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Oh EY, Han KM, Kim A, Kang Y, Tae WS, Han MR, Ham BJ. Integration of whole-exome sequencing and structural neuroimaging analysis in major depressive disorder: a joint study. Transl Psychiatry 2024; 14:141. [PMID: 38461185 PMCID: PMC10924915 DOI: 10.1038/s41398-024-02849-4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024] Open
Abstract
Major depressive disorder (MDD) is a common mental illness worldwide and is triggered by an intricate interplay between environmental and genetic factors. Although there are several studies on common variants in MDD, studies on rare variants are relatively limited. In addition, few studies have examined the genetic contributions to neurostructural alterations in MDD using whole-exome sequencing (WES). We performed WES in 367 patients with MDD and 161 healthy controls (HCs) to detect germline and copy number variations in the Korean population. Gene-based rare variants were analyzed to investigate the association between the genes and individuals, followed by neuroimaging-genetic analysis to explore the neural mechanisms underlying the genetic impact in 234 patients with MDD and 135 HCs using diffusion tensor imaging data. We identified 40 MDD-related genes and observed 95 recurrent regions of copy number variations. We also discovered a novel gene, FRMPD3, carrying rare variants that influence MDD. In addition, the single nucleotide polymorphism rs771995197 in the MUC6 gene was significantly associated with the integrity of widespread white matter tracts. Moreover, we identified 918 rare exonic missense variants in genes associated with MDD susceptibility. We postulate that rare variants of FRMPD3 may contribute significantly to MDD, with a mild penetration effect.
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Affiliation(s)
- Eun-Young Oh
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Kyu-Man Han
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
- Brain Convergence Research Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Aram Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Youbin Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woo-Suk Tae
- Brain Convergence Research Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea.
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea.
- Brain Convergence Research Center, Korea University College of Medicine, Seoul, Republic of Korea.
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Bae SH, Hwang T, Han MR. Unraveling the hypoxia modulating potential of VEGF family genes in pan-cancer. Genomics Inform 2023; 21:e44. [PMID: 37852616 PMCID: PMC10788353 DOI: 10.5808/gi.23061] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Tumor hypoxia, oxygen deprivation state, occurs in most cancers and promotes angiogenesis, enhancing the potential for metastasis. The vascular endothelial growth factor (VEGF) family genes play crucial roles in tumorigenesis by promoting angiogenesis. To investigate the malignant processes triggered by hypoxia-induced angiogenesis across pan-cancers, we comprehensively analyzed the relationships between the expression of VEGF family genes and hypoxic microenvironment based on integrated bioinformatics methods. Our results suggest that the expression of VEGF family genes differs significantly among various cancers, highlighting their heterogeneity effect on human cancers. Across the 33 cancers, VEGFB and VEGFD showed the highest and lowest expression levels, respectively. The survival analysis showed that VEGFA and placental growth factor (PGF) were correlated with poor prognosis in many cancers, including kidney renal cell and liver hepatocellular carcinoma. VEGFC expression was positively correlated with glioma and stomach cancer. VEGFA and PGF showed distinct positive correlations with hypoxia scores in most cancers, indicating a potential correlation with tumor aggressiveness. The expression of miRNAs targeting VEGF family genes, including hsa-miR-130b-5p and hsa-miR-940, was positively correlated with hypoxia. In immune subtypes analysis, VEGFC was highly expressed in C3 (inflammatory) and C6 (transforming growth factor β dominant) across various cancers, indicating its potential role as a tumor promotor. VEGFC expression exhibited positive correlations with immune infiltration scores, suggesting low tumor purity. High expression of VEGFA and VEGFC showed favorable responses to various drugs, including BLU-667, which abrogates RET signaling, an oncogenic driver in liver and thyroid cancers. Our findings suggest potential roles of VEGF family genes in malignant processes related with hypoxia-induced angiogenesis.
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Affiliation(s)
- So-Hyun Bae
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
| | - Taewon Hwang
- Department of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, Korea
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
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Choi B, Na Y, Whang MY, Ho JY, Han MR, Park SW, Song H, Hur SY, Choi YJ. MGMT Methylation Is Associated with Human Papillomavirus Infection in Cervical Dysplasia: A Longitudinal Study. J Clin Med 2023; 12:6188. [PMID: 37834832 PMCID: PMC10573962 DOI: 10.3390/jcm12196188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Cervical premalignancy/malignancy, as detected by cervical cytology or biopsy, can develop as a result of human papillomavirus (HPV) infection. Meanwhile, DNA methylation is known to be associated with carcinogenesis. In this study, we thus attempted to identify the association between MGMT methylation and persistent HPV infection using an Epi-TOP MPP assay. Integrative analysis of DNA methylation was carried out here using longitudinal cervical cytology samples of seven patients with atypical squamous cells of undetermined significance/low-grade squamous intraepithelial lesion (ASC-US/LSIL). Then, a gene expression analysis using the longitudinal cervical cytology samples and a public database (The Cancer Genome Atlas (TCGA)) was performed. Upon comparing the ASC-US or LSIL samples at the 1st collection and the paired samples at the 2nd collection more than 6 months later, we found that they became hypermethylated over time. Then, using the longitudinal data, we found that the MGMT methylation was associated with HPV infection. Moreover, TCGA dataset revealed an association between downregulated MGMT mRNA expression and poor overall survival. This decreased MGMT mRNA expression was observed to have an inverse relationship with MGMT methylation levels. In this study, we found that the MGMT methylation level could potentially serve as a valuable prognostic indicator for the transition from ASC-US/LSIL to cervical cancer.
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Affiliation(s)
- Boram Choi
- Department of Obstetrics and Gynecology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (B.C.); (Y.N.); (M.Y.W.); (J.Y.H.)
| | - Yoojin Na
- Department of Obstetrics and Gynecology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (B.C.); (Y.N.); (M.Y.W.); (J.Y.H.)
| | - Min Yeop Whang
- Department of Obstetrics and Gynecology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (B.C.); (Y.N.); (M.Y.W.); (J.Y.H.)
| | - Jung Yoon Ho
- Department of Obstetrics and Gynecology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (B.C.); (Y.N.); (M.Y.W.); (J.Y.H.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea; (M.-R.H.); (S.-W.P.)
| | - Seong-Woo Park
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea; (M.-R.H.); (S.-W.P.)
| | - Heekyoung Song
- Department of Obstetrics and Gynecology, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Incheon 21431, Republic of Korea;
| | - Soo Young Hur
- Department of Obstetrics and Gynecology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (B.C.); (Y.N.); (M.Y.W.); (J.Y.H.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea
| | - Youn Jin Choi
- Department of Obstetrics and Gynecology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (B.C.); (Y.N.); (M.Y.W.); (J.Y.H.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea
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Park AY, Han MR, Seo BK, Ju HY, Son GS, Lee HY, Chang YW, Choi J, Cho KR, Song SE, Woo OH, Park HS. MRI-based breast cancer radiogenomics using RNA profiling: association with subtypes in a single-center prospective study. Breast Cancer Res 2023; 25:79. [PMID: 37391754 PMCID: PMC10311893 DOI: 10.1186/s13058-023-01668-7] [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: 01/11/2023] [Accepted: 05/31/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND There are few prospective studies on the correlations between MRI features and whole RNA-sequencing data in breast cancer according to molecular subtypes. The purpose of our study was to explore the association between genetic profiles and MRI phenotypes of breast cancer and to identify imaging markers that influences the prognosis and treatment according to subtypes. METHODS From June 2017 to August 2018, MRIs of 95 women with invasive breast cancer were prospectively analyzed, using the breast imaging-reporting and data system and texture analysis. Whole RNA obtained from surgical specimens was analyzed using next-generation sequencing. The association between MRI features and gene expression profiles was analyzed in the entire tumor and subtypes. Gene networks, enriched functions, and canonical pathways were analyzed using Ingenuity Pathway Analysis. The P value for differential expression was obtained using a parametric F test comparing nested linear models and adjusted for multiple testing by reporting Q value. RESULTS In 95 participants (mean age, 53 years ± 11 [standard deviation]), mass lesion type was associated with upregulation of CCL3L1 (sevenfold) and irregular mass shape was associated with downregulation of MIR421 (sixfold). In estrogen receptor-positive cancer with mass lesion type, CCL3L1 (21-fold), SNHG12 (11-fold), and MIR206 (sevenfold) were upregulated, and MIR597 (265-fold), MIR126 (12-fold), and SOX17 (fivefold) were downregulated. In triple-negative breast cancer with increased standard deviation of texture analysis on precontrast T1-weighted imaging, CLEC3A (23-fold), SRGN (13-fold), HSPG2 (sevenfold), KMT2D (fivefold), and VMP1 (fivefold) were upregulated, and IGLC2 (73-fold) and PRDX4 (sevenfold) were downregulated (all, P < 0.05 and Q < 0.1). Gene network and functional analysis showed that mass type estrogen receptor-positive cancers were associated with cell growth, anti-estrogen resistance, and poor survival. CONCLUSION MRI characteristics are associated with the different expressions of genes related to metastasis, anti-drug resistance, and prognosis, depending on the molecular subtypes of breast cancer.
