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1.  Inference of SNP-Gene Regulatory Networks by Integrating Gene Expressions and Genetic Perturbations 
BioMed Research International  2014;2014:629697.
In order to elucidate the overall relationships between gene expressions and genetic perturbations, we propose a network inference method to infer gene regulatory network where single nucleotide polymorphism (SNP) is involved as a regulator of genes. In the most of the network inferences named as SNP-gene regulatory network (SGRN) inference, pairs of SNP-gene are given by separately performing expression quantitative trait loci (eQTL) mappings. In this paper, we propose a SGRN inference method without predefined eQTL information assuming a gene is regulated by a single SNP at most. To evaluate the performance, the proposed method was applied to random data generated from synthetic networks and parameters. There are three main contributions. First, the proposed method provides both the gene regulatory inference and the eQTL identification. Second, the experimental results demonstrated that integration of multiple methods can produce competitive performances. Lastly, the proposed method was also applied to psychiatric disorder data in order to explore how the method works with real data.
doi:10.1155/2014/629697
PMCID: PMC4127230  PMID: 25136606
3.  Modulation of Sodium/Iodide Symporter Expression in the Salivary Gland 
Thyroid  2013;23(8):1029-1036.
Background
Physiologic iodide-uptake, mediated by the sodium/iodide symporter (NIS), in the salivary gland confers its susceptibility to radioactive iodine–induced damage following 131I treatment of thyroid cancer. Subsequent quality of life for thyroid cancer survivors can be decreased due to recurrent sialoadenitis and persistent xerostomia. NIS expression at the three principal salivary duct components in various pathological conditions was examined to better our understanding of NIS modulation in the salivary gland.
Methods
NIS expression was evaluated by immunohistochemistry in human salivary gland tissue microarrays constructed of normal, inflamed, and neoplastic salivary tissue cores. Cumulative 123I radioactivity reflecting the combination of NIS activity with clearance of saliva secretion in submandibular and parotid salivary glands was evaluated by single-photon emission computed tomography/computed tomography imaging 24 hours after 123I administration in 50 thyroid cancer patients.
Results
NIS is highly expressed in the basolateral membranes of the majority of striated ducts, yet weakly expressed in few intercalated and excretory duct cells. The ratio of 123I accumulation between parotid and submandibular glands is 2.38±0.19. However, the corresponding ratio of 123I accumulation normalized by volume of interest is 1.19±0.06. The percentage of NIS-positive striated duct cells in submandibular salivary glands was statistically greater than in parotid salivary glands, suggesting a higher clearance rate of saliva secretion in submandibular salivary glands. NIS expression in striated ducts was heterogeneously decreased or absent in sialoadenitis. Most ductal salivary gland tumors did not express NIS. However, Warthin's tumors of striated duct origin exhibited consistent and intense NIS staining, corresponding with radioactive iodine uptake.
Conclusions
NIS expression is tightly modulated during the transition of intercalated to striated ducts and striated to excretory ducts in salivary ductal cells. NIS expression in salivary glands is decreased during inflammation and tumor formation. Further investigation may identify molecular targets and/or pharmacologic agents that allow selective inhibition of NIS expression/activity in salivary glands during radioactive iodine treatment.
doi:10.1089/thy.2012.0571
PMCID: PMC3752512  PMID: 23441638
4.  Comparison of Methylation Profiling in Cancerous and Their Corresponding Normal Tissues from Korean Patients with Breast Cancer 
Annals of Laboratory Medicine  2013;33(6):431-440.
Background
Aberrant DNA hypermethylation plays a pivotal role in carcinogenesis and disease progression; therefore, accurate measurement of differential gene methylation patterns among many genes is likely to reveal biomarkers for improved risk assessment. We evaluated the gene hypermethylation profiles of primary breast tumors and their corresponding normal tissues and investigated the association between major clinicopathological features and gene hypermethylation.
Methods
A single reaction using methylation-specific multiplex ligation-dependent probe amplification was used to analyze the DNA methylation status of 24 tumor suppressor genes in 60 cancerous tissues and their corresponding normal tissues from patients with primary breast cancer.
