Aiming at long signal acquisition time, low flux, bad signal-to-noise ratio and low intelligence in coloration biochip reader, a new kind of rapid device with high flux was developed. The device consisted of hardware system and software system. It used a charge-coupled device (CCD) as the photoelectric sensor elements and obtained the biochip microarray image. The device integrated the embedded operating system based on i.MX6 chip. The microarray image processing, data analysis and result output were achieved through the code information of the software chip. Experiments with the standard grayscale sheet and standard format chip were carried out. The results showed that the maximum measurement error was less than 0.1%, the value of R2 was 98.7%, and the value of CV was 1.096 1%. The comparison results of 200 samples showed that detection performance of the proposed device was better than that of the same kind of marketed equipment.
ObjectiveTo explore the expression of chloride intracellular channel protein 1 (CLIC1) protein in the matched colorectal normal mucosa tissue, colorectal adenoma tissue， and colorectal cancer tissue, and its relationship with tumorigenesis, tumor progression， and prognosis of patients with colorectal cancer . MethodsThe expression of CLIC1 protein was detected in 150 cases of colorectal normal mucosa tissues, 62 cases of colorectal adenoma tissues, and 187 cases of colorectal cancer tissues by using immunohistochemistry tissue microarray, and the relationships between the expression of CLIC1 protein and clinicopathologic features, and the survival rate of patients with colorectal cancer were analyzed. ResultsThe positive rate of CLIC1 protein expression in normal mucosa tissues (26.00%, 39/150), colorectal adenoma tissues (66.13%, 41/62), and colorectal cancer tissues (82.89%, 187/155) increased in turn and the difference was statistically significant (Plt;0.001). The expression of CLIC1 protein was related to TNM staging (P=0.007), but it was not related to gender (P=0.553), age (P=0.206), tumor diameter (P=0.185), tumor differentiation (P=0.062), and tumor location (P=0.598). The median survival time after surgery in patients with CLIC1 protein positive expression was 80 months, and it was 111 months in patients with CLIC1 protein negative expression. The survival rate of patients with CLIC1 protein positive expression was lower than that with CLIC1 protein negative expression by log-rank test (66.40% vs. 80.00%, P=0.031). ConclusionsThe expression of CLIC1 protein is related to the tumorigenesis and progression of colorectal cancer as well as the survival of patients with colorectal cancer. CLIC1 is a potential tumor biomarker.
Objective To explore the microRNA （miRNA） expression changes and related miRNA characteristics of colorectal cancer （CRC） with hepatic metastasis by miRNA microarray. Methods The fresh specimens of primary CRC were collected in 10 patients during operation， which with hepatic metastasis or not. miRNA microarray analysis was performed to compare the miRNA expression levels in two groups. The different expression levels of miRNA were validated by quantitative real-time PCR analysis. Results A total of six dysregulated miRNAs were identified in the CRC patients with hepatic metastasis comparing with CRC patients without hepatic metastasis， including 3 up-regulated miRNAs （miR-224， miR-1236， and miR-622） and 3 down-regulated miRNAs （miR-155， miR-342-5p， and miR-363）， and the quantitative real-time PCR result of miR-224 consisted with the microarray finding. Conclusions miR-224 may be involved in the process of CRC with hepatic metastasis pathogenesis. miR-224 would be a research direction on a new biomarker or therapic method in CRC with hepatic metastasis.
Objective To identify the expression of pleiotrophin （PTN） mRNA and protein in the colorectal cancer tissues， and to explore the clinical value of it. Methods The expressions of PTN mRNA and protein in colorectal cancer tissues （colorectal cancer group） as well as normal colorectal tissues （normal control group） were tested by using in-situ hybridization and immunohistochemistry. Results The positive rates of PTN mRNA 〔63.9% （53/83） vs. 40.7%（22/54）〕 and protein〔60.2%（50/83） vs. 33.3%（18/54）〕 in colorectal cancer group were all significantly higher than those of normal control group （P=0.008， P=0.002）. There were no significant relationship between expressions of PTN mRNA and protein with gender， age， and type of tumor （P＞0.05）， but in tissues of Ⅲ-Ⅳ stage and poor differentiation，the positive rates of PTN mRNA and protein were all higher （P＜0.05）. Conclusions The over expressions of PTN mRNA and protein in colorectal cancer tissues may directly related to the invasion and metastasis. Meanwhile， it can be used as an index to predict metastasis and prognosis of colorectal cancer.
