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Kałafut J, Czerwonka A, Czapla K, Przybyszewska-Podstawka A, Hermanowicz JM, Rivero-Müller A, Borkiewicz L. Regulation of Notch1 Signalling by Long Non-Coding RNAs in Cancers and Other Health Disorders. Int J Mol Sci 2023; 24:12579. [PMID: 37628760 PMCID: PMC10454443 DOI: 10.3390/ijms241612579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Notch1 signalling plays a multifaceted role in tissue development and homeostasis. Currently, due to the pivotal role of Notch1 signalling, the relationship between NOTCH1 expression and the development of health disorders is being intensively studied. Nevertheless, Notch1 signalling is not only controlled at the transcriptional level but also by a variety of post-translational events. First is the ligand-dependent mechanical activation of NOTCH receptors and then the intracellular crosstalk with other signalling molecules-among those are long non-coding RNAs (lncRNAs). In this review, we provide a detailed overview of the specific role of lncRNAs in the modulation of Notch1 signalling, from expression to activity, and their connection with the development of health disorders, especially cancers.
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Affiliation(s)
- Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Arkadiusz Czerwonka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Karolina Czapla
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Alicja Przybyszewska-Podstawka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Justyna Magdalena Hermanowicz
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland;
- Department of Clinical Pharmacy, Medical University of Bialystok, Waszyngtona 15, 15-274 Bialystok, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
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2
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Pan J, Huang Z, Zhang Y, Xu Y. ADAM12 as a Clinical Prognostic Indicator Associated with Tumor Immune Infiltration in Lung Adenocarcinoma. DNA Cell Biol 2022; 41:410-423. [PMID: 35377217 DOI: 10.1089/dna.2021.0764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Twenty-two functional α-disintegrin and metalloproteinases (ADAMs) have been identified in humans, 12 of which have proteolytic activity. The role of ADAMs in cancer has attracted increasing attention. However, the expression and significance of ADAMs in lung adenocarcinoma (LUAD) remain unclear. Most recently, we investigated the transcriptional data of ADAMs and related overall survival in patients with LUAD based on several databases, including TCGA, cBioPortal, Kaplan-Meier Plotter, LinkedOmics, KEGG, TIMER, and TISIDB. Knockdown of ADAM12 was performed in vitro to verify its biological function. According to our findings, 10 ADAMs exhibited significant differential expression in LUAD compared with cancer-adjacent normal tissues. ADAM12 expression was significantly higher in LUAD tissues than in paracancerous tissues, and lower ADAM12 expression was associated with better survival. Genetic alterations of ADAM12 mainly included missense mutations, amplifications, and deep deletions. ADAM12 and positively correlated genes were mainly enriched in protein digestion and absorption, extracellular matrix-receptor interaction, and adhesion plaques. ADAM12 had a moderate correlation with immune cell markers EBIP1, CCNB1, EXO1, KNTC1, PRC1, and FAM198B. Prognostic model was established based on ADAM12 and immune-related genes. In vitro experiments revealed that knocking down ADAM12 inhibited cell proliferation, migration, and invasion. ADAM12 potentially plays an important role in the occurrence of LUAD and may be utilized as an immunotherapy target and a valuable prognostic biomarker for LUAD.
