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Wang B, Shen XY, Pan LY, Li Z, Chen CJ, Yao YS, Tang DF, Gao W. The HDAC2-MTA3 interaction induces nonsmall cell lung cancer cell migration and invasion by targeting c-Myc and cyclin D1. Mol Carcinog 2023; 62:1630-1644. [PMID: 37401867 DOI: 10.1002/mc.23604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/05/2023]
Abstract
Genome-wide association studies have identified numerous single-nucleotide polymorphisms (SNPs) associated with lung cancer; however, the functions of histone deacetylase 2 (HDAC2) rs13213007 and HDAC2 in nonsmall cell lung cancer (NSCLC) remain unclear. Here we identified HDAC2 rs13213007 as a risk SNP and showed that HDAC2 was upregulated in both peripheral blood mononuclear cells (PBMCs) and NSCLC tissues with the rs13213007 A/A genotype compared with those with the rs13213007 G/G or G/A genotype. Patient clinical data indicated strong associations between rs13213007 genotype and N classification. Immunohistochemical staining confirmed that higher expression of HDAC2 was associated with NSCLC progression. Furthermore, we generated 293T cells with the rs13213007 A/A genotype using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 gene editing. Chromatin immunoprecipitation sequencing followed by motif analysis showed that HDAC2 can bind to c-Myc in rs13213007 A/A 293T cells. Cell Counting Kit-8, colony formation, wound-healing, and Transwell assays revealed that HDAC2 upregulates c-Myc and cyclin D1 expression and promotes NSCLC cell proliferation, migration, and invasion. Co-immunoprecipitation, quantitative reverse transcription-polymerase chain reaction, and western blot analysis assays showed that MTA3 interacts with HDAC2, decreases HDAC2 expression, and rescues the migration and invasion abilities of NSCLC cells. Taken together, these findings identify HDAC2 as a potential therapeutic biomarker in NSCLC.
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Affiliation(s)
- Bin Wang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Xiao-Yong Shen
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Lin-Yue Pan
- Department of Respiration, The Affiliated Zhongshan Hospital of Fudan University, Shanghai, China
| | - Zheng Li
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Chun-Ji Chen
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Yuan-Shan Yao
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Dong-Fang Tang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Wen Gao
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
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2
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Xia L, Nan B, Li Y. Statistical Inference for Cox Proportional Hazards Models with a Diverging Number of Covariates. Scand Stat Theory Appl 2023; 50:550-571. [PMID: 37408772 PMCID: PMC10321494 DOI: 10.1111/sjos.12595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 03/21/2022] [Indexed: 12/01/2022]
Abstract
For statistical inference on regression models with a diverging number of covariates, the existing literature typically makes sparsity assumptions on the inverse of the Fisher information matrix. Such assumptions, however, are often violated under Cox proportion hazards models, leading to biased estimates with under-coverage confidence intervals. We propose a modified debiased lasso method, which solves a series of quadratic programming problems to approximate the inverse information matrix without posing sparse matrix assumptions. We establish asymptotic results for the estimated regression coefficients when the dimension of covariates diverges with the sample size. As demonstrated by extensive simulations, our proposed method provides consistent estimates and confidence intervals with nominal coverage probabilities. The utility of the method is further demonstrated by assessing the effects of genetic markers on patients' overall survival with the Boston Lung Cancer Survival Cohort, a large-scale epidemiology study investigating mechanisms underlying the lung cancer.