It is generally considered that various regulatory activities between genes are contained in the gene expression datasets. Therefore, the underlying gene regulatory relationship and the biologically useful information can be found by modeling the gene regulatory network from the gene expression data. In our study, two unsupervised matrix factorization methods, independent component analysis (ICA) and nonnegative matrix factorization (NMF), were proposed to identify significant genes and model the regulatory network using the microarray gene expression data of Alzheimer's disease (AD). By bio-molecular analyzing of the pathways, the differences between ICA and NMF have been explored and the fact, which the inflammatory reaction is one of the main pathological mechanisms of AD, is also emphasized. It was demonstrated that our study gave a novel and valuable method for the research of early detection and pathological mechanism, biomarkers' findings of AD.
Objective To seek for a method of constructing the tissue microarray which contains keloid, skin around keloid, and normal skin. Methods The specimens were gained from patients of voluntary donation between March and May2009, including the tissues of keloid (27 cases), skin around keloid (13 cases), and normal skin (27 cases). The specimens were imbedded by paraffin as donor blocks. The traditional method of constructing the tissue microarray and section were modified according to the histological characteristics of the keloid and skin tissue and the experimental requirement. The tissue cores were drilled from donor blocks and attached securely on the adhesive platform which was prepared. The adhesive platform with tissue cores in situ was placed into an imbedding mold, which then was preheated briefly. Paraffin at approximately 70℃ was injected to fill the mold and then cooled to room temperature. Then HE staining, immunohistochemistry staining were performed and the results were observed by microscope. Results The constructed tissue microarray block contained 67 cores as designed and displayed smooth surface with no crack. All the cores distributed regularly, had no disintegration or manifest shift. HE staining of tissue microarray section showed that all cores had equal thickness, distinct layer, manifest contradistinction, well-defined edge, and consistent with original pathological diagnosis. Immunohistochemistry staining results demonstrated that all cores contained enough tissue dose to apply group comparison. However, in tissue microarray which was made as traditional method, many cores missed and a few cores shifted obviously. Conclusion Applying modified method can successfully construct tissue microarray which is composed of keloid, skin around keloid, and normal skin. This tissue microarray will become an effective tool of researching the pathogenesis of keloid.
Objective To study hepatocyte growth factor (HGF) and its receptor (c-met) expressions in human colorectal cancer and non-neoplasm colorectal mucosa, and the relationship with tumor angiogenesis. Methods Tissue microarrays (TMAs) were made up of 80 cases of colorectal cancer and 80 cases of nonneoplasm colorectal mucosa. The expressions of HGF and c-met were detected by immunohistochemistry (SP). CD105 was used as a marker to account microvessel density (MVD) in tumor tissue. Results HGF was over expressed in 48 cases and c-met was over expressed in 63 cases of colorectal cancer tissue, and the correlation between HGF and c-met positive expression was significant (r=0.231, Plt;0.05). The high expression rate of HGF and cmet in colorectal cancer were significantly higher than that in non-neoplasm colorectal mucosa (χ2=35.387, Plt;0.05; χ2=59.854, Plt;0.05) of colorectal cancer. The overexpression of HGF was correlated with lymph node metastasis (χ2=4.743, Plt;0.05) and TNM staging (χ2=5.576, Plt;0.05). The overexpression of c-met was correlated with differentiation (χ2=15.767, Plt;0.05) and lymph node metastasis (χ2=5.765, Plt;0.05) of colorectal cancer. MVD was different between overexpression and lowexpression colorectal cancer tissues of HGF and cmet (t=2.150, Plt;0.05; t=2.052, Plt;0.05). There was statistical correlation between HGF and cmet overexpression (r=0.259, Plt;0.05). The overexpressions of HGF and cmet were correlated with lymph metastasis in moderate differentiation cancer (χ2=13.154, Plt;0.05; χ2=5.371, Plt;0.05). Conclusions The overexpressions of HGF and c-met in colorectal cancer may be related with tumor angiogenesis. Detecting the expressions of HGF and c-met is valuable to estimate the biological character of colorectal cancer.
