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Phuong NA, Dao TT, Pham PB, Nguyen UD, Nguyen BV, Ho TH. Novel Semi-Nested Real-Time PCR Assay Leveraging Extendable Blocking Probes for Improved SHOX2 Methylation Analysis in Lung Cancer. Biomolecules 2024; 14:729. [PMID: 38927132 PMCID: PMC11201985 DOI: 10.3390/biom14060729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Lung cancer is the leading cause of cancer deaths globally, necessitating effective early detection methods. Traditional diagnostics like low-dose computed tomography (LDCT) often yield high false positive rates. SHOX2 gene methylation has emerged as a promising biomarker. This study aimed to develop and validate a novel semi-nested real-time PCR assay enhancing sensitivity and specificity for detecting SHOX2 methylation using extendable blocking probes (ExBPs). The assay integrates a semi-nested PCR approach with ExBPs, enhancing the detection of low-abundance methylated SHOX2 DNA amidst unmethylated sequences. It was tested on spiked samples with varied methylation levels and on clinical samples from lung cancer patients and individuals with benign lung conditions. The assay detected methylated SHOX2 DNA down to 0.01%. Clinical evaluations confirmed its ability to effectively differentiate between lung cancer patients and those with benign conditions, demonstrating enhanced sensitivity and specificity. The use of ExBPs minimized non-target sequence amplification, crucial for reducing false positives. The novel semi-nested real-time PCR assay offers a cost-effective, highly sensitive, and specific method for detecting SHOX2 methylation, enhancing early lung cancer detection and monitoring, particularly valuable in resource-limited settings.
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Affiliation(s)
- Ngoc Anh Phuong
- Vietnam National Lung Hospital, 463 Hoang Hoa Tham, Ba Dinh, Hanoi 10000, Vietnam;
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, No. 222 Phung Hung, Ha Dong, Hanoi 10000, Vietnam
| | - Trang Thuy Dao
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, No. 222 Phung Hung, Ha Dong, Hanoi 10000, Vietnam
| | - Phuong Bich Pham
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, No. 222 Phung Hung, Ha Dong, Hanoi 10000, Vietnam
| | - Ung Dinh Nguyen
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, No. 222 Phung Hung, Ha Dong, Hanoi 10000, Vietnam
| | - Ba Van Nguyen
- Oncology Center, 103 Military Hospital, Vietnam Military Medical University, Hanoi 10000, Vietnam
| | - Tho Huu Ho
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, No. 222 Phung Hung, Ha Dong, Hanoi 10000, Vietnam
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Cui X, Lin Q, Chen M, Wang Y, Wang Y, Wang Y, Tao J, Yin H, Zhao T. Long-read sequencing unveils novel somatic variants and methylation patterns in the genetic information system of early lung cancer. Comput Biol Med 2024; 171:108174. [PMID: 38442557 DOI: 10.1016/j.compbiomed.2024.108174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 01/25/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024]
Abstract
Lung cancer poses a global health challenge, necessitating advanced diagnostics for improved outcomes. Intensive efforts are ongoing to pinpoint early detection biomarkers, such as genomic variations and DNA methylation, to elevate diagnostic precision. We conducted long-read sequencing on cancerous and adjacent non-cancerous tissues from a patient with lung adenocarcinoma. We identified somatic structural variations (SVs) specific to lung cancer by integrating data from various SV calling methods and differentially methylated regions (DMRs) that were distinct between these two tissue samples, revealing a unique methylation pattern associated with lung cancer. This study discovered over 40,000 somatic SVs and over 180,000 DMRs linked to lung cancer. We identified approximately 700 genes of significant relevance through comprehensive analysis, including genes intricately associated with many lung cancers, such as NOTCH1, SMOC2, CSMD2, and others. Furthermore, we observed that somatic SVs and DMRs were substantially enriched in several pathways, such as axon guidance signaling pathways, which suggests a comprehensive multi-omics impact on lung cancer progression across various biological investigation levels. These datasets can potentially serve as biomarkers for early lung cancer detection and may hold significant value in clinical diagnosis and treatment applications.
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Affiliation(s)
- Xinran Cui
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China
| | - Qingyan Lin
- Department of Respiratory and Critical Care, Heilongjiang Provincial Hospital, 405 Gorokhovaya Street, Harbin, Heilongjiang, 150000, China
| | - Ming Chen
- Institute of Bioinformatics, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China
| | - Yidan Wang
- Department of Respiratory and Critical Care, Heilongjiang Provincial Hospital, 405 Gorokhovaya Street, Harbin, Heilongjiang, 150000, China
| | - Yiwen Wang
- Tanwei College, Tsinghua University, Shuangqing Road, Beijing, 100084, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China.
| | - Jiang Tao
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China.
| | - Honglei Yin
- Department of Respiratory and Critical Care, Heilongjiang Provincial Hospital, 405 Gorokhovaya Street, Harbin, Heilongjiang, 150000, China.
| | - Tianyi Zhao
- School of Medicine, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China.
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Zhou YF, Li JT, Zheng QL, Ren KL, Yi CC. METTL3-mediated m 6 A methylation of TRAF5 inhibits lung adenocarcinoma cell metastasis via activation of the PI3K/AKT/NF-κB signaling pathway. Kaohsiung J Med Sci 2024; 40:150-160. [PMID: 38088510 DOI: 10.1002/kjm2.12791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 02/03/2024] Open
Abstract
Tumor necrosis factor receptor-associated factor 5 (TRAF5) has been implicated in the pathogenesis of human malignancies. This work aimed to clarify the role of TRAF5 in lung adenocarcinoma (LUAD) progression. Herein, we uncovered that TRAF5 level was reduced in LUAD tissues. Low TRAF5 expression correlated with dismal prognosis in LUAD patients. Moreover, upregulated TRAF5 impeded cell viability, migration, and invasion, induced apoptosis in vitro, as well as impaired tumorigenicity in vivo. However, depletion of TRAF5 revealed opposing results. Moreover, TRAF5 was identified as the downstream target of methyltransferase-like 3 (METTL3)-elicited N6 -methyladenosine (m6 A) modification. METTL3 stabilized TRAF5 mRNA and positively modulated TRAF5 level. Further, TRAF5 depletion relieved the repressive phenotype caused by METTL3 addition. In addition, it was manifested that the METTL3/TRAF5 axis served as an inhibitor in LUAD through the PI3K/AKT/Nuclear Factor-Kappa B (NF-κB) signaling. Collectively, we propose that METTL3-mediated TRAF5 m6 A modification exerted as a vital tumor inhibitory function in LUAD development. The METTL3/TRAF5 axis may be a critical effector of LUAD progression.
