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Li Y, Xie F, Zheng Q, Zhang Y, Li W, Xu M, He Q, Li Y, Sun J. Non-invasive diagnosis of pulmonary nodules by circulating tumor DNA methylation: A prospective multicenter study. Lung Cancer 2024; 195:107930. [PMID: 39146624 DOI: 10.1016/j.lungcan.2024.107930] [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: 04/03/2024] [Revised: 07/08/2024] [Accepted: 08/10/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND With the popularization of computed tomography, more and more pulmonary nodules (PNs) are being detected. Risk stratification of PNs is essential for detecting early-stage lung cancer while minimizing the overdiagnosis of benign nodules. This study aimed to develop a circulating tumor DNA (ctDNA) methylation-based, non-invasive model for the risk stratification of PNs. METHODS A blood-based assay ("LUNG-TRAC") was designed to include novel lung cancer ctDNA methylation markers identified from in-house reduced representative bisulfite sequencing data and known markers from the literature. A stratification model was trained based on 183 ctDNA samples derived from patients with benign or malignant PNs and validated in 62 patients. LUNG-TRAC was further single-blindly tested in a single- and multi-center cohort. RESULTS The LUNG-TRAC model achieved an area under the curve (AUC) of 0.810 (sensitivity = 74.4 % and specificity = 73.7 %) in the validation set. Two test sets were used to evaluate the performance of LUNG-TRAC, with an AUC of 0.815 in the single-center test (N = 61; sensitivity = 67.5 % and specificity = 76.2 %) and 0.761 in the multi-center test (N = 95; sensitivity = 50.7 % and specificity = 80.8 %). The clinical utility of LUNG-TRAC was further assessed by comparing it to two established risk stratification models: the Mayo Clinic and Veteran Administration models. It outperformed both in the validation and the single-center test sets. CONCLUSION The LUNG-TRAC model demonstrated accuracy and consistency in stratifying PNs for the risk of malignancy, suggesting its utility as a non-invasive diagnostic aid for early-stage peripheral lung cancer. CLINICAL TRIAL REGISTRATION www. CLINICALTRIALS gov (NCT03989219).
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Affiliation(s)
- Ying Li
- Department of Respiratory Endoscopy, Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Engineering Research Center of Respiratory Endoscopy, Shanghai, China
| | - Fangfang Xie
- Department of Respiratory Endoscopy, Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Engineering Research Center of Respiratory Endoscopy, Shanghai, China
| | - Qiang Zheng
- Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yujun Zhang
- Department of Respiratory Endoscopy, Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Engineering Research Center of Respiratory Endoscopy, Shanghai, China
| | - Wei Li
- Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Minjie Xu
- Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Yuan Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Jiayuan Sun
- Department of Respiratory Endoscopy, Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Engineering Research Center of Respiratory Endoscopy, Shanghai, China.
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Shan Y, Teng Y, Guan C, Mao Z, Lu C, Ding W, Zhang J. Combined ultrasound endoscopy-guided fine-needle aspiration with DNA methylation of SHOX2 and RASSF1A genes to enhance the auxiliary diagnostic precision of pancreatic cancer. Heliyon 2024; 10:e34028. [PMID: 39071574 PMCID: PMC11282983 DOI: 10.1016/j.heliyon.2024.e34028] [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: 01/18/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
The purpose of this study was to assess the influence and the clinical effectiveness of the short stature homeobox 2 (SHOX2) and ras association domain family 1A (RASSF1A) genes by tissue sampling through ultrasound endoscopy-guided fine-needle aspiration (EUS-FNA) as auxiliary diagnostic tools for pancreatic cancer (PC). Methylation markers were detected in 96 patients using real-time fluorescence quantitative PCR (qPCR), and the performance of this diagnostic assay was compared with CA19-9, CEA, and puncture fluid-based exfoliative cytology using receiver operating characteristic curve (ROC) analysis. The PC group exhibited higher methylation rates for SHOX2, RASSF1A, and the combined assay of both genes compared to the control group (95.7 % vs. 54.0 %, 78.3 % vs. 36.0 %, and 73.9 % vs. 16.0 %, P < 0.05). The areas under the ROC curve (AUC) for CA19-9, CEA, liquid-based exfoliative cytology, SHOX2, RASSF1A, the combination of SHOX2 and RASSF1A, the combination assay with CEA, CA19-9, and liquid-based exfoliative cytology were 0.827, 0.692, 0.767, 0.770, 0.732, 0.870, 0.870, 0.933, and 0.900, respectively. Therefore, the methylation assay based on the combined SHOX2 and RASSF1A genes in EUS-FNA puncture fluid is more effective than using a single gene, liquid-based exfoliative cytology, or intravenous tumor markers for diagnosing PC. Combining the conventional marker CA19-9 enhances the diagnostic value, making it a promising approach to complement histology and cytology.
