• Journal of Information Processing Systems
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• v.19 no.5
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• pp.652-662
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• 2023

Identifying highly discriminating genes is a critical step in tumor recognition tasks based on microarray gene expression profile data and machine learning. Gene selection based on tree models has been the subject of several studies. However, these methods are based on a single-tree model, often not robust to ultra-highdimensional microarray datasets, resulting in the loss of useful information and unsatisfactory classification accuracy. Motivated by the limitations of single-tree-based gene selection, in this study, ensemble gene selection methods based on multiple-tree models were studied to improve the classification performance of tumor identification. Specifically, we selected the three most representative tree models: ID3, random forest, and gradient boosting decision tree. Each tree model selects top-n genes from the microarray dataset based on its intrinsic mechanism. Subsequently, three ensemble gene selection methods were investigated, namely multipletree model intersection, multiple-tree module union, and multiple-tree module cross-union, were investigated. Experimental results on five benchmark public microarray gene expression datasets proved that the multiple tree module union is significantly superior to gene selection based on a single tree model and other competitive gene selection methods in classification accuracy.

• Tuberculosis and Respiratory Diseases
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• v.65 no.6
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• pp.495-503
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• 2008

Background: Epigenetic alterations in certain genes are now known as at least important as genetic mutation in pathogenesis of cancer. Especially abnormal hypermethylation in or near promoter region of tumor suppressor genes (TSGs) are known to result in gene silencing and loss of gene function eventually. The authors tried to search for new lung cancer-specific TSGs which have CpG islands and HpaII sites, and are thought to be involved in carcinogenesis by epigenetic mechanism. Methods: Tumor tissue and corresponding adjacent normal tissue were obtained from 10 patients who diagnosed with non small cell lung cancer (NSCLC) and underwent surgery in Konyang university hospital in 2005. Methylation profiles of promoter region of 21 genes in tumor tissue & non-tumor tissue were examined with HpaII-MspI methylation microarray (Methyl-Scan DNA chip$^{(R)}$, Genomic tree, Inc, South Korea). The rates of hypermethylation were compared in tumor and non-tumor group, and as a normal control, we obtained lung tissue from two young patients with pneumothorax during bullectomies, methylation profiles were examined in the same way. Results: Among the 21 genes, 10 genes were commonly methylated in tumor, non-tumor, and control group. The 6 genes of APC, AR, RAR-b, HTR1B, EPHA3, and CFTR, among the rest of 11 genes were not methylated in control, and more frequently hypermethylated in tumor tissue than non-tumor tissue. Conclusion: In the present study, HTR1B, EPHA3, and CFTR are suggested as possible novel TSGs of NSCLC by epigenetic mechanism.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.2
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• pp.693-698
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• 2012

Breast cancer is the most frequent cancer of women worldwide, with considerable geographic and racial/ethnic variation. Data are generally derived from population based cancer registries in the developed countries but hospital data are the most reliable source in the developing countries. Ten years data from 1st Jan 2000 to 31st Dec 2009 of a cancer hospital in Pakistan were here analyzed by descriptive statistics to evaluate the clinicopathologic profile of local breast cancer patients. Among 28,740 cancer patients, 6,718 were registered as breast cancer. The female to male ratio was 100:2. Breast cancer accounted for 23% of all and 41% of female cancers. Some 46% were residents of Lahore, with a mean age of $47{\pm}12$ years. Less than 1% were at Stage 0 and 10%, 32%, 35% and 23% were at Stage I, II, III and IV respectively. Histopathology was unknown in 4% while 91%, 2% and 1% had invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC) and mucinous carcinoma respectively. Rare carcinomas accounted for the rest. Tumor grade 1, 2 and 3 was 11%, 55% and 34% among the known. Profile of breast cancer patients in Pakistan follows a pattern similar to that of other developing countries with earlier peak age and advanced disease stage at presentation. The male breast cancer accounts for higher proportion in the local population. Local women have higher frequency of IDC and lower frequency of ILC and DCIS, owing probably to a different risk profile. Use of hospital information systems and establishment of population based cancer registry is required to have accurate and detailed local data. Promotion of breast health awareness and better health care system is required to decrease the burden of advanced disease.

