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Lee YJ, Pan Y, Lim D, Park SH, Sin SI, Kwack K, Park KY. Broccoli Cultivated with Deep Sea Water Mineral Fertilizer Enhances Anti-Cancer and Anti-Inflammatory Effects of AOM/DSS-Induced Colorectal Cancer in C57BL/6N Mice. Int J Mol Sci 2024; 25:1650. [PMID: 38338927 PMCID: PMC10855752 DOI: 10.3390/ijms25031650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
This study aimed to determine the alleviating effect of broccoli grown with deep sea water mineral (DSWM) fertilizer extracted from deep sea water on the development of colorectal cancer in C57BL/6N mice treated with AOM/DSS. Naturaldream Fertilizer Broccoli (NFB) cultured with deep sea water minerals (DSWM) showed a higher antioxidant effect and mineral content. In addition, orally administered NFB, showed a level of recovery in the colon and spleen tissues of mice compared with those in normal mice through hematoxylin and eosin (H&E) staining. Orally administered NFB showed the inhibition of the expression of inflammatory cytokine factors IL-1β, IL-6, TNF, IFN-γ, and IL-12 while increasing the expression of IL-10. Furthermore, the expression of inflammatory cytokines and NF-κB in the liver tissue was inhibited, and that of inflammatory enzymes, such as COX-2 and iNOS, was reduced. In the colon tissue, the expression of p53 and p21 associated with cell cycle arrest increased, and that of Bcl-2 associated with apoptosis decreased. Additionally, the expression of Bax, Bad, Bim, Bak, caspase 9, and caspase 3 increased, indicating enhanced activation of apoptosis-related factors. These results demonstrate that oral administration of broccoli cultivated using DSWM significantly restores spleen and colon tissues and simultaneously inhibits the NF-κB pathway while significantly decreasing cytokine expression. Moreover, by inducing cell cycle arrest and activating cell apoptosis, they also suggest alleviating AOM/DSS-induced colon cancer symptoms in C57BL/6N mice.
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Affiliation(s)
- Yeon-Jun Lee
- Department of Biomedical Science, CHA University, Seongnam 13488, Republic of Korea; (Y.-J.L.); (Y.P.); (D.L.)
| | - Yanni Pan
- Department of Biomedical Science, CHA University, Seongnam 13488, Republic of Korea; (Y.-J.L.); (Y.P.); (D.L.)
| | - Daewoo Lim
- Department of Biomedical Science, CHA University, Seongnam 13488, Republic of Korea; (Y.-J.L.); (Y.P.); (D.L.)
| | - Seung-Hwan Park
- Agriculture Research Center for Carbon Neutral and Healing, Gurye-gun 57607, Republic of Korea
| | - Sin-Il Sin
- Agriculture Research Center for Carbon Neutral and Healing, Gurye-gun 57607, Republic of Korea
| | - KyuBum Kwack
- Department of Biomedical Science, CHA University, Seongnam 13488, Republic of Korea; (Y.-J.L.); (Y.P.); (D.L.)
| | - Kun-Young Park
- Graduate School of Integrative Medicine, CHA University, Seongnam 13488, Republic of Korea
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Lee SS, Park J, Oh S, Kwack K. Downregulation of LOC441461 Promotes Cell Growth and Motility in Human Gastric Cancer. Cancers (Basel) 2022; 14:cancers14051149. [PMID: 35267457 PMCID: PMC8909665 DOI: 10.3390/cancers14051149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Gastric cancer is a common tumor, with a high mortality rate. The severity of gastric cancer is assessed by TNM staging. Long noncoding RNAs (lncRNAs) play a role in cancer treatment; investigating the clinical significance of novel biomarkers associated with TNM staging, such as lncRNAs, is important. In this study, we investigated the association between the expression of the lncRNA LOC441461 and gastric cancer stage. LOC441461 expression was lower in stage IV than in stages I, II, and III. The depletion of LOC441461 promoted cell proliferation, cell cycle progression, apoptosis, cell motility, and invasiveness. LOC441461 downregulation increased the epithelial-to-mesenchymal transition, as indicated by increased TRAIL signaling and decreased RUNX1 interactions. The interaction of the transcription factors RELA, IRF1, ESR1, AR, POU5F1, TRIM28, and GATA1 with LOC441461 affected the degree of the malignancy of gastric cancer by modulating gene transcription. The present study identified LOC441461 and seven transcription factors as potential biomarkers and therapeutic targets for the treatment of gastric cancer.
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Affiliation(s)
- Sang-soo Lee
- Department of Biomedical Science, CHA University, Seongnam 13488, Korea; (S.-s.L.); (J.P.)
| | - JeongMan Park
- Department of Biomedical Science, CHA University, Seongnam 13488, Korea; (S.-s.L.); (J.P.)
| | - Sooyeon Oh
- Chaum Life Center, CHA University School of Medicine, Seoul 06062, Korea;
| | - KyuBum Kwack
- Department of Biomedical Science, CHA University, Seongnam 13488, Korea; (S.-s.L.); (J.P.)
- Correspondence: ; Tel.: +82-31-881-7141
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Oh S, Chun S, Hwang S, Kim J, Cho Y, Lee J, Kwack K, Choi SW. Vitamin D and Exercise Are Major Determinants of Natural Killer Cell Activity, Which Is Age- and Gender-Specific. Front Immunol 2021; 12:594356. [PMID: 34248925 PMCID: PMC8261050 DOI: 10.3389/fimmu.2021.594356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/08/2021] [Indexed: 01/16/2023] Open
Abstract
Background The coronavirus-19 disease (COVID-19) pandemic reminds us of the importance of immune function, even in immunologically normal individuals. Multiple lifestyle factors are known to influence the immune function. Objective The aim was to investigate the association between NK cell activity (NKA) and multiple factors including vitamin D, physical exercise, age, and gender. Methods This was a cross-sectional association study using health check-up and NKA data of 2,095 subjects collected from 2016 to 2018 in a health check-up center in the Republic of Korea. NKA was measured using the interferon-γ (IFN-γ) stimulation method. The association of NKA with 25-(OH)-vitamin D (25(OH)D) and other factors was investigated by multiple logistic regression analysis. Results The average age of subjects was 48.8 ± 11.6 years (52.9% of subjects were female). Among 2,095 subjects, 1,427 had normal NKA (NKA ≥ 500 pg IFN-γ/mL), while 506 had low NKA (100 ≤ NKA < 500 pg/mL), and 162 subjects had very low NKA (NKA < 100 pg/mL). Compared to men with low 25(OH)D serum level (< 20 ng/mL), vitamin D replete men (30–39.9 ng/mL) had significantly lower risk of very low NKA (OR: 0.358; 95% CI: 0.138, 0.929; P = 0.035). In women, both low exercise (OR: 0.529; 95% CI: 0.299, 0.939; P = 0.030) and medium to high exercise (OR: 0.522; 95% CI: 0.277, 0.981; P = 0.043) decreased the risk compared to lack of physical exercise. Interestingly, in men and women older than 60 years, physical exercise significantly decreased the risk. Older-age was associated with increased risk of very low NKA in men, but not in women. Conclusion Physical exercise and vitamin D were associated with NKA in a gender- and age-dependent manner. Age was a major risk factor of very low NKA in men but not in women.
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Affiliation(s)
- Sooyeon Oh
- Chaum Life Center, CHA University School of Medicine, Seoul, South Korea.,Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
| | - Sukyung Chun
- Chaum Life Center, CHA University School of Medicine, Seoul, South Korea
| | - Sena Hwang
- Chaum Life Center, CHA University School of Medicine, Seoul, South Korea
| | - Jongseok Kim
- Chaum Life Center, CHA University School of Medicine, Seoul, South Korea
| | - Yuri Cho
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, South Korea
| | - Jooho Lee
- Department of Gastroenterology and Hepatology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, South Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
| | - Sang-Woon Choi
- Chaum Life Center, CHA University School of Medicine, Seoul, South Korea.,School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, United States
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Kim YJ, Park Y, Park YR, Kim YS, Lee HR, Lee SJ, Kim MJ, Kwack K, Ko JJ, Lee JH. Role of RGMc as a Neogenin Ligand in Follicular Development in the Ovary. Biomedicines 2021; 9:biomedicines9030280. [PMID: 33801938 PMCID: PMC7999520 DOI: 10.3390/biomedicines9030280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 11/16/2022] Open
Abstract
There is currently no cure for infertility in women with a poor ovarian response (POR). Neogenin is reported to be abundantly expressed in the ovary; however, its role in mammalian follicular development is unclear and its ligand and signaling pathway remain uncertain. We systematically investigated the role of neogenin and the ligand repulsive guidance molecule c (RGMc) during follicular development. We treated hyperstimulated mouse ovaries with RGMc and analyzed follicular development. Furthermore, we investigated clusters of up/downregulated genes in RGMc-treated ovaries using whole-transcriptome next-generation sequencing (NGS). In addition, we investigated whether expression of up/downregulated factors identified by NGS was also altered in cumulus cells (CCs) of patients with a POR. The number of oocytes was 40% higher in RGMc-treated ovaries than in control ovaries. NGS data indicated that prostaglandin D2 (PGD2) was involved in the RGMc signaling pathway during follicular development. RGMc treatment significantly elevated the PGD2 level in culture medium of CCs obtained from patients with a POR. Our results demonstrate that RGMc as neogenin ligand promotes follicular development in ovaries via the PGD2 signaling pathway. Therefore, it may be possible to use RGMc for ovarian stimulation in patients with a POR.
