A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing

Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline’s performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.

Application of deep learning to predict advanced neoplasia using big clinical data in colorectal cancer screening of asymptomatic adults

Background/Aims@#We aimed to develop a deep learning model for the prediction of the risk of advanced colorectal neoplasia (ACRN) in asymptomatic adults, based on which colorectal cancer screening could be customized. @*Methods@#We collected data on 26 clinical and laboratory parameters, including age, sex, smoking status, body mass index, complete blood count, blood chemistry, and tumor marker, from 70,336 first-time colonoscopy screening recipients. For reference, we used a logistic regression (LR) model with nine variables manually selected from the 26 variables. A deep neural network (DNN) model was developed using all 26 variables. The area under the receiver operating characteristic curve (AUC), sensitivity, and specificity of the models were compared in a randomly split validation group. @*Results@#In comparison with the LR model (AUC, 0.724; 95% confidence interval [CI], 0.684 to 0.765), the DNN model (AUC, 0.760; 95% CI, 0.724 to 0.795) demonstrated significantly improved performance with respect to the prediction of ACRN (p < 0.001). At a sensitivity of 90%, the specificity significantly increased with the application of the DNN model (41.0%) in comparison with the LR model (26.5%) (p < 0.001), indicating that the colonoscopy workload required to detect the same number of ACRNs could be reduced by 20%. @*Conclusions@#The application of DNN to big clinical data could significantly improve the prediction of ACRNs in comparison with the LR model, potentially realizing further customization by utilizing large quantities and various types of biomedical information.

Deep Neural Network-Based Prediction of the Risk of Advanced Colorectal Neoplasia

Background/Aims@#Risk prediction models using a deep neural network (DNN) have not been reported to predict the risk of advanced colorectal neoplasia (ACRN). The aim of this study was to compare DNN models with simple clinical score models to predict the risk of ACRN in colorectal cancer screening. @*Methods@#Databases of screening colonoscopy from Kangbuk Samsung Hospital (n=121,794) and Kyung Hee University Hospital at Gangdong (n=3,728) were used to develop DNN-based prediction models. Two DNN models, the Asian-Pacific Colorectal Screening (APCS) model and the Korean Colorectal Screening (KCS) model, were developed and compared with two simple score models using logistic regression methods to predict the risk of ACRN. The areas under the receiver operating characteristic curves (AUCs) of the models were compared in internal and external validation databases. @*Results@#In the internal validation set, the AUCs of DNN model 1 and the APCS score model were 0.713 and 0.662 (p0.1). @*Conclusions@#Simple score models for the risk prediction of ACRN are as useful as DNN-based models when input variables are limited. However, further studies on this issue are warranted to predict the risk of ACRN in colorectal cancer screening because DNN-based models are currently under improvement.

Application of deep learning to predict advanced neoplasia using big clinical data in colorectal cancer screening of asymptomatic adults

Background/Aims@#We aimed to develop a deep learning model for the prediction of the risk of advanced colorectal neoplasia (ACRN) in asymptomatic adults, based on which colorectal cancer screening could be customized. @*Methods@#We collected data on 26 clinical and laboratory parameters, including age, sex, smoking status, body mass index, complete blood count, blood chemistry, and tumor marker, from 70,336 first-time colonoscopy screening recipients. For reference, we used a logistic regression (LR) model with nine variables manually selected from the 26 variables. A deep neural network (DNN) model was developed using all 26 variables. The area under the receiver operating characteristic curve (AUC), sensitivity, and specificity of the models were compared in a randomly split validation group. @*Results@#In comparison with the LR model (AUC, 0.724; 95% confidence interval [CI], 0.684 to 0.765), the DNN model (AUC, 0.760; 95% CI, 0.724 to 0.795) demonstrated significantly improved performance with respect to the prediction of ACRN (p < 0.001). At a sensitivity of 90%, the specificity significantly increased with the application of the DNN model (41.0%) in comparison with the LR model (26.5%) (p < 0.001), indicating that the colonoscopy workload required to detect the same number of ACRNs could be reduced by 20%. @*Conclusions@#The application of DNN to big clinical data could significantly improve the prediction of ACRNs in comparison with the LR model, potentially realizing further customization by utilizing large quantities and various types of biomedical information.

