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Kim J, Kwon EJ, Kim YJ, Kim D, Shin YZ, Gil D, Kim JH, Shin HD, Kim LH, Lee MO, Go YH, Cha HJ. Epigenetic repression of CHCHD2 enhances survival from single cell dissociation through attenuated Rho A kinase activity. Cell Mol Life Sci 2024; 81:38. [PMID: 38214772 PMCID: PMC10787008 DOI: 10.1007/s00018-023-05060-8] [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: 06/14/2023] [Revised: 10/18/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024]
Abstract
During in vitro culture, human pluripotent stem cells (hPSCs) often acquire survival advantages characterized by decreased susceptibility to mitochondrial cell death, known as "culture adaptation." This adaptation is associated with genetic and epigenetic abnormalities, including TP53 mutations, copy number variations, trisomy, and methylation changes. Understanding the molecular mechanisms underlying this acquired survival advantage is crucial for safe hPSC-based cell therapies. Through transcriptome and methylome analysis, we discovered that the epigenetic repression of CHCHD2, a mitochondrial protein, is a common occurrence during in vitro culture using enzymatic dissociation. We confirmed this finding through genetic perturbation and reconstitution experiments in normal human embryonic stem cells (hESCs). Loss of CHCHD2 expression conferred resistance to single cell dissociation-induced cell death, a common stress encountered during in vitro culture. Importantly, we found that the downregulation of CHCHD2 significantly attenuates the activity of Rho-associated protein kinase (ROCK), which is responsible for inducing single cell death in hESCs. This suggests that hESCs may survive routine enzyme-based cell dissociation by downregulating CHCHD2 and thereby attenuating ROCK activity. These findings provide insights into the mechanisms by which hPSCs acquire survival advantages and adapt to in vitro culture conditions.
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Affiliation(s)
- Jumee Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eun-Ji Kwon
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yun-Jeong Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dayeon Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yoon-Ze Shin
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dayeon Gil
- Korea National Stem Cell Bank, Osong, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex 202, Osong, Republic of Korea
| | - Jung-Hyun Kim
- Korea National Stem Cell Bank, Osong, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex 202, Osong, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Young-Hyun Go
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
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Cha SM, Shin HD, Kim YK, Kim SG. Finger injuries by eyebrow razor blades in infants. Hand Surg Rehabil 2023; 42:80-85. [PMID: 36336263 DOI: 10.1016/j.hansur.2022.10.004] [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] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Infants are occasionally injured while playing with their mother's eyebrow razor, and we have treated several infants with flexor tendon injuries, which in some cases were accompanied by damage to the corresponding digital nerves and/or vessels. Here, we report the outcomes in a retrospective case series, with a review of literature. Between January 2013 and October 2019, 8 patients who met our inclusion criteria were initially investigated. The inclusion criteria were: (1) injured by an eyebrow razor during fiddling or grasping, and (2) the availability of complete medical records and radiological data, with follow-up of at least 2 years. The core sutures were performed using a modified Becker (4-strand) method for flexor digitorum profundus (FDP). Nerves and/or vessels were repaired under microscopy. A long-arm mitten cast was then applied, with the fingers slightly flexed in a resting position, for 3 weeks. Then, the children were allowed to return to unrestricted activity. Formal outpatient hand therapy was not performed. Mean postnatal age was 6.3 months. The FDP was injured in zones 1 and 2 in 3 and 5 infants, respectively. Most of the infants were injured near a dressing table, in the bedroom used by their mother. The colors of these razors were all bright, except for one achromatic (white) razor. All of the razors had been left uncovered, without their cap, or were left open in the case of hinged razors. At a mean follow-up of 35.8 months, range of motion was evaluated by the Strickland and modified Strickland methods; all results were "excellent". We encountered no significant complications in any digit: neuroma, tendon retear, stiffness or necrosis. Uncapped or unfolded colorful eyebrow razors pose a high risk of tendon section with concurrent neurovascular injury in infants. Although satisfactory outcomes can be expected, it seems important to prevent the injury through fastidious parental care and changing razor design and color. LEVEL OF EVIDENCE: Level IV, retrospective case series.
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Affiliation(s)
- S M Cha
- Department of Orthopedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-Gu, 35015 Daejeon, Republic of Korea
| | - H D Shin
- Department of Orthopedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-Gu, 35015 Daejeon, Republic of Korea.
| | - Y K Kim
- Department of Orthopedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-Gu, 35015 Daejeon, Republic of Korea
| | - S G Kim
- Department of Orthopedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-Gu, 35015 Daejeon, Republic of Korea
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Kim YJ, Go YH, Jeong HC, Kwon EJ, Kim SM, Cheong HS, Kim W, Shin HD, Lee H, Cha HJ. TPX2 prompts mitotic survival via the induction of BCL2L1 through YAP1 protein stabilization in human embryonic stem cells. Exp Mol Med 2023; 55:32-42. [PMID: 36596852 PMCID: PMC9898288 DOI: 10.1038/s12276-022-00907-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/07/2022] [Accepted: 10/31/2022] [Indexed: 01/05/2023] Open
Abstract
Genetic alterations have been reported for decades in most human embryonic stem cells (hESCs). Survival advantage, a typical trait acquired during long-term in vitro culture, results from the induction of BCL2L1 upon frequent copy number variation (CNV) at locus 20q11.21 and is one of the strongest candidates associated with genetic alterations that occur via escape from mitotic stress. However, the underlying mechanisms for BCL2L1 induction remain unknown. Furthermore, abnormal mitosis and the survival advantage that frequently occur in late passage are associated with the expression of BCL2L1, which is in locus 20q11.21. In this study, we demonstrated that the expression of TPX2, a gene located in 20q11.21, led to BCL2L1 induction and consequent survival traits under mitotic stress in isogenic pairs of hESCs and human induced pluripotent stem cells (iPSCs) with normal and 20q11.21 CNVs. High Aurora A kinase activity by TPX2 stabilized the YAP1 protein to induce YAP1-dependent BCL2L1 expression. A chemical inhibitor of Aurora A kinase and knockdown of YAP/TAZ significantly abrogated the high tolerance to mitotic stress through BCL2L1 suppression. These results suggest that the collective expression of TPX2 and BCL2L1 from CNV at loci 20q11.21 and a consequent increase in YAP1 signaling promote genome instability during long-term in vitro hESC culture.
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Affiliation(s)
- Yun-Jeong Kim
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Young-Hyun Go
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Ho-Chang Jeong
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Eun-Ji Kwon
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Seong-Min Kim
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Hyun Sub Cheong
- grid.412670.60000 0001 0729 3748Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| | - Wantae Kim
- grid.254230.20000 0001 0722 6377Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hyoung Doo Shin
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Haeseung Lee
- grid.262229.f0000 0001 0719 8572College of Pharmacy, Pusan National University, Busan, 46241 Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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Baek IK, Cheong HS, Namgoong S, Kim JH, Kang SG, Yoon SJ, Kim SH, Chang JH, Kim LH, Shin HD. Two independent variants of epidermal growth factor receptor associated with risk of glioma in a Korean population. Sci Rep 2022; 12:19014. [PMID: 36347915 PMCID: PMC9643523 DOI: 10.1038/s41598-022-23217-6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Gliomas are the most common primary tumors in the brain and spinal cord. In previous GWASs, SNPs in epidermal growth factor receptor (EGFR) have been reported as risk loci for gliomas. However, EGFR variants associated with gliomas in the Korean population remain unstudied. This study explored the association of EGFR SNPs with the risk of glioma. We genotyped 13 EGFR exon SNPs in a case-control study that included 324 Korean patients diagnosed with glioma and 480 population-based controls. Statistical analyses of the association between EGFR SNPs and glioma risk were conducted using logistic regression. Both stepwise analysis and conditional logistic analysis were performed to identify independent associations among genotyped variants. We confirmed that two SNPs (rs2227983, rs1050171) were significantly associated with glioma (rs2227983: odds ratio = 1.42, Pcorr = 0.009; rs1050171: odds ratio = 1.68, Pcorr = 0.005). Additionally, the stepwise analysis and conditional logistic analysis indicated that both SNPs created variants with independent genetic effects. This study is the first to show evidence that functional variants of EGFR, namely, rs2227983 (K521R) and rs1050171 (Q787Q), are associated with an increased risk of glioma in the Korean population. Future work should confirm the functional association between EGFR variants and glioma.
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Affiliation(s)
- In Ki Baek
- grid.263736.50000 0001 0286 5954Department of Life Science, Sogang University, Seoul, 04107 Republic of Korea
| | - Hyun Sub Cheong
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Seok Namgoong
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- grid.267370.70000 0004 0533 4667Department of Medicine, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seok-Gu Kang
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seon-Jin Yoon
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea ,grid.15444.300000 0004 0470 5454Department of Biochemistry and Molecular Biology, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Se Hoon Kim
- grid.15444.300000 0004 0470 5454Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hee Chang
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Hyoung Doo Shin
- grid.263736.50000 0001 0286 5954Department of Life Science, Sogang University, Seoul, 04107 Republic of Korea ,grid.263736.50000 0001 0286 5954Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
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Youn BJ, Cheong HS, Namgoong S, Kim LH, Baek IK, Kim JH, Yoon SJ, Kim EH, Kim SH, Chang JH, Kim SH, Shin HD. Asian-specific 3'UTR variant in CDKN2B associated with risk of pituitary adenoma. Mol Biol Rep 2022; 49:10339-10346. [PMID: 36097105 DOI: 10.1007/s11033-022-07796-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/13/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Previous genomewide association studies (GWASs), single nucleotide polymorphisms (SNPs) on cyclin-dependent kinase inhibitor 2 A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and cyclin-dependent kinase inhibitor 2B antisense RNA1 (CDKN2B-AS1) were reported as risk loci for glioma, a subgroup of the brain tumor. To further characterize this association with the risk of brain tumors in a Korean population, we performed a fine-mapping association study of CDKN2A, CDKN2B, and CDKN2B-AS1. METHODS AND RESULTS A total of 17 SNPs were selected and genotyped in 1,439 subjects which were comprised of 959 patients (pituitary adenoma 335; glioma 324; meningioma 300) and 480 population controls (PCs). We discovered that a 3'untranslated region (3'UTR) variant, rs181031884 of CDKN2B (Asian-specific variant), had significant association with the risk of pituitary adenoma (PA) (Odds ratio = 0.58, P = 0.00003). Also, rs181031884 appeared as an independent causal variant among the significant variants in CDKN2A and CDKN2B, and showed dose-dependent effects on PA. CONCLUSIONS Although further studies are needed to verify the impact of this variant on PA susceptibility, our results may help to understand CDKN2B polymorphism and the risk of PA.
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Affiliation(s)
- Byeong Ju Youn
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea.,Forensic DNA Division, National Forensic Service, 26460, Wonju, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - Suhg Namgoong
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - In Ki Baek
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seon-Jin Yoon
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eui Hyun Kim
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sun Ho Kim
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea. .,Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea. .,Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.
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Choi IY, Ju HJ, Lee KJ, Shin HD. First Report of Powdery Mildew Caused by Podosphaera xanthii on Salvia farinacea in Korea. Plant Dis 2022; 106:1068. [PMID: 34402635 DOI: 10.1094/pdis-07-21-1427-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- I Y Choi
- Department of Agricultural Biology, Jeonbuk National University, Jeonju 54896, Korea
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea
| | - H J Ju
- Department of Agricultural Biology, Jeonbuk National University, Jeonju 54896, Korea
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea
| | - K J Lee
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea
| | - H D Shin
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Korea
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Cha SM, Kang JW, Shin HD, Ga IH. Acute Seymour fractures in children/adolescents overlooked as a simple nail injury: Reduction without pinning. Hand Surg Rehabil 2021; 40:171-176. [PMID: 33508522 DOI: 10.1016/j.hansur.2020.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/28/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
We retrospectively report the outcomes of several cases in which acute Seymour fractures were treated by open reduction of displaced distal bony fragments with concurrent nail repair, following complete incision and drainage without K-wire fixation. Among 21 patients surgically treated between March 2004 and December 2018, the final 12 were evaluated after at least 2 years of follow-up. All children/adolescents presented more than 24 h after the injury. All injuries were unreduced in the emergency department, with typical features of skin disruption around the eponychium/perionychium. Reduction was maintained without a K-wire after repairing the bone-periosteum-nail bed-nail plate of the distal fragment and the corresponding physis-periosteum-germinal matrix-proximal nail-fold of the proximal stump. Dorsal angulation, finger length, postoperative pain on visual analog scale (VAS), Disabilities of the Arm, Shoulder, and Hand (DASH) score, and active range of motion (ROM) were evaluated at the final follow-up. The mean patient age was 9.3 years (range, 3-13 years) and the mean time from injury to surgery was 35 h (range, 28-44 h). Only one child suffered a superficial infection; however, it resolved with 1 week of oral antibiotic treatment. At the final follow-up, mean dorsal angulation was 0.50° ± 1.24°; the length ratio compared with the corresponding contralateral phalanx was 98% (both, P > 0.05). The final pain on VAS, DASH score, and ROM ratio were 0.25 ± 0.45, 0.83 ± 1.34, and 99 ± 2%, respectively. Unreduced Seymour fractures presenting more than 24 h after the injury were treated by proper debridement and reduction of the fracture without the use of a K-wire. However, to determine whether the infection rate is definitively lower, this procedure should be compared with the conventional procedure using a K-wire. Level of Evidence: Therapeutic level IV.