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Affiliation(s)
- Lu Xia
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Bin Nan
- Department of Statistics, University of California, Irvine, Irvine, California, USA
| | - Yi Li
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
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3
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Lee YH, Do SK, Lee SY, Kang HG, Choi JE, Hong MJ, Lee JH, Lee S, Lee WK, Jeong JY, Shin KM, Park JE, Choi SH, Seo H, Yoo SS, Lee J, Cha SI, Kim CH, Park JY. Genetic Variants in Histone Modification Regions Predict Clinical Outcomes of Pemetrexed Chemotherapy in Lung Adenocarcinoma. Oncology 2023; 101:96-104. [PMID: 36257285 PMCID: PMC9932833 DOI: 10.1159/000527492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
OBJECTIVE This study was conducted to investigate the association between genetic variants in histone modification regions and clinical outcomes of PEM chemotherapy in patients with lung adenocarcinoma. METHODS Potentially functional SNPs were selected using integrated analysis of ChIP-seq and RNA-seq. The associations of 279 SNPs with chemotherapy response and overall survival (OS) were analyzed in 314 lung adenocarcinoma patients who underwent PEM chemotherapy. RESULTS Among the SNPs investigated, 18 were significantly associated with response to chemotherapy, while 28 with OS. Of these SNPs, rs549794A>G in an enhancer which is expected to regulate the expression of ribosomal protein S3 (RPS3) gene was significantly associated with both worse response to chemotherapy and worse OS (adjusted odds ratio = 0.59, 95% CI = 0.36-0.97, p = 0.04; adjusted hazard ratio = 1.44, 95% CI = 1.09-1.91, p = 0.01, respectively). Previous studies suggested that RPS3, a multi-functional protein with various extraribosomal activities, may play a role in chemotherapy resistance. Therefore, it is postulated that rs549794-induced change in the expression level of RPS3 may affect the response to PEM chemotherapy and consequently the survival outcomes in lung adenocarcinoma patients. CONCLUSION This study suggests that genetic variants in the histone modification regions may be useful for the prediction of clinical outcomes of PEM chemotherapy in advanced lung adenocarcinoma.
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Affiliation(s)
- Yong Hoon Lee
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sook Kyung Do
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shin Yup Lee
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Lung Cancer Center, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea,*Shin Yup Lee,
| | - Hyo-Gyoung Kang
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Mi Jeong Hong
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sunwoong Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won Kee Lee
- Department of Medical Informatics, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Medical Research Collaboration Center in Kyungpook National University Hospital and School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ji Yun Jeong
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Kyung Min Shin
- Department of Radiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ji Eun Park
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sun Ha Choi
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Lung Cancer Center, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea
| | - Hyewon Seo
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Soo Yoo
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Lung Cancer Center, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea
| | - Jaehee Lee
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Ick Cha
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Ho Kim
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jae Yong Park
- Departments of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea,Lung Cancer Center, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea,**Jae Yong Park,
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4
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Wang W, Shen Y, Zhang P, Liu L, Sha X, Li H, Wang S, Zhang H, Zhou Y, Shi J. Histone acetylation modification regulator-mediated tumor microenvironment infiltration characteristics and prognostic model of lung adenocarcinoma patients. J Thorac Dis 2022; 14:3886-3902. [PMID: 36389327 PMCID: PMC9641363 DOI: 10.21037/jtd-22-1000] [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: 07/18/2022] [Accepted: 09/16/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND The incidence rate of lung adenocarcinoma (LUAD) is rapidly increasing. Recent studies have reported that histone acetylation modification plays an important role in the occurrence and development of tumors. However, the potential role of modification of histone acetylation modification in the development of tumor immune microenvironment is still unclear. METHODS In this study, we comprehensively evaluated the acetylation modification patterns of LUAD samples obtained from various different databases based on 36 histone modification regulators, and constructed a prognostic model based on The Cancer Genome Atlas (TCGA) LUAD cohort using the Cox regression method. The close relationship between histone acetylation and tumor immune characteristics was further studied, including immune infiltration, immune escape and immunotherapy. Finally, we combined three cohort (GSE30219, GSE72094 and GSE50081) from Gene Expression Omnibus (GEO) database to verify the above results. RESULTS We analyzed the expression, mutation and interaction of 36 histone acetylation regulated genes. After Univariate Cox regression analysis and least absolute shrinkage and selection operator regression (LASSO), 5 genes (KAT2B, SIRT2, HDAC5, KAT8, HDAC2) were screened to establish the prognosis model and calculate the risk score. Then, patients in the TCGA cohort were divided into high- and low-risk groups based on the risk scores. Further analysis indicated that patients in the high-risk group exhibited significantly reduced overall survival (OS) compared with those in the low-risk group. The high- and low-risk groups exhibited significant differences in terms of tumor immune characteristics, such as immune infiltration, immune escape and immunotherapy. The high-risk group had lower immune score, less immune cell infiltration and higher clinical stage. Moreover, multivariate analysis revealed that this prognostic model might be a powerful prognostic predictor for LUAD. In addition, drugs sensitive for this classification were identified. Finally, the efficacy of the prognostic model was validated by cohort (GSE30219, GSE72094 and GSE50081) from GEO database. CONCLUSIONS Our study provided a robust signature for predicting changing prognosis of patients with LUAD. Thus, it appears to be a potentially useful prognostic tool. Moreover, the important relationship between histone acetylation and tumor immune microenvironment was revealed.