A scientific treatment approach for acute mast cell leukemia: using a strategy based on next-generation sequencing data

BACKGROUND: Mast cell leukemia (MCL) is the most aggressive form of systemic mastocytosis disorders. Owing to its rarity, neither pathogenesis nor standard treatment is established for this orphan disease. Hence, we tried to treat a patient with MCL based on the exome and transcriptome sequencing results of the patient's own DNA and RNA. METHODS: First, tumor DNA and RNA were extracted from bone marrow at the time of diagnosis. Germline DNA was extracted from the patient's saliva 45 days after induction chemotherapy and used as a control. Then, we performed whole-exome sequencing (WES) using the DNA and whole transcriptome sequencing (WTS) using the RNA. Single nucleotide variants (SNVs) were called using MuTect and GATK. Samtools, FusionMap, and Gene Set Enrichment Analysis were utilized to analyze WTS results. RESULTS: WES and WTS results revealed mutation in KIT S476I. Fusion analysis was performed using WTS data, which suggested a possible RARα-B2M fusion. When RNA expression analysis was performed using WTS data, upregulation of PIK3/AKT pathway, downstream of KIT and mTOR, was observed. Based on our WES and WTS results, we first administered all-trans retinoic acid, then dasatinib, and finally, an mTOR inhibitor. CONCLUSION: We present a case of orphan disease where we used a targeted approach using WES and WTS data of the patient. Even though our treatment was not successful, use of our approach warrants further validation.

Effect of Selective Cyclooxygenase 2 Inhibitor in TCDD Pre-exposed Thyroid Papillary Carcinoma Cell Line

BACKGROUND: Cyclooxygenase 2 (COX-2) is related to carcinogenesis and progression of cancer. COX-2 has been detected in thyroid cancer. This suggests that COX-2 inhibitor may be useful to control the growth of thyroid cancer cells as well as the progression of thyroid cancer. Tetrachlorodibenzodioxin (TCDD), acting as an inflammatory cytokine, directly induces the expression of COX-2. We examine whether TCDD controls the effect of COX-2 inhibitor on thyroid cancer cells. METHODS: The effects of TCDD and celecoxib on thyroid papillary carcinoma cell line (SNU790) were examined using cell proliferation and fluorescence-activated cell sorting analysis. Western blot analysis was performed to determine the expressed COX-2 levels and the cell cycle-related proteins. The matrix metalloproteinase-2 (MMP-2) expression and gelatinolytic activity were examined using real time-polymerase chain reaction and zymography. RESULTS: TCDD directly induced the growth of SNU790 and the expression of cyclin D1, cyclin A, cyclin E, p21 and COX-2. Celecoxib suppressed the growth of SNU790 and the expression of cyclin D1 and cyclin E. Celecoxib reduced the MMP-2 expression and the gelatinolytic activity, but those effects were decreased in the SNU790 by either pre-treatment with TCDD or co-treatment with TCDD and celecoxib. CONCLUSIONS: Celocoxib effect is directly reduced depending on the exposure to TCDD. TCDD exposure should be considered in the treatment with Celecoxib.

Slug suppression induces apoptosis via Puma transactivation in rheumatoid arthritis fibroblast-like synoviocytes treated with hydrogen peroxide

Inadequate apoptosis contributes to synovial hyperplasia in rheumatoid arthritis (RA). Recent study shows that low expression of Puma might be partially responsible for the decreased apoptosis of fibroblast-like synoviocytes (FLS). Slug, a highly conserved zinc finger transcriptional repressor, is known to antagonize apoptosis of hematopoietic progenitor cells by repressing Puma transactivation. In this study, we examined the expression and function of Slug in RA FLS. Slug mRNA expression was measured in the synovial tissue (ST) and FLS obtained from RA and osteoarthritis patients. Slug and Puma mRNA expression in FLS by apoptotic stimuli were measured by real-time PCR analysis. FLS were transfected with control siRNA or Slug siRNA. Apoptosis was quantified by trypan blue exclusion, DNA fragmentation and caspase-3 assay. RA ST expressed higher level of Slug mRNA compared with osteoarthritis ST. Slug was significantly induced by hydrogen peroxide (H2O2) but not by exogenous p53 in RA FLS. Puma induction by H2O2 stimulation was significantly higher in Slug siRNA-transfected FLS compared with control siRNA-transfected FLS. After H2O2 stimulation, viable cell number was significantly lower in Slug siRNA-transfected FLS compared with control siRNA-transfected FLS. Apoptosis enhancing effect of Slug siRNA was further confirmed by ELISA that detects cytoplasmic histone-associated DNA fragments and caspase-3 assay. These data demonstrate that Slug is overexpressed in RA ST and that suppression of Slug gene facilitates apoptosis of FLS by increasing Puma transactivation. Slug may therefore represent a potential therapeutic target in RA.

