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Liu J, Qu Y, Zhao Y, Liang F, Ji L, Wang Z, Li J, Zang Z, Huang H, Zhang J, Gu W, Dai L, Yang R. CCDC12 gene methylation in peripheral blood as a potential biomarker for breast cancer detection. Biomarkers 2024; 29:265-275. [PMID: 38776382 DOI: 10.1080/1354750x.2024.2358302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Aberrant DNA methylation has been identified as biomarkers for breast cancer detection. Coiled-coil domain containing 12 gene (CCDC12) implicated in tumorigenesis. This study aims to investigate the potential of blood-based CCDC12 methylation for breast cancer detection. METHODS DNA methylation level of CpG sites (Cytosine-phosphate Guanine dinucleotides) in CCDC12 gene was measured by mass spectrometry in 255 breast cancer patients, 155 patients with benign breast nodules and 302 healthy controls. The association between CCDC12 methylation and breast cancer risk was evaluated by logistic regression and receiver operating characteristic curve analysis. RESULTS A total of eleven CpG sites were analyzed. The CCDC12 methylation levels were higher in breast cancer patients. Compared to the lowest tertile of methylation level in CpG_6,7, CpG_10 and CpG_11, the highest quartile was associated with 82, 91 and 95% increased breast cancer risk, respectively. The CCDC12 methylation levels were associated with estrogen receptor (ER) and human epidermal growth factor 2 (HER2) status. In ER-negative and HER2-positive (ER-/HER2+) breast cancer subtype, the combination of four sites CpG_2, CpG_5, CpG_6,7 and CpG_11 methylation levels could distinguish ER-/HER2+ breast cancer from the controls (AUC = 0.727). CONCLUSION The hypermethylation levels of CCDC12 in peripheral blood could be used for breast cancer detection.
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Affiliation(s)
- Jingjing Liu
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Yunhui Qu
- Department of Clinical Laboratory in the First Affiliated Hospital & Key Clinical Laboratory of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Yutong Zhao
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Feifei Liang
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Longtao Ji
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Zhi Wang
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Jinyu Li
- Department of Otology, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
| | - Zishan Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Haixia Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
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2
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Hall D, Giaimo BD, Park SS, Hemmer W, Friedrich T, Ferrante F, Bartkuhn M, Yuan Z, Oswald F, Borggrefe T, Rual JF, Kovall R. The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3. Nucleic Acids Res 2022; 50:13083-13099. [PMID: 36477367 PMCID: PMC9825171 DOI: 10.1093/nar/gkac1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 10/01/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The Notch pathway transmits signals between neighboring cells to elicit downstream transcriptional programs. Notch is a major regulator of cell fate specification, proliferation, and apoptosis, such that aberrant signaling leads to a pleiotropy of human diseases, including developmental disorders and cancers. The pathway signals through the transcription factor CSL (RBPJ in mammals), which forms an activation complex with the intracellular domain of the Notch receptor and the coactivator Mastermind. CSL can also function as a transcriptional repressor by forming complexes with one of several different corepressor proteins, such as FHL1 or SHARP in mammals and Hairless in Drosophila. Recently, we identified L3MBTL3 as a bona fide RBPJ-binding corepressor that recruits the repressive lysine demethylase LSD1/KDM1A to Notch target genes. Here, we define the RBPJ-interacting domain of L3MBTL3 and report the 2.06 Å crystal structure of the RBPJ-L3MBTL3-DNA complex. The structure reveals that L3MBTL3 interacts with RBPJ via an unusual binding motif compared to other RBPJ binding partners, which we comprehensively analyze with a series of structure-based mutants. We also show that these disruptive mutations affect RBPJ and L3MBTL3 function in cells, providing further insights into Notch mediated transcriptional regulation.