ObjectiveTo analyze the expression profile changes of osteogenic-related genes during spontaneous calcification of rat bone marrow mesenchymal stem cells (BMSCs). MethodsBMSCs were isolated from 3-day-old healthy Sprague Dawley rats;cells at the 4th generation were used to establish the spontaneous calcification model in vitro. Spontaneous calcification process was recorded by inverted phase contrast microscope observation and alizarin red staining after 7 and 14 days of culture. For gene microarray analysis, cell samples were collected at 0, 7, and 14 days after culture; the differentially expressed genes were analyzed by bioinformatics methods and validated by real-time quantitative PCR (RT-qPCR) assay. ResultsRat BMSCs calcified spontaneously in vitro. When cultured for 7 days, the cells began to aggregate and were weakly positive for alizarin red staining. After 14 days of culture, obvious cellular aggregation and typical mineralized nodules were observed, the mineralized nodules were brightly positive for alizarin red staining. A total of 576 gene probe-sets expressed differentially during spontaneous calcification, corresponding 378 rat genes. Among them, 359 gene probe-sets expressed differentially between at 0 and 7 days, while only 13 gene probe-sets expressed differentially between at 7 and 14 days. The 378 differentially expressed genes were divided into 6 modes according to their expression profiles. Moreover, according to their biological functions, differentially expressed genes related to bone cell biology could be classified into 7 major groups:angiogenesis, apoptosis, bone-related genes, cell cycle, development, cell communication, and signal pathways related to osteogenic differentiation. In cell cycle group, 12 down-regulated genes were linked with each other functionally. Matrix metalloproteinase 13 (Mmp13), secreted phosphoprotein 1 (Spp1), Cxcl12, Mmp2, Mmp3, Apoe, and Itga7 had more functional connections with other genes. The results of genes Spp1, Mgp, Mmp13, Wnt inhibitory factor 1, Cxcl12, and cyclin A2 by RT-qPCR were consistent with that of gene microarray. ConclusionThe first 7 days after rat BMSCs were seeded are a key phase determining the fate of spontaneous calcification. Multiple genes related with cell communication, bone-related genes, cell cycle, transforming growth factor-β signaling pathway, mitogen-activated protein kinase signaling pathway, and Wnt signaling pathway are involved during spontaneous calcification.
Objective To study the differences in gene expression in A549 cells transfected with Forkhead box protein O1(FOXO1),and provide clues to further exploring the mechanism of FOXO1 in acute lung injury. Methods After using TNF-α to stimulate A549 cells,the eukaryotic expression vector GV230-FOXO1 was transfected into A549 cells by using lipofectamine transfection reagent.The RNA was isolated and differentially expressed genes were screened with high-throughout DNA microarray. Results The eukaryotic expression vector GV230-FOXO1 was successfully constructed and verified.High quality mRNA was isolated and prepared for microarray screening,which passed RNA quality control.The DNA microarray data indicated that 317 genes were up-regulated and 237 genes were down-regulated in A549 cells transfected with FOXO1.The function of these differentially expressed genes involved in many aspects,such as proliferation,apoptosis and differentiation. Conclusions Differentially expressed genes in A549 cells transfected with FOXO1 can be successfully screened by using DNA microarray.FOXO1 may influence the progression of the disease by changing the level of cell proliferation,apoptosis and differentiation in acute lung injury.
DNA microarray has become an essential medical genetic diagnostic tool for its high-throughput, miniaturization and automation. The design and selection of oligonucleotide probes are critical for preparing gene chips with high quality. Several sets of probe design software have been developed and are available to perform this work now. Every set of the software aims to different target sequences and shows different advantages and limitations. In this article, the research and development of these sets of software are reviewed in line with three main criteria, including specificity, sensitivity and melting temperature (Tm). In addition, based on the experimental results from literatures, these sets of software are classified according to their applications. This review will be helpful for users to choose an appropriate probe-design software. It will also reduce the costs of microarrays, improve the application efficiency of microarrays, and promote both the research and development (R&D) and commercialization of high-performance probe design software.