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Affiliation(s)
- Yu Jin Kim
- CHA Fertility Center Seoul Station, Seoul 04637, Korea; (Y.J.K.); (Y.R.P.); (Y.S.K.); (H.R.L.)
| | - YoungJoon Park
- Department of Biomedical Science, CHA University, Gyeonggi-do, Seongnam 13488, Korea;
| | - Yeo Reum Park
- CHA Fertility Center Seoul Station, Seoul 04637, Korea; (Y.J.K.); (Y.R.P.); (Y.S.K.); (H.R.L.)
| | - Young Sang Kim
- CHA Fertility Center Seoul Station, Seoul 04637, Korea; (Y.J.K.); (Y.R.P.); (Y.S.K.); (H.R.L.)
| | - Hye Ran Lee
- CHA Fertility Center Seoul Station, Seoul 04637, Korea; (Y.J.K.); (Y.R.P.); (Y.S.K.); (H.R.L.)
| | - Sang Jin Lee
- Institute of Animal Genetic Resources Affiliated with Traditional Hanwoo Co., Ltd., Boryeong 33402, Korea;
| | - Myung Joo Kim
- CHA Fertility Center Seoul Station, Seoul 04637, Korea; (Y.J.K.); (Y.R.P.); (Y.S.K.); (H.R.L.)
- Correspondence: (M.J.K.); (K.K.); (J.J.K.); (J.H.L.)
| | - KyuBum Kwack
- Department of Biomedical Science, CHA University, Gyeonggi-do, Seongnam 13488, Korea;
- Correspondence: (M.J.K.); (K.K.); (J.J.K.); (J.H.L.)
| | - Jung Jae Ko
- Department of Biomedical Science, CHA University, Gyeonggi-do, Seongnam 13488, Korea;
- Correspondence: (M.J.K.); (K.K.); (J.J.K.); (J.H.L.)
| | - Jae Ho Lee
- CHA Fertility Center Seoul Station, Seoul 04637, Korea; (Y.J.K.); (Y.R.P.); (Y.S.K.); (H.R.L.)
- Department of Biomedical Science, CHA University, Gyeonggi-do, Seongnam 13488, Korea;
- Correspondence: (M.J.K.); (K.K.); (J.J.K.); (J.H.L.)
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Ahn JW, Park Y, Kang SJ, Hwang SJ, Cho KG, Lim J, Kwack K. Correction: Ahn, J.W., et al. CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas. Cancers 2020, 12, 2543. Cancers (Basel) 2021; 13:cancers13030478. [PMID: 33514074 PMCID: PMC7866089 DOI: 10.3390/cancers13030478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Ju Won Ahn
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - YoungJoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - Su Jung Kang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - So Jung Hwang
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
| | - Kyung Gi Cho
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
| | - JaeJoon Lim
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
- Correspondence: (J.L.); (K.K.); Tel.: +82-031-780-5688 (J.L.); +82-031-725-7141 (K.K.)
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
- Correspondence: (J.L.); (K.K.); Tel.: +82-031-780-5688 (J.L.); +82-031-725-7141 (K.K.)
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Jin H, Ahn J, Park Y, Sim J, Park HS, Ryu CS, Kim NK, Kwack K. Identification of potential causal variants for premature ovarian failure by whole exome sequencing. BMC Med Genomics 2020; 13:159. [PMID: 33109206 PMCID: PMC7590468 DOI: 10.1186/s12920-020-00813-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Premature ovarian failure (POF) is a highly heterogeneous disorder that occurs in 1% of women of reproductive age. Very few causative genes and variants contributing to POF have been detected, and the disease remains incompletely understood. In this study, we used whole exome sequencing (WES) to identify potential causal variants leading to POF. METHODS WES was conducted to identify variants in 34 Korean patients with POF, alongside 10 normal controls. Detected variants were filtered using a range of characterized bioinformatics analyses, and the machine learning tools, CADD and VEST, were used to predict pathogenic variants that could cause disease. VarSome was used for a comprehensive interpretation of the variants. Potential causal variants finally screened by these analyses were confirmed using Sanger sequencing. RESULTS We identified nine potential causative variants in genes previously associated with POF in 8 of 34 (24%) Korean patients by WES variant analysis. These potentially pathogenic variants included mutations in the MCM8, MCM9, and HFM1 genes, which are involved in homologous recombination, DNA repair, and meiosis, and are established as causing POF. Using a combination of CADD and VEST, 72 coding variants were also identified in 72 genes, including ADAMTSL1 and FER1L6, which have plausible functional links to POF. CONCLUSIONS WES is a useful tool to detect genetic variants that cause POF. Accumulation and systematic management of data from a number of WES studies in specialized groups of patients with POF (family data, severe case populations) are needed to better comprehend the genetic landscape underlying POF.
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Affiliation(s)
- Haengun Jin
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - JuWon Ahn
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - YoungJoon Park
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - JeongMin Sim
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Han Sung Park
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Chang Soo Ryu
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Nam Keun Kim
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - KyuBum Kwack
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea.
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Park J, Park Y, Koh I, Kim NK, Baek KH, Yun BS, Lee KJ, Song JY, Lee E, Kwack K. Association of an APBA3 Missense Variant with Risk of Premature Ovarian Failure in the Korean Female Population. J Pers Med 2020; 10:jpm10040193. [PMID: 33114509 PMCID: PMC7720130 DOI: 10.3390/jpm10040193] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
Premature ovarian failure (POF) is a complex disease of which the etiology is influenced by numerous genetic variations. Several POF candidate genes have been reported. However, no causal genes with high odds ratio (OR) have yet been discovered. This study included 564 females of Korean ethnicity, comprising 60 patients with POF and 182 controls in the discovery set and 105 patients with POF and 217 controls in the replication set. We conducted genome-wide association analysis to search for novel candidate genes predicted to influence POF development using Axiom Precision Medicine Research Arrays and additive model logistic regression analysis. One statistically significant single nucleotide polymorphism (SNP), rs55941146, which encodes a missense alteration (Val > Gly) in the APBA3 gene, was identified with OR values for association with POF of 13.33 and 4.628 in the discovery and replication sets, respectively. No rs55941146 minor allele homozygotes were present in either cases or controls. The APBA3 protein binds FIH-1 that inhibits hypoxia inducible factor-1α (HIF-1α). HIF-1α contributes to granulosa cell proliferation, which is crucial for ovarian follicle growth, by regulating cell proliferation factors and follicle stimulating hormone-mediated autophagy. Our data demonstrate that APBA3 is a candidate novel causal gene for POF.
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Affiliation(s)
- JeongMan Park
- Institute Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Gyeonggi-do 13488, Korea; (J.P.); (Y.P.); (N.K.K.); (K.-H.B.)
| | - YoungJoon Park
- Institute Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Gyeonggi-do 13488, Korea; (J.P.); (Y.P.); (N.K.K.); (K.-H.B.)
| | - Insong Koh
- Department of Biomedical Informatics, Hanyang University, Seoul 04763, Korea;
| | - Nam Keun Kim
- Institute Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Gyeonggi-do 13488, Korea; (J.P.); (Y.P.); (N.K.K.); (K.-H.B.)
| | - Kwang-Hyun Baek
- Institute Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Gyeonggi-do 13488, Korea; (J.P.); (Y.P.); (N.K.K.); (K.-H.B.)
| | - Bo-Seong Yun
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seongnam, Gyeonggi-do 13497, Korea;
| | - Kyung Ju Lee
- Department of Obstetrics and Gynecology, Korea University Medical Center, Seoul 02841, Korea;
| | - Jae Yun Song
- Department of Preventive Medicine, College of Medicine, Korea University, Seoul 02841, Korea; (J.Y.S.); (E.L.)
| | - Eunil Lee
- Department of Preventive Medicine, College of Medicine, Korea University, Seoul 02841, Korea; (J.Y.S.); (E.L.)
| | - KyuBum Kwack
- Institute Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Gyeonggi-do 13488, Korea; (J.P.); (Y.P.); (N.K.K.); (K.-H.B.)
- Correspondence: ; Tel.: +82-31-881-7141
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Ahn JW, Park Y, Kang SJ, Hwang SJ, Cho KG, Lim J, Kwack K. CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas. Cancers (Basel) 2020; 12:cancers12092543. [PMID: 32906679 PMCID: PMC7564449 DOI: 10.3390/cancers12092543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Oligodendroglioma (OD) is a subtype of glioma occurring in the central nervous system. The 1p/19q codeletion is a prognostic marker of OD with an isocitrate dehydrogenase (IDH) mutation and is associated with a clinically favorable overall survival (OS). The long non-coding RNAs (lncRNAs) protects the mRNA from degradation by binding with the same miRNA by acting as a competitive endogenous RNA (ceRNA). Recently, although there is an increasing interest in lncRNAs on glioma studies, however, studies regarding their effects on OD and the 1p/19q codeletion remain limited. In our study, we performed in silico analyses using low-grade gliomas from datasets obtained from The Cancer Genome Atlas to investigate the effects of ceRNA with 1p/19q codeletion on ODs. We constructed 16 coding RNA–miRNA–lncRNA networks and the ceRNA network participated in ion channel activity, insulin secretion, and collagen network and extracellular matrix (ECM) changes. In conclusion, our results can provide insights into the possibility in the different tumor microenvironments and OS following 1p/19q codeletion through changes in the ceRNA network. Abstract Oligodendroglioma (OD) is a subtype of glioma occurring in the central nervous system. The 1p/19q codeletion is a prognostic marker of OD with an isocitrate dehydrogenase (IDH) mutation and is associated with a clinically favorable overall survival (OS); however, the exact underlying mechanism remains unclear. Long non-coding RNAs (lncRNAs) have recently been suggested to regulate carcinogenesis and prognosis in cancer patients. Here, we performed in silico analyses using low-grade gliomas from datasets obtained from The Cancer Genome Atlas to investigate the effects of ceRNA with 1p/19q codeletion on ODs. Thus, we selected modules of differentially expressed genes that were closely related to 1p/19q codeletion traits using weighted gene co-expression network analysis and constructed 16 coding RNA–miRNA–lncRNA networks. The ceRNA network participated in ion channel activity, insulin secretion, and collagen network and extracellular matrix (ECM) changes. In conclusion, ceRNAs with a 1p/19q codeletion can create different tumor microenvironments via potassium ion channels and ECM composition changes; furthermore, differences in OS may occur. Moreover, if extrapolated to gliomas, our results can provide insights into the consequences of identical gene expression, indicating the possibility of tracking different biological processes in different subtypes of glioma.