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Affiliation(s)
- Junfan Pan
- Department of Thoracic Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China.,Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Zhidong Huang
- Quanzhou First Hospital of Fujian Medical University, Quanzhou, China
| | - Yuan Zhang
- The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Yiquan Xu
- Department of Thoracic Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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3
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Liu L, Liu H, Luo S, Patz EF, Glass C, Su L, Lin L, Christiani DC, Wei Q. Genetic Variants of CLEC4E and BIRC3 in Damage-Associated Molecular Patterns-Related Pathway Genes Predict Non-Small Cell Lung Cancer Survival. Front Oncol 2021; 11:717109. [PMID: 34692492 PMCID: PMC8527850 DOI: 10.3389/fonc.2021.717109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022] Open
Abstract
Accumulating evidence supports a role of various damage-associated molecular patterns (DAMPs) in progression of lung cancer, but roles of genetic variants of the DAMPs-related pathway genes in lung cancer survival remain unknown. We investigated associations of 18,588 single-nucleotide polymorphisms (SNPs) in 195 DAMPs-related pathway genes with non-small cell lung cancer (NSCLC) survival in a subset of genotyping data for 1,185 patients from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial and validated the findings in another independent subset of genotyping data for 984 patients from Harvard Lung Cancer Susceptibility Study. We performed multivariate Cox proportional hazards regression analysis, followed by expression quantitative trait loci (eQTL) analysis, Kaplan-Meier survival analysis and bioinformatics functional prediction. We identified that two SNPs (i.e., CLEC4E rs10841847 G>A and BIRC3 rs11225211 G>A) were independently associated with NSCLC overall survival, with adjusted allelic hazards ratios of 0.89 (95% confidence interval=0.82-0.95 and P=0.001) and 0.82 (0.73-0.91 and P=0.0003), respectively; so were their combined predictive alleles from discovery and replication datasets (Ptrend=0.0002 for overall survival). We also found that the CLEC4E rs10841847 A allele was associated with elevated mRNA expression levels in normal lymphoblastoid cells and whole blood cells, while the BIRC3 rs11225211 A allele was associated with increased mRNA expression levels in normal lung tissues. Collectively, these findings indicated that genetic variants of CLEC4E and BIRC3 in the DAMPs-related pathway genes were associated with NSCLC survival, likely by regulating the mRNA expression of the corresponding genes.
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Affiliation(s)
- Lihua Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,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
| | - 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
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, United States
| | - Edward F Patz
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Radiology, Duke University Medical Center, Durham, NC, United States.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States
| | - Carolyn Glass
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Pathology, Duke University School of Medicine, Durham, NC, United States
| | - Li Su
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States
| | - Lijuan Lin
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States
| | - David C Christiani
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States.,Department of Medicine, Massachusetts General Hospital, Boston, MA, 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 Medical Center, Durham, NC, United States
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4
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Qu X, Zhao L, Wang M, Zhang R, Cheng L, Qiu L, Tong X, Cai S, Wei Q, Li Q. Novel functional variants in the Notch pathway and survival of Chinese colorectal cancer. Int J Cancer 2021; 149:84-96. [PMID: 33728681 DOI: 10.1002/ijc.33561] [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: 11/17/2020] [Revised: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 12/09/2022]
Abstract
Notch signaling pathway plays crucial roles in progression of colorectal cancer (CRC), likely affecting overall survival (OS). In a two-stage survival analysis of 1116 CRC patients in East China, we found that one locus at MINAR1 out of 133 genes in the Notch signaling pathway was significantly associated with OS (P < 1 × 10-6 , false discovery rate < 0.01). This locus containing seven single-nucleotide polymorphisms (SNPs) in high linkage disequilibrium (R2 = 1) is located on chromosome 15, of which the MINAR1 rs72430409 G allele was associated with a greater death risk (HR = 1.98, 95% CI = 1.55-2.54, P = 6.8 × 10-8 ). Further analysis of ChIP-sequencing data from the encyclopedia of DNA Elements showed that rs72430409 and rs72630408 were potential cis-regulatory elements for the MINAR1 promoter. Additional expression quantitative trait loci analysis revealed that rs72430409 G>A and rs72630408 A>G were correlated with increased MINAR1 expression levels in both blood cells and colon tissues. Dual luciferase assays revealed that the rs72430409 A allele increased MINAR1 promoter activity. The Cancer Genome Atlas data showed that expression levels of MINAR1 in CRC samples were significantly higher than that in normal colorectal tissue and that high expression of MINAR1 was associated with a shortened OS, likely via activating the epithelial mesenchymal transition (EMT) pathway as shown in the gene-set enrichment analysis. In vitro, RNAi-mediated silencing of MINAR1 led to decreased migration and proliferation in CRC cancer cells, and MINAR1 silencing could downregulate the expression of key effector genes in EMT and glycolysis. Larger cohort studies and further experiments are needed to validate our findings.
