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Gunes M, Rosen ST, Shachar I, Gunes EG. Signaling lymphocytic activation molecule family receptors as potential immune therapeutic targets in solid tumors. Front Immunol 2024; 15:1297473. [PMID: 38476238 PMCID: PMC10927787 DOI: 10.3389/fimmu.2024.1297473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/05/2024] [Indexed: 03/14/2024] Open
Abstract
Recently, cancer immunotherapy has revolutionized cancer treatment. Various forms of immunotherapy have a manageable safety profile and result in prolongation of overall survival in patients with solid tumors, but only in a proportion of patients. Various factors in the tumor microenvironment play critical roles and may be responsible for this lack of therapeutic response. Signaling lymphocytic activation molecule family (SLAMF) members are increasingly being studied as factors impacting the tumor immune microenvironment. SLAMF members consist of nine receptors mainly expressed in immune cells. However, SLAMF receptors have also been detected in cancer cells, and they may be involved in a spectrum of anti-tumor immune responses. Here, we review the current knowledge of the expression of SLAMF receptors in solid tumors and tumor-infiltrating immune cells and their association with patient outcomes. Furthermore, we discuss the therapeutic potential of targeting SLAMF receptors to improve outcomes of cancer therapy in solid tumors. We believe the research on SLAMF receptor-targeted strategies may enhance anti-cancer immunity in patients with solid tumors and improve clinical outcomes.
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Affiliation(s)
- Metin Gunes
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Los Angeles, CA, United States
| | - Steven T. Rosen
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Los Angeles, CA, United States
- Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Los Angeles, CA, United States
| | - Idit Shachar
- Department of System Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - E. Gulsen Gunes
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Los Angeles, CA, United States
- Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, Los Angeles, CA, United States
- Toni Stephenson Lymphoma Center, City of Hope, Los Angeles, CA, United States
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2
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Wang M, Li S, Guo W, Wang L, Huang J, Zhuo J, Lai B, Liao C, Ge T, Nie Y, Jin S, Wang M, Zhang Y, Liu Y, Li X, Zhang H. CHRAC1 promotes human lung cancer growth through regulating YAP transcriptional activity. Carcinogenesis 2021; 43:264-276. [PMID: 34718437 DOI: 10.1093/carcin/bgab103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/01/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes regulate chromatin structure and play important roles in gene expression, differentiation, development and cancer progression. Dysregulation in the subunits of the complexes often has been found in different cancers, but how they influence cancer initiation and progression is not fully understood. Here we show that Chromatin Accessibility Complex Subunit 1 (CHRAC1), the accessory subunit of chromatin remodeling complex, is highly expressed in lung cancer tissues, which correlates with poor prognosis in lung cancer patients. CHRAC1 overexpression promotes lung cancer cell proliferation and migration in vitro and tumor growth in genetically engineered Kras G12D.LSL lung adenocarcinoma mouse model. Consistent with this, CHRAC1 silencing inhibits cell proliferation and migration in lung cancer cells and suppresses tumor growth in xenograft mouse model. Further, CHRAC1 binds to the transcription co-activator Yes-associated protein (YAP), enhances the transcription of downstream target oncogenes in Hippo pathway and thus promotes the tumor growth. Together, our study defines a critical role of CHRAC1 in promoting YAP transcriptional activity and lung cancer tumorigenesis, which makes it a potential target for lung cancer.