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Affiliation(s)
- Yu-Fei Zhou
- Department of Thoracic Surgery, The People's Hospital of Dongying (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, China
| | - Jiang-Tao Li
- Department of Thoracic Surgery, The People's Hospital of Laiyang, Yantai, China
| | - Qing-Lin Zheng
- Department of Thoracic Surgery, The People's Hospital of Dongying (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, China
| | - Kun-Lun Ren
- Department of Thoracic Surgery, The People's Hospital of Dongying (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, China
| | - Cheng-Cheng Yi
- Department of Thoracic Surgery, The People's Hospital of Dongying (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, China
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Yang S, Li K, Zhang J, Liu J, Liu L, Tan Y, Xu C. Link between m6A modification and infiltration characterization of tumor microenvironment in lung adenocarcinoma. Exp Biol Med (Maywood) 2023; 248:2273-2288. [PMID: 38166412 PMCID: PMC10903232 DOI: 10.1177/15353702231214266] [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: 05/11/2023] [Accepted: 08/30/2023] [Indexed: 01/04/2024] Open
Abstract
N6-methyladenosine (m6A) RNA methylation plays a pivotal role in immune responses and the onset and advancement of cancer. Nonetheless, the precise impact of m6A modification in lung adenocarcinoma (LUAD) and its associated tumor microenvironment (TME) remains to be fully elucidated. Here, we distinguished distinct m6A modification patterns within two separate LUAD cohorts using a set of 21 m6A regulators. The TME characteristics associated with these two patterns align with the immune-inflamed and immune-excluded phenotypes, respectively. We identified 2064 m6A-related genes, which were used as a basis to divide all LUAD samples into three distinct m6A gene clusters. We applied a scoring system to evaluate the m6A gene signature of the m6A modification pattern in individual patients. To authenticate the categorization significance of m6A modification patterns, we established a correlation between m6A score and TME infiltration profiling, tumor somatic mutations, and responses to immunotherapy. A high level of m6A modification may be associated with the aggressiveness and poor prognosis of LUAD. Further studies should investigate the mechanism of action of m6A regulators and m6A-related genes to improve the diagnosis and treatment of patients with LUAD.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang 550025, China
| | - Ke Li
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Jiqin Zhang
- Department of Anesthesiology, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Jian Liu
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Lin Liu
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Ying Tan
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Chuan Xu
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
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Ji XY, Li H, Chen HH, Lin J. Diagnostic performance of RASSF1A and SHOX2 methylation combined with EGFR mutations for differentiation between small pulmonary nodules. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04745-8. [PMID: 37097393 DOI: 10.1007/s00432-023-04745-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND AND AIM Aberrant methylation of Ras association domain family 1, isoform A (RASSF1A), and short-stature homeobox gene 2 (SHOX2) promoters has been validated as a pair of valuable biomarkers for diagnosing early lung adenocarcinomas (LUADs). Epidermal growth factor receptor (EGFR) is the key driver mutation in lung carcinogenesis. This study aimed to investigate the aberrant promoter methylation of RASSF1A and SHOX2, and the genetic mutation of EGFR in 258 specimens of early LUADs. METHODS We retrospectively selected 258 paraffin-embedded samples of pulmonary nodules measuring 2 cm or less in diameter and evaluated the diagnostic performance of individual biomarker assays and multiple panels between noninvasive (group 1) and invasive lesions (groups 2A and 2B). Then, we investigated the interaction between genetic and epigenetic alterations. RESULTS The degree of RASSF1A and SHOX2 promoter methylation and EGFR mutation was significantly higher in invasive lesions than in noninvasive lesions. The three biomarkers distinguished between noninvasive and invasive lesions with reliable sensitivity and specificity: 60.9% sensitivity [95% confidence interval (CI) 52.41-68.78] and 80.0% specificity (95% CI 72.14-86.07). The novel panel biomarkers could further discriminate among three invasive pathological subtypes (area under the curve value > 0.6). The distribution of RASSF1A methylation and EGFR mutation was considerably exclusive in early LUAD (P = 0.002). CONCLUSION DNA methylation of RASSF1A and SHOX2 is a pair of promising biomarkers, which may be used in combination with other driver alterations, such as EGFR mutation, to support the differential diagnosis of LUADs, especially for stage I.
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Affiliation(s)
- Xiang-Yu Ji
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Hong Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Hui-Hui Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jie Lin
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China.
- National Virtual and Reality Experimental Education Center for Medical Morphology, Southern Medical University, Guangzhou, People's Republic of China.
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Sulewska A, Pilz L, Manegold C, Ramlau R, Charkiewicz R, Niklinski J. A Systematic Review of Progress toward Unlocking the Power of Epigenetics in NSCLC: Latest Updates and Perspectives. Cells 2023; 12:cells12060905. [PMID: 36980246 PMCID: PMC10047383 DOI: 10.3390/cells12060905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Epigenetic research has the potential to improve our understanding of the pathogenesis of cancer, specifically non-small-cell lung cancer, and support our efforts to personalize the management of the disease. Epigenetic alterations are expected to have relevance for early detection, diagnosis, outcome prediction, and tumor response to therapy. Additionally, epi-drugs as therapeutic modalities may lead to the recovery of genes delaying tumor growth, thus increasing survival rates, and may be effective against tumors without druggable mutations. Epigenetic changes involve DNA methylation, histone modifications, and the activity of non-coding RNAs, causing gene expression changes and their mutual interactions. This systematic review, based on 110 studies, gives a comprehensive overview of new perspectives on diagnostic (28 studies) and prognostic (25 studies) epigenetic biomarkers, as well as epigenetic treatment options (57 studies) for non-small-cell lung cancer. This paper outlines the crosstalk between epigenetic and genetic factors as well as elucidates clinical contexts including epigenetic treatments, such as dietary supplements and food additives, which serve as anti-carcinogenic compounds and regulators of cellular epigenetics and which are used to reduce toxicity. Furthermore, a future-oriented exploration of epigenetic studies in NSCLC is presented. The findings suggest that additional studies are necessary to comprehend the mechanisms of epigenetic changes and investigate biomarkers, response rates, and tailored combinations of treatments. In the future, epigenetics could have the potential to become an integral part of diagnostics, prognostics, and personalized treatment in NSCLC.
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Affiliation(s)
- Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Correspondence: (A.S.); (J.N.)
| | - Lothar Pilz
- Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Christian Manegold
- Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Correspondence: (A.S.); (J.N.)
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DNA Methylation Analysis of the SHOX2 and RASSF1A Panel Using Cell-Free DNA in the Diagnosis of Malignant Pleural Effusion. JOURNAL OF ONCOLOGY 2023; 2023:5888844. [PMID: 36691467 PMCID: PMC9867579 DOI: 10.1155/2023/5888844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/16/2023]
Abstract
Objectives The differential diagnosis of pleural effusion (PE) is a common but major challenge in clinical practice. This study aimed to establish a strategy based on a PE-cell-free DNA (cfDNA) methylation detection system for the differential diagnosis of malignant pleural effusion (MPE) and benign pleural effusion (BPE). Methods A total of 104 patients with PE were enrolled in this study, among which 50 patients had MPE, 9 malignant tumor patients had PE of indefinite causes, and the other 45 patients were classified as benign controls. The methylation status of short stature homeobox 2 (SHOX2) and RAS association domain family 1, isoform A (RASSF1A) was detected using PE-cfDNA specimens by real-time fluorescence quantitative PCR. Total methylation (TM) was defined as the combination of the methylation levels of SHOX2 and RASSF1A. The electrochemiluminescence immunoassay was applied to evaluate the levels of multiple serum tumor markers. Results The PE-cfDNA methylation status of either SHOX2 or RASSF1A was much higher in MPE samples than in benign controls. The combination of SHOX2 and RASSF1A methylation in PE yielded a diagnostic sensitivity of 96% and a specificity of 100%, respectively. When compared with the corresponding serum tumor marker detection results, TM showed the highest diagnostic efficiency (AUC = 0.985). Furthermore, the combination of the SHOX2 and RASSF1A methylation panels using PE-cfDNA could apparently improve the differential diagnostic efficacy of BPE and MPE and could help compensate for the deficiency of cytology. Conclusions Our results indicated that SHOX2 and RASSF1A methylation panel detection could accurately classify BPE and MPE diseases and showed better diagnostic performance than traditional serum parameters. The SHOX2 and RASSF1A methylation detection of PE-cfDNA could be a potentially effective complementary tool for cytology in the process of differential diagnosis. In summary, PE-cfDNA could be used as a promising non-invasive analyte for the auxiliary diagnosis of MPE.