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Affiliation(s)
- Xiaofei Qu
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liqin Zhao
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mengyun Wang
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruoxin Zhang
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lei Cheng
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lixin Qiu
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoxia Tong
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Sanjun Cai
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qingyi Wei
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,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
| | - Qingguo Li
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
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5
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Yoo SS, Lee JH, Hong MJ, Choi JE, Kang HG, Do SK, Kim JH, Baek SA, Choi SH, Lee WK, Lee YH, Seo H, Lee J, Lee SY, Cha SI, Kim CH, Park JY. Effect of genetic variation in Notch regulator DTX1 on SCLC prognosis compared with the effect on NSCLC prongosis. Thorac Cancer 2020; 11:2698-2703. [PMID: 32700476 PMCID: PMC7471053 DOI: 10.1111/1759-7714.13566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/30/2022] Open
Abstract
Deltex-1 (DTX1) is a negative regulator of the Notch signaling pathway. Here, we investigated the clinical effect of DTX1 rs1732786A > G, which is associated with better prognosis in patients with early-stage non-small cell lung cancer (NSCLC), in 261 patients with small cell lung cancer (SCLC). DTX1 rs1732786A > G was associated with a significantly worse chemotherapy response and lower overall survival in the codominant model (odds ratio = 0.42, 95% confidence interval [CI]: 0.26-0.66, P = 2 × 10-4 ; hazard ratio = 1.47, 95% CI: 1.17-1.84, P = 0.001, respectively). An in vitro luciferase assay was performed, and the 1732786G allele demonstrated significantly higher promoter activity than the 1732786A allele (P = 2 × 10-7 ). In summary, DTX1 rs1732786A > G was associated with poor prognosis in patients with SCLC as opposed to patients with NSCLC. KEY POINTS: SIGNIFICANT FINDINGS OF THE STUDY: DTX1 rs1732786A > G was associated with better prognosis in patients with early-stage non-small cell lung cancer (NSCLC) in our previous study. WHAT THIS STUDY ADDS: DTX1 rs1732786A > G was associated with a significantly worse chemotherapy response and lower overall survival in small cell lung cancer (SCLC).
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Affiliation(s)
- Seung Soo Yoo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, 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
| | - 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
| | - 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
| | - Sook Kyung Do
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Tumor Heterogeneity and Network (THEN) Research Center, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ji Hyun Kim
- 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
| | - Sun Ah Baek
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sun Ha Choi
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Won Kee Lee
- Biostatistics, Medical Research Collaboration Center, Kyungpook National University, Daegu, Republic of Korea
| | - Yong Hoon Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Hyewon Seo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Jae Yong Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea.,Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Republic of Korea
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6
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Wang Y, Yuan D, Zhou L, Liang Z, Zhou W, Lu J, Jiang B, You L, Guo J, Zhao YP. Transducin-Like Enhancer of Split-1 Inhibits Malignant Behaviors in vitro and Predicts a Better Prognosis in Pancreatic Ductal Adenocarcinoma. Front Oncol 2020; 10:576. [PMID: 32432037 PMCID: PMC7214815 DOI: 10.3389/fonc.2020.00576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Transducin-like enhancer of split-1 (TLE1), a member of the Groucho/TLE family of transcriptional corepressors, has been reported to be involved in the tumorigenesis of various cancers and function as a clinical prognostic indicator. However, the mechanisms and prognostic significance of TLE1 in pancreatic ductal adenocarcinoma (PDAC) have not been elucidated. Methods: In this study, western blot analyses and real-time polymerase chain reaction (RT-PCR) were employed to evaluate the expression of TLE1 and related proteins in PDAC cell lines. Wound healing, transwell migration and invasion, and Cell Counting Kit-8 (CCK-8) assays were used to determine cell line-specific differences in metastasis and proliferation. Flow cytometry was performed for cell cycle detection. RNA sequencing and bioinformatics were undertaken to explore the molecular mechanisms and potential targeted molecules of TLE1. TLE1 expression in tumor and para-tumor tissues was evaluated by tissue microarray-based immunohistochemistry using a semiquantitative method (H-score) in 262 patients with radical PDAC resection. Correlation, Kaplan-Meier survival, univariate, and multivariate analyses were also performed. Results: Our findings showed that TLE1 expression was common in PDAC cell lines. Upregulation of TLE1 inhibited PDAC cell migration, invasion, and proliferation in vitro by delaying the G0/G1 transition. Immunohistochemistry revealed that TLE1 was specifically expressed in the nucleus and at higher levels in tumor tissues compared with para-tumor tissues. Generally, high TLE1 expression was associated with no vascular invasion. In univariate analyses, high TLE1 expression was associated with longer disease-specific survival (DSS) in all patients and in 16 patient subgroups. In multivariate analyses, TLE1 expression was independently associated with DSS in all patients and four patient subgroups. Conclusion: In conclusion, these results suggest that TLE1 has an inhibitory role in PDAC progression and is a favorable prognostic indicator for patients with resectable PDAC.
