Detection of Methylated Circulating DNA as Noninvasive Biomarkers for Breast Cancer Diagnosis / 한국유방암학회지

Internationally, breast cancer is the most common female cancer, and is induced by a combination of environmental, genetic, and epigenetic risk factors. Despite the advancement of imaging techniques, invasive sampling of breast epithelial cells is the only definitive diagnostic procedure for patients with breast cancer. To date, molecular biomarkers with high sensitivity and specificity for the screening and early detection of breast cancer are lacking. Recent evidence suggests that the detection of methylated circulating cell-free DNA in the peripheral blood of patients with cancer may be a promising quantitative and noninvasive method for cancer diagnosis. Methylation detection based on a multi-gene panel, rather than on the methylation status of a single gene, may be used to increase the sensitivity and specificity of breast cancer screening. In this review, the results of 14 relevant studies, investigating the efficacy of cell-free DNA methylation screening for breast cancer diagnosis, have been summarized. The genetic risk factors for breast cancer, the methods used for breast cancer detection, and the techniques and limitations related to the detection of cell-free DNA methylation status, have also been reviewed and discussed. From this review, we conclude that the analysis of peripheral blood or other samples to detect differentially methylated cell-free DNA is a promising technique for use in clinical settings, and may improve the sensitivity of screening for both, early detection and disease relapse, and thus improve the future prognosis of patients with breast cancer.

Non-homologous DNA end joining in normal and cancer cells and its dependence on break structures

DNA double-strand breaks (DSBs) are a serious threat to the cell, for if not or miss-repaired, they can lead to chromosomal aberration, mutation and cancer. DSBs in human cells are repaired via non-homologous DNA end joining (NHEJ) and homologous recombination repair pathways. In the former process, the structure of DNA termini plays an important role, as does the genetic constitution of the cells, through being different in normal and pathological cells. In order to investigate the dependence of NHEJ on DSB structure in normal and cancer cells, we used linearized plasmids with various, complementary or non-complementary, single-stranded or blunt DNA termini, as well as whole-cell extract isolated from normal human lymphocytes, chronic myeloid leukemia K562 cells and lung cancer A549 cells. We observed a pronounced variability in the efficacy of NHEJ reaction depending on the type of ends. Plasmids with complementary and blunt termini were more efficiently repaired than the substrate with 3' protruding single-strand ends. The hierarchy of the effectiveness of NHEJ was on average, from the most effective to the least, A549/ normal lymphocytes/ K562. Our results suggest that the genetic constitution of the cells together with the substrate terminal structure may contribute to the efficacy of the NHEJ reaction. This should be taken into account on considering its applicability in cancer chemo-or radiotherapy by pharmacologically modulating NHEJ cellular responses.

Identification of Proteins That Interact with Podocin Using the Yeast 2-Hybrid System

PURPOSE: As a membrane protein at the insertion site of the slit diaphragm (SD) complex in podocyte foot processes, podocin has been reported to act as a scaffolding protein required to maintain or regulate the structural integrity of the SD. In order to identify proteins that associate or interact with podocin, we screened a mouse kidney complementary DNA (cDNA) library using a yeast 2-hybrid system. MATERIALS AND METHODS: 1) The full-length cDNA of podocin from the mouse kidney was amplified by Polymerase Chain Reaction (PCR), 2) The PCR product was cloned into a pGBKT7 vector, pGBKT7-podocin, 3) After the pGBKT7-podocin was transformed into AH109, the AH109/pGBKT7-podocin product was obtained, 4) The mouse kidney cDNA library was transformed into the AH109/pGBKT7-podocin and screened by selection steps, 5) Next, twelve clones were cultured and isolated, 6) The yeast-purified plasmids were transformed into Escherichia coli (E. coli) by heat shock, and 7) To identify the activation domain (AD)/library inserts, we digested them with Him III, and the fragments were then sequenced. RESULTS: 12 positive clones that interacted with podocin were obtained by screening a mouse kidney cDNA library using pGBKT7-podocin. Among them, only 4 clones were found to function at the podocyte where podocin is present. CONCLUSION: Additional studies are needed to clarify the role and interaction with podocin and candidates.