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Affiliation(s)
- Mingwei Wang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shasha Li
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wencong Guo
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lulu Wang
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430040, China
| | - Jiaxin Huang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Junzhe Zhuo
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Botao Lai
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chenqi Liao
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tianlan Ge
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuxuan Nie
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Su Jin
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Manxiang Wang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yanggeling Zhang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yimeng Liu
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaowen Li
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huixia Zhang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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3
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Chen Q, Qiu B, Zeng X, Hu L, Huang D, Chen K, Qiu X. Identification of a tumor microenvironment-related gene signature to improve the prediction of cervical cancer prognosis. Cancer Cell Int 2021; 21:182. [PMID: 33766042 PMCID: PMC7992856 DOI: 10.1186/s12935-021-01867-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
Background Previous studies have found that the microenvironment of cervical cancer (CESC) affects the progression and treatment of this disease. Thus, we constructed a multigene model to assess the survival of patients with cervical cancer. Methods We scored 307 CESC samples from The Cancer Genome Atlas (TCGA) and divided them into high and low matrix and immune scores using the ESTIMATE algorithm for differential gene analysis. Cervical cancer patients were randomly divided into a training group, testing group and combined group. The multigene signature prognostic model was constructed by Cox analyses. Multivariate Cox analysis was applied to evaluate the significance of the multigene signature for cervical cancer prognosis. Prognosis was assessed by Kaplan–Meier curves comparing the different groups, and the accuracy of the prognostic model was analyzed by receiver operating characteristic-area under the curve (ROC-AUC) analysis and calibration curve. The Tumor Immune Estimation Resource (TIMER) database was used to analyze the relationship between the multigene signature and immune cell infiltration. Results We obtained 420 differentially expressed genes in the tumor microenvironment from 307 patients with cervical cancer. A three-gene signature (SLAMF1, CD27, SELL) model related to the tumor microenvironment was constructed to assess patient survival. Kaplan–Meier analysis showed that patients with high risk scores had a poor prognosis. The ROC-AUC value indicated that the model was an accurate predictor of cervical cancer prognosis. Multivariate cox analysis showed the three-gene signature to be an independent risk factor for the prognosis of cervical cancer. A nomogram combining the three-gene signature and clinical features was constructed, and calibration plots showed that the nomogram resulted in an accurate prognosis for patients. The three-gene signature was associated with T stage, M stage and degree of immune infiltration in patients with cervical cancer. Conclusions This research suggests that the developed three-gene signature may be applied as a biomarker to predict the prognosis of and personalized therapy for CESC.
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Affiliation(s)
- Qian Chen
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, China.,Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Bingqing Qiu
- Department of Nuclear Medicine, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, China
| | - Xiaoyun Zeng
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Lang Hu
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, China
| | - Dongping Huang
- Department of Nutrition, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Kaihua Chen
- Department of Radiation Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, China
| | - Xiaoqiang Qiu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China.
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Liang X, Peng J, Chen D, Tang L, Liu A, Fu Z, Shi L, Wang K, Shao C. Identification of novel hub genes and lncRNAs related to the prognosis and progression of pancreatic cancer by microarray and integrated bioinformatics analysis. Gland Surg 2021; 10:1104-1117. [PMID: 33842254 PMCID: PMC8033078 DOI: 10.21037/gs-21-151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND Pancreatic cancer (PC) is one of the most invasive and metastatic neoplasms among the fatal malignancies of the digestive system. Abnormal expression of genes and long non-coding RNAs (lncRNAs) are reportedly linked to multiple cancers. However, the lncRNA-mRNA expression profiles and their molecular mechanisms in PC progression are poorly known. This study aimed to map the hub genes and lncRNAs which might play core roles in the development of PC. METHODS This study used microarray expression analysis to screen for both differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) between PC and matched adjacent non-tumor (AN) tissues. In order to clarify the functional classification of DEGs, we conducted GO and KEGG pathway enrichment analyses via the Enrichr database. LncRNA-mRNA co-expressed networks were also constructed to explore the probable core regulating DEGs and DElncRNAs. Subsequently, the hub genes and lncRNAs were validated via the ONCOMINE and GEPIA databases and the co-expressed networks. RESULTS By analyzing an mRNA-lncRNA microarray, we identified 943 mRNAs and 1,138 lncRNAs differentially expressed in PC tumors compared with the matched AN tissues. GO analysis confirmed that both up-regulated and down-regulated DEGs were enriched in multiple terms. The KEGG pathways enrichment analyses revealed that DEGs were mostly enriched in the focal adhesion and glutathione metabolism pathways, amongst others. Co-expressed networks were established to reveal the differential interactions between DEGs and DElncRNAs, and to indicate the core regulatory factors located at the core nodes of the co-expressed networks. The expression levels of potential core-regulating DEGs were validated by the GEPIA and ONCOMINE databases, and the relationship between overall survival and tumor stage and the potential core-regulating DEGs was analyzed using the GEPIA database. As a result, five genes and sixteen lncRNAs were finally considered as the hub transcripts in PC. CONCLUSIONS This study identified DEGs and DElncRNAs between PC tumors and matched AN tissues, and these transcripts were connected with malignant phenotypes in PC through different BPs and signaling pathways. Furthermore, five hub genes and sixteen lncRNAs were identified, which are expected to represent candidate diagnostic biomarkers or potential therapeutic targets for PC.