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Affiliation(s)
- Yangyang Shan
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
- Department of General Practice, Affiliated Hospital 2 of Nantong University, Nantong, Jiangsu, 226006, PR China
| | - Ying Teng
- Department of General Practice Medicine, and Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Chengqi Guan
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Zhenbiao Mao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Cuihua Lu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Weifeng Ding
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Jianfeng Zhang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
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Jin Y, Lu R, Liu F, Jiang G, Wang R, Zheng M. DNA methylation analysis in plasma for early diagnosis in lung adenocarcinoma. Medicine (Baltimore) 2024; 103:e38867. [PMID: 38996143 PMCID: PMC11245223 DOI: 10.1097/md.0000000000038867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) represents the most prevalent type of lung cancer. SHOX2 and RASSF1A methylation have been identified as important biomarkers for diagnosis and prognosis of lung cancer. Bronchoalveolar lavage fluid (BALF) exhibits good specificity and sensitivity in diagnosing pulmonary diseases, but its acquisition is challenging and may cause discomfort to patients. In clinical, plasma samples are more convenient to obtain than BALF; however, there is little research on the concurrent detection of SHOX2 and RASSF1A methylation in plasma. This study aims to assess the diagnostic value of a combined promoter methylation assay for SHOX2 and RASSF1A in early-stage LUAD using plasma samples. METHODS BALF and blood samples were obtained from 36 early-stage LUAD patients, with a control group of nineteen non-tumor individuals. The promoter methylation levels of SHOX2 and RASSF1A in all subjects were assessed using the human SHOX2 and RASSF1A gene methylation kit. RESULTS The methylation detection rate of SHOX2 and RASSF1A in plasma was 61.11%, slightly lower than that in BALF (66.7%). The Chi-square test revealed no significant difference in the methylation rate between BALF and plasma (P > 0.05). The area under the receiver operating characteristic (ROC) curve analysis for blood was 0.806 (95% CI, 0.677 to 0.900), while for BALF it was 0.781 (95% CI, 0.649 to 0.881). Additionally, we conducted an analysis on the correlation between SHOX2 and RASSF1A methylation levels in plasma with gender, age, tumor differentiation, pathologic classification, and other clinicopathological variables; however, no significant correlations were observed. CONCLUSIONS Measurement of SHOX2 and RASSF1A methylation for early diagnosis of LUAD can be achieved with high sensitivity and specificity by using plasma as a substitute for BALF samples.
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Affiliation(s)
- Yulin Jin
- Department of Thoracic Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
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Fu M, Deng F, Chen J, Fu L, Lei J, Xu T, Chen Y, Zhou J, Gao Q, Ding H. Current data and future perspectives on DNA methylation in ovarian cancer (Review). Int J Oncol 2024; 64:62. [PMID: 38757340 PMCID: PMC11095605 DOI: 10.3892/ijo.2024.5650] [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: 11/23/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Ovarian cancer (OC) represents the most prevalent malignancy of the female reproductive system. Its distinguishing features include a high aggressiveness, substantial morbidity and mortality, and a lack of apparent symptoms, which collectively pose significant challenges for early detection. Given that aberrant DNA methylation events leading to altered gene expression are characteristic of numerous tumor types, there has been extensive research into epigenetic mechanisms, particularly DNA methylation, in human cancers. In the context of OC, DNA methylation is often associated with the regulation of critical genes, such as BRCA1/2 and Ras‑association domain family 1A. Methylation modifications within the promoter regions of these genes not only contribute to the pathogenesis of OC, but also induce medication resistance and influence the prognosis of patients with OC. As such, a more in‑depth understanding of DNA methylation underpinning carcinogenesis could potentially facilitate the development of more effective therapeutic approaches for this intricate disease. The present review focuses on classical tumor suppressor genes, oncogenes, signaling pathways and associated microRNAs in an aim to elucidate the influence of DNA methylation on the development and progression of OC. The advantages and limitations of employing DNA methylation in the diagnosis, treatment and prevention of OC are also discussed. On the whole, the present literature review indicates that the DNA methylation of specific genes could potentially serve as a prognostic biomarker for OC and a therapeutic target for personalized treatment strategies. Further investigations in this field may yield more efficacious diagnostic and therapeutic alternatives for patients with OC.