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Affiliation(s)
- S M Cha
- Department of Orthopedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, 282 Munhwa-ro, Daesa-dong, Jung-gu, Daejeon, South Korea
| | - J W Kang
- Department of Orthopedic Surgery, Korea University Ansan Hospital, 123 Jeokgeum-ro, Gojan-dong, Danwon-gu, Ansan-si, Gyeonggi-do, Korea
| | - H D Shin
- Department of Orthopedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, 282 Munhwa-ro, Daesa-dong, Jung-gu, Daejeon, South Korea.
| | - I H Ga
- Department of Orthopedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, 282 Munhwa-ro, Daesa-dong, Jung-gu, Daejeon, South Korea
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Seo JY, Shin JG, Youn BJ, Namgoong S, Cheong HS, Kim LH, Kim JO, Shin HD, Kim YJ. A non-synonymous variant rs12614 of complement factor B associated with risk of chronic hepatitis B in a Korean population. BMC Med Genet 2020; 21:241. [PMID: 33334325 PMCID: PMC7745368 DOI: 10.1186/s12881-020-01177-w] [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] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022]
Abstract
Background Hepatitis B is known to cause several forms of liver diseases including chronic hepatitis B (CHB), and hepatocellular carcinoma. Previous genome-wide association study of CHB risk has demonstrated that rs12614 of complement factor B (CFB) was significantly associated with CHB risk. In this study, fine-mapping study of previously reported GWAS single nucleotide polymorphism (SNP; CFB rs12614) was performed to validate genetic effect of rs12614 on CHB susceptibility and identify possible additional causal variants around rs12614 in a Korean population. This association study was conducted in order to identify genetic effects of CFB single nucleotide polymorphisms (SNPs) and to identify additional independent CHB susceptible causal markers within a Korean population. Methods A total of 10 CFB genetic polymorphisms were selected and genotyped in 1716 study subjects comprised of 955 CHB patients and 761 population controls. Results A non-synonymous variant, rs12614 (Arg32Trp) in exon2 of CFB, had significant associations with risk of CHB (odds ratio = 0.43, P = 5.91 × 10− 10). Additional linkage disequilibrium and conditional analysis confirmed that rs12614 had independent genetic effect on CHB susceptibility with previously identified CHB markers. The genetic risk scores (GRSs) were calculated and the CHB patients had higher GRSs than the population controls. Moreover, OR was found to increase significantly with cumulative GRS. Conclusions rs12614 showed significant genetic effect on CHB risk within the Korean population. As such rs12614 may be used as a possible causal genetic variant for CHB susceptibility. Supplementary Information The online version contains supplementary material available at 10.1186/s12881-020-01177-w.
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Affiliation(s)
- Jung Yeon Seo
- Current address: Department of Core Technology, R&D Center, LG Household & Healthcare (LG H&H), Seoul, 07795, South Korea.,Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Joong-Gon Shin
- Current address: Department of Core Technology, R&D Center, LG Household & Healthcare (LG H&H), Seoul, 07795, South Korea.,Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Byeong Ju Youn
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, 04107, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, 04107, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, 04107, Republic of Korea
| | - Ji On Kim
- Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea. .,Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea. .,Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, 04107, Republic of Korea.
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
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Braun U, Nakashima C, Bakhshi M, Zare R, Shin HD, Alves RF, Sposito MB. Taxonomy and phylogeny of cercosporoid ascomycetes on Diospyros spp. with special emphasis on Pseudocercospora spp. Fungal Syst Evol 2020; 6:95-127. [PMID: 32904397 PMCID: PMC7453130 DOI: 10.3114/fuse.2020.06.06] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Indexed: 12/01/2022] Open
Abstract
A worldwide survey of cercosporoid ascomycete species on hosts of the genus Diospyros (persimmon) with key to the species based on characters in vivo is provided. Special emphasis is placed on species of the genus Pseudocercospora, which are in part also phylogenetically analysed, using a multilocus approach. Species of the latter genus proved to be very diverse, with a remarkable degree of cryptic speciation. Seven new species are described (Pseudocercospora diospyri-japonicae, P. diospyriphila, P. ershadii, P. kakiicola, P. kobayashiana, and P. tesselata), and two new names are introduced [P. kakiigena (≡ Cylindrosporium kaki, non Pseudocercospora kaki), and Zasmidium diospyri-hispidae (≡ Passalora diospyri, non Zasmidium diospyri)]. Six taxa are lectotypified (Cercospora atra, C. diospyri, C. diospyri var. ferruginea, C. flexuosa, C. fuliginosa, C. kaki), and Pseudocercospora kaki is epitypified.
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Affiliation(s)
- U Braun
- Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik und Botanischer Garten, Herbarium, Neuwerk 21, 06099 Halle (Saale), Germany
| | - C Nakashima
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - M Bakhshi
- Department of Botany, Iranian Research Institute of Plant Protection, P.O. Box 19395-1454, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - R Zare
- Department of Botany, Iranian Research Institute of Plant Protection, P.O. Box 19395-1454, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - H D Shin
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Korea
| | - R F Alves
- University of São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", 13418-900, Piracicaba, Brazil
| | - M B Sposito
- University of São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", 13418-900, Piracicaba, Brazil
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Lee JU, Son JH, Shim EY, Cheong HS, Shin SW, Shin HD, Baek AR, Ryu S, Park CS, Chang HS, Park JS. Global DNA Methylation Pattern of Fibroblasts in Idiopathic Pulmonary Fibrosis. DNA Cell Biol 2019; 38:905-914. [DOI: 10.1089/dna.2018.4557] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Jong-Uk Lee
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Ji-Hye Son
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Eun-Young Shim
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Republic of Korea
| | - Seung-Woo Shin
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Republic of Korea
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Ae Rin Baek
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Seongho Ryu
- Soonchunhyang Institute of Med-Bioscience (SIMS), Soonchunhyang University, Cheonan-Si, Republic of Korea
| | - Choon-Sik Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
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11
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Hong Y, Choi HM, Cheong HS, Shin HD, Choi CM, Kim WJ. Epigenome-Wide Association Analysis of Differentially Methylated Signals in Blood Samples of Patients with Non-Small-Cell Lung Cancer. J Clin Med 2019; 8:jcm8091307. [PMID: 31450665 PMCID: PMC6780065 DOI: 10.3390/jcm8091307] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 07/29/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is a common form of cancer and the leading cause of cancer-related deaths worldwide. Early diagnosis using noninvasive biomarkers may play an important role in increasing the survival rate of patients with lung cancer. Biomarkers of DNA methylation in blood samples may improve the early diagnosis of lung cancer. Here, we used peripheral blood samples obtained from 150 patients diagnosed with non-small-cell lung cancer (NSCLC) and 150 healthy controls. The latter were selected by frequency matching with the 150 patients with NSCLC, based on age, sex, and smoking status. Genome-wide methylation profiles were obtained using a MethylationEPIC BeadChip Kit, which covers the 850k bp cytosine–phosphate–guanine site. This analysis showed two significant differentially methylated changes (cg12169243 [DPH6] and cg25429010 [IMP3]) associated with NSCLC in current smokers, six changes (cg09245319, cg17183999 [USP7], cg06366994 [CPE], cg24992236 [MEG9], cg22144719, and cg22448179 [epidermal growth factor receptor]) associated with epidermal growth factor receptor mutation in patients with adenocarcinoma, and four changes (cg25021476 [RSL24D1], cg04989085 [FAM113B], cg20905681 [CKAP4], and cg26379694) associated with advanced-stage NSCLC compared with stage I NSCLC. The validation of these DNA methylation changes and further research on the related genes may help develop easily accessible biomarkers for the early diagnosis or prognosis of NSCLC.
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Affiliation(s)
- Yoonki Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Hye-Mi Choi
- Division of Biomedical Convergence, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, 04107, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, 04107, Korea
- Department of Life Science, Sogang University, Seoul 121-742, Korea
| | - Chang Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Woo Jin Kim
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.
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12
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Uh ST, Park JS, Koo SM, Kim YK, Kim KU, Kim MA, Shin SW, Son JH, Park HW, Shin HD, Park CS, Chang HS. Association of Genetic Variants of NLRP4 with Exacerbation of Asthma: The Effect of Smoking. DNA Cell Biol 2018; 38:76-84. [PMID: 30526007 DOI: 10.1089/dna.2018.4433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Asthma exacerbation is induced by the interaction of genes and environmental factors such as cigarette smoke. NLRP4 counteracts the activity of the inflammasome, which is responsible for asthma exacerbation. In this study, we analyzed the association of single-nucleotide polymorphisms of NLRP4 with the annual rate of exacerbation and evaluated the additive effect of smoking in 1454 asthmatics. Asthmatics possessing the minor allele of rs1696718G > A had more frequent exacerbation episodes than those homozygous for the common allele (0.59 vs. 0.36/year) and the association was present only in current and ex-smokers. There was a significant interaction between the amount smoked and rs16986718 genotypes (p = 0.014) and a positive correlation between the number of annual exacerbation episodes and amount smoked only in rs16986718G > A AA homozygotes. The prevalence of frequent exacerbators (≥2 exacerbation episodes/year) was 2.5 times higher in rs16986718G > A minor allele homozygotes than in common allele homozygotes (12.0% vs. 5.9%). Furthermore, the prevalence was 6 times higher in rs16986718G > A minor allele homozygotes who were current and ex-smokers than in nonsmokers (25.6% vs. 4.1%). The minor allele of rs16986718G > A in NLRP4 may be a genetic marker that predicts asthma exacerbation in adult asthmatics who smoke.
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Affiliation(s)
- Soo-Taek Uh
- 1 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital , Seoul, Korea
| | - Jong-Sook Park
- 2 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital , Bucheon, Korea
| | - So-My Koo
- 1 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital , Seoul, Korea
| | - Yang-Ki Kim
- 1 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital , Seoul, Korea
| | - Ki Up Kim
- 1 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital , Seoul, Korea
| | - Mi-Ae Kim
- 3 Department of Pulmonology, Allergy and Critical Care Medicine, CHA Bundang Medical Center, CHA University , Seongnam, Korea
| | - Seung-Woo Shin
- 4 Genome Research Center for Allergy and Respiratory Diseases, Soonchunhyang University Bucheon Hospital , Bucheon, Korea
| | - Ji-Hye Son
- 5 Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University , Bucheon, Korea
| | - Heung-Woo Park
- 6 Department of Internal Medicine, Seoul National University College of Medicine , Seoul, Korea
| | - Hyoung Doo Shin
- 7 Department of Life Sciences, Sogang University , Seoul, Korea
| | - Choon-Sik Park
- 2 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital , Bucheon, Korea.,4 Genome Research Center for Allergy and Respiratory Diseases, Soonchunhyang University Bucheon Hospital , Bucheon, Korea
| | - Hun Soo Chang
- 5 Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University , Bucheon, Korea
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13
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Namgoong S, Cheong HS, Kim JH, Kim LH, Seo JY, Kang SG, Yoon SJ, Kim SH, Chang JH, Shin HD. Association analysis of RTEL1 variants with risk of adult gliomas in a Korean population. PLoS One 2018; 13:e0207660. [PMID: 30462709 PMCID: PMC6248978 DOI: 10.1371/journal.pone.0207660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 02/19/2018] [Accepted: 11/04/2018] [Indexed: 01/28/2023] Open
Abstract
Previous studies have identified multiple loci for inherited susceptibility to glioma development, including the regulator of telomere elongation helicase 1 (RTEL1). However, the association between RTEL1 variants and risk of glioma has not been well understood. Therefore, we sought to comprehensively examine the genetic interaction between RTEL1 variants and risk of glioma with respect to defined histological and molecular subtypes. We employed a case-control study involving 250 adult glioma patients with previous molecular alterations and 375 population–based controls within Korean populations. Statistical analyses on the association between RTEL1 single nucleotide polymorphisms (SNPs) and glioma risk were conducted using unconditional logistic regression. Additional conditional and stepwise analyses were performed on significant RTEL1 SNPs. We detected significant associations (Bonferroni P < .05) between six SNPs (rs6089953, rs3848669, rs6010620, rs3787089, rs6062302, and rs115303435) and risk of glioma in the Korean subjects. The two coding variants, rs6062302 (D664D) and rs115303435 (A1059T), were plausibly causal variants and were independent among the significantly associated RTEL1 variants. The glioma subgroup analyses showed that the causal variants (rs6062302 and rs115303435) may be associated with increased risk of glioma regardless of histological grades and molecular alterations. This study provides a deeper understanding of relationships between RTEL1 variants and risk of glioma. Further studies are required to ascertain the impact of those variants on glioma susceptibility.
