• Interdisciplinary Bio Central
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• v.3 no.1
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• pp.5.1-5.5
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• 2011

Introduction: Many signal transduction pathways mediate cell's behavior by regulating expression level of involved genes. Abnormal behavior indicates loss of regulatory potential of pathways, and this can be attributed to loss of expression regulation of downstream genes. Therefore, function of pathways should be assessed by activity of a pathway itself and relative activity between a pathway and downstream genes, simultaneously. Results and Discussion: In this study, we suggested a new method to assess pathway's function by introducing concept of 'responsiveness'. The responsiveness was defined as a relative activity between a pathway itself and its downstream genes. The expression level of a downstream gene as a function of an upstream pathway activation characterizes disease status. In this aspect, by using the responsiveness we predicted potential progress in cancer development. We applied our method to predict primary and metastatic status of melanoma cancer. The result shows that the responsiveness-based approach achieves better performance than using gene or pathway information alone. The mean of ROC scores in the responsiveness-based approach was 0.90 for GSE7553 data set, increased more than 40% compared to a gene-based method. Moreover, identifying the abnormal regulatory patterns between pathway and its downstream genes provided more biologically interpretable information compared to gene or pathway based approaches.

• BMB Reports
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• v.45 no.12
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• pp.677-685
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• 2012

In the process of tumorigenesis, normal cells are remodeled to cancer cells and protein expression patterns are changed to those of tumor cells. A newly formed tumor microenvironment elicits the immune system and, as a result, a humoral immune response takes place. Although the tumor antigens are undetectable in sera at the early stage of tumorigenesis, the nature of an antibody amplification response to antigens makes tumor-associated autoantibodies as promising early biomarkers in cancer diagnosis. Moreover, the recent development of proteomic techniques that make neo-epitopes of tumor-associated autoantigens discovered concomitantly has opened a new area of 'immuno-proteomics', which presents tumor-associated autoantibody signatures and confers information to redefine the process of tumorigenesis. In this article, the strategies recently used to identify and validate serum autoantibodies are outlined and tumor-associated antigens suggested until now as diagnostic/prognostic biomarkers in various tumor types are reviewed. Also, the meaning of autoantibody signatures and their clinical utility in personalized medicine are discussed.

• Annals of Clinical Neurophysiology
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• v.23 no.1
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• pp.46-52
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• 2021

Background: We aimed to investigate candidates for serological biomarkers of neuropathic pain in individuals with neuromyelitis optica spectrum disorder (NMOSD). Methods: We analyzed 38 sera samples from 38 participants with NMOSD in National Cancer Center. Neuropathic pain was evaluated using the painDETECT questionnaire. Pain with neuropathic components (painDETECT score ≥ 13) was observed in 22 participants, among whom 17 had definite neuropathic pain (painDETECT score ≥ 19). The remaining 16 participants had non-neuropathic pain (painDETECT score < 13). Serum glial fibrillary acidic protein (GFAP) levels were assessed using a single-molecule array assay. Several cytokines, including tumor necrosis factor-alpha (TNF-α), interleukin (IL)-6, IL-10, and IL-17A, were measured by a multiplex bead-based immunoassay. Results: In comparison of NMOSD participants with neuropathic pain components (or definite neuropathic pain) and those with non-neuropathic pain, the absolute values of serum GFAP, TNF-α, IL-6, and IL-10 levels were higher in participants with neuropathic pain components (or definite neuropathic pain), but these findings did not reach statistical significance. Conclusions: Further larger-scale investigations to find reliable serological biomarkers for neuropathic pain in NMOSD are warranted.

• Molecules and Cells
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• v.44 no.11
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• pp.843-850
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• 2021

The rapid increase in collateral omics and phenotypic data has enabled data-driven studies for the fast discovery of cancer targets and biomarkers. Thus, it is necessary to develop convenient tools for general oncologists and cancer scientists to carry out customized data mining without computational expertise. For this purpose, we developed innovative software that enables user-driven analyses assisted by knowledge-based smart systems. Publicly available data on mutations, gene expression, patient survival, immune score, drug screening and RNAi screening were integrated from the TCGA, GDSC, CCLE, NCI, and DepMap databases. The optimal selection of samples and other filtering options were guided by the smart function of the software for data mining and visualization on Kaplan-Meier plots, box plots and scatter plots of publication quality. We implemented unique algorithms for both data mining and visualization, thus simplifying and accelerating user-driven discovery activities on large multiomics datasets. The present Q-omics software program (v0.95) is available at http://qomics.sookmyung.ac.kr.