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Affiliation(s)
- Mengyu Fu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Fengying Deng
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jie Chen
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Li Fu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jiahui Lei
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Ting Xu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
- Department of Gynecology and Obstetrics, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu 215100, P.R. China
| | - Youguo Chen
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jinhua Zhou
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Qinqin Gao
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Hongmei Ding
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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Xue Y, Zhao G, Song L, Qiao L, Huang C, Wang K, Wang T. The signature of cancer methylation markers in maternal plasma: Factors influencing the development and application of cancer liquid biopsy assay. Gene 2024; 906:148261. [PMID: 38342253 DOI: 10.1016/j.gene.2024.148261] [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: 10/16/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND DNA methylation is highly correlated with cancer and embryo development, and plasma-based methylation markers have been widely used for cancer early detection. However, whether the commonly used cancer methylation markers cause "false positives" in the plasma of pregnant women has not been comprehensively evaluated. METHODS We conducted a case-control study from February 2021 to March 2023, which included 138 pregnant women and 44 control women. Plasma cell-free DNA (cfDNA) was isolated and bisulfite-converted, and then the methylation levels of eight methylated markers related to gastrointestinal cancer (SEPT9, SDC2, C9orf50, KCNQ5, CLIP4, TFPI2, ELMO1 and ZNF582) and three markers related to lung cancer (SHOX2, RASSF1A and PTGER4) were analyzed. RESULTS When comparing the plasma of pregnant women to that of control women, SEPT9, CLIP4, ZNF582, SHOX2, RASSF1A and PTGER showed significantly higher levels of methylation (p < 0.05). These positive signals originate from the placenta/fetus rather than the mother. We found no discernible difference in DNA methylation levels between fetal cfDNA fractions of < 10 % and ≥ 10 % in pregnant women (p > 0.05), while CLIP4 and PTGER4 showed high methylation levels in the assisted fertilization group compared to the natural fertilization group (p < 0.05). CONCLUSION Our study shows that cancer and fetus/placenta exhibit similar DNA methylation patterns, and some gastrointestinal cancer and lung cancer-related methylation markers also show positives in maternal plasma. This is an important consideration in the design and application of plasma-based cancer liquid biopsy assays.
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Affiliation(s)
- Ying Xue
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Guodong Zhao
- ZJUT Yinhu Research Institute of Innovation and Entrepreneurship Fuyang District, Hangzhou, Zhejiang 311400, China; Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China.
| | - Lishuang Song
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Longwei Qiao
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Chao Huang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Kai Wang
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
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Gao J, Shi W, Wang J, Guan C, Dong Q, Sheng J, Zou X, Xu Z, Ge Y, Yang C, Li J, Bao H, Zhong X, Cui Y. Research progress and applications of epigenetic biomarkers in cancer. Front Pharmacol 2024; 15:1308309. [PMID: 38681199 PMCID: PMC11048075 DOI: 10.3389/fphar.2024.1308309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
Epigenetic changes are heritable changes in gene expression without changes in the nucleotide sequence of genes. Epigenetic changes play an important role in the development of cancer and in the process of malignancy metastasis. Previous studies have shown that abnormal epigenetic changes can be used as biomarkers for disease status and disease prediction. The reversibility and controllability of epigenetic modification changes also provide new strategies for early disease prevention and treatment. In addition, corresponding drug development has also reached the clinical stage. In this paper, we will discuss the recent progress and application status of tumor epigenetic biomarkers from three perspectives: DNA methylation, non-coding RNA, and histone modification, in order to provide new opportunities for additional tumor research and applications.