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Pan T, Wang H, Wang S, Liu F. Long Non-Coding RNA LINC01929 Facilitates Cell Proliferation and Metastasis as a Competing Endogenous RNA Against MicroRNA miR-1179 in Non-Small Cell Lung Carcinoma. Br J Biomed Sci 2022; 79:10598. [PMID: 35996496 PMCID: PMC9329516 DOI: 10.3389/bjbs.2022.10598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022]
Abstract
Introduction: Non-small cell lung carcinoma (NSCLC) constitutes most lung cancers and has a poor prognosis. LncRNAs are a potential repository for the discovery of cancer prognostic markers. This study explored the role of LINC01929 in NSCLC, both the clinical prognostic significance and the mechanism of its influence on cells. Materials and Methods: LINC01929 levels in 143 pairs of NSCLC tissues and non-cancerous tissues were detected by RT-qPCR. Kaplan-Meier curves and multivariate Cox regression assays were generated for evaluating the prognostic values of LINC01929. To evaluate the cellular function, an XTT assay and transwell invasion assays were performed. Results: LINC01929 was up-regulated in NSCLC tissues compared with healthy tissues. A positive correlation was observed between LINC01929 expression level and tumor T (p = 0.002) or N stage (p = 0.010). Patients with higher LINC01929 levels had shorter overall survival (p = 0.009). Compared with other factors, high LINC01929 expression was significantly associated with poor survival in univariate Cox analysis (HR: 2.485, 95%CI: 1.220–5.060, p = 0.012). After multivariate Cox regression assays, LINC01929 was a independent prognostic factor (HR: 3.021, 95%CI: 1.377–6.628, p = 0.006). miR-1179 was a target miRNA of LINC01929. Inhibited expression of LINC01929 significantly reduced the proliferation, migration, and invasion of NSCLC cells by targeting miR-1179. Discussion: This study revealed the upregulation of LINC01929 in NSCLC. This study supports previous studies showing LINC01929 as a potential prognostic factor for NSCLC.
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Affiliation(s)
- Tinghong Pan
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Hui Wang
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Shuai Wang
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Feng Liu
- Department of Cardiothoracic Surgery, Zhucheng People’s Hospital, Weifang, China
- *Correspondence: Feng Liu, , orcid.org/0000-0002-3218-9173
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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Masoumi F, Saraiva SM, Bouzo BL, López-López R, Esteller M, Díaz-Lagares Á, de la Fuente M. Modulation of Colorectal Tumor Behavior via lncRNA TP53TG1-Lipidic Nanosystem. Pharmaceutics 2021; 13:pharmaceutics13091507. [PMID: 34575588 PMCID: PMC8470159 DOI: 10.3390/pharmaceutics13091507] [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: 08/06/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 01/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are an emerging group of RNAs with a crucial role in cancer pathogenesis. In gastrointestinal cancers, TP53 target 1 (TP53TG1) is an epigenetically regulated lncRNA that represents a promising therapeutic target due to its tumor suppressor properties regulating the p53-mediated DNA damage and the intracellular localization of the oncogenic YBX1 protein. However, to translate this finding into the clinic as a gene therapy, it is important to develop effective carriers able to deliver exogenous lncRNAs to the targeted cancer cells. Here, we propose the use of biocompatible sphingomyelin nanosystems comprising DOTAP (DSNs) to carry and deliver a plasmid vector encoding for TP53TG1 (pc(TP53TG1)-DSNs) to a colorectal cancer cell line (HCT-116). DSNs presented a high association capacity and convenient physicochemical properties. In addition, pc(TP53TG1)-DSNs showed anti-tumor activities in vitro, specifically a decrease in the proliferation rate, a diminished colony-forming capacity, and hampered migration and invasiveness of the treated cancer cells. Consequently, the proposed strategy displays a high potential as a therapeutic approach for colorectal cancer.
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Affiliation(s)
- Farimah Masoumi
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain; (F.M.); (S.M.S.); (B.L.B.)
- Immunology Department, School of Medicine, Tehran University of Medical Sciences, Tehran 14176-13151, Iran
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon 46841-61167, Iran
| | - Sofia M. Saraiva
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain; (F.M.); (S.M.S.); (B.L.B.)
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
| | - Belén L. Bouzo
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain; (F.M.); (S.M.S.); (B.L.B.)
| | - Rafael López-López
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain
| | - Manel Esteller
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08907 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Ángel Díaz-Lagares
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
- Cancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS), SERGAS, 15706 Santiago de Compostela, Spain
- Correspondence: (A.D.-L.); (M.d.l.F.)
| | - María de la Fuente
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain; (F.M.); (S.M.S.); (B.L.B.)
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
- Correspondence: (A.D.-L.); (M.d.l.F.)
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Shi YX. Identification of the molecular function of tripartite motif containing 58 in human lung cancer. Oncol Lett 2021; 22:685. [PMID: 34434284 PMCID: PMC8335731 DOI: 10.3892/ol.2021.12946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/24/2021] [Indexed: 11/15/2022] Open
Abstract
Lung cancer is a major public health problem worldwide, with a high associated incidence and mortality. In the present study, novel epigenetic signatures were identified through genome-wide DNA methylation microarrays. The results revealed that tripartite motif containing 58 (TRIM58), a potential tumor suppressor gene exhibited high methylation and low expression in lung cancer tissue samples compared with normal tissues. Receiver operating characteristic curve analysis demonstrated that TRIM58 may be a promising early diagnostic indicator of lung cancer. In addition, the present study analyzed the role of TRIM58 in tumorigenesis and development in lung cancer A549 cells. Wound healing assay and transwell migration assay were used to investigate cell migration, and flow cytometry analysis was used to detect apoptosis. Silencing TRIM58 accelerated the proliferation and migration of lung cancer cells. In contrast, the overexpression of TRIM58 significantly inhibited the proliferation and migration of lung cancer cells and promoted apoptosis. Gene set enrichment analysis revealed that TRIM58 expression was negatively correlated with MYC targets, G2M checkpoints and the mTORC1 signaling pathway. These results of the present study suggested that TRIM58, a potential tumor suppressor gene may serve as a novel diagnostic biomarker and therapeutic target in human lung cancer.
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Affiliation(s)
- Yuan-Xiang Shi
- Institute of Clinical Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, P.R. China
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12
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Mc Cormack BA, González-Cantó E, Agababyan C, Espinoza-Sánchez NA, Tomás-Pérez S, Llueca A, Marí-Alexandre J, Götte M, Gilabert-Estellés J. miRNAs in the Era of Personalized Medicine: From Biomarkers to Therapeutics. Int J Mol Sci 2021; 22:8154. [PMID: 34360918 PMCID: PMC8348078 DOI: 10.3390/ijms22158154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
In recent years, interest in personalized medicine has considerably increased [...].
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Affiliation(s)
- Bárbara A. Mc Cormack
- Research Laboratory in Biomarkers in Reproduction, Gynaecology and Obstetrics, Research Foundation of the General University Hospital of Valencia, 46014 Valencia, Spain; (B.A.M.C.); (E.G.-C.); (C.A.); (S.T.-P.); (J.G.-E.)
| | - Eva González-Cantó
- Research Laboratory in Biomarkers in Reproduction, Gynaecology and Obstetrics, Research Foundation of the General University Hospital of Valencia, 46014 Valencia, Spain; (B.A.M.C.); (E.G.-C.); (C.A.); (S.T.-P.); (J.G.-E.)
| | - Cristina Agababyan
- Research Laboratory in Biomarkers in Reproduction, Gynaecology and Obstetrics, Research Foundation of the General University Hospital of Valencia, 46014 Valencia, Spain; (B.A.M.C.); (E.G.-C.); (C.A.); (S.T.-P.); (J.G.-E.)
- Obstetrics and Gynaecology Service, General University Hospital of Valencia Consortium, 46014 Valencia, Spain
| | - Nancy A. Espinoza-Sánchez
- Research Laboratory, Department of Gynecology and Obstetrics, Münster University Hospital, D-48149 Münster, Germany;
| | - Sarai Tomás-Pérez
- Research Laboratory in Biomarkers in Reproduction, Gynaecology and Obstetrics, Research Foundation of the General University Hospital of Valencia, 46014 Valencia, Spain; (B.A.M.C.); (E.G.-C.); (C.A.); (S.T.-P.); (J.G.-E.)
| | - Antoni Llueca
- Department of Medicine, University Jaume I, 12071 Castellón, Spain;
- Multidisciplinary Unit of Abdominal Pelvic Oncology Surgery (MUAPOS), General University Hospital of Castellón, 12004 Castellón, Spain
| | - Josep Marí-Alexandre
- Research Laboratory in Biomarkers in Reproduction, Gynaecology and Obstetrics, Research Foundation of the General University Hospital of Valencia, 46014 Valencia, Spain; (B.A.M.C.); (E.G.-C.); (C.A.); (S.T.-P.); (J.G.-E.)
| | - Martin Götte
- Research Laboratory, Department of Gynecology and Obstetrics, Münster University Hospital, D-48149 Münster, Germany;
| | - Juan Gilabert-Estellés
- Research Laboratory in Biomarkers in Reproduction, Gynaecology and Obstetrics, Research Foundation of the General University Hospital of Valencia, 46014 Valencia, Spain; (B.A.M.C.); (E.G.-C.); (C.A.); (S.T.-P.); (J.G.-E.)