Abrogation of U266 Multiple Myeloma Cell Proliferation Via Inhibition of NF-kappaB Activation by Curcumin / 대한혈액학회지

BACKGROUND: Curcumin is a naturally occurring biologically active compound, and it has been shown to possess potent anti-inflammatory, anti-tumor and anti-oxidative properties. It is known for its anti-proliferative and proapoptotic effects in several cancer cells. Curcumin's effects on the mechanisms of cell survival and the expression of various cytokines were investigated in U266 cells and the in vivo effects of curcumin were examined using an animal model. METHODS: Cell proliferation assay and flow cytometry were used to examine cell proliferation, along with cell cycle analysis. The protein expressions were analyzed by Western blotting and the expressed levels of cytokines were analyzed by the ELISA method. RESULTS: Curcumin inhibited U266 cell growth in a dose-dependent and time-dependent manner. Cell cycle analysis showed an increased sub-G1 phase, a down regulated cyclinD1 expression and an induced p21 expression. Apoptosis induced a down regulated procaspase 3 expression and it induced cleaved PARP. Curcumin inhibited the IL (interleukin)-6 induced cell signal pathway via decreasing the STAT1 an 3, Erk cyclinD1 and c-myc expressions. Also, administration of 25mg/kg curcumin to a U266 animal model inhibited cancer cell engraftment in the bone marrow and it decreased the IL-6, sIL-6R and IL-8 expression levels. CONCLUSION: Curcumin induced cell cycle arrest and apoptosis and it inhibited the IL-6 mediated signal transduction pathways in U266 cells. Similar to the in vitro results, curcumin inhibited cancer cell proliferation and the expression of cytokine in vivo.

Chromosome 22 LD Map Comparison between Korean and Other Populations

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium(LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centred'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes(frequency > or = 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

Chromosome 22 LD Map Comparison between Korean and Other Populations

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium(LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centred'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes(frequency > or = 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

Regulation of aggrecanase-1 and aggrecanase-2 expressions by hypoxia and cytokines in rheumatoid fibroblast-like synoviocytes / 대한내과학회지

BACKGROUND: While aggrecanases (aggrecanase-1 and aggrecanase-2) are substantially responsible for cartilage aggrecan breakdown in rheumatoid arthritis (RA), not much information is available on the regulation or expression of the two key aggrecanases in rheumatoid fibroblast-like synoviocytes (FLS). The aim of this study is to determine the effect of hypoxia and several cytokines on the expression of the aggrecanases in rheumatoid FLS. METHODS: FLS obtained from RA patients were cultured under hypoxic condition for 24 hours. Quantitative polymerase chain reaction assays for mRNA expression of aggrecanase-1 and aggrecanase-2 were performed on FLS cultured under hypoxia. Additionally, to see the effect of various cytokines, same experiments were conducted after treating FLS with IL-1beta, IL-6, EGF, TGF-beta and TNF-alpha, compared with control. RESULTS: Hypoxia significantly increased both aggrecanase-1 and -2 mRNA expression in rheumatoid FLS compared with normoxia. IL-1beta, IL-6, EGF, TGF-beta and TNF-alpha upregulated the mRNA expression of aggrecanase-1. Both EGF and TGF-beta upregulated the mRNA expression of aggrecanase-2, but TNF-alpha significantly downregulated the mRNA expression of aggrecanase-2. CONCLUSIONS: These results showed upregulation of aggrecanase-1 and -2 by hypoxia and differential regulation of aggrecanase-1 and -2 by various cytokines in rheumatoid FLS. It suggests that hypoxia and cytokines enhance the aggrecanase activity of RA FLS and contribute to joint destruction.

