小鼠出生后嗅球发育的基因表达差异及其特征分析

目的:通过研究小鼠嗅球全基因表达差异来寻找嗅球生后发育基因变化及其特征,为嗅球发育及相关研究提供参考依据。方法:分别取新生及成年野生型小鼠完整嗅球并独立进行RNA-seq分析,对全基因测序结果进行差异表达分析并通过检测成年与新生小鼠嗅球中差异表达基因(DEGs),利用Gene Ontology、DAVID及KEGG等数据库,结合q PCR的实验方法对部分差异表达基因进行验证,进一步分析差异表达基因在生物学上的影响。结果:成年小鼠和新生小鼠嗅球存在大量差异表达基因,其中Tfap2e,Neurod6和Tbr1等基因表达下调,同时Zfp365,Elt4以及Omp等基因表达上调,DEGs参与多种信号通路。结论:小鼠嗅球在出生后仍然处于不断发育的过程当中,这些差异表达基因主要影响细胞内代谢,细胞的分裂、分化、成熟及细胞间信号传递。     

Inflammation-related gene expression profiles of endocervical polyps

The roles of inflammation-associated genes in the pathogenesis of endocervical polyps remain unclear. We thus compared the expression levels of 509 inflammation-associated genes between endocervical polyp tissues and endocervical canal membrane tissues using a gene microarray. Sixteen inflammation-related genes were differentially expressed in endocervical polyps compared with those of normal endocervical canal membrane tissues. Expression of 8 of these 16 genes was further validated biochemically. The protein expression levels of IL-12P40, IL-17, IFN-γ, TNF-α, CCR2, and IL-11 were significantly higher in endocervical polyps than those in endocervical canal tissues, while expression of TGF-β1 and IL-10 was significantly lower (P<0.05). In addition, endocervical polyp tissues expressed IL-12P40, IL-17, IFN-γ, TNF-α, CCR2, IL-11, TGF-β1, and IL-10 mainly in the cytoplasm of the inflammatory cells and, to a lesser extent, in the acinus of the serous gland. Endocervical polyp is a polygenic disease and aberrantly expressed genes may play roles in its pathogenesis.     

胆囊皱襞位置异常与胆囊疾病关系的探讨

目的探讨胆囊皱襞异常与胆囊疾病的关系。方法我科1995年1月至2006年10月共发现5000例皱襞胆囊,根据其位置分为胆囊皱襞位置正常组（2500例）和胆囊皱襞位置异常组（2500例）,对其超声资料进行回顾性分析。结果位置正常组中正常胆囊占56%;病变胆囊44%,其中胆囊结石、慢性胆囊炎、慢性胆囊炎合并胆囊结石、急性胆囊炎、胆息肉、胆囊腺肌增生症的发病率分别为11.1%、9.2%、10.7%、8.4%、3.4%、1.1%。位置异常组中正常胆囊占12.1%;病变胆囊达87.9%,其中胆囊结石、慢性胆囊炎、慢性胆囊炎合并胆囊结石、急性胆囊炎、胆息肉、胆囊腺肌增生症的发病率分别为20%、8%、39%、12.9%、5.2%、2.8%。结论胆囊内由于皱襞位置异常,影响了胆汁的排泄及胆囊收缩功能,导致胆汁郁积,是胆囊疾病发生的病因之一,且皱襞越近底部或皱襞横贯性越大,胆囊疾病的发病率越高。     

New genes associated with rheumatoid arthritis identified by gene expression profiling

In this study, we aimed to find new genes associated with rheumatoid arthritis (RA) so that more comprehensive genes would be used for monitoring and/or diagnosing patients. Illumina digital gene expression profiling was applied in two sample types – peripheral blood mononuclear cells (PBMCs) and synovial cells to compare the gene expression pattern between 17 patients with RA and three control groups (six osteoarthritis patients, three ankylosing spondylitis patients and 17 healthy controls). Bioinformatics was performed on pathway analysis and protein–protein interaction networks. Four novel genes from PBMCs – DHRS3, TTC38, SAP30BP and LPIN2 – were found to be associated with RA and further confirmed through quantitative real‐time polymerase chain reaction. Five new differentially expressed genes (EPYC, LIFR, GLDN, TADA3 and ZNRF3) found in synovial cells were not confirmed. Pathway analyses revealed 10 significantly enriched pathways, and a protein–protein interaction network analysis showed that four novel PBMC‐derived genes were connected to previously reported genes by four intermediate genes. Therefore, we proposed that four newly identified PBMC‐derived genes could be integrated with previously reported RA‐associated genes to monitor and/or diagnose RA.     