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Affiliation(s)
- Daniel Hall
- University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, USA
| | | | - Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Wiebke Hemmer
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine 1, Albert-Einstein-Allee 23, 89081Ulm, Germany
| | - Tobias Friedrich
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, University of Giessen, 35392 Giessen, Germany
| | - Zhenyu Yuan
- University of Cincinnati College of Medicine, Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, USA
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine 1, Albert-Einstein-Allee 23, 89081Ulm, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, 35392 Giessen, Germany
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rhett A Kovall
- To whom correspondence should be addressed. Tel: +1 513 558 4631;
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Eun K, Hwang SU, Kim M, Yoon JD, Kim E, Choi H, Kim G, Jeon HY, Kim JK, Kim JY, Hong N, Park MG, Jang J, Jeong HJ, Kim SJ, Ko BW, Lee SC, Kim H, Hyun SH. Generation of reproductive transgenic pigs of a CRISPR-Cas9-based oncogene-inducible system by somatic cell nuclear transfer. Biotechnol J 2022; 17:e2100434. [PMID: 35233982 DOI: 10.1002/biot.202100434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 11/06/2022]
Abstract
Alternative cancer models that are close to humans are required to create more valuable preclinical results during oncology studies. Here, we developed a new onco-pig model via developing a CRISPR-Cas9-based Conditional Polycistronic gene expression Cassette (CRI-CPC) system to control the tumor inducing simian virus 40 large T antigen (SV40LT) and oncogenic HRASG12V. After conducting somatic cell nuclear transfer (SCNT), transgenic embryos were transplanted into surrogate mothers and five male piglets were born. Umbilical cord analysis confirmed that all piglets were transgenic. Two of them survived, and they expressed a detectable green fluorescence. We tested whether our CRI-CPC models were naturally fertile and whether the CRI-CPC system was stably transferred to the offspring. By mating with a normal female pig, four offspring piglets were successfully produced. Among them, only three male piglets were transgenic. Finally, we tested their applicability as cancer models after transduction of Cas9 into fibroblasts from each CRI-CPC pig in vitro, resulting in cell acquisition of cancerous characteristics via the induction of oncogene expression. These results showed that our new CRISPR-Cas9-based onco-pig model was successfully developed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kiyoung Eun
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.,Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Seon-Ung Hwang
- Laboratory of Veterinary Embryology and Biotechnology, Korea University, Seongbuk-gu.,Institute of Stem Cell & Regenerative Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, Republic of Korea
| | - Mirae Kim
- Laboratory of Veterinary Embryology and Biotechnology, Korea University, Seongbuk-gu.,Institute of Stem Cell & Regenerative Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, Republic of Korea
| | - Junchul David Yoon
- Laboratory of Veterinary Embryology and Biotechnology, Korea University, Seongbuk-gu.,Institute of Stem Cell & Regenerative Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, Republic of Korea
| | - Eunhye Kim
- Laboratory of Veterinary Embryology and Biotechnology, Korea University, Seongbuk-gu.,Institute of Stem Cell & Regenerative Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, Republic of Korea
| | - Hyerin Choi
- Laboratory of Veterinary Embryology and Biotechnology, Korea University, Seongbuk-gu.,Institute of Stem Cell & Regenerative Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, Republic of Korea
| | - Gahye Kim
- Laboratory of Veterinary Embryology and Biotechnology, Korea University, Seongbuk-gu.,Institute of Stem Cell & Regenerative Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, Republic of Korea
| | - Hee-Young Jeon
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.,Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jun-Kyum Kim
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.,Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jung Yun Kim
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.,Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Nayoung Hong
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.,Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Min-Gi Park
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.,Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Junseok Jang
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.,Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyeon Ju Jeong
- Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sung Jin Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Bong-Woo Ko