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Affiliation(s)
- Ju Won Ahn
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - YoungJoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - Su Jung Kang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - So Jung Hwang
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
| | - Kyung Gi Cho
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
| | - JaeJoon Lim
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
- Correspondence: (J.L.); (K.K.); Tel.: +82-031-780-5688 (J.L.); +82-031-725-7141 (K.K.)
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
- Correspondence: (J.L.); (K.K.); Tel.: +82-031-780-5688 (J.L.); +82-031-725-7141 (K.K.)
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Sim J, Ahn J, Park Y, Kim J, Kang S, Choi SH, Lee S, Hwang M, Cho J, Lim J, Oh SY, Kwack K. Transcriptomic landscape of lenalidomide‐treated NK cells: Functional enhancement by down‐regulation of CD161. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.09284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lee M, Jin H, Kim S, Ji S, Song S, Koh D, Choi J, Park J, Lee Y, Jo G, Kim J, Sim J, Ahn J, Park Y, Kwack K. Comparison of Transcriptomic Analysis between IDH1 Mutant and Wild‐type of Lower Grade Glioma. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lim J, Park Y, Kim M, Ahn J, Kwack K, Cho K. TMIC-03. UPREGULATION OF THE NLRC4 INFLAMMASOME CONTRIBUTES TO POOR PROGNOSIS IN GLIOMA PATIENTS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Inflammation in tumor microenvironments is implicated in the pathogenesis of tumor development. In particular, inflammasomes, which modulate innate immune functions, are linked to tumor growth and anticancer responses. However, the role of the NLRC4 inflammasome in gliomas remains unclear. Here, we investigated whether the upregulation of the NLRC4 inflammasome is associated with the clinical prognosis of gliomas. We analyzed the protein expression and localization of NLRC4 in glioma tissues from 11 patients by immunohistochemistry. We examined the interaction between the expression of NLRC4 and clinical prognosis via a Kaplan-Meier survival analysis. The level of NLRC4 protein was increased in brain tissues, specifically, in astrocytes, from glioma patients. NLRC4 expression was associated with a poor prognosis in glioma patients, and the upregulation of NLRC4 in astrocytomas was associated with poor survival. Furthermore, hierarchical clustering of data from the Cancer Genome Atlas dataset showed that NLRC4 was highly expressed in gliomas relative to that in a normal healthy group. Our results suggest that the upregulation of the NLRC4 inflammasome contributes to a poor prognosis for gliomas and presents a potential therapeutic target and diagnostic marker.
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Affiliation(s)
- Jaejoon Lim
- CHA University, Bundang CHA Medical Center, Seongnam, Republic of Korea
| | - Youngjoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Republic of Korea
| | - Minjun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Republic of Korea
| | - Juwon Ahn
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Republic of Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Republic of Korea
| | - Kyunggi Cho
- CHA University, Bundang CHA Medical Center, Seongnam, Republic of Korea
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Oh S, Lee JH, Kwack K, Choi SW. Natural Killer Cell Therapy: A New Treatment Paradigm for Solid Tumors. Cancers (Basel) 2019; 11:cancers11101534. [PMID: 31614472 PMCID: PMC6826624 DOI: 10.3390/cancers11101534] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/29/2019] [Accepted: 10/06/2019] [Indexed: 01/10/2023] Open
Abstract
In treatments of solid tumors, adoptive transfer of ex vivo expanded natural killer (NK) cells has dawned as a new paradigm. Compared with cytotoxic T lymphocytes, NK cells take a unique position targeting tumor cells that evade the host immune surveillance by down-regulating self-antigen presentation. Recent findings highlighted that NK cells can even target cancer stem cells. The efficacy of allogeneic NK cells has been widely investigated in the treatment of hematologic malignancies. In solid tumors, both autologous and allogeneic NK cells have demonstrated potential efficacy. In allogeneic NK cell therapy, the mismatch between the killer cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) can be harnessed to increase the antitumor activity. However, the allogeneic NK cells cause more adverse events and can be rejected by the host immune system after repeated injections. In this regard, the autologous NK cell therapy is safer. This article reviews the published results of clinical trials and discusses strategies to enhance the efficacy of the NK cell therapy. The difference in immunophenotype of the ex vivo expanded NK cells resulted from different culture methods may affect the final efficacy. Furthermore, currently available standard anticancer therapy, molecularly targeted agents, and checkpoint inhibitors may directly or indirectly enhance the efficacy of NK cell therapy. A recent study discovered that NK cell specific genetic defects are closely associated with the tumor immune microenvironment that determines clinical outcomes. This finding warrants future investigations to find the implication of NK cell specific genetic defects in cancer development and treatment, and NK cell deficiency syndrome should be revisited to enhance our understanding. Overall, it is clear that NK cell therapy is safe and promises a new paradigm for the treatment of solid tumors.
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Affiliation(s)
- Sooyeon Oh
- Chaum Life Center, CHA University School of Medicine, Seoul 06062, Korea.
- Graduate school of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Joo-Ho Lee
- Department of Gastroenterology and Hepatology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Korea.
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea.
| | - Sang-Woon Choi
- Chaum Life Center, CHA University School of Medicine, Seoul 06062, Korea.
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003, USA.
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Kim Y, Park Y, Hwang J, Kwack K. Comparative genomic analysis of the human and nematode Caenorhabditis elegans uncovers potential reproductive genes and disease associations in humans. Physiol Genomics 2018; 50:1002-1014. [DOI: 10.1152/physiolgenomics.00063.2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Reproduction is an important biological process. However, studies of human reproduction at the molecular level are limited due to the difficulty of performing in vivo studies. Hence, a mechanistic understanding of human reproduction remains still poor. Thus, it is important to use an alternative model organism for mechanistic studies of human reproduction. In this study, we used the nematode Caenorhabditis elegans as a model for studying human reproduction and identified 61 human and 535 worm reproductive genes through a combination of comparative genomic and Gene Ontology (GO) analyses. Interestingly, in terms of sex specificity, the number of male-specific genes was greater than the number of female-specific genes. Gene enrichment analysis identified biologically significant processes such as protein localization to cajal bodies/telomeres/nuclear bodies/chromosomes, helicase activity, pyrimidine biosynthesis, and determination of adult lifespan. Regarding the analysis of human reproductive diseases among the identified genes, 10 and 12 genes were identified in the human- and C. elegans-based analyses, respectively. In addition, RNA interference knockdown of a newly identified F52H2.6/DHCR24 gene increased brood size and ovulation/egg-laying rate in C. elegans. Therefore, gene identification, disease associations, and a proof-of-concept experiment using C. elegans will not only provide insights into mechanistic study of human reproduction, but also demonstrate the utility in studying human reproduction.
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Affiliation(s)
- Yongsoon Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - YoungJoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - JoonYeon Hwang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
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Kim C, Yang J, Jeong SH, Kim H, Park GH, Shin HB, Ro M, Kim KY, Park Y, Kim KP, Kwack K. Yeast-based assays for characterization of the functional effects of single nucleotide polymorphisms in human DNA repair genes. PLoS One 2018; 13:e0193823. [PMID: 29522548 PMCID: PMC5844570 DOI: 10.1371/journal.pone.0193823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/20/2018] [Indexed: 01/03/2023] Open
Abstract
DNA repair mechanisms maintain genomic integrity upon exposure to various types of DNA damage, which cause either single- or double-strand breaks in the DNA. Here, we propose a strategy for the functional study of single nucleotide polymorphisms (SNPs) in the human DNA repair genes XPD/ERCC2, RAD18, and KU70/XRCC6 and the checkpoint activation gene ATR that are essentially involved in the cell cycle and DNA damage repair. We analyzed the mutational effects of the DNA repair genes under DNA-damaging conditions, including ultraviolet irradiation and treatment with genotoxic reagents, using a Saccharomyces cerevisiae system to overcome the limitations of the human cell-based assay. We identified causal variants from selected SNPs in the present analyses. (i) R594C SNP in RAD3 (human XPD/ERCC2) caused severe reductions in the growth rate of mutant cells upon short-wavelength UV irradiation or chemical reagent treatment. (ii) The growth rates of the selected variants in RAD18, YKU70, and MEC1 were similar to those of wild-type cells on methyl methanesulfonate and hydroxyurea treated media. (iii) We also assessed the structural impact of the SNPs by analyzing differences in the structural conformation and calculating the root mean square deviation, which is a measure of the discordance of the Cα atoms between protein structures. Based on the above results, we propose that these analytical approaches serve as efficient methods for the identification of causal variants of human disease-causing genes and elucidation of yeast-cell based molecular mechanisms.
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Affiliation(s)
- Changshin Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jinmo Yang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Su-Hyun Jeong
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Hayoung Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Geun-hee Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Hwa Beom Shin
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - MyungJa Ro
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Kyoung-Yeon Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - YoungJoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Keun Pil Kim
- Department of Life Sciences, College of Natural Sciences, Chung-Ang University, Seoul, Republic of Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
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Jin LH, Kim BH, Lee JH, Lee K, Kwack K, Yim SV. Screening study for genetic polymorphisms affecting pharmacokinetics of talniflumate. Transl Clin Pharmacol 2017; 25:166-172. [PMID: 32095470 PMCID: PMC7033407 DOI: 10.12793/tcp.2017.25.4.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 11/19/2022] Open
Abstract
Talniflumate is a phthalidyl ester of niflumic acid, which has potent analgesic and anti-inflammatory effects and is widely used to treat inflammatory disorders, such as rheumatoid arthritis. To screen the possible genetic factors affecting the pharmacokinetics (PK) of talniflumate, 23 male Korean volunteers were enrolled from two separate bioequivalence studies. All subjects received 740 mg (two tablets) talniflumate in a standard 2×2 cross-over model in a randomized order. For the genetic study, PK parameters of the reference drug were used. We used Illumina Human610Quad v1.0 DNA Analysis BeadChip for whole genome single nucleotide polymorphism (SNP) analysis and whole genome genotyping data were processed by linear regression analysis for PK parameters. Whole genome analysis revealed 1498 significant SNPs (P < 0.0001) for Cmax, 65 significant SNPs (P < 0.0001) for T max, and 1491 significant SNPs (P < 0.0001) for AUC inf. For clinical pharmacological purposes, we selected SNPs from drug metabolizing enzymes and transporters, and analyzed the PK parameters of various genotypes. Two SNPs (rs11165069 from ABCA4 (p=0.00002); rs17847036 from CYP2C9 (p=0.000001)) showed significant associations with talniflumate C max. In the T max group, two SNPs (rs3787555 from CYP24A1 (p=0.00035); rs2275034 from ABCA4 (p=0.000587)) showed significant associations with talniflumate T max. In the AUC inf group, two SNPs (rs11165069 from ABCA4 (p=0.00002); rs12461006 from SLC1A6 (p=0.00008)) exhibited significant associations with talniflumate absorption. These results show that genetic factors could affect the PK parameters, and provide information that may be used in the development of personalized talniflumate therapy.