脂代谢相关三基因突变小鼠肝组织基因表达差异研究

目的研究3个脂代谢相关基因联合突变小鼠与野生型小鼠肝脏基因表达差异及其与血脂代谢紊乱和动脉粥样硬化病变的关系。方法应用BiostarM-40S型小鼠cDNA表达谱芯片检测不同基因型小鼠肝脏基因表达的差异，并观察不同年龄小鼠血浆总胆固醇和甘油三脂的浓度以及主动脉内膜形态变化。结果在被测的4000条基因中，与野生型小鼠比较，5周龄三基因突变小鼠肝脏基因表达上调92条，下调105条，脂代谢相关基因中与胆固醇合成相关的基因表达下调，与甘油三脂代谢相关的肝脂肪酶基因表达水平上调。糖代谢、细胞骨架蛋白和免疫等相关的基因表达也有明显差异。5周龄的三基因突变小鼠血浆总胆固醇和甘油三脂水平明显高于野生型小鼠，伴有主动脉内膜损伤，并随年龄增长而加重。结论三基因突变导致肝脏中与脂类、糖类以及免疫等相关的多种基因表达改变，可能共同参与了血脂代谢紊乱和动脉粥样硬化的发生发展。     

p53 tumour suppressor gene protein expression in early and advanced gallbladder carcinoma

 

Aims:

Gallbladder carcinoma is one of the most frequent malignant tumours occurring in Chile and the mortality rate in both sexes ranks among one of the highest in the world. Mutation of p53 tumour suppressor gene has been demonstrated in many tumours. Our aim was to determine protein expression of p53 gene in early and advanced gallbladder carcinoma.  

Methods and results:

Protein expression of gene p53 was studied by immunohistochemical means in 191 gallbladder carcinomas (157 primary tumours, 34 metastases) and 25 controls. In 86 out of 191 cases (45%), protein expression of gene p53 was observed. Differences related to sex, age, or race were not observed. All gallbladder controls were negative. Twenty-five per cent of well-differentiated tumours were p53 positive, while moderate or poorly differentiated carcinomas reached 50% ( P  = 0.04). p53 expression was observed in 23.5% of early carcinomas and in 48.2% of advanced carcinomas ( P  = 0.01). No differences between primary tumours and metastasis were demonstrated.  

Conclusions:

Protein expression of p53 tumour suppressor gene is observed in 45% of gallbladder carcinomas. The absence of expression in controls and in normal mucosa adjacent to tumours suggests its utility in differentiating atypical gallbladder epithelia from neoplastic lesions.     

Homeobox基因在子宫内膜异位症中的异常表达

目的 分析子宫内膜异位症(endometriosis,EM)患者生物信息,探索异位内膜(ectopic endo-metrium,EC)组织中异常表达基因.方法 获取EM患者组织测序数据,筛选差异表达基因(differentially expressed genes,DEGs),使用DAVID工具进行DEGs基因注释,...     