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Affiliation(s)
- Xing Liang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Junfeng Peng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Danlei Chen
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liang Tang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anan Liu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhiping Fu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ligang Shi
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Keqi Wang
- Department of Gastroenterology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chenghao Shao
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
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5
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Wu J, Mamidi TKK, Zhang L, Hicks C. Deconvolution of the Genomic and Epigenomic Interaction Landscape of Triple-Negative Breast Cancer. Cancers (Basel) 2019; 11:cancers11111692. [PMID: 31683572 PMCID: PMC6896043 DOI: 10.3390/cancers11111692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/07/2019] [Accepted: 10/19/2019] [Indexed: 12/26/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive form of breast cancer. Emerging evidenced suggests that both genetics and epigenetic factors play a role in the pathogenesis of TNBC. However, oncogenic interactions and cooperation between genomic and epigenomic variation have not been characterized. The objective of this study was to deconvolute the genomic and epigenomic interaction landscape in TNBC using an integrative genomics approach, which integrates information on germline, somatic, epigenomic and gene expression variation. We hypothesized that TNBC originates from a complex interplay between genomic (both germline and somatic variation) and epigenomic variation. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect entire molecular networks and signaling pathways which, in turn, drive TNBC. We addressed these hypotheses using germline variation from genome-wide association studies and somatic, epigenomic and gene expression variation from The Cancer Genome Atlas (TCGA). The investigation revealed signatures of functionally related genes containing germline, somatic and epigenetic variations. DNA methylation had an effect on gene expression. Network and pathway analysis revealed molecule networks and signaling pathways enriched for germline, somatic and epigenomic variation, among them: Role of BRCA1 in DNA Damage Response, Hereditary Breast Cancer Signaling, Molecular Mechanisms of Cancer, Estrogen-Dependent Breast Cancer, p53, MYC Mediated Apoptosis, and PTEN Signaling pathways. The investigation revealed that integrative genomics is a powerful approach for deconvoluting the genomic-epigenomic interaction landscape in TNBC. Further studies are needed to understand the biological mechanisms underlying oncogenic interactions between genomic and epigenomic factors in TNBC.
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Affiliation(s)
- Jiande Wu
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
| | - Tarun Karthik Kumar Mamidi
- Graduate Biomedical Sciences, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35233, USA.
| | - Lu Zhang
- Department of Public Health Sciences, Clemson University, 513 Edwards Hall, Clemson, SC 29634, USA.