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Affiliation(s)
- Wenmiao Wang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Yao Shen
- School of Medicine, Nantong University, Nantong, China
| | - Peng Zhang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Lei Liu
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Xinyu Sha
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Houqiang Li
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Silin Wang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Youlang Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiahai Shi
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China;,School of Public Health, Nantong University, Nantong, China
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5
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Huang Q, Liu Y, Qiu M, Lin Q, Wei X, Zhou Z, Liang X, Li R, Chen W, Zhou X, Yu H. Potentially functional variants of MAP3K14 in the NF-κB signaling pathway genes predict survival of HBV-related hepatocellular carcinoma patients. Front Oncol 2022; 12:990160. [PMID: 36119471 PMCID: PMC9478184 DOI: 10.3389/fonc.2022.990160] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022] Open
Abstract
Background The NF-κB signaling pathway plays an important role in associating inflammation with tumor development and progression. However, few studies have reported that roles of genetic variants of the NF-κB signaling pathway genes in survival of patients with HBV-related hepatocellular carcinoma (HBV-HCC), especially with regards to potentially functional SNPs. Methods We used multivariate Cox proportional hazards regression to evaluate associations between 2,060 single nucleotide polymorphisms (SNPs) in 20 NF-κB signaling pathway genes and survival of 866 HBV-HCC patients, which were randomly split (1:1) into discovery and validation datasets. Expression quantitative trait loci (eQTL) analysis was conducted to identify associations between survival-associated SNPs and mRNA expression of corresponding genes. Furthermore, online database was used to assess mRNA expression of corresponding genes and survival. Finally, receiver operating characteristic (ROC) curves were used to assess the prediction accuracy of models integrating both clinical and genetic variables on HCC survival. Results A total of 6 SNPs in MAP3K14 remained significantly associated with OS of HBV-HCC patients (P<0.05, BFDP<0.8). Further eQTL analysis demonstrated that significant correlations between the rs2074292 (G>A) A allele was associated with higher mRNA expression levels of MAP3K14 (P=0.044) in normal liver tissue, which was associated with worse survival of HBV-HCC patients. In the additive model, after adjusting for age, sex, smoking status, drinking status, AFP level, cirrhosis, embolus and BCLC stage, the combined dataset showed that HBV-HCC patients carrying the rs2074292 AA and GA genotypes (HR=1.71, 95%CI= 1.29-2.27, P=0.000) (HR=1.40, 95%CI=1.10-1.77, P=0.005) have worse OS than GG genotype, respectively. The addition of risk genotypes to the prediction models increased the AUC significantly from 71.15% to 73.11% (P=0.012) and from 72.55% to 74.21% (P=0.010) for 1-year and 3-year OS, respectively. Conclusion Our study indicated that MAP3K14 rs2074292 A allele may be a potential predictor of HBV-HCC survival, likely regulating MAP3K14 mRNA expression.