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Affiliation(s)
- Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Asan Institute for Life Sciences, University of Ulsan Collage of Medicine, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Republic of Korea
| | - Jung Yeon Seo
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Seok-Gu Kang
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seon-Jin Yoon
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
- * E-mail: (HDS); (JHC)
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
- * E-mail: (HDS); (JHC)
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14
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Cho SJ, Kim KT, Jeong HC, Park JC, Kwon OS, Song YH, Shin JG, Kang S, Kim W, Shin HD, Lee MO, Moon SH, Cha HJ. Selective Elimination of Culture-Adapted Human Embryonic Stem Cells with BH3 Mimetics. Stem Cell Reports 2018; 11:1244-1256. [PMID: 30293852 PMCID: PMC6235677 DOI: 10.1016/j.stemcr.2018.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 04/04/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 01/05/2023] Open
Abstract
The selective survival advantage of culture-adapted human embryonic stem cells (hESCs) is a serious safety concern for their clinical application. With a set of hESCs with various passage numbers, we observed that a subpopulation of hESCs at late passage numbers was highly resistant to various cell death stimuli, such as YM155, a survivin inhibitor. Transcriptome analysis from YM155-sensitive (YM155S) and YM155-resistant (YM155R) hESCs demonstrated that BCL2L1 was highly expressed in YM155R hESCs. By matching the gene signature of YM155R hESCs with the Cancer Therapeutics Response Portal dataset, BH3 mimetics were predicted to selectively ablate these cells. Indeed, short-course treatment with a sub-optimal dose of BH3 mimetics induced the spontaneous death of YM155R, but not YM155S hESCs by disrupting the mitochondrial membrane potential. YM155S hESCs remained pluripotent following BH3 mimetics treatment. Therefore, the use of BH3 mimetics is a promising strategy to specifically eliminate hESCs with a selective survival advantage. Culture-adapted hESCs against YM155/genotoxic agents mediated by high BCL-xL expression Selective cell death of culture-adapted hPSCs by BH3 mimetics Pluripotency maintenance of normal hESCs after exposure to BH3 mimetics
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Affiliation(s)
- Seung-Ju Cho
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Keun-Tae Kim
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Ho-Chang Jeong
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Ju-Chan Park
- School of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ok-Seon Kwon
- School of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yun-Ho Song
- Department of Medicine, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Joong-Gon Shin
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Seungmin Kang
- Ewha Research Center for Systems Biology, Division of Molecular & Life Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Wankyu Kim
- Ewha Research Center for Systems Biology, Division of Molecular & Life Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Mi-Ok Lee
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Sung-Hwan Moon
- Department of Medicine, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Hyuk-Jin Cha
- School of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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15
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Namgoong S, Shin JG, Cheong HS, Kim LH, Kim JO, Seo JY, Shin HD, Kim YJ. Genetic association of complement component 2 variants with chronic hepatitis B in a Korean population. Liver Int 2018; 38:1576-1582. [PMID: 29283494 DOI: 10.1111/liv.13675] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/30/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Numerous single nucleotide polymorphisms associated with an increased risk of liver diseases, chronic hepatitis B and chronic hepatitis B-related hepatocellular carcinoma have been identified. In this study, we scrutinized the genetic effects of C2 variants, which were conflicting in previous results, on the risk of chronic hepatitis B in a Korean population. METHODS We genotyped 22 common C2 genetic variants of 977 chronic hepatitis B cases including 302 chronic hepatitis B-related hepatocellular carcinoma cases and 785 population controls. Statistical analysis was performed to examine the effects of genotype on the risk of chronic hepatitis B and chronic hepatitis B-related hepatocellular carcinoma. RESULTS Logistic regression analyses showed that six C2 single nucleotide polymorphisms had significant associations with the risk of chronic hepatitis B and chronic hepatitis B-related hepatocellular carcinoma among the Korean subjects. Stepwise analysis revealed that causal markers (rs9267665 and rs10947223) were identified among the C2 variants (stepwise P = 3.32 × 10-9 and 2.04 × 10-5 respectively). In further conditional analysis with previous chronic hepatitis B-associated loci, these two single nucleotide polymorphisms were independently associated with the risk of chronic hepatitis B. In addition, we investigated the ability of genetic risk scores combining 12 multi-chronic hepatitis B loci to predict the risk of chronic hepatitis B. Individuals with higher genetic risk scores showed increased risk for chronic hepatitis B. CONCLUSIONS Our results suggested that the C2 gene might be a susceptibility locus for chronic hepatitis B in Korean populations. The cumulative genetic effects may contribute to future etiological explanations for chronic hepatitis B.
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Affiliation(s)
- Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, Korea
| | - Joong-Gon Shin
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Korea
| | - Jung Yeon Seo
- Department of Life Science, Sogang University, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
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Kim S, Cheong HS, Shin HD, Lee SS, Roh HJ, Jeon DY, Cho CY. Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip. Asian-Australas J Anim Sci 2018; 31:1691-1699. [PMID: 30056676 PMCID: PMC6212751 DOI: 10.5713/ajas.17.0419] [Citation(s) in RCA: 14] [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] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/22/2018] [Indexed: 01/07/2023]
Abstract
Objective In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average r2 value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, inter-population, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.
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Affiliation(s)
- Seungchang Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 04107, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 04107, Korea.,Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Sung-Soo Lee
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Hee-Jong Roh
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Da-Yeon Jeon
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
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17
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Lee JS, Cheong HS, Shin HD. Prediction of cholesterol ratios within a Korean population. R Soc Open Sci 2018; 5:171204. [PMID: 29410832 PMCID: PMC5792909 DOI: 10.1098/rsos.171204] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
Cholesterol ratios (total cholesterol (TC)/high-density lipoprotein cholesterol (HDL-c) and triglyceride (TG)/HDL-c) have been suggested as better indicators to predict various clinical features such as insulin resistance and heart disease. Therefore, we aimed to build a single nucleotide polymorphism (SNP) set to predict constitutional lipid metabolism. The genotype data of 7795 samples were obtained from the Korea Association Resource. Among the total of 7795 samples, 7016 subjects were used to perform 10-fold cross-validation. We selected the SNPs that showed significance constantly throughout all 10 cross-validation sets; another 779 samples were used as the final validation set. After performing the 10-fold cross-validation, the six SNPs (rs4420638 (APOC1), rs12421652 (BUD13), rs17411126 (LPL), rs6589566 (ZPR1), rs16940212 (LOC101928635) and rs10852765 (ABCA8)) were finally selected for predicting cholesterol ratios. The weighted genetic risk scores (wGRS) were calculated based on the regression slopes of the six selected SNPs. Our results showed upward trends of wGRS for both the TC/HDL-c and TG/HDL-c ratios within the 10-fold cross-validation. Similarly, the wGRS of the six SNPs also showed upward trends in analyses using the SNP selection set and final validation set. The selected six SNPs can be used to explain both the TC/HDL-c and TG/HDL-c ratios. Our results may be useful for the prospective predictions of cholesterol-related diseases.
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Affiliation(s)
- Jin Sol Lee
- Department of Life Science, Sogang University, Baekbumro 35, Mapo-gu, Seoul 04107, Republic of Korea
- Research Institute for Basic Science, Sogang University, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Taihard building 1007, Sogang University, Baekbumro 35, Mapo-gu, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Baekbumro 35, Mapo-gu, Seoul 04107, Republic of Korea
- Research Institute for Basic Science, Sogang University, Mapo-gu, Seoul, 121-742, Republic of Korea
- Department of Genetic Epidemiology, SNP Genetics, Inc., Taihard building 1007, Sogang University, Baekbumro 35, Mapo-gu, Seoul, Republic of Korea
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Chang HS, Park JS, Lee HS, Lyu J, Son JH, Choi IS, Shin HD, Park CS. Association analysis of ILVBL gene polymorphisms with aspirin-exacerbated respiratory disease in asthma. BMC Pulm Med 2017; 17:210. [PMID: 29246216 PMCID: PMC5732499 DOI: 10.1186/s12890-017-0556-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/21/2016] [Accepted: 12/07/2017] [Indexed: 12/30/2022] Open
Abstract
Background We previously reported that the ILVBL gene on chromosome 19p13.1 was associated with the risk for aspirin-exacerbated respiratory disease (AERD) and the percent decline of forced expired volume in one second (FEV1) after an oral aspirin challenge test. In this study, we confirmed the association between polymorphisms and haplotypes of the ILVBL gene and the risk for AERD and its phenotype. Methods We recruited 141 AERD and 995 aspirin-tolerant asthmatic (ATA) subjects. All study subjects underwent an oral aspirin challenge (OAC). Nine single nucleotide polymorphisms (SNPs) with minor allele frequencies above 0.05, which were present in the region from 2 kb upstream to 0.5 kb downstream of ILVBL in Asian populations, were selected and genotyped. Results In an allelic association analysis, seven of nine SNPs were significantly associated with the risk for AERD after correction for multiple comparisons. In a codominant model, the five SNPs making up block2 (rs2240299, rs7507755, rs1468198, rs2074261, and rs13301) showed significant associations with the risk for AERD (corrected P = 0.001–0.004, OR = 0.59–0.64). Rs1468198 was also significantly associated with the percent decline in FEV1 in OAC tests after correction for multiple comparisons in the codominant model (corrected P = 0.033), but the other four SNPs in hapblock2 were not. Conclusion To the best of our knowledge, this is the first report of an association between SNPs on ILVBL and AERD. SNPs on ILVBL could be promising genetic markers of this condition. Electronic supplementary material The online version of this article (10.1186/s12890-017-0556-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hun Soo Chang
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, 22, Soonchunhyang-ro, Asan, Chungcheongnam-do, 336-745, Republic of Korea.
| | - Jong Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, 1174, Jung-Dong, Wonmi-Ku, Bucheon, Gyeonggi-Do, 420-021, Republic of Korea
| | - Ho Sung Lee
- Division of Respiratory Medicine, Soonchunhyang University Chunan Hospital, Chunan-Si, Chungcheongnam-do, 336-745, Republic of Korea
| | - Jiwon Lyu
- Division of Respiratory Medicine, Soonchunhyang University Chunan Hospital, Chunan-Si, Chungcheongnam-do, 336-745, Republic of Korea
| | - Ji-Hye Son
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, 22, Soonchunhyang-ro, Asan, Chungcheongnam-do, 336-745, Republic of Korea
| | - Inseon S Choi
- Department of Allergy, Chonnam National University Medical School and Research Institute of Medical Sciences, Gwangju, 61469, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics, Inc., 1407 14th Floor, Woolim-rall'ey B, Gasan-dong, Geumcheon-Gu, Seoul, 153-803, Republic of Korea
| | - Choon-Sik Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, 1174, Jung-Dong, Wonmi-Ku, Bucheon, Gyeonggi-Do, 420-021, Republic of Korea.
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19
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Shin JG, Cheong HS, Kim JY, Lee JH, Yu SJ, Yoon JH, Cheong JY, Cho SW, Park NH, Namgoong S, Kim LH, Kim YJ, Shin HD. Identification of additional EHMT2 variant associated with the risk of chronic hepatitis B by GWAS follow-up study. Genes Immun 2017; 20:1-9. [PMID: 29238036 DOI: 10.1038/s41435-017-0004-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 02/07/2023]
Abstract
Chronic hepatitis B (CHB) is a precursor to liver cirrhosis and hepatocellular carcinoma, caused by a Hepatitis B viral infection. Genome-wide association studies (GWASs) have been conducted to find genes associated with CHB risk. In previous GWAS, EHMT2 was identified as one of the susceptibility genes for CHB. To further characterize this association and discover possible causal variants, we conducted an additional association study. A total of 11 EHMT2 single-nucleotide polymorphisms (SNP) were selected and genotyped in 3902 subjects (1046 CHB patients and 2856 controls). An additional eight imputed SNPs were also included in further analysis. As a result, rs35875104 showed a strong association with the CHB, along with the previously reported genetic marker for CHB risk, rs652888 (odds ratio (OR) = 0.53, P = 2.20 × 10-8 at rs35875104 and OR = 1.58, P = 9.90 × 10-12 at rs652888). In addition, linkage disequilibrium and conditional analysis identified one SNP (rs35875104) as a novel genetic marker for CHB susceptibility. The GRSs (genetic risk scores) were calculated to visualize the combined genetic effects of all known CHB-associated loci, including EHMT2 rs35875104, which was additionally identified in this study. The findings from the present study may be useful for further understanding of the genetic etiology of CHB.
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Affiliation(s)
- Joong-Gon Shin
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea.,Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Sogang University, Inc., Taihard building 1007, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Jason Yongha Kim
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 28 Yungun-dong, Chongro-Gu, Seoul, 110-744, Republic of Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 28 Yungun-dong, Chongro-Gu, Seoul, 110-744, Republic of Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 28 Yungun-dong, Chongro-Gu, Seoul, 110-744, Republic of Korea
| | - Jae Youn Cheong
- Department of Internal Medicine, Seoul National University Boramae Medical Center, 20 Boramae-ro 5-gil, Dongjak-gu, Seoul, 156-707, Republic of Korea
| | - Sung Won Cho
- Department of Gastroenterology, Ajou University School of Medicine, San-5 Wonchon-dong, Youngtong-gu, Suwon, 442-721, Republic of Korea
| | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, 877 Bangeojin Sunhwan-doro, Dong-gu, Ulsan, 682-714, Republic of Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics, Sogang University, Inc., Taihard building 1007, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Sogang University, Inc., Taihard building 1007, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 28 Yungun-dong, Chongro-Gu, Seoul, 110-744, Republic of Korea.
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea. .,Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea. .,Department of Genetic Epidemiology, SNP Genetics, Sogang University, Inc., Taihard building 1007, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea.