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Affiliation(s)
- Jianjun Gao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wujiang Shi
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiangang Wang
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Canghai Guan
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qingfu Dong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jialin Sheng
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinlei Zou
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhaoqiang Xu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yifei Ge
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chengru Yang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiehan Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haolin Bao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiangyu Zhong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Wu Z, Zhang W, Qu J, Liu GH. Emerging epigenetic insights into aging mechanisms and interventions. Trends Pharmacol Sci 2024; 45:157-172. [PMID: 38216430 DOI: 10.1016/j.tips.2023.12.002] [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: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Epigenetic dysregulation emerges as a critical hallmark and driving force of aging. Although still an evolving field with much to explore, it has rapidly gained significance by providing valuable insights into the mechanisms of aging and potential therapeutic opportunities for age-related diseases. Recent years have witnessed remarkable strides in our understanding of the epigenetic landscape of aging, encompassing pivotal elements, such as DNA methylation, histone modifications, RNA modifications, and noncoding (nc) RNAs. Here, we review the latest discoveries that shed light on new epigenetic mechanisms and critical targets for predicting and intervening in aging and related disorders. Furthermore, we explore burgeoning interventions and exemplary clinical trials explicitly designed to foster healthy aging, while contemplating the potential ramifications of epigenetic influences.
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Affiliation(s)
- Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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van den Broek D, Groen HJM. Screening approaches for lung cancer by blood-based biomarkers: Challenges and opportunities. Tumour Biol 2024; 46:S65-S80. [PMID: 37393461 DOI: 10.3233/tub-230004] [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] [Indexed: 07/03/2023] Open
Abstract
Lung cancer (LC) is one of the leading causes for cancer-related deaths in the world, accounting for 28% of all cancer deaths in Europe. Screening for lung cancer can enable earlier detection of LC and reduce lung cancer mortality as was demonstrated in several large image-based screening studies such as the NELSON and the NLST. Based on these studies, screening is recommended in the US and in the UK a targeted lung health check program was initiated. In Europe lung cancer screening (LCS) has not been implemented due to limited data on cost-effectiveness in the different health care systems and questions on for example the selection of high-risk individuals, adherence to screening, management of indeterminate nodules, and risk of overdiagnosis. Liquid biomarkers are considered to have a high potential to address these questions by supporting pre- and post- Low Dose CT (LDCT) risk-assessment thereby improving the overall efficacy of LCS. A wide variety of biomarkers, including cfDNA, miRNA, proteins and inflammatory markers have been studied in the context of LCS. Despite the available data, biomarkers are currently not implemented or evaluated in screening studies or screening programs. As a result, it remains an open question which biomarker will actually improve a LCS program and do this against acceptable costs. In this paper we discuss the current status of different promising biomarkers and the challenges and opportunities of blood-based biomarkers in the context of lung cancer screening.