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Affiliation(s)
- Qiongguang Huang
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Yingchun Liu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Moqin Qiu
- Department of Respiratory Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qiuling Lin
- Department of Clinical Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xueyan Wei
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Zihan Zhou
- Department of Cancer Prevention and Control, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiumei Liang
- Department of Disease Process Management, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Runwei Li
- Department of Occupational and Environmental Health, Indiana University, Bloomington, IN, United States
| | - Weiyi Chen
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Xianguo Zhou
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Hongping Yu, ; Xianguo Zhou,
| | - Hongping Yu
- School of Public Health, Guangxi Medical University, Nanning, China
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, China
- Key Cultivated Laboratory of Cancer Molecular Medicine, Health Commission of Guangxi Zhuang Autonomous Region, Nanning, China
- *Correspondence: Hongping Yu, ; Xianguo Zhou,
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6
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Li L, Li F, Hu X, Wu Z, Ren W, Wang T, Ji Z, Li N, Gu J, Sun C, Feng X, Han W, Huang J, Lei L. LAP3 contributes to IFN-γ-induced arginine depletion and malignant transformation of bovine mammary epithelial cells. BMC Cancer 2022; 22:864. [PMID: 35941558 PMCID: PMC9358085 DOI: 10.1186/s12885-022-09963-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/29/2022] [Indexed: 11/26/2022] Open
Abstract
Background IFN-γ has been traditionally recognized as an inflammatory cytokine that involves in inflammation and autoimmune diseases. Previously we have shown that sustained IFN-γ induced malignant transformation of bovine mammary epithelial cells (BMECs) via arginine depletion. However, the molecular mechanism underlying this is still unknown. Methods In this study, the amino acids contents in BMECs were quantified by a targeted metabolomics method. The acquisition of differentially expressed genes was mined from RNA-seq dataset and analyzed bioinformatically. Quantitative reverse transcription polymerase chain reaction (qRT-PCR), enzyme-linked immunosorbent assay (ELISA), western blotting, and immunohistochemistry (IHC) assay were performed to detect gene mRNA and protein expression levels. CCK-8 and would healing assays were used to detect cell proliferation and migration abilities, respectively. Cell cycle phase alternations were analyzed by flow cytometry. Results The targeted metabolomics analysis specifically discovered IFN-γ induced arginine depletion through accelerating arginine catabolism and inhibiting arginine anabolism in BMECs. Transcriptome analysis identified leucine aminopeptidase 3 (LAP3), which was regulated by p38 and ERK MAPKs, to downregulate arginine level through interfering with argininosuccinate synthetase (ASS1) as IFN-γ stimulated. Moreover, LAP3 also contributed to IFN-γ-induced malignant transformation of BMECs by upregulation of HDAC2 (histone deacetylase 2) expression and promotion of cell cycle proteins cyclin A1 and D1 expressions. Arginine supplementation did not affect LAP3 and HDAC2 expressions, but slowed down cell cycle process of malignant BMECs. In clinical samples of patients with breast cancer, LAP3 was confirmed to be upregulated, while ASS1 was downregulated compared with healthy control. Conclusions These results demonstrated that LAP3 mediated IFN-γ-induced arginine depletion to malignant transformation of BMECs. Our findings provide a potential therapeutic target for breast cancer both in humans and dairy cows. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09963-w.
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Affiliation(s)
- Li Li
- Department of First Hospital, Jilin University, Xinmin Street 1, Changchun, China
| | - Fengyang Li
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, China
| | - Xiuhong Hu
- Department of First Hospital, Jilin University, Xinmin Street 1, Changchun, China.,Shannan Hospital, Shannan, China
| | - Zengshuai Wu
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, China
| | - Wenbo Ren
- Department of First Hospital, Jilin University, Xinmin Street 1, Changchun, China
| | - Tingting Wang
- Department of First Hospital, Jilin University, Xinmin Street 1, Changchun, China
| | - Zhengchao Ji
- Department of First Hospital, Jilin University, Xinmin Street 1, Changchun, China
| | - Na Li
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, China
| | - Jingmin Gu
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, China
| | - Changjiang Sun
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, China
| | - Xin Feng
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, China
| | - Wenyu Han
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, China
| | - Jing Huang
- Department of First Hospital, Jilin University, Xinmin Street 1, Changchun, China.
| | - Liancheng Lei
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, China.