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20
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Tang CSM, Gui H, Kapoor A, Kim JH, Luzón-Toro B, Pelet A, Burzynski G, Lantieri F, So MT, Berrios C, Shin HD, Fernández RM, Le TL, Verheij JBGM, Matera I, Cherny SS, Nandakumar P, Cheong HS, Antiñolo G, Amiel J, Seo JM, Kim DY, Oh JT, Lyonnet S, Borrego S, Ceccherini I, Hofstra RMW, Chakravarti A, Kim HY, Sham PC, Tam PKH, Garcia-Barceló MM. Trans-ethnic meta-analysis of genome-wide association studies for Hirschsprung disease. Hum Mol Genet 2017; 25:5265-5275. [PMID: 27702942 DOI: 10.1093/hmg/ddw333] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/28/2016] [Indexed: 02/04/2023] Open
Abstract
Hirschsprung disease (HSCR) is the most common cause of neonatal intestinal obstruction. It is characterized by the absence of ganglia in the nerve plexuses of the lower gastrointestinal tract. So far, three common disease-susceptibility variants at the RET, SEMA3 and NRG1 loci have been detected through genome-wide association studies (GWAS) in Europeans and Asians to understand its genetic etiologies. Here we present a trans-ethnic meta-analysis of 507 HSCR cases and 1191 controls, combining all published GWAS results on HSCR to fine-map these loci and narrow down the putatively causal variants to 99% credible sets. We also demonstrate that the effects of RET and NRG1 are universal across European and Asian ancestries. In contrast, we detected a European-specific association of a low-frequency variant, rs80227144, in SEMA3 [odds ratio (OR) = 5.2, P = 4.7 × 10-10]. Conditional analyses on the lead SNPs revealed a secondary association signal, corresponding to an Asian-specific, low-frequency missense variant encoding RET p.Asp489Asn (rs9282834, conditional OR = 20.3, conditional P = 4.1 × 10-14). When in trans with the RET intron 1 enhancer risk allele, rs9282834 increases the risk of HSCR from 1.1 to 26.7. Overall, our study provides further insights into the genetic architecture of HSCR and has profound implications for future study designs.
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Affiliation(s)
- Clara Sze-Man Tang
- Department of Surgery.,Centre for Genomic Sciences.,Dr Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong SAR, China
| | | | - Ashish Kapoor
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Berta Luzón-Toro
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Anna Pelet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Grzegorz Burzynski
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Courtney Berrios
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Republic of Korea.,Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Raquel M Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Thuy-Linh Le
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Joke B G M Verheij
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ivana Matera
- UOC Genetica Medica, Istituto Giannina Gaslini, 16148 Genova, Italy
| | - Stacey S Cherny
- Centre for Genomic Sciences.,Department of Psychiatry.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Priyanka Nandakumar
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | | | - Robert M W Hofstra
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands.,Stem Cells and Regenerative Medicine, Birth Defects Research Centre UCL Institute of Child Health, London, UK
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul 110-744, Republic of Korea
| | - Pak Chung Sham
- Centre for Genomic Sciences.,Department of Psychiatry.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Paul K H Tam
- Department of Surgery.,Dr Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong SAR, China
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21
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Lee HS, Oh H, Yang SK, Baek J, Jung S, Hong M, Kim KM, Shin HD, Kim KJ, Park SH, Ye BD, Han B, Song K. X Chromosome-wide Association Study Identifies a Susceptibility Locus for Inflammatory Bowel Disease in Koreans. J Crohns Colitis 2017; 11:820-830. [PMID: 28333213 DOI: 10.1093/ecco-jcc/jjx023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/21/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND AND AIMS Genome-wide association studies of inflammatory bowel disease identified > 200 susceptibility loci only in autosomes. This study aimed to identify inflammatory bowel disease susceptibility loci on the X chromosome. METHODS We performed an X chromosome-wide association study in Korean patients with inflammatory bowel disease. We analysed X chromosome data from our recent genome-wide association studies, including 1505 cases [922 Crohn's disease and 583 ulcerative colitis] and 4041 controls during the discovery phase, followed by replication in additional 1989 cases [993 Crohn's disease, 996 ulcerative colitis] and 3491 controls. Sex-related differential effects of single nucleotide polymorphisms on disease were also evaluated. RESULTS We confirmed a significant association of a previously reported inflammatory bowel disease susceptibility locus at chromosome Xq26.3 [CD40LG-ARHGEF6; odds ratio, 1.22; 95% confidence interval, 1.16-1.28; combined p = 3.79 × 10-15]. This locus accounted for 0.18% and 0.12% of genetic variance in Crohn's disease and ulcerative colitis, respectively, and increased the total autosomal chromosome genetic variance from 6.65% to 6.83% and from 5.47% to 5.59% for Crohn's disease and ulcerative colitis risk, respectively, in the Korean population. Sex-stratified analyses did not reveal sex-related differences in effect sizes. CONCLUSIONS We confirmed the association of rs2427870 at the CD40LG-ARHGEF6 locus with an inflammatory bowel disease through an X chromosome-wide association study in a Korean population. Our data suggest that the CD40LG-ARHGEF6 locus on the X chromosome might play a role in inflammatory bowel disease pathogenesis in the Korean population.
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Affiliation(s)
- Ho-Su Lee
- Health Screening and Promotion Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyunjung Oh
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Myunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Mo Kim
- Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Kyung-Jo Kim
- Department of Gastroenterology, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, University of Ulsan College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Seoul, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
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22
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Sio CA, Jung K, Kim JH, Cheong HS, Shin E, Jang H, Yoon M, Jang H, Shin HD. Sotos syndrome associated with Hirschsprung's disease: a new case and exome-sequencing analysis. Pediatr Res 2017; 82:87-92. [PMID: 28399120 DOI: 10.1038/pr.2017.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 12/16/2016] [Accepted: 04/02/2017] [Indexed: 11/09/2022]
Abstract
BackgroundSotos syndrome (SoS) is an overgrowth disorder with various congenital anomalies and is usually accompanied by other clinical problems. However, anorectal malformations have not been documented as part of the SoS entity. Our objective is to report on a case of SoS associated with Hirschsprung's disease (HSCR) and subsequent genetic analysis.MethodsA 2-year-old boy with SoS experienced constipation since infancy and ultimately showed an aganglionic segment in the histopathologic examination, which was followed by exome-sequencing analysis.ResultsIn the genetic test for SoS diagnosis, two novel mutations of NDS1, c.2465C>A (p.Ser822Tyr) and c.4347T>A (p.Cys1449*), were observed and verified by resequencing in the patient and his parents. In further whole-exome-sequencing analysis using the patient's blood DNA, which was followed by a comparison analysis with the results of our previously reported genome-wide association study (GWAS) of HSCR, three genes (ZNF827, FGD2, and KCNJ12) with significance for HSCR from our previous GWAS were overlapped among the genes showing variants in the exome sequencing.ConclusionThis is the first reported patient with SoS and HSCR. Further studies are required to determine whether there is a genetic relationship between SoS and HSCR.
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Affiliation(s)
- Cherry Ann Sio
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Jeju, Republic of Korea
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Seoul, Republic of Korea
| | - Eun Shin
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Hyejin Jang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Miok Yoon
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Huijeong Jang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Seoul, Republic of Korea
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23
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Kim JH, Jung SM, Shin JG, Cheong HS, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Shin HD. Potential association between ITPKC genetic variations and Hirschsprung disease. Mol Biol Rep 2017; 44:307-313. [PMID: 28664405 DOI: 10.1007/s11033-017-4111-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 10/27/2016] [Accepted: 06/24/2017] [Indexed: 02/03/2023]
Abstract
Hirschsprung disease (HSCR) is a congenital and complex disorder characterized by intestinal obstruction due to the absence of enteric neurons along variable lengths of the hindgut. Our recent genome-wide association study (GWAS) has revealed regional associations with HSCR at several loci of inositol-trisphosphate 3-kinase C (ITPKC). For fine mapping, we additionally selected and genotyped a total of 12 single nucleotide polymorphisms (SNPs) of ITPKC in 187 HSCR patients and 283 unaffected controls, and performed a further combined imputation analysis based on genotype data from this second stage of fine mapping and our previous GWAS stage, totaling 902 subjects (187 HSCR cases and 715 controls). As a result, several SNPs (minimum P = 0.004) and a haplotype (P = 0.02) were found to be significantly associated with HSCR. In further in silico analyses to ascertain the potential functions of the significant variants, the change from the common allele to the rare allele of the highly conserved nonsynonymous rs76785336 showed a difference in mRNA folding structure. In the case of intronic SNPs, rs2607420 with a high consensus value was predicted to be a new splice site. Although this study has limitations (such as lack of functional evaluations, small number of cases, and further need of replication in other cohorts), our findings suggest that genetic variants of ITPKC may have a potential association with HSCR susceptibility and/or developmental diseases related to enteric nervous system development.
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Affiliation(s)
- Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Soo-Min Jung
- Department of Surgery, Konkuk University Medical Center, Seoul, 05030, Republic of Korea
| | - Joong-Gon Shin
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, 04107, Republic of Korea
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, 03080, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Jeju, 63241, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea. .,Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea.
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24
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Jeong HC, Park SJ, Choi JJ, Go YH, Hong SK, Kwon OS, Shin JG, Kim RK, Lee MO, Lee SJ, Shin HD, Moon SH, Cha HJ. PRMT8 Controls the Pluripotency and Mesodermal Fate of Human Embryonic Stem Cells By Enhancing the PI3K/AKT/SOX2 Axis. Stem Cells 2017; 35:2037-2049. [DOI: 10.1002/stem.2642] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/06/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Ho-Chang Jeong
- Department of Life Sciences, Sogang University; Seoul Republic of Korea
| | - Soon-Jung Park
- Department of Medicine; School of Medicine, Konkuk University; Seoul Republic of Korea
| | - Jong-Jin Choi
- Department of Medicine; School of Medicine, Konkuk University; Seoul Republic of Korea
| | - Young-Hyun Go
- Department of Life Sciences, Sogang University; Seoul Republic of Korea
| | - Soon-Ki Hong
- Department of Life Sciences, Sogang University; Seoul Republic of Korea
| | - Ok-Seon Kwon
- Department of Life Sciences, Sogang University; Seoul Republic of Korea
| | - Joong-Gon Shin
- Department of Life Sciences, Sogang University; Seoul Republic of Korea
- Research Institute for Basic Science, Sogang University; Seoul Republic of Korea
| | - Rae-Kwon Kim
- Department of Life Science; Research Institute for Natural Sciences, Hanyang University; Seoul Republic of Korea
| | - Mi-Ok Lee
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon Republic of Korea
| | - Su-Jae Lee
- Department of Life Science; Research Institute for Natural Sciences, Hanyang University; Seoul Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Sciences, Sogang University; Seoul Republic of Korea
- Research Institute for Basic Science, Sogang University; Seoul Republic of Korea
| | - Sung-Hwan Moon
- Department of Medicine; School of Medicine, Konkuk University; Seoul Republic of Korea
| | - Hyuk-Jin Cha
- Department of Life Sciences, Sogang University; Seoul Republic of Korea
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25
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Jung K, Koh I, Kim JH, Cheong HS, Park T, Nam SH, Jung SM, Sio CA, Kim SY, Jung E, Lee B, Kim HR, Shin E, Jung SE, Choi CW, Kim BI, Jung E, Shin HD. RNA-Seq for Gene Expression Profiling of Human Necrotizing Enterocolitis: a Pilot Study. J Korean Med Sci 2017; 32:817-824. [PMID: 28378556 PMCID: PMC5383615 DOI: 10.3346/jkms.2017.32.5.817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/27/2017] [Indexed: 12/11/2022] Open
Abstract
Necrotizing enterocolitis (NEC) characterized by inflammatory intestinal necrosis is a major cause of mortality and morbidity in newborns. Deep RNA sequencing (RNA-Seq) has recently emerged as a powerful technology enabling better quantification of gene expression than microarrays with a lower background signal. A total of 10 transcriptomes from 5 pairs of NEC lesions and adjacent normal tissues obtained from preterm infants with NEC were analyzed. As a result, a total of 65 genes (57 down-regulated and 8 up-regulated) revealed significantly different expression levels in the NEC lesion compared to the adjacent normal region, based on a significance at fold change ≥ 1.5 and P ≤ 0.05. The most significant gene, DPF3 (P < 0.001), has recently been reported to have differential expressions in colon segments. Our gene ontology analysis between NEC lesion and adjacent normal tissues showed that down-regulated genes were included in nervous system development with the most significance (P = 9.3 × 10⁻⁷; P(corr) = 0.0003). In further pathway analysis using Pathway Express based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, genes involved in thyroid cancer and axon guidance were predicted to be associated with different expression (P(corr) = 0.008 and 0.020, respectively). Although further replications using a larger sample size and functional evaluations are needed, our results suggest that altered gene expression and the genes' involved functional pathways and categories may provide insight into NEC development and aid in future research.
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Affiliation(s)
- Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Jeju, Korea
| | - Insong Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Korea
| | - Jeong Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Taejin Park
- Department of Surgery, Gyeongsang National University Hospital, Jinju, Korea
| | - So Hyun Nam
- Department of Surgery, Donga University Hospital, Busan, Korea
| | - Soo Min Jung
- Department of Surgery, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Cherry Ann Sio
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Su Yeong Kim
- Department of Surgery, Donga University Hospital, Busan, Korea
| | - Euiseok Jung
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Byoungkook Lee
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hye Rim Kim
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Eun Shin
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sung Eun Jung
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - Chang Won Choi
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Beyong Il Kim
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Eunyoung Jung
- Department of Surgery, Gyemyoung University Dongsan Hospital, Daegu, Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Korea
- Department of Life Science, Sogang University, Seoul, Korea.