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Affiliation(s)
- Yizhi Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Da Yuan
- Medical Management Office, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Zhou
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Weixun Zhou
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jun Lu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Bolun Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Junchao Guo
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yu-Pei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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7
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Lee JH, Shin KM, Lee SY, Hong MJ, Choi JE, Kang HG, Do SK, Lee WK, Lee EB, Seok Y, Jeong JY, Yoo SS, Lee J, Cha SI, Kim CH, Cho S, Jheon S, Kim YC, Oh IJ, Na KJ, Kim MS, Lee JM, Yang HC, Jung CY, Park CK, Lee MK, Kim DK, Park JY. Genetic Variant of Notch Regulator DTX1 Predicts Survival After Lung Cancer Surgery. Ann Surg Oncol 2019; 26:3756-3764. [DOI: 10.1245/s10434-019-07614-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Indexed: 08/30/2023]
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8
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Chen K, Liu H, Liu Z, Luo S, Patz EF, Moorman PG, Su L, Shen S, Christiani DC, Wei Q. Genetic variants in RUNX3, AMD1 and MSRA in the methionine metabolic pathway and survival in nonsmall cell lung cancer patients. Int J Cancer 2019; 145:621-631. [PMID: 30650190 PMCID: PMC6828159 DOI: 10.1002/ijc.32128] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/13/2018] [Accepted: 11/27/2018] [Indexed: 12/18/2022]
Abstract
Abnormal methionine dependence in cancer cells has led to methionine restriction as a potential therapeutic strategy. We hypothesized that genetic variants involved in methionine-metabolic genes are associated with survival in nonsmall cell lung cancer (NSCLC) patients. Therefore, we investigated associations of 16,378 common single-nucleotide polymorphisms (SNPs) in 97 methionine-metabolic pathway genes with overall survival (OS) in NSCLC patients using genotyping data from two published genome-wide association study (GWAS) datasets. In the single-locus analysis, 1,005 SNPs were significantly associated with NSCLC OS (p < 0.05 and false-positive report probability < 0.2) in the discovery dataset. Three SNPs (RUNX3 rs7553295 G > T, AMD1 rs1279590 G > A and MSRA rs73534533 C > A) were replicated in the validation dataset, and their meta-analysis showed an adjusted hazards ratio [HR] of 0.82 [95% confidence interval (CI) =0.75-0.89] and pmeta = 2.86 × 10-6 , 0.81 (0.73-0.91) and pmeta = 4.63 × 10-4 , and 0.77 (0.68-0.89) and pmeta = 2.07 × 10-4 , respectively). A genetic score of protective genotypes of these three SNPs revealed an increased OS in a dose-response manner (ptrend < 0.0001). Further expression quantitative trait loci (eQTL) analysis showed significant associations between these genotypes and mRNA expression levels. Moreover, differential expression analysis further supported a tumor-suppressive effect of MSRA, with lower mRNA levels in both lung squamous carcinoma and adenocarcinoma (p < 0.0001 and < 0.0001, respectively) than in adjacent normal tissues. Additionally, low mutation rates of these three genes indicated the critical roles of these functional SNPs in cancer progression. Taken together, these genetic variants of methionine-metabolic pathway genes may be promising predictors of survival in NSCLC patients.