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Affiliation(s)
- Ah Young Park
- Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Bo Kyoung Seo
- Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan City, Gyeonggi-do, 15355, Republic of Korea.
| | - Hye-Yeon Ju
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Gil Soo Son
- Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Ansan City, Gyeonggi-do, Republic of Korea
| | - Hye Yoon Lee
- Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Ansan City, Gyeonggi-do, Republic of Korea
| | - Young Woo Chang
- Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Ansan City, Gyeonggi-do, Republic of Korea
| | - Jungyoon Choi
- Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan City, Gyeonggi-do, Republic of Korea
| | - Kyu Ran Cho
- Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Eun Song
- Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ok Hee Woo
- Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyun Soo Park
- Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan City, Gyeonggi-do, 15355, Republic of Korea
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Han MR, Park AY, Seo BK, Bae MS, Kim JS, Son GS, Lee HY, Chang YW, Cho KR, Song SE, Woo OH, Ju HY, Oh H. Association between vascular ultrasound features and DNA sequencing in breast cancer: a preliminary study. Discov Oncol 2023; 14:52. [PMID: 37120792 PMCID: PMC10149538 DOI: 10.1007/s12672-023-00657-8] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/14/2023] [Indexed: 05/01/2023] Open
Abstract
There are few radiogenomic studies to correlate ultrasound features of breast cancer with genomic changes. We investigated whether vascular ultrasound phenotypes are associated with breast cancer gene profiles for predicting angiogenesis and prognosis. We prospectively correlated quantitative and qualitative features of microvascular ultrasound (vascular index, vessel morphology, distribution, and penetrating vessel) and contrast-enhanced ultrasound (time-intensity curve parameters and enhancement pattern) with genomic characteristics in 31 breast cancers. DNA obtained from breast tumors and normal tissues were analyzed using targeted next-generation sequencing of 105 genes. The single-variant association test was used to identify correlations between vascular ultrasound features and genomic profiles. Chi-square analysis was used to detect single nucleotide polymorphisms (SNPs) associated with ultrasound features by estimating p values and odds ratios (ORs). Eight ultrasound features were significantly associated with 9 SNPs (p < 0.05). Among them, four ultrasound features were positively associated with 5 SNPs: high vascular index with rs1136201 in ERBB2 (p = 0.04, OR = 7.75); large area under the curve on contrast-enhanced ultrasound with rs35597368 in PDGFRA (p = 0.04, OR = 4.07); high peak intensity with rs35597368 in PDGFRA (p = 0.049, OR = 4.05) and rs2305948 in KDR (p = 0.04, OR = 5.10); and long mean transit time with rs2275237 in ARNT (p = 0.02, OR = 10.25) and rs755793 in FGFR2 (p = 0.02, OR = 10.25). We identified 198 non-silent SNPs in 71 various cancer-related genes. Vascular ultrasound features can reflect genomic changes associated with angiogenesis and prognosis in breast cancer.
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Affiliation(s)
- Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Ah Young Park
- Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Bo Kyoung Seo
- Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan, Gyeonggi-do 15355 Republic of Korea
| | - Min Sun Bae
- Department of Radiology, Inha University Hospital and College of Medicine, Inhang-ro 27, Jung-gu, Incheon, 22332 Republic of Korea
| | - Jung Sun Kim
- Division of Hematology/Oncology, Department of Internal medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Gyeonggi-do Republic of Korea
| | - Gil Soo Son
- Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Gyeonggi-do Republic of Korea
| | - Hye Yoon Lee
- Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Gyeonggi-do Republic of Korea
| | - Young Woo Chang
- Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Gyeonggi-do Republic of Korea
| | - Kyu Ran Cho
- Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Eun Song
- Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ok Hee Woo
- Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hye-Yeon Ju
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Hyunseung Oh
- Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Gyeonggi-do Republic of Korea
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Han KM, Choi KW, Kim A, Kang W, Kang Y, Tae WS, Han MR, Ham BJ. Association of DNA Methylation of the NLRP3 Gene with Changes in Cortical Thickness in Major Depressive Disorder. Int J Mol Sci 2022; 23:ijms23105768. [PMID: 35628578 PMCID: PMC9143533 DOI: 10.3390/ijms23105768] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
The Nod-like receptor pyrin containing 3 (NLRP3) inflammasome has been reported to be a convergent point linking the peripheral immune response induced by psychological stress and neuroinflammatory processes in the brain. We aimed to identify differences in the methylation profiles of the NLRP3 gene between major depressive disorder (MDD) patients and healthy controls (HCs). We also investigated the correlation of the methylation score of loci in NLRP3 with cortical thickness in the MDD group using magnetic resonance imaging (MRI) data. A total of 220 patients with MDD and 82 HCs were included in the study, and genome-wide DNA methylation profiling of the NLRP3 gene was performed. Among the total sample, 88 patients with MDD and 74 HCs underwent T1-weighted structural MRI and were included in the neuroimaging–methylation analysis. We identified five significant differentially methylated positions (DMPs) in NLRP3. In the MDD group, the methylation scores of cg18793688 and cg09418290 showed significant positive or negative correlations with cortical thickness in the occipital, parietal, temporal, and frontal regions, which showed significant differences in cortical thickness between the MDD and HC groups. Our findings suggest that NLRP3 DNA methylation may predispose to depression-related brain structural changes by increasing NLRP3 inflammasome-related neuroinflammatory processes in MDD.
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Affiliation(s)
- Kyu-Man Han
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (K.-M.H.); (K.W.C.)
| | - Kwan Woo Choi
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (K.-M.H.); (K.W.C.)
| | - Aram Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea; (A.K.); (W.K.); (Y.K.)
| | - Wooyoung Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea; (A.K.); (W.K.); (Y.K.)
| | - Youbin Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea; (A.K.); (W.K.); (Y.K.)
| | - Woo-Suk Tae
- Brain Convergence Research Center, Korea University College of Medicine, Seoul 02841, Korea;
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
- Correspondence: (M.-R.H.); (B.-J.H.)
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea; (K.-M.H.); (K.W.C.)
- Correspondence: (M.-R.H.); (B.-J.H.)