Cloning and high level expression of gene encoding human sCR1 binding domain in E.coli / 第三军医大学学报

Objective To clone and express the gene encoding the binding domain of human soluble complement receptor type 1 (sCR1). Methods sCR1-SCR15-18 cDNA was amplified using RT-PCR from human monocytes of peripheral blood and sequenced using vector pMD-18T. Recombinant pET32-sCR1-SCR15-18 was constructed using prokaryotic expression vector pET32 and transformed into bacterium BL21. IPTG was used to induce gene expression and the obtained expression product was identified by immunoblotting. Results The gene segment that specifically encodes sCR1 was synthesized, the sequence of which was consistent with that of sCR1-SCR15-18 cDNA as registered at GenBank. A prokaryotic expression recombinant pET32-sCR1-SCR15-18 was constructed. The amount of target protein accounted for 40% of the total bacterial proteins and inclusion bodies were present in the bacteria. Immunoblotting showed a single positive band at the site of 43?10~(3). Conclusion The gene encoding sCR1-SCR15-18 was cloned from human monocytes and efficiently expressed in E.coli.

Progress in DNA Computer / 生物化学与生物物理进展

DNA computer is a new research field which combines bot h the computer science and molecular biology. DNA computer is proposed to solve a class of hard problems of mathematical complexity by using a set of DNA sequen ces encoding all candidate solutions to the computational problem of interest an d find out the correct answers by serial manipulations of biochemical reactions. DNA computer is exactly a biomolecular computer which stores a vast quantity of information with high density. DNA computer, by means of its huge parallel comp utation and brute force search strategy, can solve the NP complete problems with polynomial time. The recent advances and principle of DNA computer are introduc ed. The future development and the bioinformatical significance of DNA computer are also analyzed and discussed.

A Comparative Study of Gene Array of Cell Cycle Modulators in Human Corneal Epithelial Cells Stimulated with Epidermal Growth Factor(EGF), Hepatocyte Growth Factor(HGF), or Keratinocyte Growth Factor(KGF)

PURPOSE: To identify and differentiate genes that are up-regulated or down-regulated in human corneal epithelial cells in response to epidermal growth factor(EGF), hepatocyte growth factor(HGF) or keratinocyte growth factor(KGF). METHODS: Primary cultures of human corneal epithelial cell(HCE) were treated with 25 ng/ml of EGF, 25 ng/ml HGF, 25 ng/ml KGF, or vehicle in serum-free medium for 8 hours. Total RNA was isolated with TRIZOL(GIBCO, NY), and treated with DNAse I.P 32-labeled complementary DNA(cDNA) probes were synthesized using 6 ug of total RNA made from HCE cells. Equivalent counts of P 32-labeled cDNA probes were hybridized with the membrane of Atlas human cell cycle array at 68degreesC overnight. After sequential washing, the membranes were exposed to X-ray film for three days. These results were analyzed using Atlas Image TM 1.1 Software. RNAse protection assay was used to confirm one of known genes on the array, which was up-regulated by EGF, KGF, and HGF in the human corneal epithelial cells. RESULTS: Autoradiographic analysis showed that out of 111 genes analyzed, 22 were up- or down-regulated in EGF, 26 in HGF and 7 in KGF compared to untreated corneal epithelial cell. After different signal intensity was normalized more than 2000 by Atlas Image TM 1.1 Software, 12 genes were up-regulated and 10 genes down-regulated in EGF. HGF have 6 up-regulated genes and 1 down-regulated gene and KGF had all up-regulated 7 genes. EGF, HGF and KGF all up-regulated the expression of cyclin D1(BCL-1 oncogene) and serine/threonine-protein kinase PITALRE in the primary cultured human corneal epithelial cells. EGF and KGF both up-regulated E2F-1 pRB-binding protein gene. HGF and KGF up-regulated cyclin D2 gene. Proto-oncogene raf was down-regulated by EGF and HGF. CONCLUSIONS: The three growth factors seemed to have similar effects on the genes that contribute to cell cycle control. Studies to analyze the significance of the differences among these growth factors are ongoing.