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Affiliation(s)
- Ka Chen
- Research Center for Nutrition and Food Safety, Institute of Military Preventive Medicine, Third Military Medical University, Chongqing 400038, P. R. China
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Edward F. Patz
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Radiology, Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Patricia G. Moorman
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
| | - Li Su
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
| | - Sipeng Shen
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115 USA
| | - David C. Christiani
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115 USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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9
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Xu Y, Liu H, Liu S, Wang Y, Xie J, Stinchcombe TE, Su L, Zhang R, Christiani DC, Li W, Wei Q. Genetic variant of IRAK2 in the toll-like receptor signaling pathway and survival of non-small cell lung cancer. Int J Cancer 2018; 143:2400-2408. [PMID: 29978465 PMCID: PMC6205899 DOI: 10.1002/ijc.31660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 05/29/2018] [Accepted: 06/01/2018] [Indexed: 12/20/2022]
Abstract
The toll-like receptor (TLR) signaling pathway plays an important role in the innate immune responses and antigen-specific acquired immunity. Aberrant activation of the TLR pathway has a significant impact on carcinogenesis or tumor progression. Therefore, we hypothesize that genetic variants in the TLR signaling pathway genes are associated with overall survival (OS) of patients with non-small cell lung cancer (NSCLC). To test this hypothesis, we first performed Cox proportional hazards regression analysis to evaluate associations between genetic variants of 165 TLR signaling pathway genes and NSCLC OS using the genome-wide association study (GWAS) dataset from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). The results were further validated by the Harvard Lung Cancer Susceptibility GWAS dataset. Specifically, we identified IRAK2 rs779901 C > T as a predictor of NSCLC OS, with a variant-allele (T) attributed hazards ratio (HR) of 0.78 [95% confidence interval (CI) = 0.67-0.91, P = 0.001] in the PLCO dataset, 0.84 (0.72-0.98, 0.031) in the Harvard dataset, and 0.81 (0.73-0.90, 1.08x10-4 ) in the meta-analysis of these two GWAS datasets. In addition, the T allele was significantly associated with an increased mRNA expression level of IRAK2. Our findings suggest that IRAK2 rs779901 C > T may be a promising prognostic biomarker for NSCLC OS.
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Affiliation(s)
- Yinghui Xu
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shun Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yanru Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jichun Xie
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Thomas E. Stinchcombe
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Li Su
- Department of Environmental Health, Harvard School of Public Health, Boston, MA02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA02115, USA
| | - Ruyang Zhang
- Department of Environmental Health, Harvard School of Public Health, Boston, MA02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA02115, USA
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, MA02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA02115, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA02115, USA
| | - Wei Li
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC 27710, USA
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10
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Xu Y, Cheng L, Dai H, Zhang R, Wang M, Shi T, Sun M, Cheng X, Wei Q. Variants in Notch signalling pathway genes, PSEN1 and MAML2, predict overall survival in Chinese patients with epithelial ovarian cancer. J Cell Mol Med 2018; 22:4975-4984. [PMID: 30055028 PMCID: PMC6156353 DOI: 10.1111/jcmm.13764] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022] Open
Abstract
To identify genetic variants in Notch signalling pathway genes that may predict survival of Han Chinese patients with epithelial ovarian cancer (EOC), we analysed a total of 1273 single nucleotide polymorphisms (SNPs) within 75 Notch genes in 480 patients from a published EOC genomewide association study (GWAS). We found that PSEN1 rs165934 and MAML2 rs76032516 were associated with overall survival (OS) of patients by multivariate Cox proportional hazards regression analysis. Specifically, the PSEN1 rs165934 AA genotype was associated with a poorer survival (adjusted hazards ratio [adjHR] = 1.41, 95% CI = 1.07-1.84, and P = .014), compared with the CC + CA genotype, while MAML2 rs76032516 AA + AC genotypes were associated with a poorer survival (adjHR = 1.58, 95% CI = 1.16-2.14, P = .004), compared with the CC genotype. The combined analysis of these two SNPs revealed that the death risk increased as the number of unfavourable genotypes increased in a dose-dependent manner (Ptrend < .001). Additionally, the expression quantitative trait loci analysis revealed that the SNP rs165932 in the rs165934 LD block (r2 = .946) was associated with expression levels of PSEN1, which might be responsible for the observed association with SNP rs165934. The associations of PSEN1 rs165934 and MAML2 rs76032516 of the Notch signalling pathway genes with OS in Chinese EOC patients are novel findings, which need to be validated in other large and independent studies.
