• Title/Summary/Keyword: co-expression

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Analysis of Indoleamine 2-3 Dioxygenase (IDO) and EGFR Co-expression in Breast Cancer Tissue by Immunohistochemistry

  • Bi, Wei-Wei;Zhang, Wei-Hua;Yin, Gui-Hua;Luo, Hong;Wang, Shou-Qin;Wang, Hongran;Li, Chao;Yan, Wei-Qun;Nie, De-Zhi
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.14
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    • pp.5535-5538
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    • 2014
  • Background: To determine the amount of co-expression of IDO and EGFR in breast cancer patients. Materials and Methods:In order to obtain the distribution of co-expression of IDO and EGFR in breast cancer, we tested 110 breast cancer paraffin tissue blocks with immunohistochemical methods. Then we investigated the relationship between the diagnostic and pathologic characteristics (tumor size, lymph node status, histologic grade, the gene expression of ER, PR, HER2, p53, Ki67 and PCNA) with the situation of co-expression of IDO and EGFR by reviewing the medical records of 32 breast cancer patients. Results: Among 110 breast cancers, 32 cases demonstrated IDO and EGFR co-expression (29.1%), IDO and EGFR synchronous co-expression being found in 19.1% and asynchronous in 10.0%. Conclusions: IDO and EGFR were co-expressed in breast cancer, including synchronous and asynchronous co-expression. The results suggest that considering IDO and EGFR as two indicators for breast cancer treatment or prognosis analysis provides a potential option of individual treatment for the portion of breast cancer patients with co-expression of IDO and EGFR.

A Co-expression Network of Drought Stress-related Genes in Chinese Cabbage

  • Lee, Gi-Ho;Park, Young-Doo
    • Horticultural Science & Technology
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    • v.35 no.2
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    • pp.243-251
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    • 2017
  • Plants have evolved to adapt to abiotic stresses, such as salt, cold, and drought stress. In this study, we conducted an in-depth analysis of drought resistance mechanisms by constructing a gene co-expression network in Chinese cabbage (Brassica rapa ssp. pekinensis L.). This drought stress co-expression network has 1,560 nodes, 4,731 edges, and 79 connected components. Based on genes that showed significant co-expression in the network, drought tolerance was associated with the induction of reactive oxygen species removal by raffinose family oligosaccharides and inositol metabolism. This network could be a useful tool for predicting the functions of genes involved in drought stress resistance in Chinese cabbage.

Effect of CXCR4 and CD133 Co-expression on the Prognosis of Patients with Stage II~III Colon Cancer

  • Li, Xiao-Feng;Guo, Xiao-Guang;Yang, Yong-Yan;Liu, Ai-Yong
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.3
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    • pp.1073-1076
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    • 2015
  • Background: To explore the relationship between CXCR4, CD133 co-expression and clinicopathological features as well as prognosis of patients with phase II~III colon cancer. Materials and Methods: Forty-nine paraffin-embedded samples of tumor tissue and epithelial tissue adjacent to cancer were collected from patients with colon cancer undergoing radical surgery in Baotou Cancer Hospital from January, 2010 to June, 2011. CXCR4 and CD133 expression was detected using immunohistochemistry and its relationship with clinicopathological features and the 3-year survival rate was analyzed. Results: In the tumor tissue and colonic epithelial tissue adjacent to cancer, the positive expression rates of CXCR4 were respectively 61.2% (30/49) and 8.16% (4/49), while those of CD133 being 36.7% (18/49) and 6.12% (3/49). CXCR4 and CD133 expression in tumor tissue was not related to patient age, gender, primary focal sites, tumor size, TNM staging, histological type, tumor infiltration depth and presence or absence of lymphatic metastasis, but CXCR4 and CD133 co-expression was associated with TNM staging and lymphatic metastasis. The 3-year survival rate of patients with CXCR4 and CD133 co-expression was 27.3% (3/11), and that of the remainderwas 76.3% (29/38), the difference being significant ($X^2=7.0206$, p=0.0081). Conclusions: CXCR4 and CD133 co-expression may be a risk factor for poor prognosis of patients with stage II~III colon cancer.