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Affiliation(s)
- Daniel van den Broek
- Department of laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Khambata K, Begum S, Raut S, Mohan S, Irani D, Singh D, Bansal V, Patil A, Balasinor NH. DNA methylation biomarkers to identify epigenetically abnormal spermatozoa in male partners from couples experiencing recurrent pregnancy loss. Epigenetics 2023; 18:2252244. [PMID: 37699152 PMCID: PMC10498810 DOI: 10.1080/15592294.2023.2252244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/28/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023] Open
Abstract
Previously, we showed that DNA methylation defects in spermatozoa from male partners of couples undergoing recurrent pregnancy loss (RPL) could be a contributing paternal factor. In the present study, we aimed to determine whether the methylation levels of selected imprinted genes can be used as diagnostic markers to identify epigenetically abnormal spermatozoa sample in these cases. The methylation levels of selected imprinted genes in spermatozoa, which were previously found to be differentially methylated, were combined into a probability score (between 0-1) using multiple logistic regression. Different combinations of these genes were investigated using Receiver Operating Characteristic analysis, and the threshold values were experimentally validated in an independent cohort of 38 control and 45 RPL spermatozoa samples. Among the different combinations investigated, a combination of five imprinted genes comprising IGF2-H19 DMR, IG-DMR, ZAC, KvDMR, and PEG3 (AUC = 0.88) with a threshold value of 0.61 was selected with a specificity of 90.41% and sensitivity of 70%. The results from the validation study indicated that 97% of the control samples had probability scores below this threshold, whereas 40% of the RPL samples were above this threshold with a post-hoc power of 97.8%. Thus, this combination can correctly classify control samples and potentially identify epigenetically abnormal spermatozoa samples in the male partners of couples undergoing RPL. We propose that the combined DNA methylation levels of these imprinted genes can be used as a diagnostic tool to identify spermatozoa samples with epigenetic defects which could contribute to the pathophysiology of RPL and the couple could be counselled appropriately.
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Affiliation(s)
- Kushaan Khambata
- Gamete Immunobiology Department, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Shahina Begum
- Biostatistics Department, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Sanketa Raut
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Sweta Mohan
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Delna Irani
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Dipty Singh
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Vandana Bansal
- Department of Obstetrics and Gynecology, Nowrosjee Wadia Maternity Hospital, Mumbai, India
| | - Anushree Patil
- Clinical Research Department, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Nafisa H. Balasinor
- Neuroendocrinology Department, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health, Mumbai, India
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10
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Yang W, Chen H, Ma L, Dong J, Wei M, Xue X, Li Y, Jin Z, Xu W, Ji Z. SHOX2 promotes prostate cancer proliferation and metastasis through disruption of the Hippo-YAP pathway. iScience 2023; 26:107617. [PMID: 37664594 PMCID: PMC10470409 DOI: 10.1016/j.isci.2023.107617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
The transcription factor SHOX2 gene is critical in regulating gene expression and the development of tumors, but its biological role in prostate cancer (PCa) remains unclear. In this study, we found that SHOX2 expression was significantly raised in PCa tissues and was associated with clinicopathological features as well as disease-free survival (DFS) of PCa patients. Phenotypic tests showed that the absence of SHOX2 inhibited PCa growth and invasion, while SHOX2 overexpression promoted these effects. Mechanistically, SHOX2 was found to activate the transcription of nephronophthisis type 4 (NPHP4), a gene located downstream of SHOX2. Further analysis revealed that SHOX2 could potentially interfere with the Hippo-YAP signaling pathway through NPHP4 activation, facilitating the oncogenic behavior of PCa cells. These findings highlight SHOX2 as an oncogene in PCa and provide a basis for developing potential therapeutic approaches against this disease.
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Affiliation(s)
- Wenjie Yang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Hualin Chen
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Lin Ma
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Jie Dong
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Mengchao Wei
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Xiaoqiang Xue
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Yingjie Li
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Zhaoheng Jin
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Weifeng Xu
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Zhigang Ji
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
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11
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Petit J, Carroll G, Williams H, Pockney P, Scott RJ. Evaluation of a Multi-Gene Methylation Blood-Test for the Detection of Colorectal Cancer. Med Sci (Basel) 2023; 11:60. [PMID: 37755164 PMCID: PMC10534804 DOI: 10.3390/medsci11030060] [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: 08/10/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
Circulating tumour DNA biomarkers are an expanding field in oncology research that offer great potential but are currently often limited in value by overall cost. The aim of this study was to evaluate the efficacy of a novel multi-gene methylation blood test for the identification of colorectal cancer and throughout the spectrum of colorectal disease. Participants were recruited either prior to resection for known CRC or prior to screening colonoscopy after a positive faecal immunochemical test. Blood was collected from participants prior to their procedure being performed. The plasma was separated, and multiplex MethylLight droplet digital PCR was used to analyse for the presence of four methylated genes: SDC2, NPY, IKZF1 and SEPT9. A total of 537 participants underwent analysis. The SDC2/NPY genes showed a sensitivity of 33-54% and a specificity of 72-96%, whilst the IKZF1/SEPT9 genes showed a sensitivity of 19-42% and a specificity of 88-96%. Combining the two tests did not significantly increase the test accuracy. The sensitivity for advanced adenoma was 2-15%. There was a significant difference in the frequency of detectable methylation between the participants with CRC and those without CRC. However, neither the sensitivity nor the specificity was superior to current diagnostic screening tests.