- Songbaek Pig Farm, Jeju, 63014, Republic of Korea
| | - Sang Chul Lee
- Cronex Corporation, Cheongju, 28174, Republic of Korea
| | - Hyunggee Kim
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.,Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sang-Hwan Hyun
- Laboratory of Veterinary Embryology and Biotechnology, Korea University, Seongbuk-gu.,Institute of Stem Cell & Regenerative Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, Republic of Korea
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4
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Yang Y, Li Y, Yuan H, Liu X, Ren Y, Gao C, Jiao T, Cai Y, Zhao S. Integrative Analysis of the lncRNA-Associated ceRNA Regulatory Network Response to Hypoxia in Alveolar Type II Epithelial Cells of Tibetan Pigs. Front Vet Sci 2022; 9:834566. [PMID: 35211545 PMCID: PMC8861501 DOI: 10.3389/fvets.2022.834566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
The function of alveolar type II epithelial (ATII) cells is severely hampered by oxygen deficiency, and understanding the regulatory mechanisms controlling responses to hypoxia may assist in relieving injury induced by hypoxia. In this study, we cultured ATII cells from Tibetan pigs and Landrace pigs under hypoxic and normoxic environments to screen for differentially expressed (DE) lncRNAs, DEmiRNAs, and construct their associated ceRNA regulatory networks in response to hypoxia. Enrichment analysis revealed that target genes of DElncRNAs of Tibetan pigs and Landrace pig between the normoxic (TN, LN) and hypoxic (TL, LL) groups significantly enriched in the proteoglycans in cancer, renal cell carcinoma, and erbB signaling pathways, while the target genes of DEmiRNAs were significantly enriched in the axon guidance, focal adhesion, and mitogen-activated protein kinase (MAPK) signaling pathways. Hypoxia induction was shown to potentially promote apoptosis by activating the focal adhesion/PI3K-Akt/glycolysis pathway. The ssc-miR-20b/MSTRG.57127.1/ssc-miR-7-5p axis potentially played a vital role in alleviating hypoxic injury by regulating ATII cell autophagy under normoxic and hypoxic conditions. MSTRG.14861.4-miR-11971-z-CCDC12, the most affected axis, regulated numerous RNAs and may thus regulate ATII cell growth in Tibetan pigs under hypoxic conditions. The ACTA1/ssc-miR-30c-3p/MSTRG.23871.1 axis is key for limiting ATII cell injury and improving dysfunction and fibrosis mediated by oxidative stress in Landrace pigs. Our findings provide a deeper understanding of the lncRNA/miRNA/mRNA regulatory mechanisms of Tibetan pigs under hypoxic conditions.
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Affiliation(s)
- Yanan Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongqing Li
- Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Haonan Yuan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xuanbo Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yue Ren
- Institute of Animal Husbandry and Veterinary Medicine, Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ting Jiao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Cai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Shengguo Zhao
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5
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Du F, Peng L, Wang Q, Dong K, Pei W, Zhuo H, Xu T, Jing C, Li L, Zhang J. CCDC12 promotes tumor development and invasion through the Snail pathway in colon adenocarcinoma. Cell Death Dis 2022; 13:187. [PMID: 35217636 PMCID: PMC8881494 DOI: 10.1038/s41419-022-04617-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/10/2022] [Accepted: 02/09/2022] [Indexed: 12/02/2022]
Abstract
Integrative expression Quantitative Trait Loci (eQTL) analysis found that rs8180040 was significantly associated with Coiled-coil domain containing 12 (CCDC12) in colon adenocarcinoma (COAD) patients. Immunohistochemical staining and western blotting confirmed CCDC12 was highly expressed in COAD tissues, which was consistent with RNA-Seq data from the TCGA database. Knockdown of CCDC12 could significantly reduce proliferation, migration, invasion, and tumorigenicity of colon cancer cells, while exogenous overexpression of CCDC12 had the opposite effect. Four plex Isobaric Tags for Relative and Absolute Quantitation assays were performed to determine its function and potential regulatory mechanism and demonstrated that overexpression of CCDC12 would change proteins on the adherens junction pathway. Overexpressed Snail and knocked down CCDC12 subsequently in SW480 cells, and we found that overexpression of Snail did not significantly change CCDC12 levels in SW480 cells, while knockdown of CCDC12 reduced that of Snail. CCDC12 plays a significant role in tumorigenesis, development, and invasion of COAD and may affect the epithelial to mesenchymal transformation process of colon cancer cells by regulating the Snail pathway.