Identification of collaboration patterns of dysfunctional pathways in breast cancer

Breast cancer (BC) is the most common malignancy among women. We aimed to illuminate the molecular dysfunctional mechanisms of BC progression. The mRNA expression profile of BC {"type":"entrez-geo","attrs":{"text":"GSE15852","term_id":"15852"}}GSE15852 was downloaded from Gene Expression Omnibus database, including 43 normal samples and 43 cancer samples. Differentially expressed genes (DEGs) in BC were screened using the t-test by Benjamin and Hochberg method. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the selected DEGs were enriched using Hypergeomeric distribution model. In addition, functional similarity network among the enriched pathways was constructed to further analyze the collaboration of these pathways. We found 848 down-regulated DEGs were associated with 16 significant dysfunctional pathways, including PPAR signaling fatty acid metabolism, and 1584 up-regulated DEGs were related to 6 significant dysfunctional pathways, like cell cycle, protein export, and antigen processing and presentation in BC samples. Crosstalk network analysis of pathways indicated that pyruvate metabolism, propanoate metabolism, and glycolysis gluconeogenesis were the pathways with closest connections with other pathways in BC. In addition, other antigen processing and presentation, including 19 DEGs; PPAR signaling pathway, including 18 DEGs; and pyruvate metabolism pathway, including 13 DEGs were further analyzed. Our results suggested that dysfunctional of significant pathways can greatly affect the progression of BC. Several significant disorder pathways were enriched in our comprehensive study. They may provide guidelines to explore the dysfunctional mechanism of BC progression.     

淡色库蚊性别差异表达cDNA文库的构建和分析

目的为探讨媒介与病原、媒介与宿主的相互作用，建立传播疾病的淡色库蚊性别差异表达cDNA文库。从而筛选阻断疾病传播的疫苗候选分子。方法以淡色库蚊雌蚊成蚊为检测方（Tester）、雄蚊成蚊为驱动方（Driver），进行正向抑制性消减杂交；以雄蚊成蚊为Tester、雌蚊成蚊为Driver，进行反向抑制性消减杂交。将获得的正向抑制性消减杂交产物克隆入pGEM-T easy vector，并以菌液PCR扩增鉴定插入片段。随机抽取100个阳性克隆进行DNA序列分析，并将所得ESTs序列进行在线BLAST分析。结果从100个阳性克隆中测得98个ESTs序列，在测定的序列中与已知基因具有同源性的有57个，其余41个ESTs与已知基因不具有同源性。结论抑制性消减杂交技术建立雌蚊特异性基因文库，发现了淡色库蚊雌蚊新的ESTs序列，为性别相关基因的功能及性别调控。探讨媒介与病原、媒介与宿主的相互作用及其筛选传播阻断疫苗候选分子的研究奠定了基础。     

Distinctive expression profiles of Caveolin-1 and Notch-1 protein in patients with nasal polyps or sinonasal inverted papillomas

Background

Nasal polyposis (NP) and sinonasal inverted papillomas (SIP) are considered benign lesions capable of recurrence or malignant transformation although not with the same prevalence. Since fluctuations of Caveolin-1 and Notch-1 proteins expression have been reported in many pathologies, the current study aimed to investigate their involvement in the epithelial transformation observed in SIPs compared to NP.

Nasal mucosal gene expression in patients with allergic rhinitis with and without nasal polyps

BACKGROUND: Nasal polyps are a common problem that is difficult to diagnose and treat, in part because the cause of nasal polyposis is unknown. Although information on the pathogenesis of polyposis is lacking, there are reports suggesting that a genetic predisposition underlies this disorder. OBJECTIVE: We sought to better understand the basis of nasal polyposis associated with allergic rhinitis. We hypothesize that the expression of unique genes is associated with the nasal polyposis phenotype. METHODS: We examined 12000 human genes transcribed in the nasal mucosa of patients with allergic rhinitis with and without nasal polyps. Biopsy specimens of the mucosa of patients with and without polyps were obtained after the patients refrained from the use of topical or systemic steroid therapy for 2 weeks. RESULTS: Thirty-four genes were differentially expressed between the patient groups, including those for inflammatory molecules and putative growth factors. The greatest differential expression identified by the array analysis was for a group of genes associated with neoplasia, including mammaglobin, a gene transcribed 12-fold higher in patients with polyps compared with control patients with rhinitis alone. Quantitative RT-PCR confirmed this differential expression and documented that the number of mammaglobin mRNA copies is actually 64-fold greater in tissues of patients with polyps versus control patients. The specificity of mammaglobin protein expression was evaluated by means of immunohistochemistry, which showed specific staining in nasal polyp mucosal goblet cells only in patients with polyps. CONCLUSION: These data suggest that nasal polyposis involves deregulated cell growth, using gene activation in some ways similar to a neoplasm. In addition, mammaglobin, a gene of unknown function associated with breast neoplasia, might be related to polyp growth.     