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7
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Chen AS, Liu H, Wu Y, Luo S, Patz EF, Glass C, Su L, Du M, Christiani DC, Wei Q. Genetic variants in DDO and PEX5L in peroxisome-related pathways predict non-small cell lung cancer survival. Mol Carcinog 2022; 61:619-628. [PMID: 35502931 DOI: 10.1002/mc.23400] [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: 01/08/2022] [Revised: 03/05/2022] [Accepted: 03/10/2022] [Indexed: 01/14/2023]
Abstract
Peroxisomes play a role in lipid metabolism and regulation of reactive oxygen species, but its role in development and progression of non-small cell lung cancer (NSCLC) is not well understood. Here, we investigated the associations between 9708 single-nucleotide polymorphisms (SNPs) in 113 genes in the peroxisome-related pathways and survival of NSCLC patients from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) and the Harvard Lung Cancer Susceptibility (HLCS) study. In 1185 NSCLC patients from the PLCO trial, we found that 213 SNPs were significantly associated with NSCLC overall survival (OS) (p ≤ 0.05, Bayesian false discovery probability [BFDP] ≤ 0.80), of which eight SNPs were validated in the HLCS data set. In a multivariate Cox proportional hazards regression model, two independent SNPs (rs9384742 DDO and rs9825224 PEX5L) were significantly associated with NSCLC survival (hazards ratios [HR] of 1.17 with 95% CI [confidence interval] of 1.06-1.28 and 0.86 with 95% CI of 0.77-0.96, respectively). Patients with one or two protective genotypes had a significantly higher OS (HR: 0.787 [95% CI: 0.620-0.998] and 0.691 [95% CI: 0.543-0.879], respectively). Further expression quantitative trait loci analysis using whole blood and lung tissue showed that the minor allele of rs9384742 DDO was significantly associated with decreased messenger RNA (mRNA) expression levels and that DDO expression was also decreased in NSCLC tumor tissue. Additionally, high PEX5L expression levels were significantly associated with lower survival of NSCLC. Our data suggest that variants in these peroxisome-related genes may influence gene regulation and are potential predictors of NSCLC OS, once validated by additional studies.
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Affiliation(s)
- Allan S Chen
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yufeng Wu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Edward F Patz
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Departments of Radiology, Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Carolyn Glass
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Li Su
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mulong Du
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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8
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Genetic variants in histone modification regions are associated with the prognosis of lung adenocarcinoma. Sci Rep 2021; 11:21520. [PMID: 34728688 PMCID: PMC8563968 DOI: 10.1038/s41598-021-00909-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/20/2021] [Indexed: 11/25/2022] Open
Abstract
We investigated the association between genetic variants in the histone modification regions and the prognosis of lung adenocarcinoma after curative surgery. Potentially functional SNPs were selected using integrated analysis of ChIP-seq and RNA-seq. The SNPs were analyzed in a discovery set (n = 166) and a validation set (n = 238). The associations of the SNPs with overall survival (OS) and disease-free survival (DFS) were analyzed. A total of 279 SNPs were selected for genotyping. Among these, CAPN1 rs17583C>T was significantly associated with better OS and DFS (P = 0.001 and P = 0.007, respectively), and LINC00959 rs4751162A>G was significantly associated with worse DFS (P = 0.008). Luciferase assays showed a significantly lower promoter activity of CAPN1 in the rs17583 T allele than C allele (P = 0.008), and consistently the CT + TT genotypes had significantly lower CAPN1 expression than CC genotype (P = 0.01) in clinical samples. The rs4751162 G allele had higher promoter activity of GLRX3 than A allele (P = 0.05). The motif analyses and ChIP-qPCR confirmed that the variants are located in the active promoter/enhancer regions where transcription factor binding occurs. This study showed that genetic variants in the histone modification regions could predict the prognosis of lung adenocarcinoma after surgery.