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Rae DT, Hocum JD, Bii V, Deeg HJ, Trobridge GD. A novel retroviral mutagenesis screen identifies prognostic genes in RUNX1 mediated myeloid leukemogenesis. Oncotarget 2016; 6:30664-74. [PMID: 26384344 PMCID: PMC4741560 DOI: 10.18632/oncotarget.5133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 08/31/2015] [Indexed: 12/16/2022] Open
Abstract
Using a novel retroviral shuttle vector approach we identified genes that collaborate with a patient derived RUNX1 (AML1) mutant. RUNX1 mutations occurs in 40% of myelodysplastic syndromes (MDS). MDS are a group of hematopoietic stem cell disorders that are characterized by dysplasia that often progress to acute myeloid leukemia (AML). Our goal was to identify genes dysregulated by vector-mediated genotoxicity that may collaborate with the RUNX1 mutant (D171N). D171N expressing cells have a survival and engraftment disadvantage and require additional genetic lesions to survive and persist. By dysregulating genes near the integrated vector provirus, the shuttle vector can promote transformation of D171N cells and tag the nearby genes that collaborate with D171N. In our approach, a gammaretroviral shuttle vector that expresses D171N is used to transduce CD105+, Sca-1+ mouse bone marrow. Mutagenized cells are expanded in liquid culture and vector integration sites from surviving cells are then identified using a retroviral shuttle vector approach. We repeatedly recovered integrated vector proviruses near genes (Itpkb, Ccdc12, and Nbeal2). To assess the prognostic significance of the genes identified we examined differential expression, overall survival, and relapse free survival of AML patients with alteration in the genes identified using The Cancer Genome Atlas (TCGA) AML data set. We found that ITPKB functions as an independent factor for poor prognoses and RUNX1 mutations in conjunction with ITPKB, CCDC12, and NBEAL2 have prognostic potential in AML.
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Affiliation(s)
- Dustin T Rae
- Washington State University College of Pharmacy, Spokane, WA, USA
| | - Jonah D Hocum
- Washington State University College of Pharmacy, Spokane, WA, USA
| | - Victor Bii
- Washington State University College of Pharmacy, Spokane, WA, USA
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Grant D Trobridge
- Washington State University College of Pharmacy, Spokane, WA, USA.,School of Molecular Biosciences, Washington State University, Pullman, WA, USA
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Identification of a Potential Regulatory Variant for Colorectal Cancer Risk Mapping to 3p21.31 in Chinese Population. Sci Rep 2016; 6:25194. [PMID: 27120998 PMCID: PMC4848543 DOI: 10.1038/srep25194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/12/2016] [Indexed: 01/30/2023] Open
Abstract
Genome-wide association studies (GWAS) have established chromosome 3p21.31 as a susceptibility locus for colorectal cancer (CRC) that lacks replication and exploration in the Chinese population. We searched potentially functional single nucleotide polymorphisms (SNPs) in the linkage disequilibrium (LD) block of 3p21.31 with chromatin immunoprecipitation-sequencing (ChIP-seq) data of histone modification, and tested their association with CRC via a case-control study involving 767 cases and 1397 controls in stage 1 and 528 cases and 678 controls in stage 2. In addition to the tag SNP rs8180040 (odds ratio (OR) = 0.875, 95% confidence interval (95% CI) = 0.793−0.966, P = 0.008, P-FDR (false discovery rate) = 0.040), rs1076394 presented consistently significant associations with CRC risk at both stages with OR = 0.850 (95% CI = 0.771−0.938, P = 0.001, P-FDR = 0.005) under the additive model in combined analyses. Supported by the analyses of data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), it was suggested that rs1076394 served as an expression Quantitative Trait Loci (eQTL) for gene CCDC12 and NME6, while NME6’s expression was obviously higher in CRC tissues. Using biofeature information such as ChIP-seq and RNA sequencing (RNA-seq) data might help researchers to interpret GWAS results and locate functional variants for diseases in the post-GWAS era.
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Zhang J, Jiang K, Shen Z, Gao Z, Lv L, Ye Y, Wang S. Expression QTL-based analyses reveal the mechanisms underlying colorectal cancer predisposition. Tumour Biol 2014; 35:12607-11. [PMID: 25201067 DOI: 10.1007/s13277-014-2583-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/29/2014] [Indexed: 11/25/2022] Open
Abstract
Genome-wide association studies have identified many risk loci associated with colorectal cancer. Strategies integrating biological data sets with GWAS results will provide insights into the roles of risk single-nucleotide polymorphisms. We performed expression quantitative trait locus-based analyses using the information provided in The Cancer Genome Atlas. Analysis of the cis-expression quantitative trait loci (eQTLs) of 18 previously reported colorectal cancer risk loci resulted in the discovery of five variants that were significantly associated with gene expressions. Analysis of the trans-eQTLs identified three risk loci that affect the expression levels of a neighboring transcription factor, MYC. These findings provide a more comprehensive picture of gene expression determinants in colorectal cancer and insights into the underlying biology of risk loci.
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Affiliation(s)
- Jizhun Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, No.11 Xizhimen South St, Xicheng District, Beijing, 100044, People's Republic of China
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