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Affiliation(s)
- Li Hua Jin
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Bo-Hyung Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Kidong Lee
- Department of BioMedical Science, College of Life Science, CHA University, SeongNam 13488, Republic of Korea
| | - KyuBum Kwack
- Department of BioMedical Science, College of Life Science, CHA University, SeongNam 13488, Republic of Korea
| | - Sung-Vin Yim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
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Park HS, Lim SM, Kim S, Kim S, Kim HR, Kwack K, Lee MG, Kim JH, Moon YW. Pilot Study of a Next-Generation Sequencing-Based Targeted Anticancer Therapy in Refractory Solid Tumors at a Korean Institution. PLoS One 2016; 11:e0154133. [PMID: 27105424 PMCID: PMC4841558 DOI: 10.1371/journal.pone.0154133] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/09/2016] [Indexed: 11/22/2022] Open
Abstract
We evaluated the preliminary efficacy and feasibility of a next-generation sequencing (NGS)-based targeted anticancer therapy in refractory solid tumors at a Korean institution. Thirty-six patients with advanced cancer underwent molecular profiling with NGS with the intent of clinical application of available matched targeted agents. Formalin-fixed paraffin-embedded (FFPE) tumors were sequenced using the Comprehensive Cancer Panel (CCP) or FoundationOne in the Clinical Laboratory Improvement Amendments-certified laboratory in the USA. Response evaluations were performed according to RECIST v1.1. Four specimens did not pass the DNA quality test and 32 specimens were successfully sequenced with CCP (n = 31) and FoundationOne (n = 1). Of the 32 sequenced patients, 10 (31.3%) were ≤40 years. Twelve patients (37.5%) had received ≥3 types of prior systemic therapies. Of 24 patients with actionable mutations, five were given genotype-matched drugs corresponding to actionable mutations: everolimus to PIK3CA mutation in parotid carcinosarcoma (partial response) and tracheal squamous cell carcinoma (stable disease; 21% reduction), sorafenib to PDGFRA mutation in auditory canal adenocarcinoma (partial response), sorafenib to BRAF mutation in microcytic adnexal carcinoma (progressive disease), and afatinib to ERBB2 mutation in esophageal adenocarcinoma (progressive disease). Nineteen of 24 patients with actionable mutations could not undergo targeted therapy based on genomic testing because of declining performance status (10/24, 41.7%), stable disease with previous treatment (5/24, 20.8%), and lack of access to targeted medication (4/24, 16.7%). NGS-based targeted therapy may be a good option in selected patients with refractory solid tumors. To pursue this strategy in Korea, lack of access to clinical-grade NGS assays and a limited number of genotype-matched targeted medications needs to be addressed and resolved.
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Affiliation(s)
- Hyung Soon Park
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Sun Min Lim
- Medical Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Sora Kim
- Severance Biomedical Science Institute and Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Sangwoo Kim
- Severance Biomedical Science Institute and Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
| | - Min Goo Lee
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Joo-Hang Kim
- Medical Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Yong Wha Moon
- Medical Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
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Yun JY, Kim BH, Lee JH, Lee K, Kwack K, Yim SV. Screening study for genetic polymorphisms affecting pharmacokinetics of pioglitazone. Transl Clin Pharmacol 2016. [DOI: 10.12793/tcp.2016.24.4.194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Ji Young Yun
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Bo-Hyung Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Kidong Lee
- Department of BioMedical Science, College of Life Science, CHA University, SeongNam 13496, Republic of Korea
| | - KyuBum Kwack
- Department of BioMedical Science, College of Life Science, CHA University, SeongNam 13496, Republic of Korea
| | - Sung-Vin Yim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
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Affiliation(s)
- Sohee Im
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Bo-Hyung Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Kidong Lee
- Department of BioMedical Science, College of Life Science, CHA University, Pangyo-ro, Bundang-gu, SeongNam 13488, Korea
| | - KyuBum Kwack
- Department of BioMedical Science, College of Life Science, CHA University, Pangyo-ro, Bundang-gu, SeongNam 13488, Korea
| | - Sung-Vin Yim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
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Lee MS, Yu M, Kim KY, Park GH, Kwack K, Kim KP. Functional Validation of Rare Human Genetic Variants Involved in Homologous Recombination Using Saccharomyces cerevisiae. PLoS One 2015; 10:e0124152. [PMID: 25938495 PMCID: PMC4418691 DOI: 10.1371/journal.pone.0124152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 03/10/2015] [Indexed: 12/02/2022] Open
Abstract
Systems for the repair of DNA double-strand breaks (DSBs) are necessary to maintain genome integrity and normal functionality of cells in all organisms. Homologous recombination (HR) plays an important role in repairing accidental and programmed DSBs in mitotic and meiotic cells, respectively. Failure to repair these DSBs causes genome instability and can induce tumorigenesis. Rad51 and Rad52 are two key proteins in homologous pairing and strand exchange during DSB-induced HR; both are highly conserved in eukaryotes. In this study, we analyzed pathogenic single nucleotide polymorphisms (SNPs) in human RAD51 and RAD52 using the Polymorphism Phenotyping (PolyPhen) and Sorting Intolerant from Tolerant (SIFT) algorithms and observed the effect of mutations in highly conserved domains of RAD51 and RAD52 on DNA damage repair in a Saccharomyces cerevisiae-based system. We identified a number of rad51 and rad52 alleles that exhibited severe DNA repair defects. The functionally inactive SNPs were located near ATPase active site of Rad51 and the DNA binding domain of Rad52. The rad51-F317I, rad52-R52W, and rad52-G107C mutations conferred hypersensitivity to methyl methane sulfonate (MMS)-induced DNA damage and were defective in HR-mediated DSB repair. Our study provides a new approach for detecting functional and loss-of-function genetic polymorphisms and for identifying causal variants in human DNA repair genes that contribute to the initiation or progression of cancer.
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Affiliation(s)
- Min-Soo Lee
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Mi Yu
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Kyoung-Yeon Kim
- Department of Biomedical Science, CHA University, Seongnam, Korea
| | - Geun-Hee Park
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - KyuBum Kwack
- Department of Biomedical Science, CHA University, Seongnam, Korea
- * E-mail: (KPK); (KBK)
| | - Keun P. Kim
- Department of Life Science, Chung-Ang University, Seoul, Korea
- * E-mail: (KPK); (KBK)
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Shin C, Kwack K, Cho NH, Kim SH, Baik I. Sex-specific differences in the association of a common aldehyde dehydrogenase 2 gene polymorphism and alcohol consumption with stroke risk in a Korean population: a prospective cohort study. Nutr Res Pract 2015; 9:79-86. [PMID: 25671072 PMCID: PMC4317484 DOI: 10.4162/nrp.2015.9.1.79] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND/OBJECTIVES It is well-known that alcohol consumption is associated with stroke risk as well as with aldehyde dehydrogenase 2 gene (ALDH2) polymorphisms. However, it is unclear whether ALDH2 polymorphisms are associated with stroke risk independent of alcohol consumption and whether such association is modified by sex. We evaluated sex-specific associations of a common ALDH2 polymorphism and alcohol consumption with stroke risk in a Korean population. SUBJECTS/METHODS We conducted a prospective cohort study involving 8,465 men and women, aged 40-69 years and free of stroke between June, 2001 and January, 2003, and followed for the development of stroke. We identified new cases of stroke, which were self-reported or ascertained from vital registration data. Based on genome-wide association data, we selected a single-nucleotide polymorphism (rs2074356), which shows high linkage disequilibrium with the functional polymorphism of ALDH2. We conducted Cox proportional hazards regression analysis considering potential risk factors collected from a baseline questionnaire. RESULTS Over the median follow-up of 8 years, 121 cases of stroke were identified. Carrying the wild-type allele of the ALDH2 polymorphism increased stroke risk among men. The multivariate hazard ratio [95% confidence interval] of stroke was 2.02 [1.03-3.99] for the wild-type allele compared with the mutant alleles, but the association was attenuated after controlling for alcohol consumption. Combinations of the wild-type allele and other risk factors of stroke, such as old age, diabetes mellitus, and habitual snoring, synergistically increased the risk among men. Among women, however, the ALDH2 polymorphism was not associated with stroke risk. CONCLUSIONS The prospective cohort study showed a significant association between a common ALDH2 polymorphism and stroke risk in Korean men, but not in Korean women, and also demonstrated that men with genetic disadvantages gain more risk when having risk factors of stroke. Thus, these men may need to make more concerted efforts to control modifiable risk factors of stroke.