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Lee K, Han MR, Yeon JW, Kim B, Kim TH. Whole Transcriptome Analysis of Myeloid Dendritic Cells Reveals Distinct Genetic Regulation in Patients with Allergies. Int J Mol Sci 2020; 21:ijms21228640. [PMID: 33207814 PMCID: PMC7697962 DOI: 10.3390/ijms21228640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/23/2022] Open
Abstract
Dendritic cells (DCs) play critical roles in atopic diseases, orchestrating both innate and adaptive immune systems. Nevertheless, limited information is available regarding the mechanism through which DCs induce hyperresponsiveness in patients with allergies. This study aims to reveal novel genetic alterations and future therapeutic target molecules in the DCs from patients with allergies using whole transcriptome sequencing. Transcriptome sequencing of human BDCA-3+/CD11c+ DCs sorted from peripheral blood monocytes obtained from six patients with allergies and four healthy controls was conducted. Gene expression profile data were analyzed, and an ingenuity pathway analysis was performed. A total of 1638 differentially expressed genes were identified at p-values < 0.05, with 11 genes showing a log2-fold change ≥1.5. The top gene network was associated with cell death/survival and organismal injury/abnormality. In validation experiments, amphiregulin (AREG) showed consistent results with transcriptome sequencing data, with increased mRNA expression in THP-1-derived DCs after Der p 1 stimulation and higher protein expression in myeloid DCs obtained from patients with allergies. This study suggests an alteration in the expression of DCs in patients with allergies, proposing related altered functions and intracellular mechanisms. Notably, AREG might play a crucial role in DCs by inducing the Th2 immune response.
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Affiliation(s)
- Kijeong Lee
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea; (K.L.); (J.W.Y.); (B.K.)
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea;
| | - Ji Woo Yeon
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea; (K.L.); (J.W.Y.); (B.K.)
| | - Byoungjae Kim
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea; (K.L.); (J.W.Y.); (B.K.)
| | - Tae Hoon Kim
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea; (K.L.); (J.W.Y.); (B.K.)
- Correspondence: ; Tel.: +82-02-920-5486
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Hwang SH, Yeom H, Han BI, Ham BJ, Lee YM, Han MR, Lee M. Predicting Carcinogenic Mechanisms of Non-Genotoxic Carcinogens via Combined Analysis of Global DNA Methylation and In Vitro Cell Transformation. Int J Mol Sci 2020; 21:ijms21155387. [PMID: 32751172 PMCID: PMC7432388 DOI: 10.3390/ijms21155387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022] Open
Abstract
An in vitro cell transformation assay (CTA) is useful for the detection of non-genotoxic carcinogens (NGTXCs); however, it does not provide information on their modes of action. In this study, to pursue a mechanism-based approach in the risk assessment of NGTXCs, we aimed to develop an integrated strategy comprising an in vitro Bhas 42 CTA and global DNA methylation analysis. For this purpose, 10 NGTXCs, which were also predicted to be negative through Derek/Sarah structure-activity relationship analysis, were first tested for transforming activity in Bhas 42 cells. Methylation profiles using reduced representation bisulfite sequencing were generated for seven NGTXCs that were positive in CTAs. In general, the differentially methylated regions (DMRs) within promoter regions showed slightly more bias toward hypermethylation than the DMRs across the whole genome. We also identified 13 genes associated with overlapping DMRs within the promoter regions in four NGTXCs, of which seven were hypermethylated and six were hypomethylated. Using ingenuity pathway analysis, the genes with DMRs at the CpG sites were found to be enriched in cancer-related categories, including "cell-to-cell signaling and interaction" as well as "cell death and survival". Moreover, the networks related to "cell death and survival", which were considered to be associated with carcinogenesis, were identified in six NGTXCs. These results suggest that epigenetic changes supporting cell transformation processes occur during non-genotoxic carcinogenesis. Taken together, our combined system can become an attractive component for an integrated approach for the testing and assessment of NGTXCs.
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Affiliation(s)
- Sung-Hee Hwang
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
| | - Hojin Yeom
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
| | - Byeal-I Han
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea;
| | - Yong-Moon Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheoungju-si, Chungcheongbuk-do 28160, Korea;
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
- INU Human Genome Center, Incheon National University, Incheon 22012, Korea
- Correspondence: (M.-R.H.); (M.L.); Tel.: +82-32-835-8247 (M.L.)
| | - Michael Lee
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
- INU Human Genome Center, Incheon National University, Incheon 22012, Korea
- Correspondence: (M.-R.H.); (M.L.); Tel.: +82-32-835-8247 (M.L.)
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An JY, Min JS, Hur H, Lee YJ, Cho GS, Park YK, Jung MR, Park JH, Hyung WJ, Jeong SH, Kim YW, Yoon HM, Eom BW, Kook MC, Han MR, Nam BH, Ryu KW. Laparoscopic sentinel node navigation surgery versus laparoscopic gastrectomy with lymph node dissection for early gastric cancer: short-term outcomes of a multicentre randomized controlled trial (SENORITA). Br J Surg 2020; 107:1429-1439. [PMID: 32492186 DOI: 10.1002/bjs.11655] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/05/2020] [Accepted: 04/06/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Sentinel node navigation surgery reduces the extent of gastric and lymph node dissection, and may improve quality of life. The benefit and harm of laparoscopic sentinel node navigation surgery (LSNNS) for early gastric cancer is unknown. The SENORITA (SEntinel Node ORIented Tailored Approach) trial investigated the pathological and surgical outcomes of LSNNS compared with laparoscopic standard gastrectomy (LSG) with lymph node dissection. METHODS The SENORITA trial was an investigator-initiated, open-label, parallel-assigned, non-inferiority, multicentre RCT conducted in Korea. The primary endpoint was 3-year disease-free survival. The secondary endpoints, morbidity and mortality within 30 days of surgery, are reported in the present study. RESULTS A total of 580 patients were randomized to LSG (292) or LSNNS (288). Surgery was undertaken in 527 patients (LSG 269, LSNNS 258). LSNNS could be performed according to the protocol in 245 of 258 patients, and a sentinel node basin was detected in 237 (96·7 per cent) Stomach-preserving surgery was carried out in 210 of 258 patients (81·4 per cent). Postoperative complications occurred in 51 patients in the LSG group (19·0 per cent) and 40 (15·5 per cent) in the LSNNS group (P = 0·294). Complications with a Clavien-Dindo grade of III or higher occurred in 16 (5·9 per cent) and 13 (5·0 per cent) patients in the LSG and LSNNS groups respectively (P = 0·647). CONCLUSION The rate and severity of complications following LSNNS for early gastric cancer are comparable to those after LSG with lymph node dissection. Registration number: NCT01804998 ( http://www.clinicaltrials.gov).
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Affiliation(s)
- J Y An
- Department of Surgery, Yonsei University College of Medicine, Seoul, South Korea.,Department of Surgery, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - J-S Min
- Departments of Surgery, Dongnam Institute of Radiological and Medical Sciences, Cancer Centre, Busan, South Korea
| | - H Hur
- Ajou University School of Medicine, Suwon, South Korea
| | - Y J Lee
- Gyeongsang National University, Jinju, South Korea
| | - G S Cho
- Soonchunhyang University College of Medicine, Bucheon, South Korea
| | - Y-K Park
- Chonnam National University Medical School, Gwangju, South Korea
| | - M R Jung
- Chonnam National University Medical School, Gwangju, South Korea
| | - J-H Park
- Gyeongsang National University, Jinju, South Korea
| | - W J Hyung
- Department of Surgery, Yonsei University College of Medicine, Seoul, South Korea
| | - S-H Jeong
- Gyeongsang National University, Jinju, South Korea
| | - Y-W Kim
- Centre for Gastric Cancer.,Department of Cancer Control and Population Health, National Cancer Centre Graduate School of Cancer Science and Policy, Goyang, South Korea
| | | | | | | | - M R Han
- Biostatistics Collaboration Team, National Cancer Centre, Goyang, South Korea
| | - B-H Nam
- Clinical Design Research Centre, HERINGS Institute of Advanced Clinical and Biomedical Research, Seoul, South Korea
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Han MR, Lee SH, Park JY, Hong H, Ho JY, Hur SY, Choi YJ. Clinical Implications of Circulating Tumor DNA from Ascites and Serial Plasma in Ovarian Cancer. Cancer Res Treat 2020; 52:779-788. [PMID: 32106643 PMCID: PMC7373868 DOI: 10.4143/crt.2019.700] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/24/2020] [Indexed: 12/27/2022] Open
Abstract
Purpose The purpose of this study was to identify the clinical utility of circulating tumor DNA (ctDNA) from ascites and serial plasma samples from epithelial ovarian cancer (EOC) patients. Materials and Methods Using targeted next-generation sequencing, we analyzed a total of 55 EOC samples including ctDNA from ascites and serial plasma and gDNA from tumor tissues. Tumor tissues and ascites were collected during debulking surgeries and plasma samples were collected before and after the surgeries. Because one EOC patient underwent secondary debulking surgery, a total of 11 tumor tissues, 33 plasma samples, and 11 ascites samples were obtained from the 10 patients. Results Of the 10 patients, nine (90%) contained somatic mutations in both tumor tissues and ascites ctDNA. This mutational concordance was confirmed through correlation analysis. The mutational concordance between ascites and tumor tissues was valid in recurrent/progressive ovarian cancer. TP53 was the most frequently detected gene with mutations. ctDNA from serial plasma samples identified EOC progression/recurrence at a similar time or even more rapidly than cancer antigen 125, an established serum protein tumor marker for EOC. Conclusion Our data suggest that ascites ctDNA can be used to identify the mutational landscape of ovarian cancer for therapeutic strategy planning.