- Obstetrics and Gynaecology Service, General University Hospital of Valencia Consortium, 46014 Valencia, Spain
- Department of Paediatrics, Obstetrics and Gynaecology, University of Valencia, 46010 Valencia, Spain
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13
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Huang W, Huang H, Zhang S, Wang X, Ouyang J, Lin Z, Chen P. A Novel Diagnosis Method Based on Methylation Analysis of SHOX2 and Serum Biomarker for Early Stage Lung Cancer. Cancer Control 2021; 27:1073274820969703. [PMID: 33167712 PMCID: PMC7791477 DOI: 10.1177/1073274820969703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives: Lung cancer (LC) is often accompanied by significant methylation
abnormalities. This study aimed to develop a decision tree (DT) accompanied
the stature homeobox 2 gene (SHOX2) / prostaglandin E receptor 4 (PTGER4)
gene DNA methylation with traditional tumor marker in the differential
diagnosis of benign and malignant lung nodule. Methods: We performed a study with 104 patients enrolled in the LC group and 36
patients in the benign lung diseases group. All the clinical data of these
patients were collected through electronic medical record. Total Methylation
(TM) status of both SHOX2 and PTGER4 was defined as methylation levels of
SHOX2 plus methylation levels of PTGER4. One-way analysis was used to
compare the concentrations of serum samples and t-test was used to compare
pairwise mean values between groups. Receiver operating curve (ROC) was used
to evaluate the diagnostic value. Furthermore, the strategy was validated in
19 LC patients and 11 patients with benign lung diseases. Results: There were significant differences between the concentration of
neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), cytokeratin
19 fragments (CYFRA21 -1) and the methylation levels of SHOX2, PTGER4 and TM
in lung benign diseases and cancer group. The AUCs of NSE, CEA, CYFRA21 -1,
Methylation SHOX2, Methylation PTGER4 and TM were 0.721 (95% CI:
0.627–0.816), 0.753 (95% CI: 0.673–0.833) and 0.778(95% CI: 0.700–0.856),
0.851(0.786-0.916), 0.847(0.780-0.913) and 0.861(0.800-0.922) respectively.
We developed a DT model with TM and CYFRA21 -1 used in this study, and the
area under the curve (AUC) of DT was 0.921 and the sensitivity up to 0.856.
In the validation cohort, the AUC of SHOX2, PTGER4 and TM was also much
higher than traditional serum markers. Conclusions: Our results indicated that the DT model calculated from the TM and CYFRA21 -1
can accurately classify LC and benign diseases, which showed better
diagnostic performance than traditional serum parameter.
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Affiliation(s)
- Wenhai Huang
- Department of Thoracic Surgery, Jiangmen Centre Hospital, Jiangmen, Guangdong, China
| | - Hao Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuishen Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xueping Wang
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Juan Ouyang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhichao Lin
- Department of Thoracic Surgery, Jiangmen Centre Hospital, Jiangmen, Guangdong, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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14
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Lorenzo PM, Crujeiras AB. Potential effects of nutrition-based weight loss therapies in reversing obesity-related breast cancer epigenetic marks. Food Funct 2021; 12:1402-1414. [PMID: 33480953 DOI: 10.1039/d0fo01984d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Obesity is a modifiable risk factor of breast cancer and epigenetic marks were proposed as a relevant mechanistic link. These mechanisms can be remodelled by modifying lifestyle factors and this fact could be useful in the treatment of obesity-related breast cancer. This review aimed to reveal the current evidence on the effects of differences in body composition and lifestyle factors on the risk, treatment, and survival of breast cancer with a focus on the effects of weight loss therapies based on different nutrients, bioactive compounds, and Mediterranean and ketogenic diets to counteract obesity-related breast cancer epigenetic marks. This review was framed on the most relevant and recently published articles and abstracts selected in PubMed using key words related to epigenetics, lifestyle, dietary habits, nutrients, bioactive compounds, ketone bodies, and weight loss treatments in obesity and breast cancer. Several studies have demonstrated that lifestyle interventions, including dietary modifications towards a healthy diet pattern, are effective therapies to prevent the onset of breast cancer and to improve the survival after treatment. These therapies reduce the main factors associated with obesity that are links between adiposity and cancer, including oxidative stress, inflammation and epigenetic mechanisms. However, although sufficient evidence exists regarding the effects of nutrients, dietary patterns, and weight loss therapies to prevent breast cancer or to improve survival, the effects of these strategies on the oncological treatment response were less studied. This review summarises the current scientific evidence regarding these nutritional strategies as adjuvant therapies in the management of obesity-related breast cancer by remodelling epigenetic marks related to carcinogenesis.
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Affiliation(s)
- Paula M Lorenzo
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigacion Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.
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15
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Rodriguez-Casanova A, Costa-Fraga N, Bao-Caamano A, López-López R, Muinelo-Romay L, Diaz-Lagares A. Epigenetic Landscape of Liquid Biopsy in Colorectal Cancer. Front Cell Dev Biol 2021; 9:622459. [PMID: 33614651 PMCID: PMC7892964 DOI: 10.3389/fcell.2021.622459] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and is a major cause of cancer-related deaths worldwide. Thus, there is a clinical need to improve early detection of CRC and personalize therapy for patients with this disease. In the era of precision oncology, liquid biopsy has emerged as a major approach to characterize the circulating tumor elements present in body fluids, including cell-free DNA and RNA, circulating tumor cells, and extracellular vesicles. This non-invasive tool has allowed the identification of relevant molecular alterations in CRC patients, including some indicating the disruption of epigenetic mechanisms. Epigenetic alterations found in solid and liquid biopsies have shown great utility as biomarkers for early detection, prognosis, monitoring, and evaluation of therapeutic response in CRC patients. Here, we summarize current knowledge of the most relevant epigenetic mechanisms associated with cancer development and progression, and the implications of their deregulation in cancer cells and liquid biopsy of CRC patients. In particular, we describe the methodologies used to analyze these epigenetic alterations in circulating tumor material, and we focus on the clinical utility of epigenetic marks in liquid biopsy as tumor biomarkers for CRC patients. We also discuss the great challenges and emerging opportunities of this field for the diagnosis and personalized management of CRC patients.
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Affiliation(s)
- Aitor Rodriguez-Casanova
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Nicolás Costa-Fraga
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rafael López-López
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Laura Muinelo-Romay
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
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16
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Shi J, Chen X, Zhang L, Fang X, Liu Y, Zhu X, Zhang H, Fan L, Gu J, Zhang S, She B, Han H, Yi X. Performance Evaluation of SHOX2 and RASSF1A Methylation for the Aid in Diagnosis of Lung Cancer Based on the Analysis of FFPE Specimen. Front Oncol 2020; 10:565780. [PMID: 33425721 PMCID: PMC7793934 DOI: 10.3389/fonc.2020.565780] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022] Open
Abstract
Emerging molecular diagnostic methods are more sensitive and objective, which can overcome the intrinsic failings of morphological diagnosis. Here, a RT-PCR-based in vitro diagnostic test kit (LungMe®) was developed and characterized to simultaneously quantify the DNA methylation of SHOX2 and RASSF1A in FFPE tissue specimens. The clinical manifestations were evaluated in 251 FFPE samples with specificity and sensitivity of 90.4 and 89.8%, respectively. Furthermore, the quantitative analysis shows that the degree of SHOX2 methylation was correlated with the stages of lung cancer, but not in the case of RASSF1A. Our observation indicated that the DNA methylation of SHOX2 and RASSF1A may play different roles in cancer development. Comparison of the methylation levels of SHOX2 and RASSF1A between cancer and cancer-adjacent specimens (n = 30), showed they have “epigenetic field defect”. As additional clinical validation, the hypermethylation of SHOX2 and RASSF1A was detected not only in surgical operative specimens, but also in histopathological negative puncture biopsies. SHOX2 and RASSF1A methylation detection can be used to increase sensitivity and NPV, which provide us with a more accurate method of differential diagnosis and are likely to be rapidly applied in clinical examinations.