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
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Liang ZZ, Zhang YX, Lin Y, Liu Q, Xie XM, Tang LY, Ren ZF. Joint effects of multiple sleep characteristics on breast cancer progression by menopausal status. Sleep Med 2018; 54:153-158. [PMID: 30580187 DOI: 10.1016/j.sleep.2018.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/09/2018] [Accepted: 10/23/2018] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Sleep has been closely linked to breast cancer risk. However, the association between sleep and breast cancer prognosis remains unclear. The aim of this study was to evaluate the separate and joint effects of multiple sleep characteristics on breast cancer prognosis among Chinese women. METHODS A total of 1580 breast cancer patients were recruited between October 2008 and December 2014 and followed up until December 31, 2017 in Guangzhou. Multivariate Cox models were conducted to estimate the hazard ratios (HR) and 95% confidence intervals (95%CI) for breast cancer prognosis in association with sleep characteristics. RESULTS Long sleep duration at night (>9 h) (HR = 2.33, 95%CI: 1.01-5.42), poor sleep quality (HR = 3.08, 95%CI: 1.74-5.47), and impaired daytime function (HR = 2.49, 95%CI: 1.65-3.79) after diagnosis were associated with an increased risk of breast cancer progression. Both short sleep duration (<6 h) (HR = 2.00, 95%CI: 1.06-3.77, Pinteraction = 0.011) and long sleep duration (>9 h) (HR = 4.69, 95%CI: 1.31-16.78, Pinteraction = 0.187) increased the progression risk only among patients with impaired but not normal daytime function. In addition, daytime napping significantly modified the effect of short sleep duration on the progression (HR = 3.55, 0.59, 95%CI: 1.55-7.97, 0.23-1.53 for patients without and with daytime napping, respectively, Pinteraction = 0.005). Stratification results suggested that the associations were more evident among pre-menopausal patients, although no significant interaction was observed. CONCLUSION Our findings suggested that inadequate sleep duration to feel one's best and poor sleep quality after diagnosis were associated with an increased risk of breast cancer progression, particularly for pre-menopausal women.
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Affiliation(s)
- Zhuo-Zhi Liang
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yi-Xin Zhang
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Ying Lin
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Qiang Liu
- The Second Affiliated Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiao-Ming Xie
- The Sun Yat-sen Cancer Center, Guangzhou 510080, China
| | - Lu-Ying Tang
- The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Ze-Fang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
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Li Q, Ma R, Zhang M. XRCC1 rs1799782 (C194T) polymorphism correlated with tumor metastasis and molecular subtypes in breast cancer. Onco Targets Ther 2018; 11:8435-8444. [PMID: 30568466 PMCID: PMC6276638 DOI: 10.2147/ott.s154746] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Breast cancer, a malignant tumor with its highest incidence in women, affects physical and mental health, and can even be life-threatening. In recent years, its incidence has continued to grow, accompanied by a trend of younger onset. XRCC1 is well known as a DNA-repair gene, and its abnormal expression is related to the occurrence of various malignant tumors. METHODS In this study, we detected XRCC1 expression and investigated its association with the XRCC1 rs1799782 polymorphism. XRCC1 was overexpressed to investigate its effect on in breast cancer cells. CCK8 and clone formation efficiency assay were used to detect cell proliferation. Transwell assay was performed to confirm cell migration and invasion. Flow cytometry was used to detect cell apoptosis. RESULTS In 118 breast cancer samples, CC genotype frequency was 49.15% (58 of 118), CT genotype frequency was 42.37% (50 of 118), and TT genotype frequency was 8.48% (ten of 118). Lymphatic metastasis was associated with a higher frequency of XRCC1 rs1799782 polymorphism (P<0.05), and breast cancer patients with positive PR, HER2, and negative ER had high XRCC1 rs1799782 frequency (P<0.05). Meanwhile, XRCC1 had low expression in breast cancer (74.6%, 88 of 118) and high expression in ER-negative, PR-negative, HER2-positive and Ki67-low-expression patients. XRCC1 rs1799782 may play an important role in the development and metastasis of breast cancer. These results differ from previous studies that did not suggest that rs1799782 is effective in breast cancer. We also investigated the role of XRCC1 in breast cancer progression. CONCLUSION We have proved that XRCC1 can inhibit proliferation and invasion and promote apoptosis of breast cancer cells. XRCC1 expression was regulated by the JNK pathway. We found that the JNK inhibitor SP600125 significantly inhibited the growth of breast cancer cells, and consider it a potential drug for breast cancer.