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Shin JG, Kim JH, Park CS, Kim BJ, Kim JW, Choi IG, Hwang J, Shin HD, Woo SI. Gender-Specific Associations between CHGB Genetic Variants and Schizophrenia in a Korean Population. Yonsei Med J 2017; 58:619-625. [PMID: 28332369 PMCID: PMC5368149 DOI: 10.3349/ymj.2017.58.3.619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/09/2016] [Accepted: 12/22/2016] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Schizophrenia is a devastating mental disorder and is known to be affected by genetic factors. The chromogranin B (CHGB), a member of the chromogranin gene family, has been proposed as a candidate gene associated with the risk of schizophrenia. The secretory pathway for peptide hormones and neuropeptides in the brain is regulated by chromogranin proteins. The aim of this study was to investigate the potential associations between genetic variants of CHGB and schizophrenia susceptibility. MATERIALS AND METHODS In the current study, 15 single nucleotide polymorphisms of CHGB were genotyped in 310 schizophrenia patients and 604 healthy controls. RESULTS Statistical analysis revealed that two genetic variants (non-synonymous rs910122; rs2821 in 3'-untranslated region) were associated with schizophrenia [minimum p=0.002; odds ratio (OR)=0.72], even after correction for multiple testing (p(corr)=0.02). Since schizophrenia is known to be differentially expressed between sexes, additional analysis for sex was performed. As a result, these two genetic variants (rs910122 and rs2821) and a haplotype (ht3) showed significant associations with schizophrenia in male subjects (p(corr)=0.02; OR=0.64), whereas the significance disappeared in female subjects (p>0.05). CONCLUSION Although this study has limitations including a small number of samples and lack of functional study, our results suggest that genetic variants of CHGB may have sex-specific effects on the risk of schizophrenia and provide useful preliminary information for further study.
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Affiliation(s)
- Joong Gon Shin
- Department of Life Science, Sogang University, Seoul, Korea
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Jeong Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Chul Soo Park
- Department of Psychiatry, College of Medicine, Gyeongsang National University, Jinju, Korea
| | - Bong Jo Kim
- Department of Psychiatry, College of Medicine, Gyeongsang National University, Jinju, Korea
| | - Jae Won Kim
- Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| | - Ihn Geun Choi
- Department of Neuropsychiatry, Hallym University Hangang Sacred Heart Hospital, Seoul, Korea
| | - Jaeuk Hwang
- Department of Neuropsychiatry, Soonchunhyang University Hospital, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Korea
- Research Institute for Basic Science, Sogang University, Seoul, Korea
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea.
| | - Sung Il Woo
- Department of Neuropsychiatry, Soonchunhyang University Hospital, Seoul, Korea.
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Na HS, Lee JS, Cheong HS, Shin HJ, Kang TS, Park HJ, Shin HD, Chung MW. Expression efficiency of NAT2 haplotypes in a Korean population. Genes Genet Syst 2017; 91:277-281. [PMID: 27853051 DOI: 10.1266/ggs.15-00081] [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: 11/23/2022] Open
Abstract
Since NAT2 single-nucleotide polymorphisms (SNPs) are responsible for the efficacy of arylamines and hydrazine drugs, defining the effects of these SNPs in various ethnicities is an important factor in the development of personalized medicine. In the present study, we examined the expression efficiency of NAT2 using promoter haplotypes identified in a Korean population. To construct NAT2 promoter haplotypes, seven NAT2 promoter SNPs (rs4646241, rs4646242, rs4646243, rs4646267, rs4345600, rs4271002 and rs4646246) were genotyped in a total of 192 Korean subjects. A luciferase assay was performed using the three commonest haplotypes to evaluate enzyme expression level of NAT2 promoter haplotypes. The most common haplotype (TACGAGG) showed the lowest enzyme expression level (0.72 ± 0.06 relative light units (RLU)/[β-galactosidase]). The second (CGTAAGA) and third (TATAACA) commonest haplotypes showed intermediate and the highest enzyme expression level (0.99 ± 0.05 and 1.45 ± 0.11 RLU/[β-galactosidase]), respectively. Haplotype comparison among populations showed that Asian populations had a high proportion of the haplotype for lowest enzyme expression. Haplotype frequencies of Caucasian and African ethnicities were markedly different from those of Korean ethnicity. Results from the present study should contribute to the expansion of our current understanding of the pharmacogenetics field.
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Affiliation(s)
- Han Sung Na
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex
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Shin JG, Cheong HS, Lee K, Ju BG, Lee JH, Yu SJ, Yoon JH, Cheong JY, Cho SW, Park NH, Namgoong S, Kim LH, Kim YJ, Shin HD. Identification of novel OCT4 genetic variant associated with the risk of chronic hepatitis B in a Korean population. Liver Int 2017; 37:354-361. [PMID: 27596359 DOI: 10.1111/liv.13245] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/28/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Hepatitis B viral infection is a serious risk factor for chronic hepatitis B (CHB), cirrhosis and hepatocellular carcinoma. Recently, several genome-wide association studies (GWASs) have been conducted to identify important genetic variant associated with the risk of CHB. In our previous GWAS, TCF19 was identified as one of the susceptibility genes for CHB risk (P=4.2×10-9 at rs1419881). In order to discover possible additional causal variants around TCF19, we performed an association study by genotyping single nucleotide polymorphisms (SNPs) in OCT4, a nearby gene to TCF19. METHODS Nineteen OCT4 genetic variants were selected and genotyped in 3902 subjects (1046 CHB patients and 2856 population controls). RESULTS Logistic regression analysis revealed that OCT4 rs1265163 showed the most significant association signal for the risk of CHB (OR=1.46, P=4.78×10-12 ). Linkage disequilibrium and conditional analysis confirmed rs1265163 in OCT4 as a novel genetic marker for CHB susceptibility. The genetic risk scores (GRSs) were calculated to visualize the combined genetic effects of all known CHB-associated loci, including OCT4 rs1265163, which had been identified in this study. Individuals with higher cumulative GRSs showed significantly increased ORs. The luciferase activity of rs885952, a tagging SNP of rs1265163, showed that OCT4 promoter activity was significantly different between the wild-type and SNP mutant form (P<.05). CONCLUSIONS This follow-up study to our previous GWAS identified a possible causal genetic variant associated with the risk of CHB, and findings from this study may prove useful in the understanding of genetic susceptibility to CHB.
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Affiliation(s)
- Joong-Gon Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Kwanghyun Lee
- Department of Life Science, Sogang University, Seoul, Korea
| | - Bong-Gun Ju
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Jae Youn Cheong
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sung Won Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, Korea.,Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Lyoung Hyo Kim
- Department of Life Science, Sogang University, Seoul, Korea.,Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea.,Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
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Lee JU, Cheong HS, Shim EY, Bae DJ, Chang HS, Uh ST, Kim YH, Park JS, Lee B, Shin HD, Park CS. Gene profile of fibroblasts identify relation of CCL8 with idiopathic pulmonary fibrosis. Respir Res 2017; 18:3. [PMID: 28057004 PMCID: PMC5216573 DOI: 10.1186/s12931-016-0493-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 06/14/2016] [Accepted: 12/13/2016] [Indexed: 01/15/2023] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is characterized by the complex interaction of cells involved in chronic inflammation and fibrosis. Global gene expression of a homogenous cell population will identify novel candidate genes. Methods Gene expression of fibroblasts derived from lung tissues (8 IPF and 4 controls) was profiled, and ontology and functional pathway were analyzed in the genes exhibiting >2 absolute fold changes with p-values < 0.05. CCL8 mRNA and protein levels were quantified using real-time PCR and ELISA. CCL8 localization was evaluated by immunofluorescence staining. Results One hundred seventy eight genes differentially expressed and 15 genes exhibited >10-fold change. Among them, 13 were novel in relation with IPF. CCL8 expression was 22.8-fold higher in IPF fibroblasts. The levels of CCL8 mRNA and protein were 3 and 9-fold higher in 14 IPF fibroblasts than those in 10 control fibroblasts by real-time PCR and ELISA (p = 0.022 and p = 0.026, respectively). The CCL8 concentrations in BAL fluid was significantly higher in 86 patients with IPF than those in 41 controls, and other interstitial lung diseases including non-specific interstitial pneumonia (n = 22), hypersensitivity pneumonitis (n = 20) and sarcoidosis (n = 19) (p < 0.005, respectively). Cut-off values of 2.29 pg/mL and 0.43 pg/mL possessed 80.2 and 70.7% accuracy for the discrimination of IPF from NC and the other lung diseases, respectively. IPF subjects with CCL8 levels >28.61 pg/mL showed shorter survival compared to those with lower levels (p = 0.012). CCL8 was expressed by α-SMA-positive cells in the interstitium of IPF. Conclusions Transcriptome analysis identified several novel IPF-related genes. Among them, CCL8 is a candidate molecule for the differential diagnosis and prediction of survival. Electronic supplementary material The online version of this article (doi:10.1186/s12931-016-0493-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jong-Uk Lee
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Korea
| | - Eun-Young Shim
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Da-Jeong Bae
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea.,Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang, University Bucheon Hospital, Bucheon, Korea
| | - Soo-Taek Uh
- Division of Respiratory and Allergy Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, 1174, Jung Dong, Wonmi-Gu, Bucheon, Gyeonggi Do, 420-021, Korea
| | - Young Hoon Kim
- Division of Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University, Chunan Hospital, Cheonan, Korea
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang, University Bucheon Hospital, Bucheon, Korea
| | - Bora Lee
- Department of Biostatistic Consulting, Soon Chun Hyang Medical Center, Bucheon, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Choon-Sik Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea. .,Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang, University Bucheon Hospital, Bucheon, Korea.
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30
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Kim LH, Chang H, Namgoong S, Kim JO, Cheong HS, Lee SG, Park JS, Baek AR, Koo SM, Choi IS, Kim MK, Park HS, Park CS, Shin HD. Genetic variants of the gasdermin B gene associated with the development of aspirin-exacerbated respiratory diseases. Allergy Asthma Proc 2017; 38:4-12. [PMID: 28052796 DOI: 10.2500/aap.2017.38.4014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Aspirin-exacerbated respiratory disease (AERD) is characterized by a severe and sudden asthma attack after aspirin ingestion in patients with asthma. We studied associations with six common single nucleotide polymorphisms (SNP) of the gasdermin B gene (GSDMB). OBJECTIVE DNA obtained from 572 patients with asthma (with AERD, n = 165; and with aspirin-tolerant asthma, n = 407) and 391 normal controls was subjected to genotyping of six SNPs of GSDMB. METHODS An association analysis between GSDMB variants and AERD, with a fall rate of the forced expiratory volume in the first second of expiration (FEV1), was performed by using logistic and regression models. RESULTS Two SNPs in the intron (rs870830, rs7216389) showed significant associations with AERD (minimum p = 7.00 × 10-4 in the dominant model), even after Bonferroni correction (pcorr = 0.01 for the rs870830). Regression analysis of the genetic variants with FEV1 revealed significant associations with rs870830 and the haplotype 2 (pcorr = 4.71 × 10-4 for rs870830 and pcorr = 1.14 × 10-3 for haplotype 2, respectively). CONCLUSION We found strong associations among GSDMB polymorphisms and the presence of AERD and FEV1 in Korean patients with asthma. Our findings indicated that genetic variations of GSDMB may be associated with the development of AERD and aspirin-induced bronchospasm.
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Yang SK, Hong M, Oh H, Low HQ, Jung S, Ahn S, Kim Y, Baek J, Lee CH, Kim E, Kim KM, Ye BD, Kim KJ, Park SH, Lee HS, Lee I, Shin HD, Han B, McGovern DPB, Liu J, Song K. Identification of Loci at 1q21 and 16q23 That Affect Susceptibility to Inflammatory Bowel Disease in Koreans. Gastroenterology 2016; 151:1096-1099.e4. [PMID: 27569725 DOI: 10.1053/j.gastro.2016.08.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 12/02/2022]
Abstract
Recent genome-wide association studies have identified more than 200 regions that affect susceptibility to inflammatory bowel disease (IBD). However, identified common variants account for only a fraction of IBD heritability and largely have been identified in populations of European ancestry. We performed a genome-wide association study of susceptibility loci in Korean individuals, comprising a total of 1505 IBD patients and 4041 controls. We identified 2 new susceptibility loci for IBD at genome-wide significance: rs3766920 near PYGO2-SHC1 at 1q21 and rs16953946 in CDYL2 at 16q23. In addition, we confirmed associations, in Koreans, with 28 established IBD loci (P < 2.16 × 10-4). Our findings support the complementary value of genetic studies in different populations.
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Affiliation(s)
- Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Myunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyunjung Oh
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hui-Qi Low
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Seonjoo Ahn
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Youngjin Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Cue Hyunkyu Lee
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, Korea; Asan Institute for Life Sciences, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Eunji Kim
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, Korea; Asan Institute for Life Sciences, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea; Department of Chemistry, Seoul National University, Seoul, Korea
| | - Kyung Mo Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung-Jo Kim
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Inchul Lee
- Department of Pathology, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, Korea; Asan Institute for Life Sciences, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jianjun Liu
- Human Genetics Group, Genome Institute of Singapore, Singapore
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea.