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Affiliation(s)
- Juanhong Shi
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Xue Chen
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Long Zhang
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Xia Fang
- Department of Pulmonary and Critical Care Medicine, Dongfang Hospital Affiliated to Tongji University, Shanghai, China
| | - Yuting Liu
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Xuyou Zhu
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Haoyang Zhang
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Lichao Fan
- Department of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital Affiliated to Tongji University, Shanghai, China
| | - Jun Gu
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Suxia Zhang
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Bin She
- Academic Development, Tellgen Corporation, Shanghai, China
| | - Hongxiu Han
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
| | - Xianghua Yi
- Department of Pathology, Tongji Hospital, Tongji University, Shianghai, China
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17
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Bandera-Merchan B, Boughanem H, Crujeiras AB, Macias-Gonzalez M, Tinahones FJ. Ketotherapy as an epigenetic modifier in cancer. Rev Endocr Metab Disord 2020; 21:509-519. [PMID: 32514818 DOI: 10.1007/s11154-020-09567-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetic alterations in cancer play a variety of roles. Aberrant DNA methylation, as one of the epigenetic mechanisms, has been widely studied in both tumor and liquid biopsies and provide a useful bench mark for treatment response in cancer. Recently, several studies have reported an association between the type of diet and epigenetic modifications. Whereby there is a growing interest in finding the "anti-cancer diet formula", if such a thing exists. In this sense, ketogenic diets (KD) have reported potentially beneficial effects, which were able to prevent malignancies and decrease tumor growth. Some studies have even shown increased survival in cancer patients, reduced side effects of cytotoxic treatments, and intensified efficacy of cancer therapies. Although the biological mechanisms of KD are not well understood, it has been reported that KD may affect DNA methylation by modulating the expression of crucial genes involved in tumor survival and proliferation. However, there are many considerations to take into account to use ketotherapy in cancer, such as epigenetic mark, type of cancer, immunological and metabolic state or microbiota profile. In this review, we argue about ketotherapy as a potential strategy to consider as coadjuvant of cancer therapy. We will focus on mainly epigenetic mechanisms and dietary approach that could be included in the current clinical practice guidelines.
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Affiliation(s)
- Borja Bandera-Merchan
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain
| | - Hatim Boughanem
- Biomedical Research Institute of Malaga (IBIMA). Faculty of Science, University of Malaga, 29010, Málaga, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Manuel Macias-Gonzalez
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain.
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Francisco J Tinahones
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), 29010, Málaga, Spain
- CIBEROBN (CIBER in Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029, Madrid, Spain
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18
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Sreedurgalakshmi K, Srikar R, Rajkumari R. CRISPR-Cas deployment in non-small cell lung cancer for target screening, validations, and discoveries. Cancer Gene Ther 2020; 28:566-580. [PMID: 33191402 DOI: 10.1038/s41417-020-00256-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/14/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022]
Abstract
Continued advancements in CRISPR-Cas systems have accelerated genome research. Use of CRISPR-Cas in cancer research has been of great interest that is resulting in development of orthogonal methods for drug target validations and discovery of new therapeutic targets through genome-wide screens of cancer cells. CRISPR-based screens have also revealed several new cancer drivers through alterations in tumor suppressor genes (TSGs) and oncogenes inducing resistance to targeted therapies via activation of alternate signaling pathways. Given such dynamic status of cancer, we review the application of CRISPR-Cas in non-small cell lung cancer (NSCLC) for development of mutant models, drug screening, target validation, novel target discoveries, and other emerging potential applications. In addition, CRISPR-based approach for development of novel anticancer combination therapies is also discussed in this review.
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Affiliation(s)
- K Sreedurgalakshmi
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India.,Division of Biosimilars and Gene Therapy, R&D, Levim Biotech LLP, Chennai, Tamilnadu, India
| | - R Srikar
- Division of Biosimilars and Gene Therapy, R&D, Levim Biotech LLP, Chennai, Tamilnadu, India.
| | - Reena Rajkumari
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India.
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19
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Impact of Tumor LINE-1 Methylation Level and Neoadjuvant Treatment and Its Association with Colorectal Cancer Survival. J Pers Med 2020; 10:jpm10040219. [PMID: 33187096 PMCID: PMC7712476 DOI: 10.3390/jpm10040219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Recent studies suggest that long-interspersed nucleotide element-1 (LINE-1) hypomethylation is commonly found in colorectal cancer (CRC), and is associated with worse prognosis. However, the utility of LINE-1 methylation on the prognosis of CRC is still controversial, and may be due to the fact that some clinical and pathological features may affect LINE-1 methylation. Thus, the aim of this study was to assess the prognostic value of tumor LINE-1 methylation in CRC, through their association with the CRC clinical and pathological characteristics. Survival of sixty-seven CRC patients was evaluated according to the median of tumor LINE-1 methylation, as well as pathological and oncological variables. We also studied the association between LINE-1 methylation and pathological features, and finally, we assessed the overall and disease-free survival of LINE1 methylation, stratified by neoadjuvant treatment and further checked by multivariate Cox regression to assess the statistical interactions. LINE-1 was hypomethylated in the CRC tumor with respect to the tumor adjacent-free area (p < 0.05), without association with any other clinical and oncological features, nor with overall and disease-free survival rates for CRC. Relevantly, in neoadjuvant treatment, LINE-1 methylation was associated with survival rates. Thus, disease-free and overall survival rates of treated CRC patients were worse in the hypomethylated LINE-1 tumors than those with normal LINE-1 methylation (p = 0.004 and 0.0049, respectively). Indeed, LINE-1 was hypermethylated more in the treated patients than in the non-treated patients (p < 0.05). The present study showed that tumor LINE-1 hypomethylation was associated with worse survival rates in only treated patients. Our data suggest an interactive effect of neoadjuvant treatment and tumor LINE-1 methylation, which could be a specific-tissue biomarker to predict survival of the treated patients, and help to personalize treatment in CRC.
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20
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Bao-Caamano A, Rodriguez-Casanova A, Diaz-Lagares A. Epigenetics of Circulating Tumor Cells in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1220:117-134. [PMID: 32304083 DOI: 10.1007/978-3-030-35805-1_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid biopsy based on the analysis of circulating tumor cells (CTCs) has emerged as an important field of research. Molecular characterization of CTCs can provide insights into cancer biology and biomarkers for the clinic, representing a non-invasive powerful tool for monitoring breast cancer metastasis and predict the therapeutic response. Epigenetic mechanisms play a key role in the control of gene expression and their alteration contributes to cancer development and progression. These epigenetic modifications in CTCs have been described mainly related to modifications of the DNA methylation pattern and changes in the expression profile of noncoding RNAs. Here we summarize the recent findings on the epigenetic characterization of CTCs in breast cancer and their clinical value as tumor biomarkers, and discuss challenges and opportunities in this field.