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Affiliation(s)
- Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Korea
| | - Sug Hyung Lee
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Yoon Park
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyosun Hong
- Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Jung Yoon Ho
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Soo Young Hur
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn Jin Choi
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Park AY, Han MR, Park KH, Kim JS, Son GS, Lee HY, Chang YW, Park EK, Cha SH, Cho Y, Hong H, Cho KR, Song SE, Woo OH, Lee JH, Cha J, Seo BK. Radiogenomic Analysis of Breast Cancer by Using B-Mode and Vascular US and RNA Sequencing. Radiology 2020; 295:24-34. [PMID: 32013793 DOI: 10.1148/radiol.2020191368] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Radiogenomic investigations for breast cancer provide an understanding of tumor heterogeneity and discover image phenotypes of genetic variation. However, there is little research on the correlations between US features of breast cancer and whole-transcriptome profiling. Purpose To explore US phenotypes reflecting genetic alteration relevant to breast cancer treatment and prognosis by comparing US images of tumor with their RNA sequencing results. Materials and Methods From January to October 2016, B-mode and vascular US images in 31 women (mean age, 49 years ± 9 [standard deviation]) with breast cancer were prospectively analyzed. B-mode features included size, shape, echo pattern, orientation, margin, and calcifications. Vascular features were evaluated by using microvascular US and contrast agent-enhanced US: vascular index, vessel morphologic features, distribution, penetrating vessels, enhancement degree, order, margin, internal homogeneity, and perfusion defect. RNA sequencing was conducted with total RNA obtained from a surgical specimen by using next-generation sequencing. US features were compared with gene expression profiles, and ingenuity pathway analysis was used to analyze gene networks, enriched functions, and canonical pathways associated with breast cancer. The P value for differential expression was extracted by using a parametric F test comparing nested linear models. Results Thirteen US features were associated with various patterns of 340 genes (P < .05). Nonparallel orientation at B-mode US was associated with upregulation of TFF1 (log twofold change [log2FC] = 4.0; P < .001), TFF3 (log2FC = 2.5; P < .001), AREG (log2FC = 2.6; P = .005), and AGR3 (log2FC = 2.6; P = .003). Complex vessel morphologic structure was associated with upregulation of FZD8 (log2FC = 2.0; P = .01) and downregulation of IGF1R (log2FC = -2.0; P = .006) and CRIPAK (log2FC = -2.4; P = .01). The top networks with regard to orientation or vessel morphologic structure were associated with cell cycle, death, and proliferation. Conclusion Compared with RNA sequencing, B-mode and vascular US features reflected genomic alterations associated with hormone receptor status, angiogenesis, or prognosis in breast cancer. © RSNA, 2020 Online supplemental material is available for this article.
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Affiliation(s)
- Ah Young Park
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Mi-Ryung Han
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Kyong Hwa Park
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Jung Sun Kim
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Gil Soo Son
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Hye Yoon Lee
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Young Woo Chang
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Eun Kyung Park
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Sang Hoon Cha
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Yunjung Cho
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Hyosun Hong
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Kyu Ran Cho
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Sung Eun Song
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Ok Hee Woo
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Ju-Han Lee
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Jaehyung Cha
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
| | - Bo Kyoung Seo
- From the Department of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, 123 Jeokgeum-ro, Danwon-gu, Ansan city, Gyeonggi-do, 15355, Republic of Korea (A.Y.P., E.K.P., S.H.C., B.K.S.); Department of Radiology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea (A.Y.P.); Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (M.R.H., Y.C., H.H.); Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea (M.R.H.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.H.P.); Division of Hematology/Oncology, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.S.K.); Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (G.S.S., H.Y.L., Y.W.C.); Department of Radiology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea (K.R.C., S.E.S.); Department of Radiology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea (O.H.W.); Department of Pathology, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.H.L.); and Medical Science Research Center, Korea University Ansan Hospital, Korea University College of Medicine, Gyeonggi-do, Republic of Korea (J.C.)
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12
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Han MR, Han KM, Kim A, Kang W, Kang Y, Kang J, Won E, Tae WS, Cho Y, Ham BJ. Whole-exome sequencing identifies variants associated with structural MRI markers in patients with bipolar disorders. J Affect Disord 2019; 249:159-168. [PMID: 30772743 DOI: 10.1016/j.jad.2019.02.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/19/2018] [Revised: 01/29/2019] [Accepted: 02/10/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Bipolar disorder (BD) is one of the most heritable psychiatric disorders. A growing number of whole-exome sequencing (WES) studies for BD has been performed, however, no research has examined the association between single nucleotide variants (SNVs) from WES and structural magnetic resonance imaging (MRI) data. METHODS We sequenced whole-exomes in 53 patients with BD and 82 healthy control participants at an initial discovery stage and investigated the impacts of SNVs in risk genes from WES analysis on the cortical gray-matter thickness and integrity of white matter tracts and in the following stage. Cortical thickness and white matter integrity were investigated using the FreeSurfer and TRACULA (Tracts Constrained by UnderLying Anatomy). RESULTS We identified 122 BD-related genes including KMT2C, AHNAK, CDH23, DCHS1, FRAS1, MACF1 and RYR3 and observed 27 recurrent copy number alteration regions including gain on 8p23.1 and loss on 15q11.1 - q11.2. Among them, single nucleotide polymorphism (SNP) rs4639425 in KMT2C gene, which regulates histone H3 lysine 4 (H3K4) methylation involved in chromatin remodeling, was associated with widespread alterations of white matter integrity including the cingulum, uncinate fasciculus, cortico-spinal tract, and superior longitudinal fasciculus. LIMITATION The small sample size of patients with BD in the genome data may cause our study to be underpowered when searching for putative rare mutations. CONCLUSION This study first combined a WES approach and neuroimaging findings in psychiatric disorders. We postulate the rs4639425 may be associated with BD-related microstructural changes of white matter tracts.
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Affiliation(s)
- Mi-Ryung Han
- Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyu-Man Han
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Aram Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Wooyoung Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Youbin Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - June Kang
- Department of Brain and Cognitive Engineering, Korea University, Seoul, Republic of Korea
| | - Eunsoo Won
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woo-Suk Tae
- Brain Convergence Research Center, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea; Brain Convergence Research Center, Korea University Anam Hospital, Seoul, Republic of Korea.