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Affiliation(s)
- Qing Li
- Department of Breast and Thyroid Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, PR China,
| | - Rong Ma
- Department of Breast Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Mei Zhang
- Department of Breast and Thyroid Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, PR China,
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Spurr L, Li M, Alomran N, Zhang Q, Restrepo P, Movassagh M, Trenkov C, Tunnessen N, Apanasovich T, Crandall KA, Edwards N, Horvath A. Systematic pan-cancer analysis of somatic allele frequency. Sci Rep 2018; 8:7735. [PMID: 29769535 PMCID: PMC5956099 DOI: 10.1038/s41598-018-25462-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/11/2018] [Indexed: 12/31/2022] Open
Abstract
Imbalanced expression of somatic alleles in cancer can suggest functional and selective features, and can therefore indicate possible driving potential of the underlying genetic variants. To explore the correlation between allele frequency of somatic variants and total gene expression of their harboring gene, we used the unique data set of matched tumor and normal RNA and DNA sequencing data of 5523 distinct single nucleotide variants in 381 individuals across 10 cancer types obtained from The Cancer Genome Atlas (TCGA). We analyzed the allele frequency in the context of the variant and gene functional features and linked it with changes in the total gene expression. We documented higher allele frequency of somatic variants in cancer-implicated genes (Cancer Gene Census, CGC). Furthermore, somatic alleles bearing premature terminating variants (PTVs), when positioned in CGC genes, appeared to be less frequently degraded via nonsense-mediated mRNA decay, indicating possible favoring of truncated proteins by the tumor transcriptome. Among the genes with multiple PTVs with high allele frequency, ARID1, TP53 and NSD1 were known key cancer genes. All together, our analyses suggest that high allele frequency of tumor somatic variants can indicate driving functionality and can serve to identify potential cancer-implicated genes.
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Affiliation(s)
- Liam Spurr
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Muzi Li
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Nawaf Alomran
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Qianqian Zhang
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Paula Restrepo
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Mercedeh Movassagh
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, 01605, USA
| | - Chris Trenkov
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Nerissa Tunnessen
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Tatiyana Apanasovich
- Department of Statistics, The George Washington University, Washington, DC, 20037, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Nathan Edwards
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Anelia Horvath
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA. .,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA. .,Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA. .,Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
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9
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Liao YH, Ren JT, Zhang W, Zhang ZZ, Lin Y, Su FX, Jia WH, Tang LY, Ren ZF. Polymorphisms in homologous recombination repair genes and the risk and survival of breast cancer. J Gene Med 2017; 19. [PMID: 28940489 DOI: 10.1002/jgm.2988] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/23/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Immunoglobulin (Ig)A antibody of Epstein-Barr virus (EBV) was found to associate with breast cancer (BC), whereas IgA positivity was related to a series of genetic markers in the genes of homologous recombination repair system (HRRs). We assessed the associations of the polymorphisms in HRR genes with the risk and survival of BC. METHODS A case-control study was conducted with 1551 bc cases and 1605 age-matched healthy controls between October 2008 and March 2012 in the Guangzhou Breast Cancer Study (GZBCS), China, and the case population were followed up until 31 January 2016. Five single nucleotide polymorphisms of candidate genes in HRR system were genotyped. Odds ratios (ORs) and hazards ratios (HRs) were calculated using multivariate logistic regression and Cox proportional hazards regression to estimate the risk and prognostic effect, respectively. RESULTS RFC1 rs6829064 (AA) was associated with an increased BC risk [OR = 1.35; 95% confidence interval (CI) = 1.06-1.73] compared to the wild genotype (GG). NRM rs1075496 (GT/TT versus GG) was associated with a worse progression-free survival (PFS) and the HR was 1.34 (95% CI = 1.01-1.78), particularly among advanced patients. LIG3 rs1052536 (CT/TT versus CC) was associated with a better PFS and the HR was 0.70 (95% CI = 0.53-0.93). However, RAD54L rs1710286 and RPA1 rs11078676 were not observed to be associated with either the risk or survival of BC. CONCLUSIONS The findings of the present study suggest that the polymorphisms in HRR genes were associated with BC risk (RFC1 rs6829064) and prognosis (NRM rs1075496 and LIG3 rs1052536), whereas RAD54L rs1710286 and RPA1 rs11078676 had null associations with BC.