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Affiliation(s)
- Yuan Xu
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Lei Cheng
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Hongji Dai
- Department of Epidemiology and BiostatisticsKey Laboratory of Cancer Prevention and TherapyTianjinChina
- Key Laboratory of Breast Cancer Prevention and TherapyMinistry of EducationNational Clinical Research Center for CancerTianjin Medical University Cancer Institute and HospitalTianjinChina
| | - Ruoxin Zhang
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Mengyun Wang
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Tingyan Shi
- Ovarian Cancer ProgramDivision of Gynecologic OncologyDepartment of Gynecology and ObstetricsFudan University Zhongshan HospitalShanghaiChina
| | - Menghong Sun
- Department of PathologyTissue BankFudan University Shanghai Cancer CenterShanghaiChina
| | - Xi Cheng
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Qingyi Wei
- Cancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
- Duke Cancer InstituteDuke University Medical CenterDurhamNCUSA
- Department of Population Health SciencesDuke University School of MedicineDurhamNCUSA
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11
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Chammaa M, Malysa A, Redondo C, Jang H, Chen W, Bepler G, Fernandez-Valdivia R. RUMI is a novel negative prognostic marker and therapeutic target in non-small-cell lung cancer. J Cell Physiol 2018; 233:9548-9562. [PMID: 29953591 DOI: 10.1002/jcp.26858] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/22/2018] [Indexed: 12/12/2022]
Abstract
Recent comprehensive next-generation genome and transcriptome analyses in lung cancer patients, several clinical observations, and compelling evidence from mouse models of lung cancer have uncovered a critical role for Notch signaling in the initiation and progression of non-small-cell lung cancer (NSCLC). Notably, Rumi is a "protein O-glucosyltransferase" that regulates Notch signaling through O-glucosylation of Notch receptors, and is the only enzymatic regulator whose activity is required for both ligand-dependent and ligand-independent activation of Notch. We have conducted a detailed study on RUMI's involvement in NSCLC development and progression, and have further explored the therapeutic potential of its targeting in NSCLC. We have determined that Rumi is highly expressed in the alveolar and bronchiolar epithelia, including club cells and alveolar type II cells. Remarkably, RUMI maps to the region of chromosome 3q that corresponds to the major signature of neoplastic transformation in NSCLC, and is markedly amplified and overexpressed in NSCLC tumors. Notably, RUMI expression levels are predictive of poor prognosis and survival in NSCLC patients. Our data indicates that RUMI modulates Notch activity in NSCLC cells, and that its silencing dramatically decreases cell proliferation, migration, and survival. RUMI downregulation causes severe cell cycle S-phase arrest, increases genome instability, and induces late apoptotic-nonapoptotic cell death. Our studies demonstrate that RUMI is a novel negative prognostic factor with significant therapeutic potential in NSCLC, which embodies particular relevance especially when considering that, while current Notch inhibitory strategies target only ligand-dependent Notch activation, a large number of NSCLCs are driven by ligand-independent Notch activity.