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Affiliation(s)
- Aida Bao-Caamano
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
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21
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Oldani M, Fabbri M, Melchioretto P, Callegaro G, Fusi P, Gribaldo L, Forcella M, Urani C. In vitro and bioinformatics mechanistic-based approach for cadmium carcinogenicity understanding. Toxicol In Vitro 2020; 65:104757. [PMID: 31904401 PMCID: PMC7166080 DOI: 10.1016/j.tiv.2020.104757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/28/2019] [Accepted: 01/01/2020] [Indexed: 02/07/2023]
Abstract
Cadmium is a toxic metal able to enter the cells through channels and transport pathways dedicated to essential ions, leading, among others, to the dysregulation of divalent ions homeostasis. Despite its recognized human carcinogenicity, the mechanisms are still under investigation. A powerful tool for mechanistic studies of carcinogenesis is the Cell Transformation Assay (CTA). We have isolated and characterized by whole genome microarray and bioinformatics analysis of differentially expressed genes (DEGs) cadmium-transformed cells from different foci (F1, F2, and F3) at the end of CTA (6 weeks). The systematic analysis of up- and down-regulated transcripts and the comparison of DEGs in transformed cells evidence different functional targets and the complex picture of cadmium-induced transformation. Only 34 in common DEGs are found in cells from all foci, and among these, only 4 genes are jointly up-regulated (Ccl2, Ccl5, IL6 and Spp1), all responsible for cytokines/chemokines coding. Most in common DEGs are down-regulated, suggesting that the switching-off of specific functions plays a major role in this process. In addition, the comparison of dysregulated pathways immediately after cadmium treatment with those in transformed cells provides a valuable means to the comprehension of the overall process. Cell transformation Assay and toxicogenomics are integrated to study cadmium carcinogenesis mechanisms Inflammatory response is the only common feature in Cd-transformed cells from all different foci Switching-off of specific functions plays a major role in Cd-induced carcinogenesis Comparison of triggering signals and deregulated pathways in transformed cells provides hints on cadmium mechanisms
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Affiliation(s)
- Monica Oldani
- Department of Biotechnology and Biosciences, University of Milan - Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Marco Fabbri
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215, USA
| | - Pasquale Melchioretto
- Department of Earth and Environmental Sciences, University of Milan - Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Giulia Callegaro
- Department of Earth and Environmental Sciences, University of Milan - Bicocca, Piazza della Scienza 1, 20126 Milan, Italy; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, The Netherlands
| | - Paola Fusi
- Department of Biotechnology and Biosciences, University of Milan - Bicocca, Piazza della Scienza 3, 20126 Milan, Italy; Integrated Models for Prevention and Protection in Environmental and Occupational Health, (MISTRAL) Interuniversity Research Center, Italy
| | - Laura Gribaldo
- European Commission, DG Joint Research Centre, Via Fermi 2749, 21027 Ispra, VA, Italy.
| | - Matilde Forcella
- Department of Biotechnology and Biosciences, University of Milan - Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Chiara Urani
- Department of Earth and Environmental Sciences, University of Milan - Bicocca, Piazza della Scienza 1, 20126 Milan, Italy; Integrated Models for Prevention and Protection in Environmental and Occupational Health, (MISTRAL) Interuniversity Research Center, Italy
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22
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Villalba M, Exposito F, Pajares MJ, Sainz C, Redrado M, Remirez A, Wistuba I, Behrens C, Jantus-Lewintre E, Camps C, Montuenga LM, Pio R, Lozano MD, de Andrea C, Calvo A. TMPRSS4: A Novel Tumor Prognostic Indicator for the Stratification of Stage IA Tumors and a Liquid Biopsy Biomarker for NSCLC Patients. J Clin Med 2019; 8:E2134. [PMID: 31817025 PMCID: PMC6947244 DOI: 10.3390/jcm8122134] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/19/2022] Open
Abstract
Relapse rates in surgically resected non-small-cell lung cancer (NSCLC) patients are between 30% and 45% within five years of diagnosis, which shows the clinical need to identify those patients at high risk of recurrence. The eighth TNM staging system recently refined the classification of NSCLC patients and their associated prognosis, but molecular biomarkers could improve the heterogeneous outcomes found within each stage. Here, using two independent cohorts (MDA and CIMA-CUN) and the eighth TNM classification, we show that TMPRSS4 protein expression is an independent prognostic factor in NSCLC, particularly for patients at stage I: relapse-free survival (RFS) HR, 2.42 (95% CI, 1.47-3.99), p < 0.001; overall survival (OS) HR, 1.99 (95% CI, 1.25-3.16), p = 0.004). In stage IA, high levels of this protein remained associated with worse prognosis (p = 0.002 for RFS and p = 0.001 for OS). As TMPRSS4 expression is epigenetically regulated, methylation status could be used in circulating tumor DNA from liquid biopsies to monitor patients. We developed a digital droplet PCR (ddPCR) method to quantify absolute copy numbers of methylated and unmethylated CpGs within the TMPRSS4 and SHOX2 (as control) promoters in plasma and bronchoalveolar lavage (BAL) samples. In case-control studies, we demonstrated that TMPRSS4 hypomethylation can be used as a diagnostic tool in early stages, with an AUROC of 0.72 (p = 0.008; 91% specificity and 52% sensitivity) for BAL and 0.73 (p = 0.015; 65% specificity and 90% sensitivity) for plasma, in early stages. In conclusion, TMPRSS4 protein expression can be used to stratify patients at high risk of relapse/death in very early stages NSCLC patients. Moreover, analysis of TMPRSS4 methylation status by ddPCR in blood and BAL is feasible and could serve as a non-invasive biomarker to monitor surgically resected patients.
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Affiliation(s)
- Maria Villalba
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain;
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
| | - Francisco Exposito
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain;
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
| | - Maria Jose Pajares
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain;
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
| | - Cristina Sainz
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
| | - Miriam Redrado
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
| | - Ana Remirez
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (I.W.); (C.B.)
| | - Carmen Behrens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (I.W.); (C.B.)
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
- Molecular Oncology Laboratory, FIHGUV & Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Carlos Camps
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
- Department of Medicine, Universitat de Valencia, 46022 Valencia, Spain
| | - Luis M. Montuenga
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain;
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
| | - Ruben Pio
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Maria Dolores Lozano
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain;
- Department of Pathology, University of Navarra Clinic, 31008 Pamplona, Spain
| | - Carlos de Andrea
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain;
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
- Department of Pathology, University of Navarra Clinic, 31008 Pamplona, Spain
| | - Alfonso Calvo
- IDISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.V.); (F.E.); (M.J.P.); (C.S.); (M.R.); (A.R.); (L.M.M.); (R.P.); (C.d.A.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain;
- CIBERONC, ISC-III, 28029 Madrid, Spain; (E.J.-L.); (C.C.)
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23
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Montgomery M, Srinivasan A. Epigenetic Gene Regulation by Dietary Compounds in Cancer Prevention. Adv Nutr 2019; 10:1012-1028. [PMID: 31100104 PMCID: PMC6855955 DOI: 10.1093/advances/nmz046] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/07/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Traditionally, cancer has been viewed as a set of diseases that are driven by the accumulation of genetic mutations, but we now understand that disruptions in epigenetic regulatory mechanisms are prevalent in cancer as well. Unlike genetic mutations, however, epigenetic alterations are reversible, making them desirable therapeutic targets. The potential for diet, and bioactive dietary components, to target epigenetic pathways in cancer is now widely appreciated, but our understanding of how to utilize these compounds for effective chemopreventive strategies in humans is in its infancy. This review provides a brief overview of epigenetic regulation and the clinical applications of epigenetics in cancer. It then describes the capacity for dietary components to contribute to epigenetic regulation, with a focus on the efficacy of dietary epigenetic regulators as secondary cancer prevention strategies in humans. Lastly, it discusses the necessary precautions and challenges that will need to be overcome before the chemopreventive power of dietary-based intervention strategies can be fully harnessed.
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Affiliation(s)
- McKale Montgomery
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK,Address correspondence to MM (E-mail: )
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24
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Leiro-Fernandez V, De Chiara L, Rodríguez-Girondo M, Botana-Rial M, Valverde D, Núñez-Delgado M, Fernández-Villar A. Methylation Assessment for the Prediction of Malignancy in Mediastinal Adenopathies Obtained by Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration in Patients with Lung Cancer. Cancers (Basel) 2019; 11:cancers11101408. [PMID: 31547177 PMCID: PMC6826358 DOI: 10.3390/cancers11101408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022] Open
Abstract
The evaluation of mediastinal lymph nodes is critical for the correct staging of patients with lung cancer (LC). Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive technique for mediastinal staging, though unfortunately lymph node micrometastasis is often missed by cytological analysis. The aim of this study was to evaluate the predictive capacity of methylation biomarkers and provide a classification rule for predicting malignancy in false negative EBUS-TBNA samples. The study included 112 patients with a new or suspected diagnosis of LC that were referred to EBUS-TBNA. Methylation of p16/INK4a, MGMT, SHOX2, E-cadherin, DLEC1, and RASSF1A was quantified by nested methylation-specific qPCR in 218 EBUS-TBNA lymph node samples. Cross-validated linear regression models were evaluated to predict malignancy. According to EBUS-TBNA and final diagnosis, 90 samples were true positives for malignancy, 110 were true negatives, and 18 were false negatives. MGMT, SHOX2, and E-cadherin were the methylation markers that better predicted malignancy. The model including sex, age, short axis diameter and standard uptake value of adenopathy, and SHOX2 showed 82.7% cross-validated sensitivity and 82.4% specificity for the detection of malignant lymphadenopathies among negative cytology samples. Our results suggest that the predictive model approach proposed can complement EBUS-TBNA for mediastinal staging.