Integrated bioinformatics analysis for differentially expressed genes and signaling pathways identification in gastric cancer

Background: Gastric cancer (GC) has a high mortality rate in cancer-related deaths worldwide. Currently, the pathogenesis of gastric cancer progression remains unclear. Here, we identified several vital candidate genes related to gastric cancer development and revealed the potential pathogenic mechanisms using integrated bioinformatics analysis.Methods: Two microarray datasets from Gene Expression Omnibus (GEO) database integrated. Limma package was used to analyze differentially expressed genes (DEGs) between GC and matched normal specimens. DAVID was utilized to conduct Gene ontology (GO) and KEGG enrichment analysis. The relative expression of OLFM4, IGF2BP3, CLDN1 and MMP1were analyzed based on TCGA database provided by UALCAN. Western blot and quantitative real time PCR assay were performed to determine the protein and mRNA levels of OLFM4, IGF2BP3, CLDN1 and MMP1 in GC tissues and cell lines, respectively.Results: We downloaded the expression profiles of {"type":"entrez-geo","attrs":{"text":"GSE103236","term_id":"103236"}}GSE103236 and {"type":"entrez-geo","attrs":{"text":"GSE118897","term_id":"118897"}}GSE118897 from the Gene Expression Omnibus (GEO) database. Two integrated microarray datasets were used to obtain differentially expressed genes (DEGs), and bioinformatics methods were used for in-depth analysis. After gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments analysis, we identified 61 DEGs in common, of which the expression of 34 genes were elevated and 27 genes were decreased. GO analysis displayed that the biological functions of DEGs mainly focused on negative regulation of growth, fatty acid binding, cellular response to zinc ion and calcium-independent cell-cell adhesion. KEGG pathway analysis demonstrated that these DEGs mainly related to the Wnt and tumor signaling pathway. Interestingly, we found 4 genes were most significantly upregulated in the DEGs, which were OLFM4, IGF2BP3, CLDN1 and MMP1. Then, we confirmed the upregulation of these genes in STAD based on sample types. In the final, western blot and qRT-PCR assay were performed to determine the protein and mRNA levels of OLFM4, IGF2BP3, CLDN1 and MMP1 in GC tissues and cell lines.Conclusion: In our study, using integrated bioinformatics to screen DEGs in gastric cancer could benefit us for understanding the pathogenic mechanism underlying gastric cancer progression. Meanwhile, we also identified four significantly upregulated genes in DEGs from both two datasets, which might be used as the biomarkers for early diagnosis and prevention of gastric cancer.     

Metaplastic polyps and polyposis of the colorectum

Five hundred and fifty-four colorectal metaplastic polyps have been studied histologically. Whilst most lesions were small and sessile, 16.1% measured greater than 0.5 cm in diameter and 0.9% were greater than 1 cm. The larger polyps were frequently pedunculated and occasionally showed a tubulo-villous or villous pattern. A structural similarity between the larger metaplastic polyps and colorectal adenomas is illustrated and the importance of the distinction of metaplastic from dysplastic epithelium in the differentiation of these lesions is stressed. Other unusual features of metaplastic polyps are described. Evidence is given to suggest that males have a greater propensity to develop metaplastic polyps than females. A search for metaplastic-like areas in other colorectal polyps revealed that they are rare (0.6%) in adenomas, but relatively frequent (20.8%) in juvenile polyps. Finally, seven patients with multiple metaplastic polyps of the colorectum are described, in whom a diagnosis of adenomatous polyposis had been made at some stage in their management. Six of the seven patients were males and the mean age at presentation was 37.4 years. Larger metaplastic polyps were frequent in these cases. The necessity for histological confirmation in all cases of intestinal polyposis is stressed, and the possibility that 'metaplastic polyposis' is a pathological entity is discussed.