• Journal of Digestive Cancer Research
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• v.10 no.2
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• pp.65-73
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• 2022

A breakthrough in immunotherapy has changed the outlook for metastatic colorectal cancer (mCRC) treatment as the immune surveillance evasion mechanism of tumor cells has been continuously elucidated. Immune checkpoint inhibitors (ICI), such as pembrolizumab, nivolumab, and ipilimumab, which block immune checkpoint receptors or ligands have been approved for the treatment of mismatch repair deficient (dMMR)/microsatellite instability-high (MSI-H) mCRC based on numerous clinical studies. However, 50% of dMMR/MSI-H mCRC and most mismatch repair proficient/microsatellite stable mCRC remained unresponsive to current immunotherapy. Clinical trials on combination therapy that adds various treatments, such as target agents, chemotherapy, or radiation therapy to ICI, have been actively conducted to overcome this immunotherapy limitation. Further studies on safety and efficacy are needed although several trials presented promising data. Additionally, dMMR/MSI-H, tumor mutation burden, and programmed cell death ligand-1 expression have been studied as biomarkers for predicting the treatment response to immunotherapy, but the discovery and validation of more sensitively predictable biomarkers remained necessary. Thus, this study aimed to review recent studies on immunotherapy in mCRC, summarize the efficacy and limitation of immunotherapy, and describe the biomarkers that predict treatment response.

• Toxicological Research
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• v.14 no.4
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• pp.515-523
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• 1998

Oxidative stress by reactive oxygen species (ROS) damages cellular DNA, RNA, proteins, lipids and others causing various diseases such as cancer, arthritis, and heart diseases. 8-Hydroxyguanine (8-OHG) is one of the products formed from DNA or RNA damaged by ROS. Since high amounts of 8-OHG can be excreted in urine, it may serve as a potential biomarker indicating the level of oxidative damage to nucleic acids. Residents in industrial area with severe air pollution are expected to be affected by higher level of oxidative stress from pollutants like polyaromatic hydrocarbons (PAHs), etc. Smokers are also expected to be damaged by higher level of oxidative stress from cigarette smoke components like PAHs than non-smokers. To examine if the determination of the urinary concentration of 8-OHG could be used as exposure biomarker for the oxidative stress caused by air-pollutants, this study was performed to determine and compare the urinary concentrations of 8-OHG in smokers and non-smokers, or non-polluted area residents and polluted area residents. Urine samples were collected and purified by a strong cation exchange and cellulose partition column, then analyzed by HPLC with electrochemical detector at 600 ㎷ potential. Concentrations of urinary 8-OHG in non-smokers and smokers of Seoul area college male students were determined as 15.12$\pm$9.68 (ng/mg creatinine) and 34.72$\pm$11.72 (ng/mg creatinine), respectively, showing significantly higher level of 8-OHG in smokers than in non-smokers. Urine samples of elementary school students were collected from Sokcho area, which is known to be non-polluted, and 3 representative polluted areas; Yocheon industrial area, Ulsan urban and Ulsan industrial area. The concentrations of 8-OHG in these samples were 12.42$\pm$8.27 (ng/ mg creatinine, Sokcho), 22.55$\pm$9.12 (ng/mg creatinine, Yocheon), 17.41$\pm$2.30 (ng/mg creatinine, Ulsan urban), 55.04$\pm$39.73 (ng/mg creatinine, Ulsan industrial). Thus, samples from polluted area tend to have higher level of 8-OHG and the levels of Yocheon and Ulsan industrial area were significantly higher than that of Sokcho area. The results indicate that the residents of polluted industrial area or smokers are more severely exposed to oxidative stress probably caused by air pollutants like PAHs. Thus, the determination of urinary 8-OHG concentration could be used as biomarker for the extent of body exposure to oxidative stress caused by various pollutants.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3369-3375
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• 2014

Background: C-reactive protein (CRP), considered as a prototypical inflammatory cytokine, has been proposed to be involved in tumor progression through inflammation. Recent studies have indicated CRP as a progostic predictor for urological cancers, but the results remain controversial. Materials and Methods: A systematic search of Medline, Scopus and the Cochrane Library was performed to identify eligible studies published between Jan 1, 2001 and Sep 1, 2013. Outcomes of interest were collected from studies comparing overall survival (OS), cancer-specific survival (CSS) and relapse-free survival (RFS) in patients with elevated CRP levels and those having lower levels. Studies were pooled, and combined hazard ratio (HR) of CRP with its 95% confidence interval (CI) for survival were used for the effect size estimate. Results: A total of 43 studies (7,490 patients) were included in this meta-analysis (25 for RCC, 10 for UC, and 8 for PC). Our pooled results showed that elevated serum CRP level was associated with poor OS (HR: 1.26, 95%CI: 1.22-1.30) and RFS (HR: 1.38 95%CI: 1.29-1.47), respectively. For CSS the pooled HR (HR: 1.33, 95%CI: 1.28-1.39) for higher CRP expression could strongly predict poorer survival in urological cancers. Simultaneously, elevated serum CRP was also significantly associated with poor prognosis in the subgroup analysis. Conclusions: Our pooled results demonstrate that a high serum level of CRP as an inflammation biomarker denotes a poor prognosis of patients with urological cancers. Further large prospective studies should be performed to confirm whether CRP, as a biomarker of inflammation, has a prognostic role in urological cancer progression.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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• pp.9785-9790
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• 2014

