that regulate these pathways were found though the signaling pathways enrichment of common differentially expressed genes. Among them, 11 genes were associated with lymph node metastasis of EC and formed a protein-protein interaction network. PI3K-Akt signaling pathway may be an important signaling pathway for lymph node metastasis in EC. VEGFC and IRS1 may be the important candidate genes related to the regulation of lymph node metastasis in EC. Conclusion: Eight signaling pathways and 11 differentially expressed genes were identified to be associated with lymph node metastasis in EC by bioinformatics analysis.

Bioinformatics analysis of genes related to the progress of cervical intraepithelial neoplasia / 中国肿瘤临床

Objective:To investigate the potential genes associated with cervical intraepithelial neoplasia (CIN) progression through mi-croarray expression profiling data analysis and bioinformatics approaches. Methods:mRNA expression microarray data related to CIN progression were screened from GEO database for the first time. They were re-analyzed by bioinformatics analysis. Results: Two mRNA expression microarray datasets were obtained from the GEO database. Pathway enrichment analysis of the common differen-tially expressed genes identified 3 signaling pathways associated with CIN progression, including Wnt, Endocytosis, and Vibrio cholerae infection. Fourteen differentially expressed genes were also identified. Biological annotation and text mining showed that 3 genes were directly related to CIN progression, and 9 other genes were associated with tumor progression and recurrence. GeneMania tool analysis demonstrated the protein interaction network formed between all the differentially expressed genes and the 24 reported genes. CCND2 and TGFBR2 formed direct interaction with many reported genes. Conclusion:Three signaling pathways and 14 differen-tially expressed genes were associated with CIN progression, as indicated by microarray data analysis results.

Biological Pathway Extension Using Microarray Gene Expression Data

Biological pathways are known as collections of knowledge of certain biological processes. Although knowledge about a pathway is quite significant to further analysis, it covers only tiny portion of genes that exists. In this paper, we suggest a model to extend each individual pathway using a microarray expression data based on the known knowledge about the pathway. We take the Rosetta compendium dataset to extend pathways of Saccharomyces cerevisiae obtained from KEGG (Kyoto Encyclopedia of genes and genomes) database. Before applying our model, we verify the underlying assumption that microarray data reflect the interactive knowledge from pathway, and we evaluate our scoring system by introducing performance function. In the last step, we validate proposed candidates with the help of another type of biological information. We introduced a pathway extending model using its intrinsic structure and microarray expression data. The model provides the suitable candidate genes for each single biological pathway to extend it.

Study of Apoptosis and Gene Expression Pattern Related to Human Degenerative Intervertebral Disc Tissue / 中国康复理论与实践

@#ObjectiveTo investigate the relationship between the degenerative mechanisms of lumbar intervertebral disc (LID) and apoptosis.MethodsThe total RNAs were isolated from human LID tissues. Both the mRNAs from the degeneration and normal LID were reversely transcribed to the cDNAs. The cDNAs were labeled with the incorporations of fluorescent dUTP, for preparing the hybridization probes. The mixed probes were then hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for the fluorescent signals and analyzed by computer image analysis. The apoptotic status and the expression of Bcl-2 and Bax in 12 cases of degenerative LID and 10 cases of normal LID were detected with TdT-mediated dUTP-biotin nick end labeling (TUNEL) and immunohistochemistry methods.ResultsAmong the 4096 targets, there were 10 genes related to apoptosis. The expression related to Bax protein gene was up-regulated and it was down-regulated for Bcl-2 protein. In group of normal LID, the average apoptotic index (AI) was (24.897±3.620); percentage of Bcl-2 positive cells was (31.440±4.150)%; percentage of Bax positive cells was (29.372±2.588)%, average optical density (OD) values of positive particles were (0.183± 0.010 ), ( 0.203 ±0.012) and (0.169±0.005) respectively. In group of degenerative LID, the average AI was (49.232±3.440); percentage of Bcl-2 positive cells was (18.239±2.470)%; percentage of Bax positive cells was (52.349±3.764)%; average OD values of positive particles were (0.152±0.003), (0.310±0.008) and (0.262±0.014) respectively. There were significantly differences in AI and expressions of Bcl-2 and Bax proteins between normal LID and degenerative LID (P<0.05).ConclusionCell apoptosis plays an important role in the process of LID degeneration. Both Bcl-2 and Bax take part in the occurrence and progression of LID.

Analysis of Gene Expression Pattern of Lumbar Intervertebral Disc Degeneration in Human / 中国康复理论与实践

@#ObjectiveTo investigate the gene expression changes in normal and degeneration lumbar intervertebral disc in humans, providing information for clinical. MethodsThe PCR products of 4096 human genes were spotted onto a kind of chemical-material-coated-glass slides. The total RNAs were isolated from the tissues. Both the mRNAs from the degeneration and normal lumbar intervertebral disc in humans were reversely transcribed to the cDNAs, which used as the hybridization probes with the incorporations of fluorescent dUTP. The mixed probes were then hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for the fluorescent signals and analyzed with computer image analysis. ResultsAmong the 4096 targets, there were 706 genes whose expression levels differed between the degeneration and normal lumbar intervertebral disc in all cases, comprising 298 up-regulated and 358 down-regulated ones. ConclusionDNA microarray technology is an effective technique in screening for differently expressed genes between the degeneration and normal lumbar intervertebral disc. Cell apoptosis plays an important role in the process of lumbar intervertebral disc degeneration.

Modeling Colon Cancer Gene Logic Network With mRNA Microarray Data / 生物化学与生物物理进展

Analysis of cellular pathways and networks in terms of logic relations is important to decipher the networks of molecular interactions that underlie cellular function.A computational approach for identifying lower and higher order gene logic associations was presented on the base of graph coloring theory and applied it to the colon cancer mRNA microarray data.Then the logic relationships of 51 oncogenes and cancer suppressor genes are analyzed and the logic association network of them was constructed.The signal pathway of TGF? from the network model was found and verified by the colon cancer pathway of KEGG.The model reveals many higher order logic relationships of cancer genes.These relationships illustrate the complexities that arise in cancer cellular networks because of interacting pathways.The results show that this method is feasible and is expected to give a reference to the medical molecular biologist.