Results
In cancerous breast tissues, 21 of 24 genes displayed promoter methylation in one or more samples. The most frequently methylated genes included RASSF1 (43.3%), APC (31.7%), CDKN2B (25.0%), CDH13 (23.3%), GSTP1 (16.7%), and BRCA1 (10%). APC was associated with lymph node metastasis, and BRCA1 was associated with negative estrogen receptor and negative progesterone receptor expression. In normal breast tissues, 8 of 24 tumor suppressor genes displayed promoter hypermethylation; CDKN2B (28.3%) and RASSF1 (8.3%) hypermethylation were most frequently observed.
Conclusions
RASSF1 and CDKN2B hypermethylation in Korean breast cancer patients were the most frequent in cancerous tissue and corresponding normal tissue, respectively. Our data indicates that methylation of specific genes is a frequent event in morphologically normal breast tissues adjacent to breast tumors as well as the corresponding breast cancers. This study also suggests that gene methylation is linked to various pathological features of breast cancer; however, this requires confirmation in a larger study.
doi:10.3343/alm.2013.33.6.431
PMCID: PMC3819443  PMID: 24205493
Breast cancer; Epigenetics; Carcinogenesis; Methylation
5.  Anthocyanins from Vitis coignetiae Pulliat Inhibit Cancer Invasion and Epithelial-Mesenchymal Transition, but These Effects Can Be Attenuated by Tumor Necrosis Factor in Human Uterine Cervical Cancer HeLa Cells 
Recently we have demonstrated that anthocyanins from fruits of Vitis coignetiae Pulliat (AIMs) have anticancer effects. Here, we investigate the effects of AIMs on cell proliferation and invasion as well as epithelial-mesenchymal transition (EMT) which have been linked to cancer metastasis in human uterine cervical cancer HeLa cells. AIMs inhibited the invasion of HeLa cells in a dose-dependent manner. AIMs inhibited MMP-9 expression in a dose-dependent manner. AIMs inhibited the motility of HeLa cells in a wound healing test. AIMs still suppressed NF-κB activation induced by TNF. AIMs also inhibited EMT in HeLa cells. AIMs suppressed vimentin, N-cadherin, and β-catenin expression and induced E-cadherin. AIMs also suppressed expression of β-catenin and Snail, which was regulated by GSK-3. These effects of AIMs were also limited in the HeLa cells treated with TNF. In conclusion, this study indicates that AIMs have anticancer effects by suppressing NF-κB-regulated genes and EMT, which relates to suppression of IκBα phosphorylation and GSK-3 activity, respectively. However, the effects of AIMs were attenuated in the TNF-high condition.
doi:10.1155/2013/503043
PMCID: PMC3705752  PMID: 23864892
6.  A framework for personalized medicine: prediction of drug sensitivity in cancer by proteomic profiling 
Proteome Science  2012;10(Suppl 1):S13.
Background
The goal of personalized medicine is to provide patients optimal drug screening and treatment based on individual genomic or proteomic profiles. Reverse-Phase Protein Array (RPPA) technology offers proteomic information of cancer patients which may be directly related to drug sensitivity. For cancer patients with different drug sensitivity, the proteomic profiling reveals important pathophysiologic information which can be used to predict chemotherapy responses.
Results
The goal of this paper is to present a framework for personalized medicine using both RPPA and drug sensitivity (drug resistance or intolerance). In the proposed personalized medicine system, the prediction of drug sensitivity is obtained by a proposed augmented naive Bayesian classifier (ANBC) whose edges between attributes are augmented in the network structure of naive Bayesian classifier. For discriminative structure learning of ANBC, local classification rate (LCR) is used to score augmented edges, and greedy search algorithm is used to find the discriminative structure that maximizes classification rate (CR). Once a classifier is trained by RPPA and drug sensitivity using cancer patient samples, the classifier is able to predict the drug sensitivity given RPPA information from a patient.
Conclusion
In this paper we proposed a framework for personalized medicine where a patient is profiled by RPPA and drug sensitivity is predicted by ANBC and LCR. Experimental results with lung cancer data demonstrate that RPPA can be used to profile patients for drug sensitivity prediction by Bayesian network classifier, and the proposed ANBC for personalized cancer medicine achieves better prediction accuracy than naive Bayes classifier in small sample size data on average and outperforms other the state-of-the-art classifier methods in terms of classification accuracy.
doi:10.1186/1477-5956-10-S1-S13
PMCID: PMC3380735  PMID: 22759571
7.  Cyclosporine A treatment for relapsed subcutaneous panniculitis-like T-cell lymphoma: a case with long-term follow-up 
The Korean Journal of Hematology  2012;47(2):146-149.