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Affiliation(s)
- Chol Shin
- Department of Internal Medicine, Korea University Ansan Hospital, Ansan 425-707, Korea. ; Institute of Human Genomic Study, Korea University Ansan Hospital, Ansan 425-707, Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 463-712, Korea
| | - Nam H Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon 443-380, Korea
| | - Seong Hwan Kim
- Department of Internal Medicine, Korea University Ansan Hospital, Ansan 425-707, Korea
| | - Inkyung Baik
- Department of Foods and Nutrition, College of Natural Sciences, Kookmin University, 77 Jeongneung-ro Seongbuk-gu Seoul 136-702, Korea
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Abstract
Expression levels of monoamine oxidase A (MAOA), the enzyme that related to monoamine neurotransmitters metabolism such as serotonin, are related to schizophrenia and autism spectrum disorder. Forkhead box protein P2 (FOXP2), a transcription factor, is associated with abnormal language development and is expressed in several areas of the central nervous system in response to serotonin. For this reason, we undertook interaction analysis between MAOA and FOXP2 in autism spectrum disorder, including testing the verbal communication score of the childhood autism rating scale. In interaction analysis, the FOXP2-TCGC (rs12531289-rs1350135-rs10230087-rs2061183) diplotype and MAOA-TCG (rs6323-rs1801291-rs3027407) haplotype were significantly associated with autism spectrum disorder in males. However, when the interaction term was omitted, neither MAOA nor FOXP2 was associated with autism spectrum disorder or verbal communication. These results indicate that language and speech ability is affected by an interaction between FOXP2 and MAOA, but not by either gene separately.
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Affiliation(s)
- YoungJoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
| | - SeongSik Won
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
| | - Min Nam
- Seoul Metropolitan Children's Hospital, Heolleungno, Seocho-gu, Seoul, Korea
| | - Joo-Ho Chung
- Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
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Pyun JA, Kim S, Kwack K. Interaction between thyroglobulin and ADAMTS16 in premature ovarian failure. Clin Exp Reprod Med 2014; 41:120-4. [PMID: 25309856 PMCID: PMC4192452 DOI: 10.5653/cerm.2014.41.3.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/29/2014] [Accepted: 09/06/2014] [Indexed: 11/16/2022] Open
Abstract
Objective The aim of the present study was to examine whether interactions between polymorphisms in the thyroglobulin and ADAM metallopeptidase with thrombospondin type 1 motif, 16 (ADAMTS16) genes are associated with the development of premature ovarian failure (POF). Methods A total of 75 patients with POF and 196 controls were involved in this study. We used a GoldenGate assay to genotype single nucleotide polymorphisms (SNPs). Logistic regression analysis was performed to identify POF-associated polymorphisms and synergistic interactions between polymorphisms in the thyroglobulin and ADAMTS16 genes. Results Single gene analyses using logistic regression analysis showed no significant association between polymorphisms in the two genes and POF. In the results from interaction analyses, we found seven synergistic interactions between the polymorphisms in thyroglobulin and ADAMTS16, although there was no combination showing p-values lower than the significant threshold using the Bonferroni correction. When the AG genotype was present at the rs853326 missense SNP, the A and G alleles at the tagging SNPs rs16875268 and rs13168665 showed significant interactions (odds ratios=5.318 and 16.2 respectively; 95% confidence intervals, 1.64-17.28 and 2.08-126.4; p=0.0054 and 0.0079). Conclusion Synergistic interactions between polymorphisms in the thyroglobulin and ADAMTS16 genes were associated with an increased risk of POF development in Korean women.
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Affiliation(s)
- Jung-A Pyun
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
| | - Sunshin Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
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Park J, Ro M, Pyun JA, Nam M, Bang HJ, Yang JW, Choi KS, Kim SK, Chung JH, Kwack K. MTHFR 1298A>C is a risk factor for autism spectrum disorder in the Korean population. Psychiatry Res 2014; 215:258-9. [PMID: 24295761 DOI: 10.1016/j.psychres.2013.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/07/2013] [Accepted: 11/09/2013] [Indexed: 11/17/2022]
Affiliation(s)
- JungWon Park
- Department of Biomedical Science, College of Life Science, CHA University, 222 Yatapdong, Bundanggu, Seongnamsi, Gyeonggido 463-836, Republic of Korea
| | - Myungja Ro
- Department of Biomedical Science, College of Life Science, CHA University, 222 Yatapdong, Bundanggu, Seongnamsi, Gyeonggido 463-836, Republic of Korea
| | - Jung-A Pyun
- Department of Biomedical Science, College of Life Science, CHA University, 222 Yatapdong, Bundanggu, Seongnamsi, Gyeonggido 463-836, Republic of Korea
| | - Min Nam
- Department of Psychiatry, Seoul Metropolitan Children's Hospital, 260 Heolleungno, Seocho-gu, Seoul, Republic of Korea
| | - Hee Jung Bang
- Department of Psychology, College of Social Science, Ewha Womans University, Seoul, Republic of Korea
| | - Jae Won Yang
- Department of Psychiatry, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Republic of Korea
| | - Kyung-Sik Choi
- Department of Elementary Special Education, College of Social Science, Joongbu University, Chungnam, Republic of Korea
| | - Su Kang Kim
- Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Joo-Ho Chung
- Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, 222 Yatapdong, Bundanggu, Seongnamsi, Gyeonggido 463-836, Republic of Korea.
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25
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Abstract
STUDY QUESTION Do single nucleotide polymorphisms (SNPs) or synergistic interactions between SNPs and diplotypes within the insulin-like growth factor 2 receptor (IGF2R) and ADAM metallopeptidase with thrombospondin type 1 motif, 19 (ADAMTS19), contribute to premature ovarian failure (POF)? SUMMARY ANSWER Synergistic interactions were detected between SNPs, including a non-synonymous SNP, and diplotypes within IGF2R and ADAMTS19 which may contribute to POF; however, there was no correlation with POF in a single SNP model after Bonferroni correction. WHAT IS KNOWN ALREADY IGF2R regulates free IGF2 level, which is involved in steroidogenesis in bovine granulosa cells. ADAMTS19 expression is higher in the murine embryonic ovary than in the embryonic testis during sexual differentiation, and an ADAMTS19 SNP (rs246246) showed a possible association with POF in a genome-wide association study in Caucasian women. STUDY DESIGN, SIZE, DURATION This study analyzed interactions between SNPs and diplotypes within IGF2R and ADAMTS19 as well as SNPs within the two genes. In Stage I, a total of 120 patients with POF and 152 female controls were recruited. All patients were diagnosed with POF at the CHA hospital in Seoul, Korea, and were recruited between 1994 and 2004. The 152 controls were recruited from Chungju, Korea, as part of another study that was conducted from April 2002 to March 2004. For Stage II, we obtained genotype data for an additional 1641 female controls, recruited in Ansung and Ansan from 2001 to 2008, from the Korean Genome Epidemiology Study (KoGES). PARTICIPANTS/MATERIALS, SETTING, METHODS In Stage I, the GoldenGate assay with VeraCode technology was used to genotype SNPs in IGF2R and ADAMTS19. In Stage II, we obtained genotype data for IGF2R and ADAMTS19 using Affymetrix Genome-Wide Human SNP array 5.0 and imputed data by the IMPUTE program from the KoGES. To identify POF-associated SNPs, logistic regression analysis in an additive model was performed using the PLINK tool. Synergistic interactions between SNPs and diplotypes within IGF2R and ADAMTS19 were analyzed by logistic regression analysis in three alternative models. MAIN RESULTS AND THE ROLE OF CHANCE In Stage I, 13 combinations of SNPs showed significant synergistic interactions after Bonferroni correction [the strongest association had odds ratio (OR) = 5.77, 95% confidence interval (CI): 2.26-14.75, P = 0.00025]. In Stage II and combined analyses, two and four combinations, respectively, of the significant results in Stage I showed significant synergistic interactions after Bonferroni correction. For interactions between diplotypes in block 2 of IGF2R and block 3 of ADAMTS19 in Stage I, we found 17 synergistic interactions with P < 0.0001, but there was no significant interaction after Bonferroni correction. In Stage II and combined analyses, we found that three and seven combinations in the same blocks, respectively, showed significant synergistic interactions after Bonferroni correction (strongest association: OR = 4.12, 95% CI: 2.22-7.62, P = 6.74E-06). LIMITATIONS, REASONS FOR CAUTION The sample size for patients with POF in this study was small but, compared with recent reports describing associations between SNPs and POF and considering the low prevalence of POF (1%), the sample size is considered to be reasonable. These results should be confirmed in large-scale studies involving different ethnic groups. WIDER IMPLICATIONS OF THE FINDINGS Our results may ultimately provide predictive markers for women at a high risk of POF. STUDY FUNDING/COMPETING INTERESTS This study was supported by grants from Basic Science Research Program through the National Research Foundation of Korea (NRF), which is funded by the Ministry of Education (2009-0093821, 2011-0010637). There are no competing interests.
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Affiliation(s)
- J-A Pyun
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 463-836, Republic of Korea
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26
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Abstract
Background It was previously reported that an association analysis based on haplotype clusters increased power over single-locus tests, and that another association test based on diplotype trend regression analysis outperformed other, more common association approaches. We suggest a novel algorithm to combine haplotype cluster- and diplotype-based analyses. Methods Diplotyper combines a novel algorithm designed to cluster haplotypes of interest from a given set of haplotypes with two existing tools: Haploview, for analyses of linkage disequilibrium blocks and haplotypes, and PLINK, to generate all possible diplotypes from given genotypes of samples and calculate linear or logistic regression. In addition, procedures for generating all possible diplotypes from the haplotype clusters and transforming these diplotypes into PLINK formats were implemented. Results Diplotyper is a fully automated tool for performing association analysis based on diplotypes in a population. Diplotyper was tested through association analysis of hepatic lipase (LIPC) gene polymorphisms or diplotypes and levels of high-density lipoprotein (HDL) cholesterol. Conclusions Diplotyper is useful for identifying more precise and distinct signals over single-locus tests.