• The Journal of Pediatrics of Korean Medicine
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• v.22 no.1
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• pp.113-121
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• 2008

Objectives In human myeloid leukemia cells, there are no specific features of apoptosis compared with apoptosis in other cell types. Solanum nigrum L.(SNL) is a deciduous tree, which is widely distributed in Korea with reported anti-tumor, anti-inflammatory and non-specific immune-enhancing properties. Although the plant has been clinically used for treating a variety of diseases, its bioactive ingredients are unknown and its mode of action potential has never been investigated. Thus anti-tumor property of methanol extract was investigated. Methods In this study, anti-tumor property of methanol extract was investigated by determining its in vitro growth-inhibitory effects on human myeloid leukemia cells. XTT proliferation assay, DNA fragmentation, immunoblot analysis, densitometric analysis were used. Results 1. The methanol fraction of the extracts of SNL induced mitochondria-mediated apoptosis in human myeloid leukemia cells. 2. The methanol fraction exhibited relatively higher cytotoxic activity in a dose-dependent manner than chloroform, and hexane fraction. 3. Typical ladder profile of Oligonucleosomal fragments were appeared. 4. The secreted cytosolic cytochrome C level was increased by treatment of methanol fraction. Conclusions Methanol fraction of SNL is capable of inducing apoptosis in human myeloid leukemia cells.

• Food Science and Biotechnology
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• v.14 no.6
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• pp.854-859
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• 2005

Although action modes of equol and genistein have been extensively studied, their precise roles in tumor cells remain elusive. To address possible effects of these compounds on protein expression in mammary tumor cells, proteins modulated in MCF-7 mammary tumor cells when incubated in absence and presence of 10 uM equol or genistein were identified through 2-dimensional gel electrophoresis, MALDI-TOF MS/MS, and NCBInr database search using Mascot software. Most proteins differentially expressed in MCF-7 cells after treatment with 10 uM genistein or equol were identified as being the same. Exposure to both compounds caused decreased cellular expression of RNA-binding protein regulatory subunit and oncogene DJ1 tubulin beta-1 chain, and increased expression of heterogeneous ribonucleoproteins F and L, KH-type splicing regulatory protein, and translation elongation factor EF-Tu precursor. Genistein and equol at dose used in this study showed common action mechanism.

• Genomics & Informatics
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• v.11 no.4
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• pp.164-173
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• 2013

Genomic instability, which occurs through both genetic mechanisms (underlying inheritable phenotypic variations caused by DNA sequence-dependent alterations, such as mutation, deletion, insertion, inversion, translocation, and chromosomal aneuploidy) and epigenomic aberrations (underlying inheritable phenotypic variations caused by DNA sequence-independent alterations caused by a change of chromatin structure, such as DNA methylation and histone modifications), is known to promote tumorigenesis and tumor progression. Mechanisms involve both genomic instability and epigenomic aberrations that lose or gain the function of genes that impinge on tumor suppression/prevention or oncogenesis. Growing evidence points to an epigenome-wide disruption that involves large-scale DNA hypomethylation but specific hyper-methylation of tumor suppressor genes, large blocks of aberrant histone modifications, and abnormal miRNA expression profile. Emerging molecular details regarding the modulation of these epigenetic events in cancer are used to illustrate the alterations of epigenetic molecules, and their consequent malfunctions could contribute to cancer biology. More recently, intriguing evidence supporting that genetic and epigenetic mechanisms are not separate events in cancer has been emerging; they intertwine and take advantage of each other during tumorigenesis. In addition, we discuss the collusion between epigenetics and genetics mediated by heterochromatin protein 1, a major component of heterochromatin, in order to maintain genome integrity.

• Journal of Pharmacopuncture
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• v.19 no.2
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• pp.114-121
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• 2016

Objectives: Lung cancer remains a deadly disease with unsatisfactory overall survival. Cisplatin, a standard platinum (Pt)-based chemotherapeutic agent, has the potential to inhibit the growth of lung cancer. Its use, however, is occasionally limited by severe organ toxicity. However, until now, no systematic study has been conducted to verify its efficacy with proper experimental support in vivo. Therefore, we examined whether biosynthesized Pt nanoparticles (NPs) inhibited human lung cancer in vitro and in vivo to validate their use in alternative and complementary medicine. Methods: We evaluated the in vitro and the in vivo anticancer efficiencies of biosynthesized Pt NPs in a subcutaneous xenograft model with A549 cells. Severe combined immune deficient mice (SCID) were divided into four groups: group 1 being the vehicle control group and groups 2, 3 and 4 being the experimental groups. Once the tumor volume had reached $70-75mm^3$, the progression profile of the tumor growth kinetics and the body weights of the mice were measured every week for 6 weeks after oral administration of Pt NPs. Doses of Pt NPs of 500, 1,000 and 2,000 mg/kg of body weight were administered to the experimental groups and a dose of honey was administered to the vehicle control group. The efficacy was quantified by using the delay in tumor growth following the administration of Pt NPs of A549 human-lung-cancer xenografts growing in SCID mice. Results: The in vitro cytotoxicity evaluation indicated that Pt NPs, in a dose-dependent manner, inhibited the growth of A549 cells, and the in vivo evaluation showed that Pt NPs at the mid and high doses effectively inhibited and delayed the growth of lung cancer in SCID mice. Conclusion: These findings confirm the antitumor properties of biosynthesized Pt NPs and suggest that they may be a cost-effective alternative for the treatment of patients with lung cancer.