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Affiliation(s)
- May Chammaa
- Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan
| | - Agnes Malysa
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Carlos Redondo
- Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan
| | - Hyejeong Jang
- Biostatistics Core, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Wei Chen
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Biostatistics Core, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan.,Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, Michigan.,Tumor Biology and Microenvironment Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Gerold Bepler
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, Michigan.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Rodrigo Fernandez-Valdivia
- Department of Pathology, Wayne State University School of Medicine, Detroit, Michigan.,Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, Michigan.,Tumor Biology and Microenvironment Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
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12
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Li W, Zhou J, Chen Y, Zhang G, Jiang P, Hong L, Shen Y, Wang X, Gong X. Cigarette smoke enhances initiation and progression of lung cancer by mutating Notch1/2 and dysregulating downstream signaling molecules. Oncotarget 2017; 8:115128-115139. [PMID: 29383147 PMCID: PMC5777759 DOI: 10.18632/oncotarget.22924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/19/2017] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the primary cause of cancer related deaths in the western world and smoking significantly increases the risk of developing lung cancer. Smoking enhances lung cancer initiation and progression. The effects of cigarette smoke on lung cancer are mediated by the presence of highly mutagenic substances, including nicotine, leading to mutations in oncogenes and tumor suppressor genes. An emerging pathway in cancer is the Notch signaling pathway which is essential for embryonic lung development and tissue homeostasis. The role of Notch signaling in lung cancer remains controversial and no studies have directly linked cigarette exposure to mutations in Notch. Therefore, we investigated the direct effect of Notch signaling pathways on cigarette-induced lung tumors and the correlation between smoking and mutations in Notch leading to altered downstream signaling. Human cell lines, mouse models and clinical lung cancer samples were utilized in this study. Cigarette-induced in vitro human lung cancer models and in vivo mouse models demonstrated strong effects of cigarette exposure on the Notch signaling pathway. Immunohistochemistry (IHC) of 50 clinical samples collected from smokers and non-smokers with and without lung cancer also demonstrated a link between smoking and changes in Notch signaling. Finally, 34 lung cancer samples analyzed through direct sequencing indicated smoking significantly increased small nucleotide polymorphisms (SNPs) in Notch 1 and 2 and specific SNPs significantly modulated expression levels of downstream signaling pathway molecules. Taken together, these results demonstrate a direct effect of smoking on the Notch signaling pathway leading to lung cancer initiation and progression.
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Affiliation(s)
- Wei Li
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China.,Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu 233004, China
| | - Jihong Zhou
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu 233004, China
| | - Yuqing Chen
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China.,Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu 233004, China
| | - Gengyan Zhang
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China.,Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu 233004, China
| | - Peng Jiang
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China.,Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu 233004, China
| | - Lei Hong
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China.,Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu 233004, China
| | - Yuangbing Shen
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China.,Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu 233004, China
| | - Xiaojing Wang
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China.,Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu 233004, China
| | - Xiaomeng Gong
- Department of Pathology, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
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13
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Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC. Oncotarget 2017; 8:15349-15363. [PMID: 28146432 PMCID: PMC5362490 DOI: 10.18632/oncotarget.14856] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/16/2017] [Indexed: 01/23/2023] Open
Abstract
Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have accelerated the genome-wide characterization of HNSCC. However, comprehensive pipelines with statistical algorithms that account for HNSCC biology and perform independent confirmatory and functional validation of candidates are needed to identify the most biologically relevant genes. We applied outlier statistics to high throughput gene expression data, and identified 76 top-scoring candidates with significant differential expression in tumors compared to normal tissues. We identified 15 epigenetically regulated candidates by focusing on a subset of the genes with a negative correlation between gene expression and promoter methylation. Differential expression and methylation of 3 selected candidates (BANK1, BIN2, and DTX1) were confirmed in an independent HNSCC cohorts from Johns Hopkins and TCGA (The Cancer Genome Atlas). We further performed functional evaluation of NOTCH regulator, DTX1, which was downregulated by promoter hypermethylation in tumors, and demonstrated that decreased expression of DTX1 in HNSCC tumors maybe associated with NOTCH pathway activation and increased migration potential.