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Affiliation(s)
- Joel Petit
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Georgia Carroll
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Henry Williams
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
| | - Peter Pockney
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Rodney J. Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
- Pathology North, Newcastle, NSW 2305, Australia
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12
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Xue Y, Huang C, Pei B, Wang Z, Dai Y. An overview of DNA methylation markers for early detection of gastric cancer: current status, challenges, and prospects. Front Genet 2023; 14:1234645. [PMID: 37560387 PMCID: PMC10407555 DOI: 10.3389/fgene.2023.1234645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023] Open
Abstract
Background: Gastric cancer (GC) is one of the most common malignancies, with a low 5-year survival rate. However, if diagnosed at an early stage, it can be cured by endoscopic treatment and has a good prognosis. While gastrointestinal X-ray and upper endoscopy are used as national GC screening methods in some GC high-risk countries, such as Japan and Korea, their radiation exposure, invasiveness, and high cost suggest that they are not the optimal tools for early detection of GC in many countries. Therefore, a cost-effective, and highly accurate method for GC early detection is urgently needed in clinical settings. DNA methylation plays a key role in cancer progression and metastasis and has been demonstrated as a promising marker for cancer early detection. Aims and methods: This review provides a comprehensive overview of the current status of DNA methylation markers associated with GC, the assays developed for GC early detection, challenges in methylation marker discovery and application, and the future prospects of utilizing methylation markers for early detection of GC. Through our analysis, we found that the currently reported DNA methylation markers related to GC are mainly in the early discovery stage. Most of them have only been evaluated in tissue samples. The majority of non-invasive assays developed based on blood lack standardized sampling protocols, pre-analytical procedures, and multicenter validation, and they exhibit insufficient sensitivity for early-stage GC detection. Meanwhile, the reported GC DNA methylation markers are generally considered pan-cancer markers. Conclusion: Therefore, future endeavors should focus on identifying additional methylation markers specific to GC and establishing non-invasive diagnostic assays that rely on these markers. These assays should undergo multicenter, large-scale prospective validation in diverse populations.
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Affiliation(s)
- Ying Xue
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Chao Huang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Bing Pei
- Department of Clinical Laboratory, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, Jiangsu, China
| | - ZhenZhen Wang
- Department of Laboratory Medicine, Affiliated Xuzhou Maternity and Child Healthcare Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yanmiao Dai
- Department of Spleen and Stomach Diseases, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
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13
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Li T, Patel KB, Yu X, Yao S, Wang L, Chung CH, Wang X. Unveiling targeted cell-free DNA methylation regions through paired methylome analysis of tumor and normal tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546654. [PMID: 37425680 PMCID: PMC10327111 DOI: 10.1101/2023.06.27.546654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Liquid biopsy analysis of cell-free DNA (cfDNA) has revolutionized cancer research by enabling non-invasive assessment of tumor-derived genetic and epigenetic changes. In this study, we conducted a comprehensive paired-sample differential methylation analysis (psDMR) on reprocessed methylation data from two large datasets, CPTAC and TCGA, to identify and validate differentially methylated regions (DMRs) as potential cfDNA biomarkers for head and neck squamous cell carcinoma (HNSC). Our hypothesis is that the paired sample test provides a more suitable and powerful approach for the analysis of heterogeneous cancers like HNSC. The psDMR analysis revealed a significant number of overlapped hypermethylated DMRs between two datasets, indicating the reliability and relevance of these regions for cfDNA methylation biomarker discovery. We identified several candidate genes, including CALCA, ALX4, and HOXD9, which have been previously established as liquid biopsy methylation biomarkers in various cancer types. Furthermore, we demonstrated the efficacy of targeted region analysis using cfDNA methylation data from oral cavity squamous cell carcinoma and nasopharyngeal carcinoma patients, further validating the utility of psDMR analysis in prioritizing cfDNA methylation biomarkers. Overall, our study contributes to the development of cfDNA-based approaches for early cancer detection and monitoring, expanding our understanding of the epigenetic landscape of HNSC, and providing valuable insights for liquid biopsy biomarker discovery not only in HNSC and other cancer types.