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Lee JS, Cheong HS, Koh Y, Ahn KS, Shin HD, Yoon SS. MCM7 polymorphisms associated with the AML relapse and overall survival. Ann Hematol 2016; 96:93-98. [PMID: 27837251 DOI: 10.1007/s00277-016-2844-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/25/2016] [Indexed: 11/30/2022]
Abstract
The minichromosome maintenance complex component 7 (MCM7) encodes a member of MCM complex, which plays a critical role in the initiation of gene replication. Due to the importance of MCM complex, MCM7 gene has been regarded as a candidate gene for cancer development. In the present study, seven MCM7 polymorphisms were genotyped in 344 subjects composed of 103 acute myeloid leukemia (AML) patients and 241 normal controls to examine the possible associations between MCM7 polymorphisms and the risk of AML. MCM7 polymorphisms were not associated with the risk of AML (P > 0.05). However, MCM7 polymorphisms were significantly related to the relapse of AML and overall survival. The rs2070215 (N144S) showed a protective effect to the risk of AML relapse (OR = 0.37; P corr = 0.02). In haplotype analyses, the ht1 and ht2 showed significant associations with the risk of AML relapse (P corr = 0.02-0.03). In addition, rs1534309 showed an association with the overall survival of AML patients. Patients with major homozygote genotype (CC) of rs1534309 showed a higher survival rate than the patients with other genotypes (CG and GG). The results of the present study indicate that MCM7 polymorphisms may be able to predict the prognosis of AML patients.
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MESH Headings
- Adolescent
- Adult
- Aged
- Female
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Male
- Middle Aged
- Minichromosome Maintenance Complex Component 7/genetics
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/mortality
- Polymorphism, Single Nucleotide/genetics
- Survival Rate/trends
- Young Adult
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Affiliation(s)
- Jin Sol Lee
- Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea
- Department of Life Science, Sogang University, Seoul, 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, South Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehang-ro, Jongno-gu, Seoul, 110-744, South Korea
| | - Kwang-Sung Ahn
- Functional Genome Institute, PDXen Biosystem Inc., Seoul, South Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, 121-742, Republic of Korea
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, South Korea
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehang-ro, Jongno-gu, Seoul, 110-744, South Korea.
- Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea.
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Bae JS, Koh I, Cheong HS, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Sul JH, Park WY, Kim JH, Shin HD. A genome-wide association analysis of chromosomal aberrations and Hirschsprung disease. Transl Res 2016; 177:31-40.e6. [PMID: 27370899 DOI: 10.1016/j.trsl.2016.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 12/10/2015] [Revised: 05/12/2016] [Accepted: 06/06/2016] [Indexed: 12/12/2022]
Abstract
Hirschsprung disease (HSCR) is a neurocristopathy characterized by the absence of intramural ganglion cells along variable lengths of the gastrointestinal tract. Although the RET proto-oncogene is considered to be the main risk factor for HSCR, only about 30% of the HSCR cases can be explained by variations in previously known genes including RET. Recently, copy number variation (CNV) and loss of heterozygosity (LOH) have emerged as new ways to understand human genomic variation. The goal of this present study is to identify new HSCR genetic factors related to CNV in Korean patients. In the genome-wide genotyping, using Illumina's HumanOmni1-Quad BeadChip (1,140,419 markers), of 123 HSCR patients and 432 unaffected subjects (total n = 555), a total of 8,188 CNVs (1 kb ∼ 1 mb) were identified by CNVpartition. As a result, 16 CNV regions and 13 LOH regions were identified as associated with HSCR (minimum P = 0.0005). Two top CNV regions (deletions at chr6:32675155-32680480 and chr22:20733495-21607293) were successfully validated by additional real-time quantitative polymerase chain reaction analysis. In addition, 2 CNV regions (6p21.32 and 22q11.21) and 2 LOH regions (3p22.2 and 14q23.3) were discovered to be unique to the HSCR patients group. Regarding the large-scale chromosomal aberrations (>1 mb), 11 large aberrations in the HSCR patients group were identified, which suggests that they may be a risk factor for HSCR. Although further replication in a larger cohort is needed, our findings may contribute to the understanding of the etiology of HSCR.
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Affiliation(s)
- Joon Seol Bae
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - InSong Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Aran 13gil 15, Jeju, Republic of Korea
| | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Calif, USA; Semel Center for Informatics and Personalized Genomics, University of California, Los Angeles, Calif, USA
| | - Woong-Yang Park
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea; Department of Life Science, Sogang University, Seoul, Republic of Korea.
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Lee MK, Cheong HS, Koh Y, Ahn KS, Yoon SS, Shin HD. Genetic Association of PARP15 Polymorphisms with Clinical Outcome of Acute Myeloid Leukemia in a Korean Population. Genet Test Mol Biomarkers 2016; 20:696-701. [PMID: 27610459 DOI: 10.1089/gtmb.2016.0007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIMS Some members of the poly ADP-ribose polymerase (PARP) protein family have been regarded as targets for the therapeutic inhibition of cancer. Among these PARP genes, poly ADP-ribose polymerase family, member 15 (PARP15) is a candidate gene for cancer development due to its ability to regulate gene transcription and its reported association with apoptosis. The current study investigated the possible association between PARP15 single-nucleotide polymorphisms and the risk of acute myeloid leukemia (AML). In addition, we analyzed the effects of the PARP15 polymorphisms on the clinical phenotypes associated with cytosine arabinose (AraC) chemotherapy in AML patients. METHODS Ten PARP15 polymorphisms were genotyped via TaqMan assay in a total of 344 Korean subjects, including 103 AML patients and 241 normal controls. The genetic effects of the polymorphisms on the risk of AML and the clinical phenotypes were analyzed using Statistical Analysis System (SAS) software. RESULTS The results from a Cox regression analysis for overall survival revealed that two polymorphisms were associated with increased overall survival and the signal for rs17208928 was retained after correcting for multiple tests (pcorr < 0.05). CONCLUSIONS These results suggest the possibility that the PARP15 gene may be a potential therapeutic target in AML patients although much larger scale studies are needed for validation.
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Affiliation(s)
- Min Kyung Lee
- 1 Department of Life Science, Sogang University , Seoul, Republic of Korea
| | - Hyun Sub Cheong
- 2 Cancer Research Institute, Seoul National University Hospital , Seoul, Republic of Korea.,3 Department of Genetic Epidemiology, SNP Genetics, Inc. , Seoul, Republic of Korea
| | - Youngil Koh
- 4 Department of Internal Medicine, Seoul National University College of Medicine , Seoul, Republic of Korea
| | - Kwang-Sung Ahn
- 5 Functional Genome Institute , PDXen Biosystem, Inc., Seoul, Republic of Korea
| | - Sung-Soo Yoon
- 2 Cancer Research Institute, Seoul National University Hospital , Seoul, Republic of Korea.,4 Department of Internal Medicine, Seoul National University College of Medicine , Seoul, Republic of Korea.,6 Clinical Research Institute, Seoul National University Hospital , Seoul, Republic of Korea
| | - Hyoung Doo Shin
- 1 Department of Life Science, Sogang University , Seoul, Republic of Korea.,3 Department of Genetic Epidemiology, SNP Genetics, Inc. , Seoul, Republic of Korea
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Kim JH, Lee C, Cheong HS, Koh Y, Ahn KS, Kim HL, Shin HD, Yoon SS. SLC29A1 (ENT1) polymorphisms and outcome of complete remission in acute myeloid leukemia. Cancer Chemother Pharmacol 2016; 78:533-40. [DOI: 10.1007/s00280-016-3103-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/06/2016] [Indexed: 02/08/2023]
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Shin JG, Kim DY, Seo JM, Oh JT, Park KW, Kim HY, Park BL, Kim JH, Shin HD. Potential association of VAMP5 polymorphisms with total colonic aganglionosis in Hirschsprung disease. Neurogastroenterol Motil 2016; 28:1055-63. [PMID: 26970437 DOI: 10.1111/nmo.12807] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/29/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital bowel disease caused by the absence of nerve cells in portions of the intestine. Our recent genome-wide association study has identified a variant (rs1254900) of vesicle-associated membrane protein 5 (VAMP5) as a potential risk locus for total colonic aganglionosis (TCA) in HSCR. In addition, VAMP5 is a member of the VAMP/synaptobrevin protein complex, which participates in nerve signal transduction by regulating the vesicular fusion of the neurotransmitter in synaptic transmission. METHODS A total of 11 single nucleotide polymorphisms (SNPs), including those in the functionally important coding region, were selected on the basis of linkage disequilibrium and genotyped in 187 HSCR patients and 283 unaffected controls by using a TaqMan assay. Logistic analysis was conducted to investigate the possible association between VAMP5 SNPs and the risk of HSCR. KEY RESULTS Genetic variants of VAMP5 showed increased association signals in the TCA subgroup of HSCR patients (minimum p = 9.69 × 10(-5) , OR = 3.93 at rs10206961) compared to other subgroups, even after Bonferroni correction (pcorr = 0.002). In haplotype analysis, three haplotypes (BL1_ht1, BL2_ht1, and BL2_ht2) were associated with the risk of TCA (minimum pcorr = 0.005). In additional combined analysis after imputation based on our previous GWAS, five SNPs still retained significant associations with the TCA subtype (minimum pcorr = 0.006 at rs10206961). CONCLUSIONS & INFERENCES Considering that differential genetic effects on the development of the enteric nervous system, our results suggest that VAMP5 may be associated with the TCA of HSCR. However, further replications and functional evaluations are required.
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Affiliation(s)
- J-G Shin
- Department of Life Science, Sogang University, Seoul, Korea
| | - D-Y Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J-M Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - J-T Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - K-W Park
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - H-Y Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - B L Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - J-H Kim
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - H D Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
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Kim LH, Park BL, Cheong HS, Namgoong S, Kim JO, Kim JH, Shin JG, Park CS, Kim BJ, Kim JW, Choi IG, Hwang J, Shin HD, Woo SI. Genome-wide association study with the risk of schizophrenia in a Korean population. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:257-65. [PMID: 26531332 DOI: 10.1002/ajmg.b.32400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 10/23/2015] [Indexed: 11/10/2022]
Abstract
Schizophrenia is regarded as a multifactorial and polygenic brain disorder that is attributed to different combinations of genetic and environmental risk factors. Recently, several genome-wide association studies (GWASs) of schizophrenia have identified numerous risk factors, but the replication results remain controversial and ambiguous. To identify schizophrenia susceptibility loci in the Korean population, we performed a GWAS using the Illumina HumanOmni1-Quad V1.0 Microarray. We genotyped 1,140,419 single nucleotide polymorphisms (SNPs) in 350 Korea schizophrenia patients and 700 control subjects, and approximately 620,001 autosomal SNPs were passed our quality control. In the case-control analysis, the rs9607195 A>G on intergenic area 250 kb away from the ISX gene and the rs12738007 A>G on the intron of the MECR gene were the most strongly associated SNPs with the risk of schizophrenia (P = 6.2 × 10(-8) , OR = 0.50 and P = 3.7 × 10(-7) , OR = 2.39, respectively). In subsequent fine-mapping analysis, 6 SNPs of MECR were genotyped with 310 schizophrenia patients and 604 control subjects. The association of the MECR rs12738007, a top ranked-SNP in GWAS, was replicated (P = 1.5 × 10(-2) , OR = 1.53 in fine mapping analysis, P = 1.5 × 10(-6) , OR = 1.90 in combined analysis). The identification of putative schizophrenia susceptibility loci could provide new insights into genetic factors related with schizophrenia and clues for the development of diagnosis strategies.
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Affiliation(s)
- Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Suhg Namgoong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Joong-Gon Shin
- Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Chul Soo Park
- Department of Psychiatry, College of Medicine, Gyeongsang National University, Gyeongsang Nam Do, Republic of Korea
| | - Bong-Jo Kim
- Department of Psychiatry, College of Medicine, Gyeongsang National University, Gyeongsang Nam Do, Republic of Korea
| | - Jae Won Kim
- Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju-ro, Gyeongsang Nam Do, Republic of Korea
| | - Ihn-Geun Choi
- Department of Neuropsychiatry, Hallym University, Han-Gang Sacred Heart Hospital, Yeongdeungpo-gu, Seoul, Republic of Korea
| | - Jaeuk Hwang
- Department of Neuropsychiatry, Soonchunhyang University Hospital, Yongsan-gu, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Sung-Il Woo
- Department of Neuropsychiatry, Soonchunhyang University Hospital, Yongsan-gu, Seoul, Republic of Korea
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Namgoong S, Cheong HS, Kim JO, Kim LH, Na HS, Koh IS, Chung MW, Shin HD. Comparison of genetic variations of the SLCO1B1, SLCO1B3, and SLCO2B1 genes among five ethnic groups. Environ Toxicol Pharmacol 2015; 40:692-697. [PMID: 26409184 DOI: 10.1016/j.etap.2015.08.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/30/2015] [Accepted: 08/31/2015] [Indexed: 06/05/2023]
Abstract
Organic anion-transporting polypeptide (OATP; gene symbol, SLCO) transporters are generally involved in the uptake of multiple drugs and their metabolites at most epithelial barriers. The pattern of single-nucleotide polymorphisms (SNPs) in these transporters may be determinants of interindividual variability in drug disposition and response. The objective of this study was to define the distribution of SNPs of three SLCO genes, SLCO1B1, SLCO1B3, and SLCO2B1, in a Korean population and other ethnic groups. The study was screened using the Illumina GoldenGate assay for genomic DNA from 450 interethnic subjects, including 11 pharmacogenetic core variants and 76 HapMap tagging SNPs. The genotype distribution of the Korean population was similar to East Asian populations, but significantly different from African American and European American cohorts. These interethnic differences will be useful information for prospective studies, including genetic association and pharmacogenetic studies of drug metabolism by SLCO families.
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Affiliation(s)
- Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, Republic of Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Ji On Kim
- Department of Life Science, Sogang University, Seoul, Republic of Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Life Science, Sogang University, Seoul, Republic of Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Han Sung Na
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk-do, Republic of Korea
| | - In Song Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Myeon Woo Chung
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk-do, Republic of Korea.