Gene Co-Expression Network Analysis of Reproductive Traits in Bovine Genome

  • Lim, Dajeong;Cho, Yong-Min;Lee, Seung-Hwan;Chai, Han-Ha;Kim, Tae-Hun
    • Reproductive and Developmental Biology
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    • v.37 no.4
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    • pp.185-192
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    • 2013
  • Many countries have implemented genetic evaluation for fertility traits in recent years. In particular, reproductive trait is a complex trait and need to require a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with reproductive trait, we applied a weighted gene co-expression network analysis from expression value of bovine genes. We identified three co-expressed modules associated with reproductive trait from bovine microarray data. Hub genes (ZP4, FHL2 and EGR4) were determined in each module; they were topologically centered with statistically significant value in the gene co-expression network. We were able to find the highly co-expressed gene pairs with a correlation coefficient. Finally, the crucial functions of co-expressed modules were reported from functional enrichment analysis. We suggest that the network-based approach in livestock may an important method for analyzing the complex effects of candidate genes associated with economic traits like reproduction.

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle

  • Lim, Dajeong;Lee, Seung-Hwan;Kim, Nam-Kuk;Cho, Yong-Min;Chai, Han-Ha;Seong, Hwan-Hoo;Kim, Heebal
    • Asian-Australasian Journal of Animal Sciences
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    • v.26 no.1
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    • pp.19-29
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    • 2013
  • Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

Co-expression of Survivin and Bcl-2 in Primary Brain Tumors : Their Potential Effect on Anti-apoptosis

  • Ryu, Je-Il;Kim, Choong-Hyun;Cheong, Jin-Hwan;Bak, Koang-Hum;Kim, Jae-Min;Oh, Suck-Jun
    • Journal of Korean Neurosurgical Society
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    • v.40 no.1
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    • pp.1-5
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    • 2006
  • Objective : Survivin is an inhibitor of apoptosis protein[IAP], which inhibits apoptosis through a pathway distinct from the Bcl-2 family members. Overexpression of survivin and Bcl-2 have been commonly reported in human neoplasms. The authors investigate whether there is a synergistic effect on the anti-apoptosis rate of primary brain tumors "in situ" based on the co-expression of survivin and Bcl-2. Methods : One hundred and two brain tumor patients who had been resected were included in this study. Survivin tin and Bcl-2 were detected by Western blotting analysis, while apoptosis was examined by DNA fragmentation analysis. An anti-apoptotic rate was assessed in these brain tumor samples based on the expression of survivin and Bcl-2 or co-expression of both. Results : Survivin and Bcl-2 were expressed in 57[55.9%] and 53[52.0%] of 102 brain tumor samples studied respectively, and co-expressed in 31[30.4%]. The percentage of astrocytic and meningeal tumors expressing survivin was significantly correlated with histological grades; however, Bcl-2 was not correlated [p=0.106]. The anti-apoptotic rate in primary brain tumors with survivin, Bcl-2, and both was detected in 49[86.0%] of 57 samples, 42[79.9%] of 53 samples, and 27[87.1%] of 31 samples, respectively. Their difference in the frequency of anti-apoptosis was not significant. Conclusion : Survivin or Bcl-2 is involved in the anti-apoptosis. However, it suggests that co-expression of survivin and Bcl-2, together, have no synergistic effect on the anti-apoptotic properties of the primary brain tumors.