Background: The aim of this study is to examine the association of urinary cesium with breast cancer risk. Materials and Methods: We collected survey data and urine specimens from 240 women with incident invasive breast cancer before their treatment and 246 age-matched female controls between October 2009 and July 2010. Urinary concentrations of cesium were determined by inductively coupled plasma mass spectrometry. Interviews were conducted by face-to-face to obtain information on potential breast cancer risk factors. Logistic regression analysis was used to estimate the associations. Results: Creatinine-adjusted levels [median ($25^{th}$, $75^{th}$) ug/g] of cesium in cases and controls were 17.6 (13.1, 24.0) and 19.3 (15.3, 25.7), respectively. After adjustment for potential risk factors, women in the second and highest tertile of cesium showed a decreased risk of breast cancer in a dose-dependent manner as compared with those in the lowest tertile [ORs and 95% CIs: 0.75 (0.46-1.22) and 0.50 (0.30-0.82), respectively]. This decrease was more evident in women with ER positive or localized clinical stage in an exploratory stratification analysis. Conclusions: These findings suggest that cesium may have anticancer efficacy and urinary cesium has potential as a biomarker for breast cancer risk assessment.

• Journal of Biomedical Engineering Research
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• v.38 no.5
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• pp.227-231
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• 2017

Early diagnosis of pancreatic cancer had been considered one of the important barrier for successful therapy since the five year survival rate after treatment of pancreatic cancer was critically low. Nonetheless, patients often miss the golden time of treatment because they rarely visit the hospital until their symptoms are severe. To overcome these problems, a lot of information about the patient's symptoms should be applied as biomarkers for early diagnosis. For this reason, a biomarker for early detection of pancreatic cancer (CA19-9) has been developed as a diagnostic kit. However, since the diagnosis is not accurate enough, pancreatic symptoms (abdominal pain, jaundice, anorexia, diabetes, etc.) and biomarkers (CA19-9) should be considered together. We develop an intelligent diagnostic system that considers CA19-9 and the incidence of pancreatic cancer for pancreatic symptoms that was determined by studying a large number of patient information. It shows a higher accuracy than one using CA19-9 alone. It may increase the survival rate of pancreatic cancer because it can diagnose pancreatic cancer early.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6557-6562
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• 2013

Objective: Specific promoters could improve efficiency and ensure the safety of gene therapy. The aim of our study was to screen examples for lung cancer. Methods: The firefly luciferase gene was used as a reporter, and promoters based on serum markers of lung cancer were cloned. The activity and specificity of seven promoters, comprising CEACAM5 (carcinoembryonic antigen, CEA), GRP (Gastrin-Releasing Peptide), KRT19 (cytokeratin 19, KRT), SFTPB (surfactant protein B, SP-B), SERPINB3 (Squamous Cell Carcinoma Antigen, SCCA), SELP (Selectin P, Granule Membrane Protein 140kDa, Antigen CD62, GMP) and DKK1 (Dickkopf-1) promoters were compared in lung cancer cells to obtain cancer-specific examples with strong activity. Results: The CEACAM5, DKK1, GRP, SELP, KRT19, SERPINB3 and SFTPB promoters were cloned. Furthermore, we successfully constructed recombinant vector pGL-CEACAM5 (DKK1, GRP, SELP, KRT19, SERPINB3 and SFTPB) contained the target gene. After cells were transfectedwith recombinant plasmids, we found that the order of promoter activity from high to low was SERPINB3, DKK1, SFTPB, KRT19, CEACAM5, SELP and GRP and the order for promoters regarding specificity and high potential were SERPINB3, DKK1, SELP, SFTPB, CEACAM5, KRT19 and GRP. Conclusion: The approach adopted is feasible to screen for new tumour specific promoters with biomarkers. In addition, the screened lung-specific promoters might have potential for use in lung cancer targeted gene therapy research.