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.
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Kim LH, Cheong HS, Shin JG, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Koh I, Kim JH, Shin HD. Genetic variants of IL-11 associated with risk of Hirschsprung disease. Neurogastroenterol Motil 2015; 27:1371-7. [PMID: 26172388 DOI: 10.1111/nmo.12629] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 06/15/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital and heterogeneous disorder characterized by the absence of enteric ganglia during enteric nervous system (ENS) development. Our recent genome-wide association study has identified a variant (rs6509940) of interleukin-11 (IL-11) as a potential susceptible locus for HSCR. As interleukins play important roles in the ENS, we further studied associations with HSCR of nine common single nucleotide polymorphisms (SNPs) on IL-11. METHODS Biopsy specimens or surgical materials from all patients that were tested for histological examination based on the absence of the enteric ganglia were collected. A total of nine SNPs on IL-11 were genotyped in 187 HSCR patients and 283 unaffected controls using TaqMan genotyping assay. KEY RESULTS Combined analysis revealed that several SNPs (minimum p = 1.57 × 10(-7) ) showed statistically significant associations with HSCR, even after Bonferroni correction (pcorr = 1.73 × 10(-6) for the SNP). Moreover, the most common haplotype was strongly associated with HSCR (pcorr = 2.20 × 10(-6) ). In further analysis among three HSCR subtypes (short segment, S-HSCR; long segment, L-HSCR; total colonic aganglionosis, TCA) based on the extent of aganglionic segment, the result showed a different association pattern depending on the subtypes (minimum pcorr = 6.12 × 10(-5) for rs6509940 in S-HSCR; but no significant SNP in L-HSCR and TCA). CONCLUSIONS & INFERENCES Although further replication in a larger cohort and functional evaluations are needed, our findings suggest that genetic variations of IL-11 may be associated with the risk of HSCR and/or the mechanisms related to ENS development.
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Affiliation(s)
- L H Kim
- Department of Life Science, Sogang University, Seoul, Korea
| | - H S Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - J-G Shin
- Department of Life Science, Sogang University, Seoul, Korea
| | - J-M Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - D-Y Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J-T Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - H-Y Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - K Jung
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Korea
| | - I Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Korea
| | - J-H Kim
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - H D Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
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Jung K, Kim JH, Cheong HS, Shin E, Kim SH, Hwang JY, Lee E, Yoon MO, Kim SH, Sio CA, Shin HD, Jung SE. Gene expression profile of necrotizing enterocolitis model in neonatal mice. Int J Surg 2015; 23:28-34. [PMID: 26403067 DOI: 10.1016/j.ijsu.2015.09.049] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/11/2015] [Accepted: 09/14/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND Necrotizing enterocolitis (NEC) characterized by intestinal necrosis is one of the most common gastrointestinal emergencies in newborns. The main purpose of this study was to evaluate the whole genome expression levels in a NEC mouse model controlled with breast milk. METHODS This study induced a NEC model in mice of gestational ages of 18-21 days by intensive hypoxic insult and permitted breast-feeding instead of formula feeding. After evaluating the NEC status in the small intestines of neonatal mice by histological examination, a genome-wide gene expression profile study was completed using microarray analysis. RESULTS A total of 72 genes (38 down-regulated and 34 up-regulated) were observed to have significantly different expression profiles in the NEC mouse model compared with the normal control animals, based on a significance at fold change ≥ 2 and P < 0.05. In particular, down-regulated Hist1h2aa and up-regulated Ube2i showed the most significant signals (P = 0.0008 for both genes). In an additional gene ontology analysis, the endopeptidase related categories (specifically, serine-type endopeptidase inhibitor activity, P = 8.95 × 10(-5); Pcorr = 0.008) appeared to affect NEC development in the mouse model. CONCLUSION Although replications and functional evaluations are needed, our results suggest that several genes may have different expression profiles in the NEC mouse model. In particular, endopeptidase related genes (which are also known to be relevant to NEC), as identified through gene ontology analysis, may represent attractive targets for future research.
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Affiliation(s)
- Kyuwhan Jung
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 153-803, Republic of Korea
| | - Eun Shin
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Seong-Ho Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Ji-Yeon Hwang
- Preclinical Experimental Center, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Eunyoung Lee
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Mi-Ok Yoon
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Seong-Hee Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Cherry Ann Sio
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea; Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea.
| | - Sung-Eun Jung
- Department of Surgery, Seoul National University Children's Hospital, Seoul 110-773, Republic of Korea.
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Hyo Kim L, Sub Cheong H, Koh Y, Ahn KS, Lee C, Kim HL, Doo Shin H, Yoon SS. Cytidine deaminase polymorphisms and worse treatment response in normal karyotype AML. J Hum Genet 2015; 60:749-54. [PMID: 26354033 DOI: 10.1038/jhg.2015.105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/20/2015] [Accepted: 07/30/2015] [Indexed: 11/09/2022]
Abstract
The cytidine deaminase (CDA) catalyzes the irreversible hydrolytic deamination of the cytarabine (AraC) into a 1-β-D-arabinofuranosyluracil (AraU), an inactive metabolite that plays a crucial role in lowering the amount of AraC, a key chemotherapeutic drug, in the treatment of patients with acute myeloid leukemia (AML). In this study, we hypothesized that CDA polymorphisms were associated with the AraC metabolism for AML treatment and/or related clinical phenotypes. We analyzed 16 polymorphisms of CDA among 50 normal karyotype AML (NK-AML) patients, 45 abnormal karyotype AML (AK-AML) patients and 241 normal controls (NC). Several polymorphisms and haplotypes, rs532545, rs2072671, rs471760, rs4655226, rs818194 and CDA-ht3, were found to have a strong correlation with NK-AML compared with NC and these polymorphisms also revealed strong linkage disequilibrium with each other. Among them, rs2072671 (79A>C), which is located in a coding region and the resultant amino acid change K27Q, showed significant associations with NK-AML compared with NC (P=0.009 and odds ratio=2.44 in the dominant model). The AC and CC genotypes of rs2072671 (79A>C) were significantly correlated with shorter overall survival rates (P=0.03, hazard ratio=1.84) and first complete remission duration (P=0.007, hazard ratio=3.24) compared with the AA genotype in the NK-AML patients. Our results indicate that rs2072671 in CDA may be an important prognostic marker in NK-AML patients.
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Affiliation(s)
- Lyoung Hyo Kim
- Department of Life Science, Sogang University, Seoul, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kwang-Sung Ahn
- Functional Genome Institute, PDXen Biosystem, Seoul, Republic of Korea
| | - Chansu Lee
- Cancer Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
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Cheong HS, Lee JH, Yu SJ, Yoon JH, Lee HS, Cheong JY, Cho SW, Park NH, Park BL, Namgoong S, Kim LH, Shin HD, Kim YJ. Association of VARS2-SFTA2 polymorphisms with the risk of chronic hepatitis B in a Korean population. Liver Int 2015; 35:1934-40. [PMID: 25404243 DOI: 10.1111/liv.12740] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/13/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Hepatitis B virus (HBV) infection is the most serious risk factor for chronic hepatitis B (CHB), cirrhosis, and hepatocellular carcinoma. Recently, several genome-wide association studies (GWASs) identified important variants associated with the risk of CHB in Asian populations. Specifically, our previous GWAS identified the VARS2-SFTA2 gene region as one of the genetic risk loci for CHB. METHODS To further characterize this association and to isolate possible causal variants within it, we performed an additional association study by genotyping more SNPs in the vicinity of the VARS2 and SFTA2 genes. In all, 14 SNPs of VARS2-SFTA2 were analysed among a total of 3902 subjects (1046 cases and 2856 controls). RESULTS Logistic regression analysis revealed that six SNPs, including the previously reported rs2532932, were significantly associated with the risk of CHB (P = 1.7 × 10(-10) ~0.002). Further linkage disequilibrium and conditional analysis identified two variants (rs9394021 and rs2517459) as new markers of genetic risk factors for CHB rather than the reported SNP from our previous study (rs2532932). To evaluate the cumulative risk for CHB based on all known genetic factors, genetic risk score (GRS) were calculated. As anticipated, the distribution of the number of risk alleles in cases vs. controls clearly differed according to the GRS. Similarly, the odds ratios (ORs) were increased (OR = 0.32-3.97). CONCLUSION Our findings show that common variants in the VARS2-SFTA2 gene region are significantly associated with CHB in a Korean population, which may be useful in further understanding genetic susceptibility to CHB.
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Affiliation(s)
- Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Hyo-Suk Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Sung Won Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Suhg Namgoong
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Yoon-Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
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Shin JG, Park BL, Kim LH, Namgoong S, Kim JO, Chang HS, Park JS, Jang AS, Park SW, Kim DJ, Kim KU, Kim YG, Uh ST, Seo KH, Kim YH, Koh I, Park CS, Shin HD. Association study of polymorphisms in interferon-γ receptor genes with the risk of pulmonary tuberculosis. Mol Med Rep 2015; 12:1568-78. [PMID: 25815589 DOI: 10.3892/mmr.2015.3544] [Citation(s) in RCA: 8] [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: 05/29/2014] [Accepted: 02/23/2015] [Indexed: 11/05/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by mycobacterium, which most commonly affects the lungs. The adaptive immune response in Mycobacterium tuberculosis is predominantly mediated by the interferon-γ (IFN-γ) signaling pathway, which is regulated by IFN-γ receptors (IFNGR). IFN-γ activates the transcription of a number of genes that are important in immune responses, thus the appropriate function of IFNGR appears to be important in host defense against mycobacteria. In the present study, 22 genetic variants in IFNGR1 and IFNGR2 were genotyped in 673 patients and 592 normal controls to investigate the association between IFNGR1 and IFNGR2 polymorphisms and the risk of TB. Statistical analyses revealed that four genetic variants in IFNGR1, rs9376269, rs9376268, rs9376267 and rs56251346 were marginally associated with the risk of TB (P = 0.02-0.04), while other single nucleotide polymorphisms in IFNGR1 and IFNGR2 did not exhibit any associations. However, the significance of the four genetic variants rs9376269, rs9376268, rs9376267 and rs56251346 was eliminated following a multiple testing correction of the data (P>0.05). The present results revealed that certain genetic variants in IFNGR genes may be associated with TB development, which may be useful preliminary data for future investigation.
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Affiliation(s)
- Joong-Gon Shin
- Department of Life Science, Sogang University, Seoul 121‑742, Republic of Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121‑742, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Life Science, Sogang University, Seoul 121‑742, Republic of Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, Seoul 121‑742, Republic of Korea
| | - Ji On Kim
- Department of Life Science, Sogang University, Seoul 121‑742, Republic of Korea
| | - Hun Soo Chang
- Soonchunhyang Medical Science Research Institute, Soonchunhyang University Bucheon Hospital, Bucheon, Gyeonggi‑do 420‑020, Republic of Korea
| | - Jong Sook Park
- Genome Research Center for Allergy and Respiratory Diseases, Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Gyeonggi‑do 420‑020, Republic of Korea
| | - An Soo Jang
- Genome Research Center for Allergy and Respiratory Diseases, Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Gyeonggi‑do 420‑020, Republic of Korea
| | - Sung Woo Park
- Genome Research Center for Allergy and Respiratory Diseases, Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Gyeonggi‑do 420‑020, Republic of Korea
| | - Do Jin Kim
- Genome Research Center for Allergy and Respiratory Diseases, Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Gyeonggi‑do 420‑020, Republic of Korea
| | - Ki Up Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, Seoul 140-743, Republic of Korea
| | - Yang Gee Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, Seoul 140-743, Republic of Korea
| | - Soo-Taek Uh
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, Seoul 140-743, Republic of Korea
| | - Ki Hyun Seo
- Division of Allergy and Respiratory Medicine, Soonchunhyang University, Cheonan Hospital, Cheonan, Hoseo 30240, Republic of Korea
| | - Young Hoon Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University, Cheonan Hospital, Cheonan, Hoseo 30240, Republic of Korea
| | - Insong Koh
- Department of Physiology, Hanyang University College of Medicine, Seoul 133-791, Republic of Korea
| | - Choon Sik Park
- Genome Research Center for Allergy and Respiratory Diseases, Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Gyeonggi‑do 420‑020, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul 121‑742, Republic of Korea
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Cha SM, Shin HD, Kim KC, Park IY. Extensive curettage using a high-speed burr versus dehydrated alcohol instillation for the treatment of enchondroma of the hand. J Hand Surg Eur Vol 2015; 40:384-91. [PMID: 24369364 DOI: 10.1177/1753193413517204] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 11/22/2013] [Indexed: 02/03/2023]
Abstract
The purpose of this retrospective study was to compare the clinical and radiological outcomes of patients treated with different adjuvant methods after curettage for enchondromas of the hand. Sixty-two patients with enchondroma were treated with high-speed burring (29 patients) or alcohol instillation (33 patients) after curettage. The mean follow-up was 40.8 months. No significant differences in the visual analogue scale, Disabilities of the Arm, Shoulder, and Hand scores, total range of active motion, grip strength, and complete healing time were observed between the groups. The distribution of the results of the formula by Wilhelm and Feldmeier were not significantly different between the groups. No surgery-related complications, postoperative pathological fractures, or recurrence was found in either group. For the treatment of enchondroma in the metacarpal and proximal phalanx, alcohol instillation immediately after curettage was as effective as extensive curettage using a high-speed burr.