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Affiliation(s)
- Virginia Leiro-Fernandez
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
- Correspondence: (L.D.C.); (V.L.-F.)
| | - Loretta De Chiara
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Correspondence: (L.D.C.); (V.L.-F.)
| | - Mar Rodríguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
- SiDOR Research Group, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
| | - Maribel Botana-Rial
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
| | - Diana Valverde
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain;
| | - Manuel Núñez-Delgado
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
| | - Alberto Fernández-Villar
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
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25
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Zou Y, Zhang B, Mao Y, Zhang H, Hong W. Long non-coding RNA OECC promotes cell proliferation and metastasis through the PI3K/Akt/mTOR signaling pathway in human lung cancer. Oncol Lett 2019; 18:3017-3024. [PMID: 31452780 PMCID: PMC6704322 DOI: 10.3892/ol.2019.10644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
Lung cancer is one of the most common malignancies worldwide; however, its detailed molecular mechanism remains largely unknown. Long non-coding RNAs (lncRNAs) have been identified to serve critical roles in tumorigenesis. The aim of the present study was to investigate the role of a newly identified lncRNA, overexpressed in colorectal cancer (OECC), in human lung cancer. It was initially revealed that the relative transcript level of OECC was highly upregulated in clinical human lung cancer tissues as well as in cultured lung cancer cells. Knockdown of OECC with specific short hairpin RNAs in lung cancer cell lines A549 and 95D inhibited colony formation and cell viability, as evidenced using colony formation assays and cell proliferation assays. Furthermore, depletion of OECC in A549 and 95D cells suppressed migration and invasion, which was verified using Transwell assays. RNA-sequence analysis suggested that the phosphoinositide 3-kinase/protein kinase B (Akt)/mammalian target of rapamycin signaling pathway was positively regulated by OECC in lung cancer cells A549. In addition, overexpression of Akt in OECC-depleted A549 and 95D cells reversed the suppression of proliferation and migration caused by OECC depletion. The results of the present study identified lncRNA OECC as a novel regulator of lung cancer progression and provided new clues for the clinical treatment of lung cancer.
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Affiliation(s)
- Yimin Zou
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Bin Zhang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yanxiong Mao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Hao Zhang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Wei Hong
- Guangzhou Medical University-Guangzhou Institute of Biomedicine and Health Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510030, P.R. China
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26
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Gillespie SL, Hardy LR, Anderson CM. Patterns of DNA methylation as an indicator of biological aging: State of the science and future directions in precision health promotion. Nurs Outlook 2019; 67:337-344. [PMID: 31248628 DOI: 10.1016/j.outlook.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND A rapidly expanding literature suggests that individuals of the same chronological age show significant variation in biological age. PURPOSE The purpose of this article is to review the literature surrounding epigenetic age as estimated by DNA methylation, involving the addition or removal of methyl groups to DNA that can alter gene expression without changing the DNA sequence. METHODS This state of the science literature review summarizes current approaches in epigenetic age determination and applications of aging algorithms. FINDINGS A number of algorithms estimate epigenetic age using DNA methylation markers, primarily among adults. Algorithm application has focused on determining predictive value for risk of disease and death and identifying antecedents to age acceleration. Several studies have incorporated epigenetic age to evaluate intervention effectiveness. DISCUSSION As the research community continues to refine aging algorithms, there may be opportunity to promote health from a precision health perspective.
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Affiliation(s)
- Shannon L Gillespie
- Martha S. Pitzer Center for Women, Children, & Youth, College of Nursing, The Ohio State University, Columbus, OH.
| | - Lynda R Hardy
- Center for Research and Health Analytics, College of Nursing, The Ohio State University, Columbus, OH
| | - Cindy M Anderson
- Martha S. Pitzer Center for Women, Children, & Youth, College of Nursing, The Ohio State University, Columbus, OH
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27
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Calderón-Aparicio A, Orue A. Precision oncology in Latin America: current situation, challenges and perspectives. Ecancermedicalscience 2019; 13:920. [PMID: 31281417 PMCID: PMC6546257 DOI: 10.3332/ecancer.2019.920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Anti-cancer cytotoxic treatments like platinum-derived compounds often show low therapeutic efficacy, high-risk side effects and resistance. Hence, targeted treatments designed to attack only tumour cells avoiding these harmful side effects are highly needed in clinical practice. Due to this, precision oncology has arisen as an approach to specifically target alterations present only in cancer cells, minimising side effects for patients. It involves the use of molecular biomarkers present in each kind of tumour for diagnosis, prognosis and treatment. Since these biomarkers are specific for each cancer type, physicians use them to stratify, diagnose or take the best therapeutic options for each patient depending on the features of the specific tumour. AIM This review aims to describe the current situation, limitations, advantages and perspectives about precision oncology in Latin America. MAIN BODY For many years, many biomarkers have been used in a clinical setting in developed countries. However, in Latin American countries, their broad application has not been affordable partially due to financial and technical limitations associated with precarious health systems and poor access of low-income populations to quality health care. Furthermore, the genetic mixture in Latin American populations could generate differences in treatment responses from one population to another (pharmacoethnicity) and this should be evaluated before establishing precision therapy in particular populations. Some research groups in the region have done a lot of work in this field and these data should be taken as a starting point to establish networks oriented to finding clinically useful cancer biomarkers in Latin American populations. CONCLUSION Latin America must create policies allowing excluded populations to gain access to health systems and next generation anti-cancer drugs, i.e. high-cost targeted therapies to improve survival. Also, cancer clinical research must be oriented to establish cancer biomarkers adapted to specific populations with different ethnicity, allowing the improvement of patient outcomes.
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Affiliation(s)
- Ali Calderón-Aparicio
- Tumor Cell Biology Laboratory, Instituto Venezolano de Investigaciones Científicas IVIC, Centro de Microbiología, Caracas 1020A, Venezuela
| | - Andrea Orue
- Tumor Cell Biology Laboratory, Instituto Venezolano de Investigaciones Científicas IVIC, Centro de Microbiología, Caracas 1020A, Venezuela
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28
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Wu W, Wang X, Shan C, Li Y, Li F. Minichromosome maintenance protein 2 correlates with the malignant status and regulates proliferation and cell cycle in lung squamous cell carcinoma. Onco Targets Ther 2018; 11:5025-5034. [PMID: 30174440 PMCID: PMC6109654 DOI: 10.2147/ott.s169002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Minichromosome maintenance protein 2 (MCM2), which is a member of MCM family, has been found to be a relevant marker for progression and prognosis in a variety of human cancers. Due to lack of effective therapeutic target in lung squamous cell carcinoma (LUSC) patients, the aim of our study was to screen and identify biomarkers which are associated to clinicopathological characteristics including prognosis in LUSC patients. Methods The expression status of MCM2 in lung cancer was analyzed using the publicly available Gene Expression Omnibus databases (GSE3268 and GSE10245). The mRNA and protein expression of MCM2 in lung cancer tissues and cell lines was detected by quantitative real-time PCR and Western blot, and the association between MCM2 expression and clinicopathological factors was analyzed by immunohistochemistry. The loss-of-function study of MCM2 was conducted in LUSC cell lines. Results In our study, we found MCM2 expression was increased in LUSC tissues compared with paired adjacent normal lung tissues or lung adenocarcinoma tissues through analyzing microarray data sets (GSE3268 and GSE10245), which confirmed that MCM2 mRNA and protein were overexpressed in LUSC tissues and cell lines. Meanwhile, we analyzed the association between MCM2 protein expression and clinicopathological characteristics of LUSC patients, and found high expression of MCM2 protein was obviously associated with malign differentiated degree, advanced clinical stage, large tumor size, more lymph node metastasis and present distant metastasis. The survival analysis showed MCM2 overexpression was an independent unfavorable prognostic factor for LUSC patients. Conclusion MCM2 is involved in the development and progression of LUSC as an oncogene, and thereby may act as a potential therapeutic target for LUSC patients.