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Affiliation(s)
- Yu-Huang Liao
- The School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jun-Ting Ren
- The School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wei Zhang
- The School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zheng-Zheng Zhang
- The School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ying Lin
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Feng-Xi Su
- The Second Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei-Hua Jia
- The Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Lu-Ying Tang
- The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ze-Fang Ren
- The School of Public Health, Sun Yat-sen University, Guangzhou, China
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10
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He P, Xia W, Wang L, Wu J, Guo YF, Zeng KQ, Wang MJ, Bing PF, Xie FF, Lu X, Zhang YH, Lei SF, Deng FY. Identification of expression quantitative trait loci (eQTLs) in human peripheral blood mononuclear cells (PBMCs) and shared with liver and brain. J Cell Biochem 2017; 119:1659-1669. [PMID: 28792098 DOI: 10.1002/jcb.26325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 08/02/2017] [Indexed: 12/21/2022]
Abstract
PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified. We identified 443 cis- and 2386 trans-eSNPs (FDR <0.05), which regulated 128 and 635 target genes, respectively. A transcriptome-wide expression regulation network was constructed, highlighting the importance of 28 pleiotropic eSNPs and 18 dually (cis- and trans-) regulated genes. Three genes, that is, TIPRL, HSPB8, and EGLN3, were commonly regulated by hundreds of eSNPs and constituted a very complex interaction network. Strikingly, the missense SNP rs371513 trans- regulated 25 target genes, which were functionally related to poly(A) RNA binding. Among 8904 eQTLs (P < 0.001) identified herein in PBMCs, a minority (163) was overlapped with lymphoblastoid, monocytes, liver, and/or brain. Besides, two cis-eSNPs in PBMC were confirmed by AEI. The present results demonstrated a comprehensive expression regulation network for human PBMCs and may provide novel insights into the pathogenesis of immunological diseases related to PBMCs.
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Affiliation(s)
- Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Wei Xia
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Lan Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Jian Wu
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yu-Fan Guo
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Ke-Qin Zeng
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Ming-Jun Wang
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Peng-Fei Bing
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Fang-Fei Xie
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yong-Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
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11
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Restrepo P, Movassagh M, Alomran N, Miller C, Li M, Trenkov C, Manchev Y, Bahl S, Warnken S, Spurr L, Apanasovich T, Crandall K, Edwards N, Horvath A. Overexpressed somatic alleles are enriched in functional elements in Breast Cancer. Sci Rep 2017; 7:8287. [PMID: 28811643 PMCID: PMC5557904 DOI: 10.1038/s41598-017-08416-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022] Open
Abstract
Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant allele fraction from corresponding RNA and DNA sequence data from patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between allele prevalence and functionality in known cancer-implicated genes from the Cancer Gene Census (CGC). We document significant allele-preferential expression of functional variants in CGC genes and across the entire dataset. Notably, we find frequent allele-specific overexpression of variants in tumor-suppressor genes. We also report a list of over-expressed variants from non-CGC genes. Overall, our analysis presents an integrated set of features of somatic allele expression and points to the vast information content of the asymmetric alleles in the cancer transcriptome.