Apoptosis Induction by Curcumin in Human Myelogenous Leukemia Cell Lines / 대한혈액학회지

BACKGROUND: Curcumin, a naturally occurring biologically active compound extracted from rhizomes of Curcuma species, has been shown to possess potent anti-inflammatory, anti-tumor and anti-oxidative properties. The effects and possible mechanism of this agent were investigated on 2 human myelogenous leukemic cell lines. METHODS: K562 and KG-1 cells were the two cell lines selected. The MTT assay and flow cytometry were used to assess the cytotoxicity and for cell cycle analysis, respectively. The protein expressions were analyzed by Western blotting; the caspase activity was also checked. RESULTS: Both cell lines showed dose-dependent susceptibility to curcumin, and the cell cycle analysis showed an increased sub-G1 phase in the KG-1 cells. In the K562 cell, curcumin down regulated the expressions of PCNA (proliferating cell nuclear antigen) and cyclins D1 and B1. The expression of Akt was also down-regulated, but caspase-3 was activated to induce cleaved PARP (polyadenosine ribose polymerase) and apoptosis. However, the expression of phospho-Erk was unaffected. Co-treatment of cyclosporin A (CsA) with curcumin resulted in an attenuation of apoptosis in the K562 cells, implying curcumin-induced apoptosis is dependent on the release of cytochrome c from the mitochondria. CONCLUSION: Curcumin induced cell cycle arrest and apoptosis in both human myelogenous leukemic cell lines, with the apoptosis appearing to be dependent on the release of cytochrome c from the mitochondria.

Effect of Hypoxia on Cytokine Production in Rheumatoid Fibroblast-Like Synoviocytes / 대한류마티스학회지

OBJECTIVE: Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by increased production of cytokines, proliferation of fibroblast-like synoviocytes (FLS) and joint destruction. It is well known that the involved joints in RA are hypoxic. Hypoxia may play a role in the pathogenesis of RA. We thought that hypoxia might alter the production of cytokines by FLS and these changes could affect the biologic behaviors of FLS. Based on that, we investigated whether hypoxia affects the production of cytokines in FLS and the effect of these changes on matrix metalloproteinases (MMPs) expression. METHODS: Fibroblast-like synoviocytes from human rheumatoid synovial tissue obtained duringjoint replacement surgery were cultured in vitro. Hypoxic culture was performed by incubating cells in BBL? Gaspak pouchTM anaerobic system. After incubation under hypoxic condition for 24 hr, the concentrations of various cytokines in culture supernatants were determined by ELISA. To determine the effect of highly expressed cytokines on MMP expression, we performed ELISA of MMP-1, MMP-2 and MMP-3 in cultured FLS, after stimulation with respective cytokines. RESULTS: In hypoxic state, IL-6, IL-8 and vascular endothelial growth factor (VEGF) concentrations were significantly increased compared to those in normoxic condition. However, there were little differences in IL-1, IL-2, IL-4, TNF-alpha and TGF-beta. Stimulation of FLS with IL-6 and IL-8 showed the increased concentrations of MMP-1, MMP-2 and MMP-3. CONCLUSION: Hypoxic environment of rheumatoid synovium might affect FLS to produce proinflammatory and proangiogenic cytokine such as IL-6 and IL-8. These cytokines again could stimulate MMPs production in FLS leading to joint destruction.

Regulation of Matrix Metalloproteinases and Tissue Inhibitor of Metalloproteinase-1 Expression by Hypoxia in Rheumatoid and Osteoarthritis Fibroblast-Like Synoviocytes / 대한류마티스학회지