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13
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Shin S, Park HC, Kim MS, Han MR, Lee SH, Jung SH, Lee SH, Chung YJ. Whole-exome sequencing identified mutational profiles of squamous cell carcinomas of anus. Hum Pathol 2018; 80:1-10. [PMID: 29555573 DOI: 10.1016/j.humpath.2018.03.008] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/13/2022]
Abstract
Anal squamous cell carcinoma (ASCC), either with human papillomavirus (+) or (-), is a neoplastic disease with frequent recurrence and metastasis. To characterize ASCC genomes, we attempted to disclose novel alterations of ASCC genomes and other genetic features including mutation signatures. We performed whole-exome sequencing and copy number alteration (CNA) profiling for 8 ASCC samples from 6 patients (2 cases with primary and recurrent/metastatic tumors). We found known ASCC mutations (TP53, CDKN2A, and PIK3CA) and CNAs (gains on 3q and 19q and losses on 11q and 13q). In addition, we discovered novel mutations in HRAS and ARID1A and CNAs (gain on 8q and losses 5q, 9p, 10q, and 19p) that had not been reported in ASCCs. We identified 4 signature patterns of the mutations (signatures 1 and 2 with deamination of 5-methyl-cytosin, signature 3 with APOBEC, and signature 4 with mismatch repair) in the ASCCs. Although signatures 1 to 3 have been detected in other SCCs, signature 4 was first identified in ASCCs. In addition, we first found that ASCCs harbored chromothripsis, copy-neutral losses of heterozygosity, and focal amplification of KLF5 super-enhancer. Analyses of primary and recurrent/metastatic pair genomes revealed that driver events in development and progression of ASCC might not be uniform. Our data indicate that ASCCs may have similar mutation and CNA profiles to other SCCs, but that there are unique genomic features of ASCCs as well. Our data may provide useful information for ASCC pathogenesis and for developing clinical strategies for ASCC.
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Affiliation(s)
- Sun Shin
- Department of Microbiology, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Hyeon-Chun Park
- Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Min Sung Kim
- Department of Pathology, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Cancer Evolution Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Mi-Ryung Han
- Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Sung Hak Lee
- Department of Hospital Pathology, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Seung Hyun Jung
- Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Cancer Evolution Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Sug Hyung Lee
- Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Department of Pathology, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Cancer Evolution Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
| | - Yeun-Jun Chung
- Department of Microbiology, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Cancer Evolution Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
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14
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Jung SH, Kim MS, Shin S, Han MR, Cho YJ, Kim SY, Lee SH, Chung YJ. Abstract 3385: Genomic landscapes of pulmonary sclerosing hemangioma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3385] [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: 11/16/2022]
Abstract
Abstract
Pulmonary sclerosing hemangioma (PSH) is a benign tumor that usually presents as a solitary, well-defined mass in the lung. The PSH predominantly affects females with a higher incidence in the Far East. Histologically, the tumor cells in PSH consist of two cell types (cuboidal epithelial and polygonal stromal cells). Immunohistochemical and ultrastructural studies have identified that both cells are derived from undifferentiated respiratory epithelium that is the histologic origin of lung adenocarcinoma as well. Previous studies have shown that PSH and adenocarcinoma in the lung share some immunohistochemical and genetic features. However, as for somatic mutations, whereas many driver genes for lung adenocarcinomas have been identified, there have not been any candidate driver mutations identified in PSHs, except for low frequency mutations in β-catenin and TP53. Frequent somatic mutations identified in lung adenocarcinomas such as KRAS and EGFR have not been detected in PSH, suggesting that genomic alterations of these two lung tumors might be different from each other. Also, there is no evidence of PSH progression to lung cancers. These earlier data indicate that despite the common cellular origin of PSH and lung adenocarcinoma, genetic mechanisms for their development may be different. Based on the established concept that PSH is a true tumor, we hypothesize that it may harbor somatic mutations. In this study, we conducted whole exome sequencing of 44 PSHs and identified recurrent somatic mutations of AKT1 (43.2%) and β-catenin (4.5%). We used a second subset of 24 PSHs to confirm the high frequency of AKT1 mutations (overall 31/68, 45.6%; p.E17K, 33.8%) and recurrent β-catenin mutations (overall 3/68, 4.4%). Of the PSHs without AKT1 mutations, two exhibited AKT1 copy gain. AKT1 mutations existed in both epithelial and stromal cells. In two separate PSHs from one patient, we observed two different AKT1 mutations, indicating they were not disseminated but independent arising tumors. Since the AKT1 mutations were not found to co-occur with β-catenin mutations (or any other known driver alterations) in any of the PSHs studied, we speculate that this may be a single most common driver alteration to develop PSHs. Our study revealed genomic differences between PSHs and lung adenocarcinomas including a high rate of AKT1 mutation in PSHs. These genomic features of PSH discovered in the present study provide clues to understanding the biology of PSH and for differential genomic diagnosis of lung tumors.
Citation Format: Seung-Hyun Jung, Min Sung Kim, Sun Shin, Mi-Ryung Han, Yu Jin Cho, So Youn Kim, Sug Hyung Lee, Yeun-Jun Chung. Genomic landscapes of pulmonary sclerosing hemangioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3385. doi:10.1158/1538-7445.AM2017-3385
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Affiliation(s)
- Seung-Hyun Jung
- 1Cancer Evolution Research Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Min Sung Kim
- 1Cancer Evolution Research Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sun Shin
- 2Integrated Research Center for Genome Polymorphism, Catholic University of Korea, Seoul, Republic of Korea
| | - Mi-Ryung Han
- 2Integrated Research Center for Genome Polymorphism, Catholic University of Korea, Seoul, Republic of Korea
| | - Yu Jin Cho
- 2Integrated Research Center for Genome Polymorphism, Catholic University of Korea, Seoul, Republic of Korea
| | - So Youn Kim
- 2Integrated Research Center for Genome Polymorphism, Catholic University of Korea, Seoul, Republic of Korea
| | - Sug Hyung Lee
- 1Cancer Evolution Research Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- 2Integrated Research Center for Genome Polymorphism, Catholic University of Korea, Seoul, Republic of Korea
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Guo X, Lin W, Cai Q, Shi J, Sun Y, Pan X, Han MR, Wen W, Li B, Long J, Chen J, Zheng W. Abstract 1441: A comprehensive cis-eQTL analysis revealed target genes in breast cancer susceptibility loci identified in genome-wide association studies. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1441] [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: 11/16/2022]
Abstract
Abstract
Genome-wide association studies (GWAS) have identified approximately 107 common single nucleotide polymorphisms (index SNPs) for breast cancer risk. The target genes and underlying mechanisms for the large majority of the identified associations remain unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using transcriptome data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (N = 1,981), The Cancer Genome Atlas (TCGA) (N = 458), and the Genotype-Tissue Expression (GTEx) project (N = 183). We identified a total of 58 genes including SSBP4 at Benjamini-Hochberg adjusted P < 0.05 in at least one dataset and another gene, PAX9, at P < 0.05 with consistent association directions in all three datasets. Using data from the Encyclopedia of DNA Elements (ENCODE), we selected functional SNPs and showed that some alternative alleles could significantly change promoter activities of their target genes compared to reference alleles using luciferase reporter assays. The effects of target gene expression for those alleles were in line with eQTL observations. In addition, we validated the genes SETD9 and SSBP4 using Sequenom allelotype technique from 235 adjacent normal breast tissues and observed the allelic-specific expression associated with their index SNPs. This study revealed novel biological mechanisms for associations of genetic susceptibility risk loci for breast cancer.