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Affiliation(s)
- Paula Restrepo
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Mercedeh Movassagh
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, 01605, USA
| | - Nawaf Alomran
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Christian Miller
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Muzi Li
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Chris Trenkov
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Yulian Manchev
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Sonali Bahl
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Stephanie Warnken
- Computational Biology Institute, The George Washington University, Washington, DC, 20037, USA
| | - Liam Spurr
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Tatiyana Apanasovich
- Department of Statistics, The George Washington University, Washington, DC, 20037, USA
| | - Keith Crandall
- Computational Biology Institute, The George Washington University, Washington, DC, 20037, USA
| | - Nathan Edwards
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Anelia Horvath
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA. .,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA. .,Department of Statistics, The George Washington University, Washington, DC, 20037, USA. .,Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
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12
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Zhu RM, Lin W, Zhang W, Ren JT, Su Y, He JR, Lin Y, Su FX, Xie XM, Tang LY, Ren ZF. Modification effects of genetic polymorphisms in FTO, IL-6, and HSPD1 on the associations of diabetes with breast cancer risk and survival. PLoS One 2017; 12:e0178850. [PMID: 28591216 PMCID: PMC5462388 DOI: 10.1371/journal.pone.0178850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 05/21/2017] [Indexed: 12/29/2022] Open
Abstract
The contribution of diabetes to breast cancer remains uncertain among Chinese females, which may result from different genetic factors. We evaluated the associations of diabetes, combined with the polymorphisms in the genes of fat mass and obesity-associated gene (FTO), interleukin 6 (IL-6), and heat shock protein 60 (HSPD1), with breast cancer risk and survival in a Chinese Han population. The information on the history of diabetes was collected from 1551 incident breast cancer cases and 1605 age-frequency matched controls in Guangzhou, China. In total, 1168 cases were followed up. Diabetes was associated with both an increased risk of breast cancer [OR (95%CI): 1.67 (1.11, 2.52)] and a poor overall survival and progression free survival for breast cancer patients [HRs (95%CIs): 2.66 (1.10, 6.44) and 2.46 (1.29, 4.70), respectively]. IL-6 rs1800796 and HSPD1 rs2605039 had interactions with diabetes on breast cancer risk. Among women with CC genotype of IL-6 rs1800796 or GG genotype of HSPD1 rs2605039, diabetic individuals had a remarkably increased risk of breast cancer compared to non-diabetic women with ORs and 95%CIs of 2.53 (1.45, 4.41) and 6.40 (2.29, 17.87), respectively. GT/TT genotypes of HSPD1 rs2605039 was also associated with a better progression free survival for breast cancer patients [HR (95%CI): 0.70 (0.49, 0.99)]. Our results suggest that the contribution of diabetes to breast cancer risk might be modified by IL-6 rs1800796 and HSPD1 rs2605039. Diabetes and HSPD1 rs2605039 might also influence breast cancer prognosis.
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Affiliation(s)
- Rui-Mei Zhu
- Department of Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Wei Lin
- Department of Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Wei Zhang
- Department of Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Jun-Ting Ren
- Department of Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Yi Su
- Department of Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-Sen University, Guangzhou, China
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jian-Rong He
- The Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Ying Lin
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Feng-Xi Su
- The Second Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiao-Ming Xie
- The Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Lu-Ying Tang
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- * E-mail: (LT); (ZR)
| | - Ze-Fang Ren
- Department of Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-Sen University, Guangzhou, China
- * E-mail: (LT); (ZR)
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13
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Hamdi Y, Soucy P, Adoue V, Michailidou K, Canisius S, Lemaçon A, Droit A, Andrulis IL, Anton-Culver H, Arndt V, Baynes C, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borresen-Dale AL, Brand JS, Brauch H, Brenner H, Broeks A, Burwinkel B, Chang-Claude J, Couch FJ, Cox A, Cross SS, Czene K, Darabi H, Dennis J, Devilee P, Dörk T, Dos-Santos-Silva I, Eriksson M, Fasching PA, Figueroa J, Flyger H, García-Closas M, Giles GG, Goldberg MS, González-Neira A, Grenaker-Alnæs G, Guénel P, Haeberle L, Haiman CA, Hamann U, Hallberg E, Hooning MJ, Hopper JL, Jakubowska A, Jones M, Kabisch M, Kataja V, Lambrechts D, Marchand LL, Lindblom A, Lubinski J, Mannermaa A, Maranian M, Margolin S, Marme F, Milne RL, Neuhausen SL, Nevanlinna H, Neven P, Olswold C, Peto J, Plaseska-Karanfilska D, Pylkäs K, Radice P, Rudolph A, Sawyer EJ, Schmidt MK, Shu XO, Southey MC, Swerdlow A, Tollenaar RA, Tomlinson I, Torres D, Truong T, Vachon C, Van Den Ouweland AMW, Wang Q, Winqvist R, Investigators KC, Zheng W, Benitez J, Chenevix-Trench G, Dunning AM, Pharoah PDP, Kristensen V, Hall P, Easton DF, Pastinen T, Nord S, Simard J. Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21. Oncotarget 2016; 7:80140-80163. [PMID: 27792995 PMCID: PMC5340257 DOI: 10.18632/oncotarget.12818] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/13/2016] [Indexed: 12/02/2022] Open