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Affiliation(s)
- Wei Wu
- Department of Respiratory Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, People's Republic of China,
| | - Xianwei Wang
- Department of Respiratory Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, People's Republic of China,
| | - Changting Shan
- Department of Respiratory Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, People's Republic of China,
| | - Yong Li
- Department of Emergency, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, People's Republic of China
| | - Fengzhu Li
- Department of Paediatric Surgery, Jining No 1 People's Hospital, Jining, Shandong 272011, People's Republic of China
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29
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Pinker K, Chin J, Melsaether AN, Morris EA, Moy L. Precision Medicine and Radiogenomics in Breast Cancer: New Approaches toward Diagnosis and Treatment. Radiology 2018; 287:732-747. [PMID: 29782246 DOI: 10.1148/radiol.2018172171] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Precision medicine is medicine optimized to the genotypic and phenotypic characteristics of an individual and, when present, his or her disease. It has a host of targets, including genes and their transcripts, proteins, and metabolites. Studying precision medicine involves a systems biology approach that integrates mathematical modeling and biology genomics, transcriptomics, proteomics, and metabolomics. Moreover, precision medicine must consider not only the relatively static genetic codes of individuals, but also the dynamic and heterogeneous genetic codes of cancers. Thus, precision medicine relies not only on discovering identifiable targets for treatment and surveillance modification, but also on reliable, noninvasive methods of identifying changes in these targets over time. Imaging via radiomics and radiogenomics is poised for a central role. Radiomics, which extracts large volumes of quantitative data from digital images and amalgamates these together with clinical and patient data into searchable shared databases, potentiates radiogenomics, which is the combination of genetic and radiomic data. Radiogenomics may provide voxel-by-voxel genetic information for a complete, heterogeneous tumor or, in the setting of metastatic disease, set of tumors and thereby guide tailored therapy. Radiogenomics may also quantify lesion characteristics, to better differentiate between benign and malignant entities, and patient characteristics, to better stratify patients according to risk for disease, thereby allowing for more precise imaging and screening. This report provides an overview of precision medicine and discusses radiogenomics specifically in breast cancer. © RSNA, 2018.
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Affiliation(s)
- Katja Pinker
- From the Department of Radiology, Breast Imaging Service, Memorial Sloan-Kettering Cancer Center, New York, NY (K.P., J.C., E.A.M.); and Center for Advanced Imaging Innovation and Research, Laura and Isaac Perlmutter Cancer Center, New York University of Medicine, 160 E 34th St, New York, NY 10016 (A.N.M., L.M.)
| | - Joanne Chin
- From the Department of Radiology, Breast Imaging Service, Memorial Sloan-Kettering Cancer Center, New York, NY (K.P., J.C., E.A.M.); and Center for Advanced Imaging Innovation and Research, Laura and Isaac Perlmutter Cancer Center, New York University of Medicine, 160 E 34th St, New York, NY 10016 (A.N.M., L.M.)
| | - Amy N Melsaether
- From the Department of Radiology, Breast Imaging Service, Memorial Sloan-Kettering Cancer Center, New York, NY (K.P., J.C., E.A.M.); and Center for Advanced Imaging Innovation and Research, Laura and Isaac Perlmutter Cancer Center, New York University of Medicine, 160 E 34th St, New York, NY 10016 (A.N.M., L.M.)
| | - Elizabeth A Morris
- From the Department of Radiology, Breast Imaging Service, Memorial Sloan-Kettering Cancer Center, New York, NY (K.P., J.C., E.A.M.); and Center for Advanced Imaging Innovation and Research, Laura and Isaac Perlmutter Cancer Center, New York University of Medicine, 160 E 34th St, New York, NY 10016 (A.N.M., L.M.)
| | - Linda Moy
- From the Department of Radiology, Breast Imaging Service, Memorial Sloan-Kettering Cancer Center, New York, NY (K.P., J.C., E.A.M.); and Center for Advanced Imaging Innovation and Research, Laura and Isaac Perlmutter Cancer Center, New York University of Medicine, 160 E 34th St, New York, NY 10016 (A.N.M., L.M.)
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30
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Potential Micronutrients and Phytochemicals against the Pathogenesis of Chronic Obstructive Pulmonary Disease and Lung Cancer. Nutrients 2018; 10:nu10070813. [PMID: 29941777 PMCID: PMC6073117 DOI: 10.3390/nu10070813] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 12/13/2022] Open
Abstract
Lung cancer and chronic obstructive pulmonary disease have shared etiology, including key etiological changes (e.g., DNA damage and epigenetics change) and lung function impairment. Focusing on those shared targets may help in the prevention of both. Certain micronutrients (vitamins and minerals) and phytochemicals (carotenoids and phenols) have potent antioxidant or methyl-donating properties and thus have received considerable interest. We reviewed recent papers probing into the potential of nutrients with respect to lung function preservation and prevention of lung cancer risk, and suggest several hypothetical intervention patterns. Intakes of vitamins (i.e., A, C, D, E, B12), carotenoids, flavonoids, curcumins, resveratrol, magnesium, and omega-3 fatty acids all show protective effects against lung function loss, some mainly by improving average lung function and others through reducing decline rate. Dietary interventions early in life may help lung function reserve over the lifespan. Protective nutrient interventions among smokers are likely to mitigate the effects of cigarettes on lung health. We also discuss their underlying mechanisms and some possible causes for the inconsistent results in observational studies and supplementation trials. The role of the lung microbiome on lung health and its potential utility in identifying protective nutrients are discussed as well. More prospective cohorts and well-designed clinical trials are needed to promote the transition of individualized nutrient interventions into health policy.
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Ma XP, Zhang W, Wu BQ, Qin J. Correlations Between mRNA Levels of Centrosomal Protein 55 (CEP55) and Clinical Features of Patients with Lung Cancer. Med Sci Monit 2018; 24:3093-3097. [PMID: 29750778 PMCID: PMC5973496 DOI: 10.12659/msm.907266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The aim of this study was to investigate the prognostic relevance of CEP55 in lung cancer (LC). Material/Methods LC microarray profile GSE30219 was obtained from the GEO database. The 2-sample t test was performed to clarify the difference in CEP55 expression between LC and normal lung tissue. The chi-square test and logistic regression analysis were preformed to investigate the relationship between CEP55 expression and the clinical features of LC patients. Log-rank test and Cox proportional hazards regression analysis were conducted to evaluate the disease-free survival (DFS) and overall survival (OS) of LC patients. Gene set enrichment analysis was conducted to investigate the related mechanisms. Results CEP55 was significantly increased in LC cells relative to normal lung tissues (P<0.0001). Univariate and multivariate correlation analyses demonstrated that CEP55 expression was associated with advanced T and N staging of LC (P<0.0001). Survival analyses indicated that CEP55 expression was an independent risk factor for DFS (HR: 1.515, 95% CI: 1.277–1.797, P<0.0001) and OS (HR: 1.436, 95% CI: 1.278–1.615). CEP55 might affect the proliferation of LC cells through Myc signaling, DNA repair, and G2M checkpoint. Conclusions Our results indicated that CEP55 was increased in LC cells and was associated with poor clinical outcomes of LC patients, and could be a prognostic biomarker for LC.
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Affiliation(s)
- Xue-Ping Ma
- Department of General Surgery, Peace Hospital of Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| | - Wenping Zhang
- Department of Cardiothoracic Surgery, Peace Hospital of Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| | - Bu-Qiang Wu
- Department of General Surgery, Peace Hospital of Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| | - Jun Qin
- Department of General Surgery, Peace Hospital of Changzhi Medical College, Changzhi, Shanxi, China (mainland)
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