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Affiliation(s)
- Sunshin Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
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27
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Ro M, Kim S, Pyun JA, Shin C, Cho NH, Lee JY, Koh I, Kwack K. Association between arachidonate 5-lipoxygenase-activating protein (ALOX5AP) and lung function in a Korean population. Scand J Immunol 2012; 76:151-7. [PMID: 22537113 DOI: 10.1111/j.1365-3083.2012.02712.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Arachidonate 5-lipoxygenase-activating protein (ALOX5AP) plays a role in the 5-lipoxygenase (LO) pathway, which includes the LTC(4), LTD(4), LTE(4) and LTB(4). These leukotrienes are known causative factors of asthma, allergy, atopy and cardiovascular diseases. ALOX5AP lacks enzyme activity and acts by helping 5-LO function. In this study, healthy and general subjects who live in rural and urban areas of Korea were tested for the association of ALOX5AP polymorphisms with lung function. Lung function was also estimated by calculating the predicted values for forced expiratory volume in one second (FEV(1) _%PRED) and the proportion of the forced vital capacity exhaled in the first second (FEV(1) /FVC_PRED). The linear regression was adjusted for residence area, gender, age, height and smoking status. The analysis revealed associations between FEV(1) and the single-nucleotide polymorphism (SNP) rs9506352 and the haplotype TCAC (permuted P-value < 0.05). The linkage disequilibrium block that included the significant SNPs overlapped with SNPs that were revealed previously to associate with myocardial infarction and asthma and to affect lung function. This study is the first to demonstrate the association between lung function and ALOX5AP polymorphisms in a healthy and general population.
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Affiliation(s)
- M Ro
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
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28
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Ro M, Park J, Nam M, Bang HJ, Yang J, Choi KS, Kim SK, Chung JH, Kwack K. Association between peroxisomal biogenesis factor 7 and autism spectrum disorders in a Korean population. J Child Neurol 2012; 27:1270-5. [PMID: 22378669 DOI: 10.1177/0883073811435507] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Autism spectrum disorder is a neurodevelopmental disorder characterized by deficits in social communication, impaired reciprocal social interaction, and repetitive patterns of behaviors or interests. Although the cause of autism spectrum disorder remains elusive, the present study identified peroxisomal biogenesis factor 7 (PEX7) as a gene associated with autism spectrum disorder, and this association was examined in a Korean population. PEX7 encodes a cytosolic receptor for peroxisome targeting signal 2 of peroxisomal matrix enzymes that are targeted to and translocated into the peroxisome. PEX7 defects are associated with rhizomelic chondrodysplasia punctata type 1 and Refsum disease. Mutations in PEX7 are related to a variety of mild to severe clinical symptoms, including mental retardation. The analysis of 9 intronic single nucleotide polymorphisms in 214 patients with autism spectrum disorder and 258 controls revealed the association of 2 single nucleotide polymorphisms and 1 haplotype with autism spectrum disorder (P < .05).
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Affiliation(s)
- MyungJa Ro
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea
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29
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Ahn DH, Rah H, Choi YK, Jeon YJ, Min KT, Kwack K, Hong SP, Hwang SG, Kim NK. Association of the miR-146aC>G, miR-149T>C, miR-196a2T>C, and miR-499A>G polymorphisms with gastric cancer risk and survival in the Korean population. Mol Carcinog 2012; 52 Suppl 1:E39-51. [PMID: 23001871 DOI: 10.1002/mc.21962] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 08/06/2012] [Accepted: 08/23/2012] [Indexed: 12/18/2022]
Abstract
We investigated whether four common microRNA polymorphisms (miR-146aC>G [rs2910164], miR-149T>C [rs2292832], miR-196a2T>C [rs11614913], and miR-499A>G [rs3746444]) are associated with the susceptibility and prognosis of gastric cancer in the Korean population. The four microRNA single-nucleotide polymorphisms (SNPs) were identified in a case-control study (461 patients; 447 controls) by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis in the Korean population. When patients were stratified into diffuse and intestinal-type gastric cancer groups, subjects with the miR-499AG and AG + GG genotypes had reduced adjusted odds ratios (AORs) for diffuse-type gastric cancer (AOR = 0.54 with 95% confidence interval [CI] = 0.31-0.97; AOR = 0.57 with 95% CI = 0.33-0.97). In the stratified analyses for gastric cancer risk, the miR-146aGG and CG + GG genotypes were associated with increased risk of gastric cancers among the non-smokers, whereas the miR-149TC and TC + CC genotypes showed lower risk of gastric cancer in males. The miR-196a2CC genotype was associated with elevated gastric cancer risk among females. For gastric cancer prognosis, intestinal-type gastric cancer patients with miR-146aCG + GG genotypes had significantly higher survival rates (log-rank P = 0.030) than patients with the CC genotype, and patients with the miR-499AA genotype had significantly increased survival rates compared to patients with the AG + GG genotypes (log-rank P = 0.013). When miR-146aCG + GG and miR-499AA genotypes were combined, the survival rate of intestinal-type gastric cancer patients was elevated (log-rank P < 0.001). No association was found between gastric or diffuse-type cancer prognosis and other miRNAs. Our data demonstrate that specific miRNA SNPs are associated with gastric cancer susceptibility (miR-499A>G) and prognosis (miR-146aC>G and miR-499A>G) in the Korean population depending on gastric cancer type.
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Affiliation(s)
- Dae Ho Ahn
- Department of Surgery, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
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30
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Abstract
Granulysin (GNLY) is found in cytotoxic granules of cytolytic T lymphocytes and natural killer (NK) cells, which are critical for hepatitis B virus (HBV) clearance. GNLY cytotoxicity plays an important role in the defense against viruses or intracellular bacteria. We hypothesized that genetic variation in the GNLY gene could affect the resistance of hosts against HBV infection. We compared the distribution frequencies of GNLY polymorphisms between an HBV-induced chronic liver disease (CLD) group and a spontaneous recovery (SR) control group to determine whether GNLY polymorphisms play a role in HBV clearance. A total of 117 patients in the SR group and 230 patients in the CLD group were enrolled. Samples derived from complex infections, including hepatitis C and human immunodeficiency virus, and those associated with insufficient clinical information (10 samples in SR and 24 samples in CLD) were excluded from the study. The final analysis included 107 SR and 206 CLD samples. DNA was extracted from peripheral blood, and GNLY genotypes were determined by the GoldenGate(®) method. The genotype distribution of the single-nucleotide polymorphisms (SNPs) rs2886767 (C>T), rs1561285 (G>C), and rs11127 (T>C) were significantly different between the SR and CLD groups in a recessive model (p<0.015). These three SNPs were in a complete linkage disequilibrium (LD) block. Diplotype distributions of haplotype (HT) 1 (C-G-T) and HT2 (T-C-C) were significantly different between the SR and CLD groups in a recessive model (p=0.025) and a dominant model (p=0.008). All p-values remained significant after multiple comparisons. GNLY polymorphism genotypes and diplotypes were associated with the chronicity of HBV. These data suggested that genetic variation of GNLY may be an important factor in HBV clearance through the CD8+ T or NK cell-mediated removal of HBV-infected cells from the host.
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Affiliation(s)
- Geun-Hee Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Republic of Korea
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31
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Pyun JA, Kim S, Cha DH, Ko JJ, Kwack K. Epistasis between the HSD17B4 and TG polymorphisms is associated with premature ovarian failure. Fertil Steril 2012; 97:968-73. [PMID: 22265031 DOI: 10.1016/j.fertnstert.2011.12.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 12/19/2011] [Accepted: 12/21/2011] [Indexed: 01/22/2023]
Abstract
OBJECTIVE To identify whether epistasis between TG and HSD17B4 and whether polymorphisms in HSD17B4 are associated with premature ovarian failure (POF). DESIGN Case-control genetic association study. SETTING Research laboratory of a university. PATIENT(S) Female patients with POF (98) and controls (218) of Korean ethnicity participated in this study. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Genotype distribution, haplotype (HT) inference, and gene-gene interaction. RESULT(S) Distribution of one haplotype (A-G-A-A-G-G) on the HSD17B4 gene was significantly different between the POF group and the control group in a dominant model. In addition, the combined effect of the single nucleotide polymorphisms (SNPs) HSD17B4 rs28943592 and TG rs2076740 was significantly associated with POF (odds ratio = 7.74, 95% confidence interval = 1.67-35.94), although a significant association was not observed in the single SNP model. CONCLUSION(S) A haplotype in the HSD17B4 gene was identified that was significantly associated with resistance to POF. In addition, epistasis between two missense SNPs (rs28943592, rs2076740) located in HSD17B4 and TG was significantly associated with susceptibility to POF.
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Affiliation(s)
- Jung-A Pyun
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
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32
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Han W, Kim KY, Yang SJ, Noh DY, Kang D, Kwack K. SNP-SNP interactions between DNA repair genes were associated with breast cancer risk in a Korean population. Cancer 2011; 118:594-602. [PMID: 21751184 DOI: 10.1002/cncr.26220] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 03/23/2011] [Accepted: 04/01/2011] [Indexed: 01/23/2023]
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) in nucleotide excision repair (NER) pathway genes may modulate DNA repair capacity and increase susceptibility to breast cancer (BC). A case-control study was conducted by evaluating genes involved in DNA repair to identify polymorphisms associated with BC. METHODS The 384 SNPs of 38 candidate genes were genotyped using the Illumina GoldenGate method. Genotypes were determined in a case-control study that consisted of 346 BC patients and 361 controls. Odds ratios and 95% confidence intervals were computed using logistic regression models. Multiple logistic regression models adjusted for age, family history of BC, and body mass index were used. RESULTS Gene-gene interaction analysis among the DNA repair pathway genes showed significant effects on BC risk. ERCC2 rs50872 (TC genotype) in combination with XPA rs2808668 (TC genotype) and rs1800975 (AG genotype) was strongly associated with an increased risk of BC (P = .0004 and .0002, P(Bonferroni) = .023 and .014, respectively). Moreover, the T-G (including rs2808668 and rs1800975) haplotype in XPA combined with the ERCC2 T allele in rs50872 carriers was also associated with additive risk effect of BC (odds ratios: 2.58, 2.62, and 3.49, respectively). CONCLUSION Genetic variation in DNA repair genes involved in NER mechanisms increased the risk of BC development. These results suggested that a stronger combined effect of SNPs via gene-gene interaction may help to predict BC risk.