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14
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Epigenetic modification of TLE1 induce abnormal differentiation in diabetic mice intestinal epithelium. Mol Cell Biochem 2017; 438:85-96. [PMID: 28744818 DOI: 10.1007/s11010-017-3116-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 07/15/2017] [Indexed: 12/20/2022]
Abstract
The intestinal epithelium cells (IECs) in diabetes mellitus (DM) patients have been proven to be abnormally differentiated. During the differentiation of IECs, epigenetic modification acts as an important regulator. In this study, we aimed to examine the epigenetic alteration of Transducin-like Enhancer of Split 1 (TLE1), a multitask transcriptional co-repressor, contributing to the differentiation homeostasis in IECs of DM mice. The IECs of type 2 diabetic mice model were isolated and collected. Methylation states of whole genomic DNA promoter regions were investigated by microarray. Methylated-specific PCR was used to detect the methylation state of TLE1 promoter in DM mice IECs. The expression of TLE1, Hes1, and differentiated cell markers were measured through real-time PCR, Western blots, and immunohistochemistry; by transfection assay, TLE1 or Hes1 was independently down-regulated in intestinal epithelium cell line, IEC-6. Subsequent modulation on TLE1, Hes1, and differentiated intestinal cell markers were detected. Global gene promoter regions in DM intestinal epithelium were less methylated comparing to normal control. The expression of TLE1 was significantly increased via hypomethylated activation in DM mice IECs. Hes1 was significantly suppressed and the terminal cell markers abnormally expressed in DM mice IECs (P < 0.05). Inhibition or induction on the abundance of TLE1 in IEC-6 cell line resulted in the corresponding dysregulation of Hes1 and intestinal epithelium differentiation (P < 0.05). Demethylation of TLE1 promoter region activates the self-expression in diabetic mice IECs. Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice.
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15
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Zhu M, Geng L, Shen W, Wang Y, Liu J, Cheng Y, Wang C, Dai J, Jin G, Hu Z, Ma H, Shen H. Exome-Wide Association Study Identifies Low-Frequency Coding Variants in 2p23.2 and 7p11.2 Associated with Survival of Non-Small Cell Lung Cancer Patients. J Thorac Oncol 2017; 12:644-656. [PMID: 28104536 DOI: 10.1016/j.jtho.2016.12.025] [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: 05/30/2016] [Revised: 11/23/2016] [Accepted: 12/15/2016] [Indexed: 01/10/2023]
Abstract
INTRODUCTION A growing body of evidence has suggested that low-frequency or rare coding variants might have strong effects on the development and prognosis of cancer. Here, we aim to assess the role of low-frequency and rare coding variants in the survival of NSCLC in Chinese populations. METHODS We performed an exome-wide scan of 247,870 variants in 1008 patients with NSCLC and replicated the promising variants by using imputed genotype data of The Cancer Genome Atlas (TCGA) with a Cox regression model. Gene-based and pathway-based analysis were also performed for nonsynonymous or splice site variants. Additionally, analysis of gene expression data in the TCGA was used to increase the reliability of candidate loci and genes. RESULTS A low-frequency missense variant in chaperonin containing TCP1 subunit 6A gene (CCT6A) (rs33922584: adjusted hazard ratio [HRadjusted] = 1.75, p = 6.06 × 10-4) was significantly related to the survival of patients with NSCLC, which was further replicated by the TCGA samples (HRadjusted = 4.19, p = 0.015). Interestingly, the G allele of rs33922584 was significantly associated with high expression of CCT6A (p = 0.019) that might induce the worse survival in the TCGA samples (HRadjusted = 1.15, p = 0.047). Besides, rs117512489 in gene phospholipase B1 gene (PLB1) (HR = 2.02, p = 7.28 × 10-4) was also associated with survival of the patients with NSCLC in our samples, but it was supported only by gene expression analysis in the TCGA (HRadjusted = 1.15, p = 0.023). Gene-based and pathway-based analysis revealed a total of 32 genes, including CCT6A and 34 potential pathways might account for the survival of NSCLC, respectively. CONCLUSION These results provided more evidence for the important role of low-frequency or rare variants in the survival of patients with NSCLC.
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Affiliation(s)
- Meng Zhu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Liguo Geng
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Wei Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yuzhuo Wang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jia Liu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yang Cheng
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China.
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
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