Abstract
There are significant inter-individual differences in the levels of gene expression. Through modulation of gene expression, cis-acting variants represent an important source of phenotypic variation. Consequently, cis-regulatory SNPs associated with differential allelic expression are functional candidates for further investigation as disease-causing variants. To investigate whether common variants associated with differential allelic expression were involved in breast cancer susceptibility, a list of genes was established on the basis of their involvement in cancer related pathways and/or mechanisms. Thereafter, using data from a genome-wide map of allelic expression associated SNPs, 313 genetic variants were selected and their association with breast cancer risk was then evaluated in 46,451 breast cancer cases and 42,599 controls of European ancestry ascertained from 41 studies participating in the Breast Cancer Association Consortium. The associations were evaluated with overall breast cancer risk and with estrogen receptor negative and positive disease. One novel breast cancer susceptibility locus on 4q21 (rs11099601) was identified (OR = 1.05, P = 5.6x10-6). rs11099601 lies in a 135 kb linkage disequilibrium block containing several genes, including, HELQ, encoding the protein HEL308 a DNA dependant ATPase and DNA Helicase involved in DNA repair, MRPS18C encoding the Mitochondrial Ribosomal Protein S18C and FAM175A (ABRAXAS), encoding a BRCA1 BRCT domain-interacting protein involved in DNA damage response and double-strand break (DSB) repair. Expression QTL analysis in breast cancer tissue showed rs11099601 to be associated with HELQ (P = 8.28x10-14), MRPS18C (P = 1.94x10-27) and FAM175A (P = 3.83x10-3), explaining about 20%, 14% and 1%, respectively of the variance inexpression of these genes in breast carcinomas.
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Affiliation(s)
- Yosr Hamdi
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
| | - Véronique Adoue
- Institut National de la Santé et de la Recherche Médicale U1043, Toulouse, France
- Centre National de la Recherche Scientifique, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Sander Canisius
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Audrey Lemaçon
- Centre de Recherche du CHU de Québec – Université Laval, Faculté de Médecine, Département de Médecine Moléculaire, Université Laval, Quebec, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec – Université Laval, Faculté de Médecine, Département de Médecine Moléculaire, Université Laval, Quebec, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlevand Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Anne-Lise Borresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Judith S. Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - NBCS Collaborators
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
- Section of Oncology, Institute of Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
- Department of Breast-Endocrine Surgery, Akershus University Hospital, Lørenskog, Norway
- Department of Breast and Endocrine Surgery, Oslo University Hospital, Ullevål, Oslo, Norway
- Department of Research, Vestre Viken, Drammen, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- National Advisory Unit on Late Effects after Cancer Treatment, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Oncology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter A. Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | | | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Mark S. Goldberg
- Department of Medicine, McGill University, Montreal, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, Canada
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Grethe Grenaker-Alnæs
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, VilleJuif, France
| | - Lothar Haeberle
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Michael Jones
- Division of Genetics and Epidemiology, the Institute of Cancer Research, London, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Vesa Kataja
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Central Finland Hospital District, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Diether Lambrechts
- Vesalius Research Center, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | | | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mel Maranian
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Patrick Neven
- Multidisciplinary Breast Center, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dijana Plaseska-Karanfilska
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione Istituto Di Ricovero e Cura a Carattere, Scientifico, Istituto Nazionale Tumori, Milan, Italy
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Elinor J. Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology & Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rob A.E.M. Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, VilleJuif, France
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras, Valencia, Spain
| | | | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D. P. Pharoah
- Centre 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, UK
| | - Vessela Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Douglas F. Easton
- Centre 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, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
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