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Affiliation(s)
- Wonshik Han
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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Kim S, Pyun JA, Cha DH, Ko JJ, Kwack K. Epistasis between FSHR and CYP19A1 polymorphisms is associated with premature ovarian failure. Fertil Steril 2011; 95:2585-8. [DOI: 10.1016/j.fertnstert.2010.12.042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/20/2010] [Accepted: 12/20/2010] [Indexed: 01/14/2023]
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Kim J, Pyun JA, Cho SW, Lee K, Kwack K. Lymph node metastasis of gastric cancer is associated with the interaction between poly (ADP-ribose) polymerase 1 and matrix metallopeptidase 2. DNA Cell Biol 2011; 30:1011-7. [PMID: 21612407 DOI: 10.1089/dna.2011.1250] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1), which plays a critical role in the base excision DNA repair mechanism, and matrix metallopeptidase 2 (MMP2), a member of the matrix metalloprotease family, are involved in tumor formation and metastasis, respectively. In the present study, the possible association of single nucleotide polymorphisms (SNPs) and gene-gene interaction between PARP1 and MMP2 with the increased incidence of gastric cancer (GC) development and lymph node metastasis (LNM) was investigated in a Korean population. Samples were obtained from 326 patients with chronic gastritis and 153 patients with GC and genotyped using the GoldenGate® method. The PARP1 rs1136410 genotype showed a significant association with the frequency of LNM of GC (odds ratio [OR] = 2.19, p = 0.02), LNM stage (p = 0.035), and tumor invasion (p = 0.035). The allele frequency of MMP2 rs243865 was not associated with the development of GC or with the development of LNM of GC. Epistasis between the PARP1 SNP and the MMP2 SNP was associated with the development of LNM of GC. The combination of the MMP2 rs243865 CC genotype and the PARP1 rs1136410 CC or CC+CT genotypes showed a high risk of LNM of GC (OR = 2.47, p = 0.01; OR = 2.28, p = 0.01, respectively). In summary, PARP1 is associated with the risk of LNM of GC and the stage of LNM and tumor invasion. Epistasis between PARP1 rs1136410 and MMP2 rs243865 increased the risk of LNM of GC.
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Affiliation(s)
- JiHye Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Republic of Korea
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35
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Pyun JA, Kang H, Kim J, Cha DH, Kwack K. Thyroglobulin gene is associated with premature ovarian failure. Fertil Steril 2010; 95:397-400. [PMID: 20864102 DOI: 10.1016/j.fertnstert.2010.08.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 07/05/2010] [Accepted: 08/18/2010] [Indexed: 02/06/2023]
Abstract
Variants of the thyroglobulin gene were significantly associated with premature ovarian failure in a Korean population. Three single nucleotide polymorphisms and one haplotype were found to be associated with a significant increase in the risk for premature ovarian failure.
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Affiliation(s)
- Jung-A Pyun
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Republic of Korea
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36
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Jeon HJ, Choi JH, Jung IH, Park JG, Lee MR, Lee MN, Kim B, Yoo JY, Jeong SJ, Kim DY, Park JE, Park HY, Kwack K, Choi BK, Kwon BS, Oh GT. CD137 (4–1BB) Deficiency Reduces Atherosclerosis in Hyperlipidemic Mice. Circulation 2010; 121:1124-33. [DOI: 10.1161/circulationaha.109.882704] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
The tumor necrosis factor receptor superfamily, which includes CD40, LIGHT, and OX40, plays important roles in atherosclerosis. CD137 (4-1BB), a member of the tumor necrosis factor receptor superfamily, has been reported to be expressed in human atherosclerotic lesions. However, limited information is available on the precise role of CD137 in atherosclerosis and the effects of blocking CD137/CD137 ligand signaling on lesion formation.
Methods and Results—
We generated CD137-deficient apolipoprotein E–knockout mice (
ApoE
−/−
CD137
−/−
) and LDL-receptor–knockout mice (
Ldlr
−/−
CD137
−/−
) to investigate the role of CD137 in atherogenesis. The deficiency of CD137 induced a reduction in atherosclerotic plaque lesions in both atherosclerosis mouse models, which was attributed to the downregulation of cytokines such as interferon-γ, monocyte chemoattractant protein-1, and tumor necrosis factor-α. CD137 signaling promoted the production of inflammatory molecules, including monocyte chemoattractant protein-1, interleukin-6, vascular cell adhesion molecule-1, and intercellular adhesion molecule-1, in endothelial cells. Stimulation of CD137 ligand signaling activated monocytes/macrophages and augmented the production of proinflammatory cytokines in atherosclerotic vessels.
Conclusions—
CD137/CD137 ligand signaling plays multiple roles in the progression of atherosclerosis, and thus, blockade of this pathway is a promising therapeutic target for the disease.
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Affiliation(s)
- Hyung Jun Jeon
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Jae-Hoon Choi
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - In-Hyuk Jung
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Jong-Gil Park
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Mi-Ran Lee
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Mi-Ni Lee
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Bora Kim
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Ji-Young Yoo
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Se-Jin Jeong
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Dae-Yong Kim
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Jeong Euy Park
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Hyun-Young Park
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - KyuBum Kwack
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Beom Kyu Choi
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Byoung S. Kwon
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
| | - Goo Taeg Oh
- From the Division of Life and Pharmaceutical Science (H.J.J., J.-H.C., I.-H.J., J.-G.P., M.-R.L., M.-N.L., B.K., J.-Y.Y., S.-J.J., G.T.O.), Ewha Womans University, Seoul, Korea; Laboratory of Cellular Physiology and Immunology (J.-H.C.), The Rockefeller University, New York, NY; Departments of Veterinary Pathology (I.-H.J., D.-Y.K.) and Biochemistry (J.-G.P.), College of Veterinary Medicine, Seoul National University, Seoul, Korea; Samsung Medical Center (J.E.P.), Sungkyungkwan University School of
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Yi CH, Lee SK, Cheong JY, Cho SW, Kwack K. Single nucleotide polymorphisms and the linkage disequilibrium at the LDL receptor gene in Koreans. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0365-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ahn HJ, Lee WJ, Kwack K, Kwon YD. FGF2 stimulates the proliferation of human mesenchymal stem cells through the transient activation of JNK signaling. FEBS Lett 2009; 583:2922-6. [DOI: 10.1016/j.febslet.2009.07.056] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 07/27/2009] [Accepted: 07/30/2009] [Indexed: 02/08/2023]
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Abstract
Human leukocyte antigen (HLA)-G is an immune modulator that inhibits the functions of cytotoxic T lymphocytes and natural killer cells. Immune modulation of HLA-G plays an important role in the prevention of fetal rejection. We found a novel substitution at nucleotide position 195 (G-T), codon 41 (Ala), in exon 2 of HLA-G. This substitution does not change the amino acid (GCG-->GCT).
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Affiliation(s)
- J-G Kim
- School of Biological Science and Technology, Pochon CHA University, Sungnam, Korea
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Kwack K, Pyun JA, Kim KY, Lee SK, Oh AR, Kim MH, Kang H, Won S, Lee KJ, Cho SW, Kim JG. A haplotype of the HLA-DRA gene promoter region was associated with susceptibility to gastric cancer in a Korean population (88.1). The Journal of Immunology 2009. [DOI: 10.4049/jimmunol.182.supp.88.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Gastric cancer, the second leading cause of mortality by cancer in the world, shows particularly high incidence and mortality in Korea. To screen the causative genes or loci that control the transition from gastritis to gastric cancer, whole genome approach was applied using Illumina's 510S SNP chip technology. One of the interesting associated genes, HLA-DRA1 was investigated. HLA-DRA gene is very limited in polymorphism compared to the highly polymorphic HLA-DRB1, 3, 4, and 5 loci. HLA-DR alpha protein has roles as a non-polymorphic partner for HLA DR-beta for transport and surface expression as a functional HLA-class II protein. The expression level of the HLA-DR alpha/beta on the cell surface may be controlled by the transcriptional level of the HLA-DR alpha. To test this hypothesis, we tested susceptibility to gastric cancer compared to gastritis in terms of SNPs, haplotypes, and diplotypes covering the HLA-DRA promoter region. To find causative SNP(s), the whole linkage disequilibrium (LD) region of the significant haplotype using more than 20 Koreans were sequenced. We found that a diplotype composed of significantly associated SNPs and a haplotype was associated with susceptibility to gastric cancer significantly. These data suggested that the expression level of HLA-DRA might control the HLA-DR protein levels on the cell surface.
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Affiliation(s)
- KyuBum Kwack
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
| | - Jung-A Pyun
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
| | - Kyoung-Yeon Kim
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
| | - Seung Ku Lee
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
| | - Ah Reum Oh
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
| | - Min-Ho Kim
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
| | - HyunJun Kang
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
| | - SungSik Won
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
| | - Kwang-Jae Lee
- 2Gastroenterology, Ajou University School of Medicine, Suwon, Korea, Republic of
| | - Sung Won Cho
- 2Gastroenterology, Ajou University School of Medicine, Suwon, Korea, Republic of
| | - Jeong-Geun Kim
- 1School of Biological Science and Technology, Pochon CHA Univ., Seungnam, Korea, Republic of
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Kang H, Lee SK, Kim MH, Choi H, Lee SH, Kwack K. Acyl-CoA synthetase long-chain family member 6 is associated with premature ovarian failure. Fertil Steril 2009; 91:1339-43. [DOI: 10.1016/j.fertnstert.2008.03.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 03/13/2008] [Accepted: 03/13/2008] [Indexed: 10/21/2022]
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Lee SK, Yi CH, Kim MH, Cheong JY, Cho SW, Yang SJ, Kwack K. Genetic association between functional haplotype of collagen type III alpha 1 and chronic hepatitis B and cirrhosis in Koreans. ACTA ACUST UNITED AC 2008; 72:539-48. [PMID: 19000145 DOI: 10.1111/j.1399-0039.2008.01144.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Collagen type III alpha 1 (COL3A1) is one of the extracelluar matrix (ECM) proteins. The expression of COL3A1 is closely related to chronic liver diseases. In this study, we investigated whether single nucleotide polymorphisms (SNPs) of COL3A1 confer genetic susceptibility to patients with hepatitis B virus-infected liver diseases including chronic hepatitis B (CH), liver cirrhosis (CIR), and hepatocellular carcinoma (HCC). A total of 399 Korean (KOR) people, 111 patients with CH, 95 patients with CIR, 86 patients with HCC, and 107 spontaneously recovery, were genotyped for 16 SNPs of the COL3A1 gene. The 'A' allele of rs3106796 was highly associated with the CH [odds ratio (OR) = 1.62, P = 0.01], CIR (OR = 1.67, P = 0.01), and HCC (OR = 1.59, P = 0.03). There were six polymorphic SNPs that could be divided into two linkage disequilibrium (LD) blocks. The haplotype pattern of the KOR control seems to be similar to the patterns displayed in the Japanese, Chinese, and Caucasian populations sampled in the International HapMap project. Haplotype 3 (A-G-A) of the LD block 2 was significantly associated with CH (OR = 2.23, P = 0.02), CIR (OR = 2.24, P = 0.03), and HCC (OR = 2.27, P = 0.03). Moreover, diplotype analysis showed that they had increased relative risk for CH and CIR in the two diplotypes, dt3 (A-G-A/G-G-A; OR = 4.05, P = 0.01) and dt6 (A-A-A/A-G-A; OR = 7.42, P = 0.01 and OR = 5.84, P = 0.05) against dt1 (G-G-A/G-G-A), the most common diplotype in both KOR groups. In vitro reporter gene assays showed that the constructs containing the 'G' allele of rs3106796 appear to exert lower transcriptional activity of COL3A1 than the 'A' allele, depending on the promoter types.