Citation Format: Xingyi Guo, Weiqiang Lin, Qiuyin Cai, Jiajun Shi, Yaqiong Sun, Xiao Pan, Mi-Ryung Han, Wanqing Wen, Bingshan Li, Jirong Long, Jianghua Chen, Wei Zheng. A comprehensive cis-eQTL analysis revealed target genes in breast cancer susceptibility loci identified in genome-wide association studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1441. doi:10.1158/1538-7445.AM2017-1441
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Affiliation(s)
- Xingyi Guo
- 1Vanderbilt University School of Medicine, Nashville, TN
| | - Weiqiang Lin
- 2Zhejiang University School of Medicine, Hangzhou, China
| | - Qiuyin Cai
- 1Vanderbilt University School of Medicine, Nashville, TN
| | - Jiajun Shi
- 1Vanderbilt University School of Medicine, Nashville, TN
| | - Yaqiong Sun
- 1Vanderbilt University School of Medicine, Nashville, TN
| | - Xiao Pan
- 2Zhejiang University School of Medicine, Hangzhou, China
| | - Mi-Ryung Han
- 1Vanderbilt University School of Medicine, Nashville, TN
| | - Wanqing Wen
- 1Vanderbilt University School of Medicine, Nashville, TN
| | - Bingshan Li
- 1Vanderbilt University School of Medicine, Nashville, TN
| | - Jirong Long
- 1Vanderbilt University School of Medicine, Nashville, TN
| | - Jianghua Chen
- 2Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zheng
- 1Vanderbilt University School of Medicine, Nashville, TN
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16
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Han MR, Zheng W, Cai Q, Gao YT, Zheng Y, Bolla MK, Michailidou K, Dennis J, Wang Q, Dunning AM, Brennan P, Chen ST, Choi JY, Hartman M, Ito H, Lophatananon A, Matsuo K, Miao H, Muir K, Sangrajrang S, Shen CY, Teo SH, Tseng CC, Wu AH, Yip CH, Kang D, Xiang YB, Easton DF, Shu XO, Long J. Evaluating genetic variants associated with breast cancer risk in high and moderate-penetrance genes in Asians. Carcinogenesis 2017; 38:511-518. [PMID: 28419251 PMCID: PMC5963497 DOI: 10.1093/carcin/bgx010] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 01/10/2017] [Accepted: 01/21/2017] [Indexed: 12/13/2022] Open
Abstract
Over the past 20 years, high-penetrance pathogenic mutations in genes BRCA1, BRCA2, TP53, PTEN, STK11 and CDH1 and moderate-penetrance mutations in genes CHEK2, ATM, BRIP1, PALB2, RAD51C, RAD50 and NBN have been identified for breast cancer. In this study, we investigated whether there are additional variants in these 13 genes associated with breast cancer among women of Asian ancestry. We analyzed up to 654 single nucleotide polymorphisms (SNPs) from 6269 cases and 6624 controls of Asian descent included in the Breast Cancer Association Consortium (BCAC), and up to 236 SNPs from 5794 cases and 5529 controls included in the Shanghai Breast Cancer Genetics Study (SBCGS). We found three missense variants with minor allele frequency (MAF) <0.05: rs80358978 (Gly2508Ser), rs80359065 (Lys2729Asn) and rs11571653 (Met784Val) in the BRCA2 gene, showing statistically significant associations with breast cancer risk, with P-values of 1.2 × 10-4, 1.0 × 10-3 and 5.0 × 10-3, respectively. In addition, we found four low-frequency variants (rs8176085, rs799923, rs8176173 and rs8176258) in the BRCA1 gene, one common variant in the CHEK2 gene (rs9620817), and one common variant in the PALB2 gene (rs13330119) associated with breast cancer risk at P < 0.01. Our study identified several new risk variants in BRCA1, BRCA2, CHEK2, and PALB2 genes in relation to breast cancer risk in Asian women. These results provide further insights that, in addition to the high/moderate penetrance mutations, other low-penetrance variants in these genes may also contribute to breast cancer risk.
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Affiliation(s)
- Mi-Ryung Han
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203,USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203,USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203,USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai200032, China
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul Brennan
- International Agency for Research on Cancer, 69372 Lyon CEDEX 08, France
| | - Shou-Tung Chen
- Department of Surgery, Changhua Christian Hospital,Changhua City 50006,Taiwan
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
- Department of Surgery, National University Health System, Singapore 119228, Singapore
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer CenterResearch Institute, Nagoya 464-8681, Japan
- Department of Epidemiology, Nagoya University Graduates School of Medicine, Nagoya 466-8550, Japan
| | - Hui Miao
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
- Institute of Population Health, University of Manchester, Manchester M13 9PL, UK
| | | | - Chen-Yang Shen
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- School of Public Health, China Medical University, Taichong 40402, Taiwan
| | - Soo Hwang Teo
- Cancer Research Initiatives Foundation, Subang Jaya, Selangor 47500, Malaysia
| | - Chiu-Chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles CA 90032, USA
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles CA 90032, USA
| | - Cheng Har Yip
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur 59100, Malaysia and
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai200032, China
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203,USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203,USA
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Han MR, Long J, Choi JY, Low SK, Kweon SS, Zheng Y, Cai Q, Shi J, Guo X, Matsuo K, Iwasaki M, Shen CY, Kim MK, Wen W, Li B, Takahashi A, Shin MH, Xiang YB, Ito H, Kasuga Y, Noh DY, Matsuda K, Park MH, Gao YT, Iwata H, Tsugane S, Park SK, Kubo M, Shu XO, Kang D, Zheng W. Genome-wide association study in East Asians identifies two novel breast cancer susceptibility loci. Hum Mol Genet 2016; 25:3361-3371. [PMID: 27354352 DOI: 10.1093/hmg/ddw164] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/04/2016] [Accepted: 05/20/2016] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is one of the most common malignancies among women worldwide. Genetic factors have been shown to play an important role in breast cancer aetiology. We conducted a two-stage genome-wide association study (GWAS) including 14 224 cases and 14 829 controls of East Asian women to search for novel genetic susceptibility loci for breast cancer. Single nucleotide polymorphisms (SNPs) in two loci were found to be associated with breast cancer risk at the genome-wide significance level. The first locus, represented by rs12118297 at 1p22.3 (near the LMO4 gene), was associated with breast cancer risk with odds ratio (OR) and (95% confidence interval (CI)) of 0.91 (0.88-0.94) and a P-value of 4.48 × 10- 8 This association was replicated in another study, DRIVE GAME-ON Consortium, including 16 003 cases and 41 335 controls of European ancestry (OR = 0.95, 95% CI = 0.91-0.99, P-value = 0.019). The second locus, rs16992204 at 21q22.12 (near the LINC00160 gene), was associated with breast cancer risk with OR (95% CI) of 1.13 (1.07-1.18) and a P-value of 4.63 × 10 - 8 The risk allele frequency for this SNP is zero in European-ancestry populations in 1000 Genomes Project and thus its association with breast cancer risk cannot be assessed in DRIVE GAME-ON Consortium. Functional annotation using the ENCODE data indicates that rs12118297 might be located in a repressed element and locus 21q22.12 may affect breast cancer risk through regulating LINC00160 expressions and interaction with oestrogen receptor signalling. Our findings provide additional insights into the genetics of breast cancer.