OBJECTIVE: The rheumatoid synovium is a hypoxic environment and hypoxia has been implicated to have a role in the pathogenesis of rheumatoid arthritis (RA). In this work, we tried to investigate the effect of hypoxia on the expression of matrix metalloproteinase (MMP)-1, -3 and tissue inhibitor of metalloproteinase (TIMP)-1 in rheumatoid and osteoarthritis (OA) fibroblast-like synoviocytes (FLS). METHODS: FLS obtained from RA and OA patients were cultured under normoxic or hypoxic condition for 48 hours. Western blot analyses for MMP-1, -3 and TIMP-1 were performed. TIMP-1 mRNA levels were measured by Northern blot analysis. RESULTS: Hypoxia increased MMP-1 expression in rheumatoid FLS compared with normoxia. TIMP-1 expression was decreased by hypoxia in rheumatoid FLS in both protein and mRNA levels. On the other hand, hypoxia did not significantly affect MMP-1, -3 and TIMP-1 expressions in OA FLS. CONCLUSION: These results suggest that microenvironment such as hypoxia may directly contribute to joint destruction in RA by increasing the ratio of MMP-1 to TIMP-1 production in FLS.

Cytokine profiles in synovial fluid of rheumatoid arthritis / 대한내과학회지

BACKGROUND: The assay of cytokines and their soluble receptors in the synovial fluid of inflammatory arthropathy may be useful in studying pathogenetic and immunoregulatory mechanisms of different arthritis. The aim of this study is to investigate cytokine profiles in rheumatoid arthritis and to find the characteristic pattern of cytokine concentration in rheumatoid arthritis according to the clinical manifestations. METHODS: We measured the concentration of TNF-alpha, IL-1 beta, IL-2, IL-6, IL-8 and IL-10, soluble TNF receptor I, II, IL-1 soluble receptor 2 and IL-6 soluble receptor in synovial fluid from the patients with rheumatoid arthritis using ELISA method. We compared these data with result from osteoarthritis patients. In rheumatoid arthritis, we investigated differences of cytokine profile according to clinical manifestations such as duration of disease, radiographic bone erosions and existence of rheumatoid factor. RESULTS: All of the concentrations of cytokines except IL-2 were significantly elevated in synovial fluid of rheumatoid arthritis than osteoarthritis. When we grouped RA patients according to existence of rheumatoid factor and compared the concentration of cytokines, there were no significant differences between seropositive and seronegative group. We also compared early and late disease, and erosive and non-erosive group but there were no significant differences in cytokine level. CONCLUSION: Our data support the results from other studies that concentration of pro-inflammatory or anti-inflammatory cytokines were elevated in rheumatoid arthritis than osteoarthritis. However, we cannot find the relationship between clinical findings and cytokine profiles in joint fluid.

Differentiation Related Gene (Drg-1) as a Molecular Marker during the Treatment of in vitro Intermittent Androgen Deprivation in prostate Cancer / 대한비뇨기과학회지

PURPOSE: recent studies have reported that the expression of Drg-1 is up-regulated by androgen. It has been suggested that Drg-1 gene be used as a molecular marker for prostate cancer therapies like PSA. To de termine the role of Drg-1 gene as a molecular marker during intermittent androgen deprivation(IAD) therapy, we investigated the expression of Drg-1 and compared it with PSA expression in human prostate cancer cell lines treated with dihydrotestosterone (DHT) continuously or intermittently. MATERIALS AND METHODS: Two prostate cancer cells having different status of androgen receptor [LNCaP (androgen dependent) and PC-3 (androgen independent)] were used in this study. To know the change in PSA and Drg-1 expression after DHT treatment the cells were cultured in steroid-free RPMI media for 24 hours. 10(-7) and 10(-8)M of DHT and 10(-7)M bicalutimide was added into the cells and then cultured for 72 hours. And we established in vitro IAD model using LNCaP cells. Northern analyses were performed to determine the expression level of both PSA and Drg-1genes. Also, western analyses were performed to determine the protein level of proliferating cellular nuclear antigen and androgen receptor. RESULTS: Transcripts of Drg-1 were detected in both LNCaP and PC-3 cells but PSA was not expressed in PC-3 cells. The expression of Drg-1gene in LNCaP cells was up-regulated by 10(-8)M of DHT like PSA gene and down-regulated by 10(-7)M bicalutamide. In the treatment of intermittent androgen deprivation, the expression pattern of Drg-1was similar to that of PSA. However, up-regulation of PSA was detected earlier than of Drg-1. CONCLUSIONS: Based on observation, Drg-1 was up-regulated by androgen and down-regulated by anti-androgen. This suggests that Drg-1gene is useful for determining the androgen independency of prostate cancer during IAD.