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Li X, Zou Y, Li T, Wong TKF, Bushey RT, Campa MJ, Gottlin EB, Liu H, Wei Q, Rodrigo A, Patz EF. Genetic Variants of CLPP and M1AP Are Associated With Risk of Non-Small Cell Lung Cancer. Front Oncol 2021; 11:709829. [PMID: 34604049 PMCID: PMC8479179 DOI: 10.3389/fonc.2021.709829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/20/2021] [Indexed: 11/23/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) are often associated with distinct phenotypes in cancer. The present study investigated associations of cancer risk and outcomes with SNPs discovered by whole exome sequencing of normal lung tissue DNA of 15 non-small cell lung cancer (NSCLC) patients, 10 early stage and 5 advanced stage. Methods DNA extracted from normal lung tissue of the 15 NSCLC patients was subjected to whole genome amplification and sequencing and analyzed for the occurrence of SNPs. The association of SNPs with the risk of lung cancer and survival was surveyed using the OncoArray study dataset of 85,716 patients (29,266 cases and 56,450 cancer-free controls) and the Prostate, Lung, Colorectal and Ovarian study subset of 1,175 lung cancer patients. Results We identified 4 SNPs exclusive to the 5 patients with advanced stage NSCLC: rs10420388 and rs10418574 in the CLPP gene, and rs11126435 and rs2021725 in the M1AP gene. The variant alleles G of SNP rs10420388 and A of SNP rs10418574 in the CLPP gene were associated with increased risk of squamous cell carcinoma (OR = 1.07 and 1.07; P = 0.013 and 0.016, respectively). The variant allele T of SNP rs11126435 in the M1AP gene was associated with decreased risk of adenocarcinoma (OR = 0.95; P = 0.027). There was no significant association of these SNPs with the overall survival of lung cancer patients (P > 0.05). Conclusions SNPs identified in the CLPP and M1AP genes may be useful in risk prediction models for lung cancer. The previously established association of the CLPP gene with cancer progression lends relevance to our findings.
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Affiliation(s)
- Xianghan Li
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Yiran Zou
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Teng Li
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thomas K F Wong
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ryan T Bushey
- Department of Radiology, Duke University Medical Center, Durham, NC, United States
| | - Michael J Campa
- Department of Radiology, Duke University Medical Center, Durham, NC, United States
| | - Elizabeth B Gottlin
- Department of Radiology, Duke University Medical Center, Durham, NC, United States
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States.,Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Allen Rodrigo
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Edward F Patz
- Department of Radiology, Duke University Medical Center, Durham, NC, United States.,Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States
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10
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Pan L, Niu Z, Gao Y, Wang L, Liu Z, Liu J, Sun J, Pei H. Silencing of CREB Inhibits HDAC2/TLR4/NF-κB Cascade to Relieve Severe Acute Pancreatitis-Induced Myocardial Injury. Inflammation 2021; 44:1565-1580. [PMID: 33725236 DOI: 10.1007/s10753-021-01441-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 02/06/2021] [Accepted: 02/19/2021] [Indexed: 02/08/2023]
Abstract
The purpose of the present study is to investigate the role of CREB in cardiomyocytes proliferation in regulation of HDAC2-dependent TLR4/NF-κB pathway in severe acute pancreatitis (SAP)-induced myocardial injury. The SAP rat model was developed by injecting sodium touracholate into SD rats and then infected with lentivirus vectors expressing sh-CREB in the presence/absence of LPS. The pathological alterations of rat pancreatic and cardiac tissues were observed by HE staining. TUNEL assay was used to study apoptosis of cardiomyocytes. Next, the loss- and gain-function assay was conducted in LPS-induced myocardial injury cardiomyocytes to define the roles of CREB, HDAC2, and TLR4 in cardiomyocyte proliferation, apoptosis, inflammation, and myocardial injury in vitro. ChIP assay was used to study the enrichment of CREB bound to HDAC2 promoter. RT-qPCR and Western blot analysis were used to detect the expressions of related mRNA and proteins in the NF-κB pathway, respectively. CREB was found to be overexpressed in both SAP tissues and cells. CREB directly bound to the promoter of HDAC2 and activated its expression. Overexpressed CREB or HDAC2 inhibited proliferation and promoted apoptosis of cardiomyocytes. Suppression of CREB inhibited the HDAC2/TLR4/NF-κB cascade to promote proliferation and inhibit apoptosis of cardiomyocytes. The in vitro results were validated in vivo experiments. Coherently, suppression of CREB can inhibit HDAC2/TLR4/NF-κB cascade to promote cardiomyocyte proliferation, thus ameliorating SAP-induced myocardial injury.