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Affiliation(s)
- Mi-Ryung Han
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jirong Long
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Siew-Kee Low
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama 351-0198, Japan
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju 61469, South Korea.,Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun 58128, South Korea
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Qiuyin Cai
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jiajun Shi
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Xingyi Guo
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan.,Department of Epidemiology, Nagoya University Graduates School of Medicine, Nagoya 464-8681, Japan
| | - Motoki Iwasaki
- Epidemiology Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo 104-0045, Japan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Taiwan Biobank, Academia Sinica, Taipei 115, Taiwan.,College of Public Health, China Medical University, Taichung 404, Taiwan
| | - Mi Kyung Kim
- Division of Cancer Epidemiology and Management, National Cancer Center, Gyeonggi-do 10408, South Korea
| | - Wanqing Wen
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama 351-0198, Japan
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju 61469, South Korea
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai 200032, China
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Yoshio Kasuga
- Department of Surgery, Nagano Matsushiro General Hospital, Nagano 381-1231, Japan
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea.,Department of Surgery, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, Tokyo 108-8639, Japan
| | - Min Ho Park
- Department of Surgery, Chonnam National University Medical School, Gwangju 61469, South Korea
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai 200032, China
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Central Hospital, Nagoya 464-8681, Japan
| | - Shoichiro Tsugane
- Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo 104-0045, Japan
| | - Sue K Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama 351-0198, Japan
| | - Xiao-Ou Shu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Wei Zheng
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
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Han MR, Shu XO, Cai Q, Gao YT, Zheng Y, Michailidou K, Dennis J, Bolla MK, Wang Q, Choi JY, Hartman M, Kang D, Lophatananon A, Miao H, Matsuo K, Muir K, Sangrajrang S, Shen CY, Teo SH, Wu AH, Dunning AM, Pharoah PDP, Easton DF, Zheng W, Long J. Abstract 2780: Evaluation of genetic variants in high and moderate-penetrance breast cancer susceptibility genes in East Asians. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2780] [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: 11/16/2022]
Abstract
Abstract
Breast cancer is the most common invasive cancer in females worldwide. Over the past 20 years, pathogenic mutations in high-penetrance genes (BRCA1, BRCA2, PTEN and TP3) and moderate-penetrance genes (CHEK2, ATM, BRIP1, PALB2, RAD51C, STK11, CDH1, RAD50, and NBN) have been identified for breast cancer. Most of these germline mutations were discovered in women of European ancestry. In the present study, we aimed to investigate whether there were additional variants in these genes associated with breast cancer among women of Asian ancestry. Genotype data of up to 584 SNPs from the Breast Cancer Association Consortium (BCAC) including 6,269 cases and 6,624 controls and Shanghai Breast Cancer Genetics Study (SBCGS) including 5,768 cases and 5,703 controls were analyzed. Among 18 reported pathogenic mutations included in the dataset, 12 were monomorphic. Rare allele was observed for the remaining 6 mutations and one of them showed a significant association with P value of 0.0096. Among the remaining SNPs that were not previously reported to be pathogenic, 17 SNPs showed nominal association with P<0.05 in the Asian populations. Notably, SNP rs80359065 in the BRCA2 gene showed significant association with OR (95% CI) of 1.46 (1.15-1.84) and P value of 1.8 × 10−3 in the BCAC, and OR (95% CI) of 1.14 (1.03-1.27) and P value of 1.3 × 10−2 in the SBCGS. In the combined data, the OR (95% CI) was 1.23 (1.13-1.32) and the P value reached 7.0 × 10−5, lower than the bonferroni corrected P value (9.1 × 10−5). This SNP has a minor allele frequency (MAF) of 1% in the present study, more prevalent than reported pathogenic mutations. Another variant in the BRCA2 gene, rs80358978, was also associated with breast cancer with P value of 5.8 × 10−3 in the combined dataset. In the BRCA1 gene, three low-frequency variants with MAF<0.1% were associated with breast cancer, including rs8176085, rs799923, and rs1799950 with P values of 8.7 × 10−4, 1.0 × 10−3, and 5.8 × 10−3, respectively. Two common variants with MAF>10% in the RAD50 gene were also associated with breast cancer with P value of 1.0 × 10−3 and 2.1 × 10−3 for rs17772583 and rs2244012, respectively. Our study identified several new risk variants in the BRCA1, BRCA2 and RAD50 genes in relation to breast cancer risk in East Asian women and showed that many of the previously reported pathogenic mutations in the high/moderate penetrance genes of breast cancer are rare in our study population comprising largely sporadic breast cancer patients of East Asian ancestry.
Citation Format: Mi-Ryung Han, Xiao-Ou Shu, Qiuyin Cai, Yu-Tang Gao, Ying Zheng, Kyriaki Michailidou, Joe Dennis, Manjeet K. Bolla, Qin Wang, Ji-Yeob Choi, Mikael Hartman, Daehee Kang, Artitaya Lophatananon, Hui Miao, Keitaro Matsuo, Kenneth Muir, Sulee Sangrajrang, Chen-Yang Shen, Soo Hwang Teo, Anna H Wu, Alison M. Dunning, Paul D. P. Pharoah, Douglas F. Easton, Wei Zheng, Jirong Long. Evaluation of genetic variants in high and moderate-penetrance breast cancer susceptibility genes in East Asians. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2780. doi:10.1158/1538-7445.AM2015-2780
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Affiliation(s)
- Mi-Ryung Han
- 1Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Xiao-Ou Shu
- 1Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Qiuyin Cai
- 1Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Yu-Tang Gao
- 2Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Ying Zheng
- 3Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Kyriaki Michailidou
- 4Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Joe Dennis
- 4Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Manjeet K. Bolla
- 4Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Qin Wang
- 4Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Ji-Yeob Choi
- 5Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Mikael Hartman
- 6Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore
| | - Daehee Kang
- 7Department of Preventive Medicine, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Artitaya Lophatananon
- 8Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK, Institute of Population Health, University of Manchester, Manchester, United Kingdom
| | - Hui Miao
- 6Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore
| | - Keitaro Matsuo
- 9Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Kenneth Muir
- 8Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK, Institute of Population Health, University of Manchester, Manchester, United Kingdom
| | | | - Chen-Yang Shen
- 11Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, School of Public Health, China Medical University, Taichong, Taiwan
| | - Soo Hwang Teo
- 12Cancer Research Initiatives Foundation, Subang Jaya, Selangor, Malaysia, Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Anna H Wu
- 13Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Alison M. Dunning
- 14Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D. P. Pharoah
- 15Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Douglas F. Easton
- 15Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Wei Zheng
- 1Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Jirong Long
- 1Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
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Han MR, Deming-Halverson S, Cai Q, Wen W, Shrubsole MJ, Shu XO, Zheng W, Long J. Evaluating 17 breast cancer susceptibility loci in the Nashville breast health study. Breast Cancer 2014; 22:544-51. [PMID: 24510657 DOI: 10.1007/s12282-014-0518-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 01/23/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND Genome-wide association studies have discovered multiple genetic loci associated with breast cancer risk. Investigating these loci would be helpful to evaluate previous findings and identify causal variants for breast cancer. We evaluated index SNPs in 17 of these loci in a study of 1,511 cases and 1,454 controls of European descent. METHODS We investigated the overall association with breast cancer and among subtypes defined as ER+ (estrogen receptor positive), ER- (estrogen receptor negative) and triple-negative breast cancer (TNBC). Combined effects of SNPs on breast cancer risk were assessed via a genetic risk score. We evaluated the contribution of both genetic variants and traditional risk factors to a breast cancer risk assessment model. RESULTS Five of the 17 SNPs were significantly associated (P ≤ 0.05) with overall breast cancer in the same direction as previously reported: rs13387042 (2q35/TNP1), rs4973768 (3p24/SLC4A7), rs2046210 (6q25/ESR1), rs1219648 (10q26/FGFR2), and rs4784227 (16q12/TOX3). When stratified by breast cancer subtype, all five SNPs were associated (P < 0.05) with ER+ cancer, three with ER- cancer (rs13387042, rs1219648, and rs4784227), and one with TNBC (rs1219648). A GRS, based on those five significant SNPs, showed strong association with overall breast cancer with ORs (95 % CI) of 1.48 (1.22-1.79), 1.85 (1.52-2.25) and 2.26 (1.82-2.80), respectively, for each quartile, (P = 2.0 × 10(-15)). Traditional risk factors, including previous benign breast disease, breast cancer family history and parity, were significantly associated with breast cancer risk in the present study. These factors, together with the GRS, were used to build a breast cancer risk assessment model with a c statistic of 0.6321 from receiver operating characteristic analysis. The contribution of the GRS to the model was greater than prior benign breast disease, family history and parity with the c statistic change of 0.0374, 0.0324, 0.0103, 0.0012, respectively. CONCLUSIONS Our study demonstrates that five SNPs were associated with overall breast cancer, with stronger association for ER+ than ER- cancer as previously reported, and suggests that a risk assessment model incorporating the GRS from five loci is useful in identifying women at high risk of breast cancer.