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Affiliation(s)
- S K Lee
- Medical Genomics Laboratory, Graduate School of Life Science and Biotechnology, Pochon CHA University, Seongnam, Korea
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Kim HJ, Kim MH, Choe BK, Kim JW, Park JK, Cho AR, Bae H, Shin DH, Yim SV, Kwack K, Kwon YK, Chung JH. Genetic association between 5'-upstream single-nucleotide polymorphisms of PDGFRB and schizophrenia in a Korean population. Schizophr Res 2008; 103:201-8. [PMID: 18541413 DOI: 10.1016/j.schres.2008.04.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 04/15/2008] [Accepted: 04/20/2008] [Indexed: 10/22/2022]
Abstract
PDGFRB is located on chromosome 5q31-q32, a chromosomal region identified by linkage analyses to contain a susceptibility gene for schizophrenia (SCZ). Recent research has focused on the role of the N-methyl-d-aspartate (NMDA) receptor in the pathogenesis of SCZ. D4 dopamine receptor-mediated transactivation of the gene encoding platelet-derived growth factor receptor beta (PDGFRB) has immediate effects on synaptic neurotransmission via calcium-dependent inactivation of NMDA receptors. In this study, we investigate the association between the PDGFRB gene and SCZ in a Korean population. We screened 6 single-nucleotide polymorphisms (SNPs) in the 5'-upstream region of PDGFRB and conducted a case-control study of 381 SCZ patients and 752 controls. The genotype and haplotype frequencies of 3 of the 6 SNPs [SNP1 (g.-1924T>C, rs3756314), SNP3 (g.-1772A>G, rs3756312) and SNP4 (rs3756311, g.-1658G>A)] were significantly associated with SCZ [SNP1, corrected p=0.012 (co-dominant model), 0.002 (Dominant model), and 0.506 (Recessive model); SNP3 and 4, corrected p=0.003, 0.009, and 0.049]. Haplotype analysis also revealed that ht1 (CGG) and ht2 (TAA) were significantly associated with SCZ (ht1, corrected p=0.018, 0.340, and 0.010; ht2, corrected p=0.002, 0.009, and 0.016). Transient transfection in neuronal cells revealed that ht1 had higher luciferase activity than the vector alone. Furthermore, Pdgfrb expression was increased in the frontal cortex and hippocampus in a mouse model of SCZ induced by MK801. We conclude that SNPs of the 5'-upstream region of PDGFRB are associated with SCZ in a Korean population. These are weak positives that require future studies to confirm these results.
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Affiliation(s)
- Hak-Jae Kim
- Kohwang Medical Research Institute, School of Medicine, Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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Kang H, Lee SK, Kim MH, Song J, Bae SJ, Kim NK, Lee SH, Kwack K. Parathyroid hormone-responsive B1 gene is associated with premature ovarian failure. Hum Reprod 2008; 23:1457-65. [PMID: 18349106 DOI: 10.1093/humrep/den086] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Premature ovarian failure (POF) is a complex and heterogeneous disorder that is influenced by multiple genetic components. Here, we performed a two-stage association study to identify POF-associated genes. METHODS A first stage linkage disequilibrium (LD)-based genome-wide association study was performed using 24 pairs of patients with POF and matched controls and a high-throughput BeadChip assay with 109365 single-nucleotide polymorphisms (SNPs) that are scattered throughout the genome in an exon-centric and evenly spaced manner. A region that was shown to be strongly associated with POF was then tested again for POF association in the second stage by using a larger sample size (101 cases and 87 controls) and additional putative causal SNPs. RESULTS The first stage analysis revealed that many regions were associated with POF, with part of chromosome 7p14 that contains the parathyroid hormone responsive-B1 (PTHB1) gene showing the strongest association. A POF-susceptible haplotype of PTHB1 (ht1, 'GAAAG', P = 0.00034) and a POF-resistant haplotype (ht2, 'TGTGC') were also identified. The association between POF and two PTHB1 SNPs (rs3884597 and rs6944723) and part of ht1 was confirmed in the second stage analysis. The additional SNP, rs11773504, was considered as a putative causal variant causing an amino acid change, Ala to Thr. CONCLUSIONS We showed for the first time that PTHB1 is strongly associated with POF, and ht1 confers susceptibility to POF. While causative SNPs were not identified, the polymorphism of the non-synonymous SNP rs11773504 and the repeated association of ht1 with POF suggest that PTHB1 may contribute to POF pathogenesis.
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Affiliation(s)
- Hyunjun Kang
- Medical Genomics Laboratory, Pochon CHA University, Gyeonggi-do, Korea
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Abstract
In the present study, a novel human leucocyte antigen-G allele, G*010113, was identified via direct sequencing from donor gDNA in a Korean population. This allele differs from G*01010201 by a single nucleotide substitution, C to T, in codon 169 of exon 3 but did not result in any amino acid change.
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Affiliation(s)
- H Kang
- Medical Genomics Laboratory, CHA Research Institute, Pochon CHA University, Sungnam, Korea
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Kwack K, Lee SK, Kim M, Nam M, Bang HJ, Yang JW, Choe K, Kim SK, Hong MS, Chung J, Kim HG. Positive association between the mesoderm specific transcript gene and autism spectrum disorder in a Korean male population. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.906.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- KyuBum Kwack
- CHA Research InstitutePochon CHA UniversitySeungnam‐siRepublic of Korea
| | - Seung Ku Lee
- CHA Research InstitutePochon CHA UniversitySeungnam‐siRepublic of Korea
| | - Min‐ho Kim
- CHA Research InstitutePochon CHA UniversitySeungnam‐siRepublic of Korea
| | - Min Nam
- Department of PsychologyEwha Womans UniversitySeoulRepublic of Korea
| | - Hee Jung Bang
- Department of PsychologyEwha Womans UniversitySeoulRepublic of Korea
| | - Jae Won Yang
- Department of NeuropsychiatryKorea UniversitySeoulRepublic of Korea
| | | | - Su Kang Kim
- Kohwang Medical Research InstituteKyung Hee UniversitySeoulRepublic of Korea
| | - Mee Suk Hong
- Kohwang Medical Research InstituteKyung Hee UniversitySeoulRepublic of Korea
| | - Joo‐Ho Chung
- Kohwang Medical Research InstituteKyung Hee UniversitySeoulRepublic of Korea
| | - Hyoun Geun Kim
- CHA Research InstitutePochon CHA UniversitySeungnam‐siRepublic of Korea
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Pyun JA, Kang H, Lee SK, Kim M, Kim HG, Kim K, Kim J, Oh AR, Won S, Kang EJ, Kwack K. Association between the polymorphisms in protein L‐isoaspartate (D‐aspartate) O‐methyltransferase gene and premature ovarian failure. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.1123.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jung A Pyun
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - HyunJun Kang
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - Seung Ku Lee
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - Min‐ho Kim
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - Hyoun Geun Kim
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - Kyoung‐Yeon Kim
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - Jeong‐Geun Kim
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - Ah Reum Oh
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - Seongsik Won
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - Eun Joo Kang
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
| | - KyuBum Kwack
- Pochon CHA UniversityCHA research instituteSeongnamRepublic of Korea
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Lee SK, Yi C, Kim M, Cheong JY, Cho SW, Kang JJ, Yang S, Kwack K. Genetic variations of the carbonic anhydrase gene were associated with hepatocellular carcinoma in Korean population. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.1124.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Min‐Ho Kim
- Pochon CHA UniversitySeongnamRepublic of Korea
| | | | - Sung Won Cho
- Ajou University School of MedicineSuwonRepublic of Korea
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Kang H, Lee SK, Kim HG, Kim K, Kim J, Oh AR, Pyun JA, Kim M, Won S, Kang EJ, Lee S, Kwack K. Identification of premature ovarian failure‐associated genes using linkage disequilibrium‐based genome‐wide association study. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.1123.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- HyunJun Kang
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Seung Ku Lee
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Hyoun Geun Kim
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Kyoung‐Yeon Kim
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Jeong‐Geun Kim
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Ah Reum Oh
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Jung A Pyun
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Min‐Ho Kim
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - SeongSik Won
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Eun Joo Kang
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
| | - Sook‐Hwan Lee
- Genome Research Center for Reproductive Medicine and InfertilitySeoulRepublic of Korea
| | - KyuBum Kwack
- Pochon CHA UniversityCHA Research InstituteSeongnamRepublic of Korea
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