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Affiliation(s)
- Longfei Pan
- Department of Emergency, the Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, 710004, Xi'an, Shaanxi Province, People's Republic of China.
| | - Zequn Niu
- Department of Emergency, the Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, 710004, Xi'an, Shaanxi Province, People's Republic of China
| | - Yanxia Gao
- Department of Emergency, the Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, 710004, Xi'an, Shaanxi Province, People's Republic of China
| | - Liming Wang
- Department of Emergency, the Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, 710004, Xi'an, Shaanxi Province, People's Republic of China
| | - Zhong Liu
- Department of Emergency, the Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, 710004, Xi'an, Shaanxi Province, People's Republic of China
| | - Jie Liu
- Department of Emergency, the Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, 710004, Xi'an, Shaanxi Province, People's Republic of China
| | - Jiangli Sun
- Department of Emergency, the Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, 710004, Xi'an, Shaanxi Province, People's Republic of China
| | - Honghong Pei
- Department of Emergency, the Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, 710004, Xi'an, Shaanxi Province, People's Republic of China
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11
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Zhao YC, Tang D, Yang S, Liu H, Luo S, Stinchcombe TE, Glass C, Su L, Shen S, Christiani DC, Wei Q. Novel Variants of ELP2 and PIAS1 in the Interferon Gamma Signaling Pathway Are Associated with Non-Small Cell Lung Cancer Survival. Cancer Epidemiol Biomarkers Prev 2020; 29:1679-1688. [PMID: 32493705 DOI: 10.1158/1055-9965.epi-19-1450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/12/2020] [Accepted: 05/29/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND IFNγ is a pleiotropic cytokine that plays critical immunomodulatory roles in intercellular communication in innate and adaptive immune responses. Despite recognition of IFNγ signaling effects on host defense against viral infection and its utility in immunotherapy and tumor progression, the roles of genetic variants of the IFNγ signaling pathway genes in survival of patients with cancer remain unknown. METHODS We used a discovery genotyping dataset from the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (n = 1,185) and a replication genotyping dataset from the Harvard Lung Cancer Susceptibility Study (n = 984) to evaluate associations between 14,553 genetic variants in 150 IFNγ pathway genes and survival of non-small cell lung cancer (NSCLC). RESULTS The combined analysis identified two independent potentially functional SNPs, ELP2 rs7242481G>A and PIAS1 rs1049493T>C, to be significantly associated with NSCLC survival, with a combined HR of 0.85 (95% confidence interval, 0.78-0.92; P < 0.0001) and 0.87 (0.81-0.93; P < 0.0001), respectively. Expression quantitative trait loci analyses showed that the survival-associated ELP2 rs7242481A allele was significantly associated with increased mRNA expression levels of elongator acetyltransferase complex subunit 2 (ELP2) in 373 lymphoblastoid cell lines and 369 whole-blood samples. The PIAS1 rs1049493C allele was significantly associated with decreased mRNA expression levels of PIAS1 in 383 normal lung tissues and 369 whole-blood samples. CONCLUSIONS Genetic variants of IFNγ signaling genes are potential prognostic markers for NSCLC survival, likely through modulating the expression of key genes involved in host immune response. IMPACT Once validated, these variants could be useful predictors of NSCLC survival.
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Affiliation(s)
- Yu Chen Zhao
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Dongfang Tang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Sen Yang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | - Thomas E Stinchcombe
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina.,Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Carolyn Glass
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina.,Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Li Su
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Sipeng Shen
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - David C Christiani
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina. .,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina.,Department of Medicine, Duke University Medical Center, Durham, North Carolina
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