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Affiliation(s)
- Mi-Ryung Han
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
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Han MR, Schellenberg GD, Wang LS. Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study. BMC Neurol 2010; 10:90. [PMID: 20932310 PMCID: PMC2964649 DOI: 10.1186/1471-2377-10-90] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 10/08/2010] [Indexed: 11/25/2022] Open
Abstract
Background Alzheimer's disease (AD) is common and highly heritable with many genes and gene variants associated with AD in one or more studies, including APOE ε2/ε3/ε4. However, the genetic backgrounds for normal cognition, mild cognitive impairment (MCI) and AD in terms of changes in cerebrospinal fluid (CSF) levels of Aβ1-42, T-tau, and P-tau181P, have not been clearly delineated. We carried out a genome-wide association study (GWAS) in order to better define the genetic backgrounds to these three states in relation to CSF levels. Methods Subjects were participants in the Alzheimer's Disease Neuroimaging Initiative (ADNI). The GWAS dataset consisted of 818 participants (mainly Caucasian) genotyped using the Illumina Human Genome 610 Quad BeadChips. This sample included 410 subjects (119 Normal, 115 MCI and 176 AD) with measurements of CSF Aβ1-42, T-tau, and P-tau181P Levels. We used PLINK to find genetic associations with the three CSF biomarker levels. Association of each of the 498,205 SNPs was tested using additive, dominant, and general association models while considering APOE genotype and age. Finally, an effort was made to better identify relevant biochemical pathways for associated genes using the ALIGATOR software. Results We found that there were some associations with APOE genotype although CSF levels were about the same for each subject group; CSF Aβ1-42 levels decreased with APOE gene dose for each subject group. T-tau levels tended to be higher among AD cases than among normal subjects. From adjusted result using APOE genotype and age as covariates, no SNP was associated with CSF levels among AD subjects. CYP19A1 'aromatase' (rs2899472), NCAM2, and multiple SNPs located on chromosome 10 near the ARL5B gene demonstrated the strongest associations with Aβ1-42 in normal subjects. Two genes found to be near the top SNPs, CYP19A1 (rs2899472, p = 1.90 × 10-7) and NCAM2 (rs1022442, p = 2.75 × 10-7) have been reported as genetic factors related to the progression of AD from previous studies. In AD subjects, APOE ε2/ε3 and ε2/ε4 genotypes were associated with elevated T-tau levels and ε4/ε4 genotype was associated with elevated T-tau and P-tau181P levels. Pathway analysis detected several biological pathways implicated in Normal with CSF β-amyloid peptide (Aβ1-42). Conclusions Our genome-wide association analysis identified several SNPs as important factors for CSF biomarker. We also provide new evidence for additional candidate genetic risk factors from pathway analysis that can be tested in further studies.
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Affiliation(s)
- Mi-Ryung Han
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Han W, Han MR, Kang JJ, Bae JY, Lee JH, Bae YJ, Lee JE, Shin HJ, Hwang KT, Hwang SE, Kim SW, Noh DY. Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer. BMC Cancer 2006; 6:92. [PMID: 16608533 PMCID: PMC1459182 DOI: 10.1186/1471-2407-6-92] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 04/12/2006] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A considerable proportion of estrogen receptor (ER)-positive breast cancer recurs despite tamoxifen treatment, which is a serious problem commonly encountered in clinical practice. We tried to find novel prognostic markers in this subtype of breast cancer. METHODS We performed array comparative genomic hybridization (CGH) with 1,440 human bacterial artificial chromosome (BAC) clones to assess copy number changes in 28 fresh-frozen ER-positive breast cancer tissues. All of the patients included had received at least 1 year of tamoxifen treatment. Nine patients had distant recurrence within 5 years (Recurrence group) of diagnosis and 19 patients were alive without disease at least 5 years after diagnosis (Non-recurrence group). RESULTS Potential prognostic variables were comparable between the two groups. In an unsupervised clustering analysis, samples from each group were well separated. The most common regions of gain in all samples were 1q32.1, 17q23.3, 8q24.11, 17q12-q21.1, and 8p11.21, and the most common regions of loss were 6q14.1-q16.3, 11q21-q24.3, and 13q13.2-q14.3, as called by CGH-Explorer software. The average frequency of copy number changes was similar between the two groups. The most significant chromosomal alterations found more often in the Recurrence group using two different statistical methods were loss of 11p15.5-p15.4, 1p36.33, 11q13.1, and 11p11.2 (adjusted p values < 0.001). In subgroup analysis according to lymph node status, loss of 11p15 and 1p36 were found more often in Recurrence group with borderline significance within the lymph node positive patients (adjusted p = 0.052). CONCLUSION Our array CGH analysis with BAC clones could detect various genomic alterations in ER-positive breast cancers, and Recurrence group samples showed a significantly different pattern of DNA copy number changes than did Non-recurrence group samples.
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MESH Headings
- Adult
- Aged
- Antineoplastic Agents, Hormonal/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Breast Neoplasms/chemistry
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/radiotherapy
- Breast Neoplasms/surgery
- Carcinoma, Ductal, Breast/chemistry
- Carcinoma, Ductal, Breast/drug therapy
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/radiotherapy
- Carcinoma, Ductal, Breast/secondary
- Carcinoma, Ductal, Breast/surgery
- Chemotherapy, Adjuvant
- Chromosomes, Artificial, Bacterial
- Cluster Analysis
- Combined Modality Therapy
- Cyclophosphamide/administration & dosage
- DNA, Neoplasm/genetics
- Disease-Free Survival
- Estrogen Receptor Modulators/therapeutic use
- Estrogens
- Female
- Fluorouracil/administration & dosage
- Humans
- Life Tables
- Mastectomy
- Methotrexate/administration & dosage
- Middle Aged
- Neoplasm Metastasis
- Neoplasm Proteins/analysis
- Neoplasms, Hormone-Dependent/chemistry
- Neoplasms, Hormone-Dependent/drug therapy
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/radiotherapy
- Neoplasms, Hormone-Dependent/surgery
- Nucleic Acid Hybridization
- Oligonucleotide Array Sequence Analysis
- Prognosis
- Radiotherapy, Adjuvant
- Receptors, Estrogen/analysis
- Tamoxifen/therapeutic use
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Affiliation(s)
- Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Mi-Ryung Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | | | - Ji-Yeon Bae
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | | | | | - Jeong Eon Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Hyuk-Jae Shin
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Ki-Tae Hwang
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Eun Hwang
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Dong-Young Noh
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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Bae JY, Ahn SJ, Lee JE, Kim JE, Han MR, Han W, Kim SW, Shin HJ, Lee SJ, Park D, Noh DY. BetaPix-a enhances the activity of phospholipase Cgamma1 by binding SH3 domain in breast cancer. J Cell Biochem 2005; 94:1010-6. [PMID: 15597340 DOI: 10.1002/jcb.20357] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Phospholipase C-gamma1 (PLCgamma1) plays a critical role in cell growth and proliferation by generating the second messengers, diacylglycerol and 1, 4, 5-inositol triphosphate. To investigate the roles of Src homology domain 2 and domain 3 of PLCgamma1 in PLCgamma1-mediated cell signaling, we characterized some proteins binding to these domains in the MCF7 and MDA-MB-231 breast cancer cell lines. Of the several proteins that bind to glutathione-S-transferase-SH2/SH2/SH3, we identified an 85 kDa protein that binds to the SH3 domain of PLCgamma1 as the guanine nucleotide exchange factor, p21-activated protein kinase-interacting exchange factor-a (betaPix-a). BetaPix-a co-immunoprecipitated with PLCgamma1 in breast cancer tissues extracts and in MCF7 and MDA-MB-231 cell extracts. In addition, PDGF-stimulated PLCgamma1 activity was elevated in betaPix-a-overexpressing NIH3T3 cells. Our results suggest that betaPix-a binds to the Src homology domain 3 of PLCgamma1 and promotes tumor growth in breast cancer by enhancing the activity PLCgamma1.
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Affiliation(s)
- Ji-Yeon Bae
- Cancer Research Institute, College of Medicine, Seoul National University, Yongon-dong, Chongno-gu, Seoul 110-744, South Korea
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