Increased Expression of Caveolin-1 in Renal Cell Carcinoma / 대한비뇨기과학회지

No abstract available.

Enhanced induction of Bax gene expression in H460 and H1299 cells with the combined treatment of cisplatin and adenovirus mediated wt-p53 gene transfer

Cytotoxic effect of either cisplatin or p53 gene transfection of lung cancer cells may be different depending on the p53 status of cells. We investigated cytotoxic effects on the combined treatment of cisplatin and adenovirus mediated p53 gene transfer (Avp53) in both H460 and H1299 cells in vitro. The results showed the highest numbers of apoptotic cells in both H460 and H1299 cells following the combined treatment regardless of p53 status in comparison with either cisplatin or Avp53 alone. The expression levels of p53, p21, Bax and ICE were examined to understand a possible cellular signal path of the combined treatment. In western analyses, the patterns of phosphorylated p53 protein were different between Avp53 and combined treatment. The expressions of p21 and Bax were increased in combined treatment, whereas the cleaved form of ICE (20 kD) was not detected. These results suggest that cisplatin induced p53 protein phosphorylation and may activate the downstream of p53 gene expression such as p21 and Bax. The enhanced apoptosis of lung cancer cells by the combined treatment may be useful in the development of clinical therapeutic modality of lung tumors.

Regulation of Gene Expression in Murine Renal Cell Carcinoma Cells Growing in Ectopic or Orthotopic Organs of Syngenic Mice / 대한암학회지

PURPOSE: The biologic behavior of tumor cells is partially controlled by the microenvironment. We investigated the expression levels of several genes involved in metastasis and drug response in RENCA cells growing in ectopic (skin) and orthotopic (kidney) sites. MATERIALS AND METHODS: Murine renal carcinoma cells were injected into kidney (orthotopic) and subcutis (ectopic) of syngeneic mice. Mice were treated with doxorubicin (DXR) (8 mg/kg) on days 8 and 15 after tumor cell implantation. Drug response was measured both in vivo and ex vivo by measuring tumor size and MTT assay. We also performed an in situ mRNA hybridization to estimate the expression levels of mdr (multidrug resistance), EGFR (epidermal growth factor receptor) and type IV collagenase. RESULTS: RENCA cells growing in the kidney of syngeneic mice produced metastatic lesions in the lung (57% of mice), while the same cells growing in the subcutis did not. Tumors growing in the kidney were more resistant to DXR than tumors growing in the subcutis. MTT assays revealed that tumor cells derived from kidney were more resistant to DXR than those cells from subcutis. In situ hybridization analyses showed that transcripts of EGFR and type IV collagenase genes in kidney tumors were higher than those of subcutaneous tumors but mdr expression showed no difference between the two tumors. CONCLUSION: These results demonstrate that the organ environment influences the drug responsive ness and the expression of EGFR and type IV collagenase genes in murine renal cell carcinoma cells.

Correlation between VEGF Expression and Prognostic Factors in Breast Cancer / 대한암학회지

PURPOSE: Archival tissues of breast cancer patients were examined for VEGF expression to evaluate the relationship with other clinicopathologic factors and prognostic significance of VEGF in breast cancer. MATERIALS AND METHODS: Paraffin sections from 76 patients with invasive breast cancer who have been treated at Samsung Medical Center from December, 1994 to April, 1998 were examined for VEGF expression by immunohistochemical staining using anti-VEGF antibody. We analyzed relationships between VEGF expression and tumor size, tumor stage, metastasis, steroid honnone receptors, p53, disease recurrence and survival. RESULTS: Immunostaining showed variable VEGF positivity in the malignant cells and VEGF was detected more frequently in tumors than in adjacent non-tumorous breast tissues. 74 out of 76 (97.4%) was positive for VEGF. We found that the expression of VEGF was strongly correlated with the stages of breast tumor (P=0.020), lymph node metastasis (P=0.043) and PR (P=0.016). However, we could not find statistically significant relationship between VEGF expression and tumor size, ER, p53 and distant metastasis. CONCLUSION: VEGF may be a useful prognostic indicator in patients with breast cancer, especially correlated with tumor stage and lymph node metastasis. This result warrants further study to confirm our findings.