• Journal of Nutrition and Health
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• v.33 no.6
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• pp.632-638
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• 2000

This study was designed to observe the effect of green tea on colon tumor incidence and biomarkers of colon carcinogenesis in 1, 2-dimethlhydrazine-treated rats. Male Sprague Dawley rats at 7 weeks of age were divided into two groups: control and green tea(GT) groups. Control rats had distilled water as drinking water but GT group received green tea extracts(2.5%, w/v water) as drinking water throughout the experiment periods. All rats were fed the experimental diet containing 15% fat by weight for 20 weeks. and were i.m. injected with DMH for 6 weeks to give total dose of 180mg/kg body weight. Tumor incidence was reduced in GT group (39%) compared with control group (56%) Green tea significantly reduced cell proliferation (total cells per crypt, crypt length and proliferative zone) in colonic mucosa and also significantly reduced the levels of preformed prostalandin E2(PGE2) and thromboxance B2(TXB2) in colonic mucosa but the fatty acid profile of total lipid in colonic mucosa was not significantly influenced by green tea. However the relative percent of C20:4 and the levels f preformed PGE2 and TXB2. were significantly higher in tumor tissue compared with normal surrounding mucosa.Green tea increased the fecal excretion of total bile acid but not scondary bile acid which is known as one of promoters for colon cancer,. These results suggest that green tea could have preventive effect against colon cancer when consumed daily by influencing on antioxidant effect and the metabolism of arachidonic acid.

• Journal of Biomedical Engineering Research
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• v.33 no.4
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• pp.169-176
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• 2012

Tumor cell morphology is closely related to its migratory behaviors. An active tumor cell has a highly irregular shape, whereas a spherical cell is inactive. Thus, quantitative analysis of cell features is crucial to determine tumor malignancy or to test the efficacy of anticancer treatment. We use 3D time-lapse phase-contrast microscopy to analyze single cell morphology because it enables to observe long-term activity of living cells without photobleaching and phototoxicity, which is common in other fluorescence-labeled microscopy. Despite this advantage, there are image-level drawbacks to phase-contrast microscopy, such as local light effect and contrast interference ring. Therefore, we first corrected for non-uniform illumination artifacts and then we use intensity distribution information to detect cell boundary. In phase contrast microscopy image, cell is normally appeared as dark region surrounded by bright halo ring. Due to halo artifact is minimal around the cell body and has non-symmetric diffusion pattern, we calculate cross sectional plane which intersects center of each cell and orthogonal to first principal axis. Then, we extract dark cell region by analyzing intensity profile curve considering local bright peak as halo area. Finally, we calculated the Fourier descriptor that morphological characteristics of cell to classify tumor cells into active and inactive groups. We validated classification accuracy by comparing our findings with manually obtained results.

• Journal of Nutrition and Health
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• v.26 no.7
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• pp.829-838
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• 1993

This study was designed to compare the effect of different dietary fats on the incidence of colorectal tumor, the level of plasma thromboxane B2(TXB2) and fatty acid profiles of platelet and colonic mucosal lipids in N - methyl - N - nitro - N - nitrosoguanidine(MNNG) - treated rats. Male Sprague Dawley rats, at 8 weeks old, were divided into 2 groups and infused intrarectally with saline(control group) or with 2mg MNNG(carcinogen-treated group) twice a week for 3 weeks. Each group was again divided into 4 groups and fed one of four diets(BT, CO, PO, FO) containing dietary fat at 9%(w/w) level for 37 weeks, Dietary fats were beef tallow(7.2%)+corn oil(1.8%) for BT, corn oil(9.0%) for CO, perilla oil(9.0%) for PO, fish oil (6.5%)+corn oil (2.5%) for FO diets. MNNG-treated rats had colonic tumor, while no tumors(adenocarcinoma and adenoma) than others. Tumor sizes in BT-MNNG rats ranged from 2mm papillary form to 15mm of polypoid. However, the size of tumors in PO-MNNG or FO-MNNG rats could not be measured by gross examination. BT-MNNG and CO-MNNG groups were higher in the level of plasma TXB2 and the ratio of c20 : 4/c20 :5 platelet. PO-MNNG groups were lower in the ratio of c20 : 4/c20 : 5(p<0.05) in fatty acid of colonic mucosal lipids suggesting that perilla oil and fish oil could reduce the level of PGE2 and TXB2 by modifying its precursor content and restrain tumor promotion in colon. Effect of perilla oil rich in $\alpha$-linolenic acid on colon carcinogenesis was similar to that of fish oil and thus perilla oil could have a protective effect against colon cancer possibly by inhibiting the production of arachidonic acid metabolite.