Subcutaneous panniculitis-like T-cell lymphoma (SPTL) is a distinctive lymphoma characterized by an infiltration of subcutaneous tissue by neoplastic cytotoxic T cells. There was no distinction between TCR alpha/beta phenotype and TCR gamma/delta phenotype, and anthracycline-based chemotherapy was usually used for both. Here, we report a patient with recurrent SPTL who achieved a second long-term complete remission by repeated cyclosporine A (CsA) treatment. From 2000 to 2001, the patient received anthracycline-based combination chemotherapy. However, the treatment did not induce long-term remission. In 2002, he received cyclosporine treatment for about 6 months. This resulted in a 5-year remission that ended in relapse in 2008. He received CsA treatment once again and attained a second long-term remission. This case suggests that re-treatment with CsA can be a good option for relapsed SPTL cases and can result in long-term remission.
doi:10.5045/kjh.2012.47.2.146
PMCID: PMC3389065  PMID: 22783363
Subcutaneous panniculitis-like T-cell lymphoma; Cyclosporine; Treatment outcome
8.  Osteoclast-like Giant Cell Tumor of Parotid Gland with a Carcinomatous Component: A Case Report 
Korean Journal of Pathology  2012;46(3):297-301.
The giant cell tumor of the salivary gland is very rare, and 20 cases have been reported in the English-language literature. We report an additional case. A 57-year old man had noticed a mass in the right parotid area for several weeks. The diagnosis using aspiration cytology was a giant cell tumor possibly with a carcinomatous component. Superficial parotidectomy was carried out. The resected parotid gland contained a 1.8 cm-sized well-circumscribed brownish tumor. Histologically the tumor consisted of evenly distributed osteoclast-like giant cells, mononuclear cells and two small foci of a carcinomatous component. The osteoclast-like giant cells and mononuclear cells were positive for vimentin and CD68, and the carcinomatous component was positive for cytokeratin and epithelial membrane antigen. There was no metastatic lesion in the cervical lymph nodes. We believe this is the first case in Korea of an osteoclast-like giant cell tumor of the parotid gland.
doi:10.4132/KoreanJPathol.2012.46.3.297
PMCID: PMC3479769  PMID: 23110019
Giant cell tumors; Salivary glands
9.  Radiation-induced brain injury: retrospective analysis of twelve pathologically proven cases 
Radiation Oncology Journal  2011;29(3):147-155.
Purpose
This study was designed to determine the influencing factors and clinical course of pathologically proven cases of radiation-induced brain injury (RIBI).
Materials and Methods
The pathologic records of twelve patients were reviewed; these patients underwent surgery following radiotherapy due to disease progression found by follow-up imaging. However, they were finally diagnosed with RIBI. All patients had been treated with 3-dimensional conventional fractionated radiotherapy and/or radiosurgery for primary or metastatic brain tumors with or without chemotherapy. The histological distribution was as follows: two falx meningioma, six glioblastoma multiform (GBM), two anaplastic oligodendroglioma, one low grade oligodendroglioma, and one small cell lung cancer with brain metastasis.
Results
Radiation necrosis was noted in eight patients and the remaining four were diagnosed with radiation change. Gender (p = 0.061) and biologically equivalent dose (BED)3 (p = 0.084) were the only marginally influencing factors of radiation necrosis. Median time to RIBI was 7.3 months (range, 0.5 to 61 months). Three prolonged survivors with GBM were observed. In the subgroup analysis of high grade gliomas, RIBI that developed <6 months after radiotherapy was associated with inferior overall survival rates compared to cases of RIBI that occurred ≥6 months (p = 0.085).