Weighted Gene Co-expression Network Analysis in Identification of Endometrial Cancer Prognosis Markers

  • Zhu, Xiao-Lu;Ai, Zhi-Hong;Wang, Juan;Xu, Yan-Li;Teng, Yin-Cheng
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.9
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    • pp.4607-4611
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    • 2012
  • Objective: Endometrial cancer (EC) is the most common gynecologic malignancy. Identification of potential biomarkers of EC would be helpful for the detection and monitoring of malignancy, improving clinical outcomes. Methods: The Weighted Gene Co-expression Network Analysis method was used to identify prognostic markers for EC in this study. Moreover, underlying molecular mechanisms were characterized by KEGG pathway enrichment and transcriptional regulation analyses. Results: Seven gene co-expression modules were obtained, but only the turquoise module was positively related with EC stage. Among the genes in the turquoise module, COL5A2 (collagen, type V, alpha 2) could be regulated by PBX (pre-B-cell leukemia homeobox 1)1/2 and HOXB1(homeobox B1) transcription factors to be involved in the focal adhesion pathway; CENP-E (centromere protein E, 312kDa) by E2F4 (E2F transcription factor 4, p107/p130-binding); MYCN (v-myc myelocytomatosis viral related oncogene, neuroblastoma derived [avian]) by PAX5 (paired box 5); and BCL-2 (B-cell CLL/lymphoma 2) and IGFBP-6 (insulin-like growth factor binding protein 6) by GLI1. They were predicted to be associated with EC progression via Hedgehog signaling and other cancer related-pathways. Conclusions: These data on transcriptional regulation may provide a better understanding of molecular mechanisms and clues to potential therapeutic targets in the treatment of EC.

Rad51 Regulates Reprogramming Efficiency through DNA Repair Pathway

  • Lee, Jae-Young;Kim, Dae-Kwan;Ko, Jeong-Jae;Kim, Keun Pil;Park, Kyung-Soon
    • Development and Reproduction
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    • v.20 no.2
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    • pp.141-147
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    • 2016
  • Rad51 is a key component of homologous recombination (HR) to repair DNA double-strand breaks and it forms Rad51 recombinase filaments of broken single-stranded DNA to promote HR. In addition to its role in DNA repair and cell cycle progression, Rad51 contributes to the reprogramming process during the generation of induced pluripotent stem cells. In light of this, we performed reprogramming experiments to examine the effect of co-expression of Rad51 and four reprogramming factors, Oct4, Sox2, Klf4, and c-Myc, on the reprogramming efficiency. Co-expression of Rad51 significantly increased the numbers of alkaline phosphatase-positive colonies and embryonic stem cell-like colonies during the process of reprogramming. Co-expression ofRad51 significantly increased the expression of epithelial markers at an early stage of reprogramming compared with control cells. Phosphorylated histone H2AX (${\gamma}H2AX$), which initiates the DNA double-strand break repair system, was highly accumulated in reprogramming intermediates upon co-expression of Rad51. This study identified a novel role of Rad51 in enhancing the reprogramming efficiency, possibly by facilitating mesenchymal-to-epithelial transition and by regulating a DNA damage repair pathway during the early phase of the reprogramming process.

High-Level Expression of Human Cytochrome P450 3A4 by Co-Expression with Human Molecular Chaperone HDJ-1 (Hsp40)

  • Ahn, Tae-Ho;Yun, Chul-Ho
    • Archives of Pharmacal Research
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    • v.27 no.3
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    • pp.319-323
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    • 2004
  • Cytochrome P450 (CYP) 3A4 is of great interest because of its important roles in the oxidation of numerous drugs and xenobiotics. HDJ-1, a molecular chaperone in human, is known to assist the correct folding of unfolded proteins. To achieve a high yield of recombinant human CYP3A4 in Escherichia coli, the CYP3A4 encoding gene was co-expressed with the chaperone HDJ-1, under the control of an inducible tac promoter in a bicistronic format. The levels of expression of the CYP3A4 in the bicistronic construct reached up to 715 nmol $(liter culture)^{-1}$ within 16 h at $37^{\circ}C$, which was about a 3.3-fold increase compared to that of the CYP3A4 alone without the HDJ-1. By co-expression with HDJ-1, the catalytic activity of CYP3A4 was also increased by -15-fold. The amount of activity increase was similar to that of the CYP production at the whole cell level. The present over-expression system may be useful for the rapid production of large amounts of active CYP3A4 in E. coli.