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Affiliation(s)
- S M Cha
- Department of Orthopaedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon, Korea
| | - H D Shin
- Department of Orthopaedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon, Korea
| | - K C Kim
- Department of Orthopaedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon, Korea
| | - I Y Park
- Department of Orthopaedic Surgery, Regional Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon, Korea
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Bae JS, Park BL, Cheong HS, Kim JH, Kim JY, Namgoong S, Kim JO, Park CS, Kim BJ, Lee CS, Kim JW, Choi WH, Shin TM, Hwang J, Koh IS, Shin HD, Woo SI. Association analysis of PDE4B polymorphisms with schizophrenia and smooth pursuit eye movement abnormality in a Korean population. Gen Physiol Biophys 2015; 34:277-84. [PMID: 25926551 DOI: 10.4149/gpb_2015004] [Citation(s) in RCA: 3] [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] [Received: 08/29/2014] [Accepted: 02/06/2015] [Indexed: 11/08/2022]
Abstract
Schizophrenia is a debilitating mental disorder with a high heritability rate. Located on chromosome 1p31.3, the human cAMP-specific 3',5'-cyclic phosphodiesterase 4B (PDE4B) gene has been considered as an important candidate gene for the risk of schizophrenia. Several genetic association studies reported the association between PDE4B polymorphisms and the risk of schizophrenia in Caucasian, African American, Indian, and Japanese populations. The aim of this study is to examine the association of PDE4B variations with schizophrenia and smooth pursuit eye movement (SPEM) abnormality in a Korean population. A case-control association analysis was carried out by comparing the genotype distribution of eight PDE4B polymorphisms between 457 schizophrenia patients and 386 normal healthy subjects. Differences in the frequency distribution of PDE4B single nucleotide polymorphisms (SNPs) and haplotypes were analyzed by logistic regression analyses controlling for age as a covariate. Statistical analyses revealed nominal significant associations of rs1040716, rs472952, rs1321177, and rs2144719 with the risk of schizophrenia (p = 0.02~0.05). The rs11208756 polymorphism showed a nominal significant association with SPEM abnormality (p = 0.05). In a meta-analysis with Japanese and Korean populations, three SNPs (rs472952, rs1040716, and rs2180335) revealed significant associations with schizophrenia (meta-p value = 0.0038~0.019). Our results support previously reported association of PDE4B variations with schizophrenia in other populations. The findings in this study add a new evidence for the involvement of PDE4B gene in schizophrenia etiology.
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Affiliation(s)
- Joon Seol Bae
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul 135-710, Republic of Korea
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Kim LH, Cheong HS, Namgoong S, Kim JO, Kim JH, Park BL, Cho SW, Park NH, Cheong JY, Koh I, Shin HD, Kim YJ. Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci of STAT4 and HLA-DQ in a Korean population. Infect Genet Evol 2015; 33:72-6. [PMID: 25913043 DOI: 10.1016/j.meegid.2015.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/03/2015] [Accepted: 04/15/2015] [Indexed: 12/14/2022]
Abstract
A recent genome-wide association study (GWAS) for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) identified two loci (rs7574865 in STAT4 and rs9275319 in HLA-DQ) in a Chinese population. We attempted to replicate the associations between the two SNP loci and the risk of HCC in a Korean population. The rs7574865 in STAT4 and rs9275319 in HLA-DQ were genotyped in a total of 3838 Korean subjects composed of 287 HBV-related hepatocellular carcinoma patients, 671 chronic hepatitis B virus (CHB) patients, and 2880 population controls using TaqMan genotyping assay. Gene expression was measured by microarray. A logistic regression analysis revealed that rs7574865 in STAT4 and rs9275319 in HLA-DQ were associated with the risk of CHB (OR = 1.25, P = 0.0002 and OR = 1.57, P= 1.44 × 10(-10), respectively). However, these loci were no association with the risk of HBV-related HCC among CHB patients. In the gene expression analyses, although no significant differences in mRNA expression of nearby genes according to genotypes were detected, a significantly decreased mRNA expression in HCC subjects was observed in STAT4, HLA-DQA1, and HLA-DQB1. Although the genetic effects of two HCC susceptibility loci were not replicated, the two loci were found to exert susceptibility effects on the risk of CHB in a Korean population. In addition, the decreased mRNA expression of STAT4, HLA-DQA1, and HLA-DQB1 in HCC tissue might provide a clue to understanding their role in the progression to HCC.
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Affiliation(s)
- Lyoung Hyo Kim
- Department of Life Science, Sogang University, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Jeong-Hyun Kim
- Department of Life Science, Sogang University, Republic of Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Sung Won Cho
- Department of Gastroenterology, Ajou University School of Medicine, Republic of Korea
| | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, Republic of Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Republic of Korea
| | - InSong Koh
- Department of Physiology, College of Medicine, Han Yang University, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea.
| | - Yoon-Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Republic of Korea.
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Forero DA, López-León S, Shin HD, Park BL, Kim DJ. Meta-analysis of six genes (BDNF, DRD1, DRD3, DRD4, GRIN2B and MAOA) involved in neuroplasticity and the risk for alcohol dependence. Drug Alcohol Depend 2015; 149:259-63. [PMID: 25660313 DOI: 10.1016/j.drugalcdep.2015.01.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 01/24/2023]
Abstract
BACKGROUND Alcohol-related problems have a large impact on human health, accounting for around 4% of deaths and 4.5% of disability-adjusted life-years around the world. Genetic factors could explain a significant fraction of the risk for alcohol dependence (AD). Recent meta-analyses have found significant pooled odds ratios (ORs) for variants in the ADH1B, ADH1C, DRD2 and HTR2A genes. METHODS In the present study, we carried out a meta-analysis of common variants in 6 candidate genes involved in neurotransmission and neuroplasticity: BDNF, DRD1, DRD3, DRD4, GRIN2B and MAOA. We carried out a systematic search for published association studies that analyzed the genes of interest. Relevant articles were retrieved and demographic and genetic data were extracted. Pooled ORs were calculated using a random-effects model using the Meta-Analyst program. Dominant, recessive and allelic models were tested and analyses were also stratified by ethnicity. RESULTS Forty two published studies were included in the current meta-analysis: BDNF-rs6265 (nine studies), DRD1-rs4532 (four studies), DRD3-rs6280 (eleven studies), DRD4-VNTR (seven studies), GRIN2B-rs1806201 (three studies) and MAOA-uVNTR (eight studies). We did not find significant pooled ORs for any of the six genes, under different models and stratifying for ethnicity. CONCLUSIONS In terms of the number of candidate genes included, this is one of the most comprehensive meta-analyses for genetics of AD. Pooled ORs did not support consistent associations with any of the six candidate genes tested. Future studies of novel genes of functional relevance and meta-analyses of quantitative endophenotypes could identify further susceptibility molecular factors for AD.
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Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.
| | | | - Hyoung Doo Shin
- Laboratory of Genomic Diversity, Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Republic of Korea
| | - Dai-Jin Kim
- Department of Psychiatry, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Kim JH, Cheong HS, Kim LH, Shin HJ, Na HS, Chung MW, Shin HD. Direct sequencing for comprehensive screening of LDLR genetic polymorphisms among five ethnic populations. Genes Genomics 2015. [DOI: 10.1007/s13258-014-0244-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Chang HS, Shin SW, Lee TH, Bae DJ, Park JS, Kim YH, Uh ST, Choi BW, Kim MK, Choi IS, Park BL, Shin HD, Park CS. Development of a genetic marker set to diagnose aspirin-exacerbated respiratory disease in a genome-wide association study. Pharmacogenomics J 2015; 15:316-21. [PMID: 25707394 DOI: 10.1038/tpj.2014.78] [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] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/28/2014] [Accepted: 11/05/2014] [Indexed: 12/27/2022]
Abstract
We developed a genetic marker set of single nucleotide polymorphisms (SNPs) by summing risk scores of 14 SNPs showing a significant association with aspirin-exacerbated respiratory disease (AERD) from our previous 660 W genome-wide association data. The summed scores were higher in the AERD than in the aspirin-tolerant asthma (ATA) group (P=8.58 × 10(-37)), and were correlated with the percent decrease in forced expiratory volume in 1 s after aspirin challenge (r(2)=0.150, P=5.84 × 10(-30)). The area under the curve of the scores for AERD in the receiver operating characteristic curve was 0.821. The best cutoff value of the summed risk scores was 1.01328 (P=1.38 × 10(-32)). The sensitivity and specificity of the best scores were 64.7% and 85.0%, respectively, with 42.1% positive and 93.4% negative predictive values. The summed risk score may be used as a genetic marker with good discriminative power for distinguishing AERD from ATA.
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Affiliation(s)
- H S Chang
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan, Republic of Korea
| | - S W Shin
- Asthma Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - T H Lee
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan, Republic of Korea
| | - D J Bae
- Department of Medical Bioscience, Graduate School, Soonchunhyang University, Asan, Republic of Korea
| | - J S Park
- 1] Asthma Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea [2] Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Y H Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Republic of Korea
| | - S T Uh
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - B W Choi
- Department of Internal Medicine, Chung-Ang University Yongsan Hospital, Seoul, Republic of Korea
| | - M K Kim
- Division of Internal Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - I S Choi
- Department of Allergy, Chonnam National University, Gwangju, Republic of Korea
| | - B L Park
- Department of Genetic Epidemiology, SNP Genetics Incorporation, Seoul, Republic of Korea
| | - H D Shin
- 1] Department of Genetic Epidemiology, SNP Genetics Incorporation, Seoul, Republic of Korea [2] Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - C S Park
- 1] Asthma Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea [2] Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
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Choi IY, Cheong SS, Joa JH, Cho SE, Shin HD. First Report of Powdery Mildew Caused by Podosphaera xanthii on Sechium edule in Korea. Plant Dis 2015; 99:162. [PMID: 30699759 DOI: 10.1094/pdis-10-14-1011-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sechium edule (Jacq.) Sw. (Cucurbitaceae, chayote, mirliton) is native to Mexico and Central America. Several trials have recently been conducted to determine the ability of chayote cultivars to grow under the climatic and soil conditions of South Korea. In April 2013, chayote plants were observed showing typical symptoms of powdery mildew in a glasshouse in Jeju City, Korea. Powdery mildew colonies were circular to irregular, forming white patches on both sides of the leaves. As the disease progressed, entire leaves were covered with white mycelium, followed by leaf withering and premature senescence. The same symptoms were also found on chayote plants in a polyethylene-film-covered greenhouse in Iksan City, Korea, in 2014. Voucher specimens were deposited in the Korea University Herbarium (KUS-F27289, F27422, F28186). Hyphae were flexuous to straight, branched, septate, and 5 to 7 μm wide. Appressoria on the mycelium were nipple-shaped or nearly absent. Conidiophores were straight, 150 to 240 × 10 to 12 μm and produced three to seven immature conidia in chains with a crenate outline. Foot-cells of conidiophores were straight, cylindric, and 52 to 85 μm long. Conidia were hyaline, ellipsoid-ovoid to barrel-shaped, measured 27 to 36 × 16 to 23 μm with a length/width ratio of 1.3 to 2.0, and had distinct fibrosin bodies. Simple to forked germ tubes were produced from the lateral position of conidia. No chasmothecia were found. These structures are typical of the powdery mildew Euoidium anamorph of the genus Podosphaera. Dimensions of foot-cells and conidia were within the ranges provided for P. xanthii (Castagne) U. Braun & Shishkoff, and the length/width ratio of conidia, appressorial characteristics, and conidial germination patterns also conformed to the standard description (2). To confirm the identification, the complete internal transcribed spacer (ITS) region of rDNA of isolate KUS-F27289 was amplified with primers ITS1 and ITS4 and sequenced directly. The resulting 473-bp sequence was deposited in GenBank (Accession No. KM657960). A GenBank BLAST search of the Korean isolate showed 99% similarity with P. xanthii isolates from cucurbitaceous hosts (e.g., AB774155 to AB774158, AB040321, JQ340082, etc.). Pathogenicity was confirmed through inoculation tests by gently pressing a diseased leaf onto young leaves of three asymptomatic, potted chayote plants. Three non-inoculated plants were used as controls. Plants were maintained in a greenhouse at 24 to 34°C. Inoculated leaves started to develop symptoms after 5 days, whereas the control plants remained symptomless. The pathogenicity test was carried out twice with similar results. Powdery mildews of chayote caused by Podosphaera species have been reported in Australia, South Africa, Portugal, India, China, and the United States (1,3,4). To our knowledge, this is the first report of powdery mildew caused by P. xanthii on chayote in Korea. Since chayote production was only recently started on a commercial scale in Korea, powdery mildew infections may pose a serious threat to the safe production of this vegetable. References: (1) P. Baiswar et al. Australas. Plant Dis. Notes 3:160, 2008. (2) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No. 11. CBS, Utrecht, 2012. (3) D. F. Farr and A. Y. Rossman. Fungal Databases. Syst. Mycol. Microbiol. Lab. Online publication, ARS, USDA, Retrieved October 4, 2014. (4) R. Singh et al. Plant Dis. 93:1348, 2009.
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Affiliation(s)
- I Y Choi
- Jeollabuk-do Agricultural Research and Extension Services, Iksan 570-704, Korea
| | - S S Cheong
- Jeollabuk-do Agricultural Research and Extension Services, Iksan 570-704, Korea
| | - J H Joa
- Agricultural Research Center for Climate Change, National Institute of Horticultural and Herbal Science, Jeju 690-150, Korea
| | - S E Cho
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 136-701, Korea
| | - H D Shin
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul 136-701, Korea
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