Conclusion
Our study demonstrated that RIBI could occur in early periods after conventional fractionated brain radiotherapy within normal tolerable dose ranges. Studies with a larger number of patients are required to identify the strong influencing factors for RIBI development.
doi:10.3857/roj.2011.29.3.147
PMCID: PMC3429897  PMID: 22984665
Radiation necrosis; Radiation injury; Chemoradiation; Brain tumor
10.  Learning biological network using mutual information and conditional independence 
BMC Bioinformatics  2010;11(Suppl 3):S9.
Background
Biological networks offer us a new way to investigate the interactions among different components and address the biological system as a whole. In this paper, a reverse-phase protein microarray (RPPM) is used for the quantitative measurement of proteomic responses.
Results
To discover the signaling pathway responsive to RPPM, a new structure learning algorithm of Bayesian networks is developed based on mutual Information, conditional independence, and graph immorality. Trusted biology networks are thus predicted by the new approach. As an application example, we investigate signaling networks of ataxia telangiectasis mutation (ATM). The study was carried out at different time points under different dosages for cell lines with and without gene transfection. To validate the performance ofthe proposed algorithm, comparison experiments were also implemented using three well-known networks. From the experiment results, our approach produces more reliable networks with a relatively small number of wrong connection especially in mid-size networks. By using the proposed method, we predicted different networks for ATM under different doses of radiation treatment, and those networks were compared with results from eight different protein protein interaction (PPI) databases.
Conclusions
By using a new protein microarray technology in combination with a new computational framework, we demonstrate an application of the methodology to the study of biological networks of ATM cell lines under low dose ionization radiation.
doi:10.1186/1471-2105-11-S3-S9
PMCID: PMC2863068  PMID: 20438656
11.  Diagnostic Value of Galectin-3, HBME-1, Cytokeratin 19, High Molecular Weight Cytokeratin, Cyclin D1 and p27kip1 in the Differential Diagnosis of Thyroid Nodules 
Journal of Korean Medical Science  2007;22(4):621-628.
The distinction between benign and malignant thyroid tumors is critical for the management of patients with thyroid nodules. We applied immunohistochemical staining for galectin-3, HBME-1, cytokeratin 19 (CK19), high molecular weight cytokeratin (HMWCK), cyclin D1 and p27kip1 in 295 thyroid lesions to determine their diagnostic accuracy. The expression of all markers was significantly associated with differentiated thyroid carcinoma (DTC).The sensitivity for the diagnosis of DTC was 94.7% with galectin-3, 91.3% with HBME-1, and 90.3% with CK19. The specificities of these markers were 95.5%, 69.7%, and 83.1%, respectively. Combining these markers, co-expression of galectin-3 and CK19 or galectin-3 and HBME-1 was seen in 93.2% of carcinomas but in none of the benign nodules. Comparing follicular variant of papillary carcinoma (FVPC) with follicular carcinoma (FC), the expression of galectin-3, CK19, and HMWCK was significantly higher in FVPC. When comparing FC with FA, the expression of galectin-3 and HBME-1 was significantly higher in FC. These results suggest that 1) galectin-3 is a useful marker in the distinction between benign and malignant thyroid tumors, 2) the combined use of HBME-1 and CK19 can increase the diagnostic accuracy, and 3) the use of CK19 and HMWCK can aid in the differential diagnosis between PC and FC.
doi:10.3346/jkms.2007.22.4.621
PMCID: PMC2693809  PMID: 17728499
Thyroid Neoplasm; Papillary Carcinoma; Follicular Carcinoma; Galectin 3; HBME-1; Cytokeratin 19
12.  Prenatal Sonographic and MR Imaging Findings of Extensive Fetal Lymphangioma: A Case Report 
Korean Journal of Radiology  2003;4(4):260-263.
We report the imaging findings in a case of fetal lymphangioma involving the retroperitoneum and right lower extremity, and diagnosed by ultrasonography and magnetic resonance (MR) imaging at 26 weeks of gestation. Prenatal ultrasonograms and T2-weighted single-shot fast spin-echo MR images clearly revealed an extensive, multilocular cystic mass with internal hemorrhage in the retroperitoneum extending to the lower extremity.
doi:10.3348/kjr.2003.4.4.260
PMCID: PMC2698106  PMID: 14726645
Fetus, MR; Fetus, neoplasms; Fetus, US; Lymphangioma

Results 1-12 (12)