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Affiliation(s)
- Tingyi Li
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, 33612, USA
| | - Krupal B Patel
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, 33612, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, 33612, USA
| | - Sijie Yao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, 33612, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, 33612, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, 33612, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, 33612, USA
- Moffitt Cancer Center Immuno-Oncology Program, Tampa, Florida, 33612, USA
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14
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Hu S, Tao J, Peng M, Ye Z, Chen Z, Chen H, Yu H, Wang B, Fan JB, Ni B. Accurate detection of early-stage lung cancer using a panel of circulating cell-free DNA methylation biomarkers. Biomark Res 2023; 11:45. [PMID: 37101220 PMCID: PMC10134678 DOI: 10.1186/s40364-023-00486-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Lung cancer remains the leading cause of cancer mortality worldwide. Early detection of lung cancer helps improve treatment and survival. Numerous aberrant DNA methylations have been reported in early-stage lung cancer. Here, we sought to identify novel DNA methylation biomarkers that could potentially be used for noninvasive early diagnosis of lung cancers. METHODS This prospective-specimen collection and retrospective-blinded-evaluation trial enrolled a total of 317 participants (198 tissues and 119 plasmas) comprising healthy controls, patients with lung cancer and benign disease between January 2020 and December 2021. Tissue and plasma samples were subjected to targeted bisulfite sequencing with a lung cancer specific panel targeting 9,307 differential methylation regions (DMRs). DMRs associated with lung cancer were identified by comparing the methylation profiles of tissue samples from patients with lung cancer and benign disease. Markers were selected with minimum redundancy and maximum relevance algorithm. A prediction model for lung cancer diagnosis was built through logistic regression algorithm and validated independently in tissue samples. Furthermore, the performance of this developed model was evaluated in a set of plasma cell-free DNA (cfDNA) samples. RESULTS We identified 7 DMRs corresponding to 7 differentially methylated genes (DMGs) including HOXB4, HOXA7, HOXD8, ITGA4, ZNF808, PTGER4, and B3GNTL1 that were highly associated with lung cancer by comparing the methylation profiles of lung cancer and benign nodule tissue. Based on the 7-DMR biomarker panel, we developed a new diagnostic model in tissue samples, termed "7-DMR model", to distinguish lung cancers from benign diseases, achieving AUCs of 0.97 (95%CI: 0.93-1.00)/0.96 (0.92-1.00), sensitivities of 0.89 (0.82-0.95)/0.92 (0.86-0.98), specificities of 0.94 (0.89-0.99)/1.00 (1.00-1.00), and accuracies of 0.90 (0.84-0.96)/0.94 (0.89-0.99) in the discovery cohort (n = 96) and the independent validation cohort (n = 81), respectively. Furthermore, the 7-DMR model was applied to noninvasive discrimination of lung cancers and non-lung cancers including benign lung diseases and healthy controls in an independent validation cohort of plasma samples (n = 106), yielding an AUC of 0.94 (0.86-1.00), sensitivity of 0.81 (0.73-0.88), specificity of 0.98 (0.95-1.00), and accuracy of 0.93 (0.89-0.98). CONCLUSION The 7 novel DMRs could be promising methylation biomarkers that merits further development as a noninvasive test for early detection of lung cancer.
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Affiliation(s)
- Shuo Hu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | | | | | - Zhujia Ye
- Anchordx Medical Co., Ltd, Guangzhou, China
| | - Zhiwei Chen
- Anchordx Medical Co., Ltd, Guangzhou, China
- AnchorDx Inc, Fremont, CA, USA
| | | | - Haifeng Yu
- The Fifth People's Hospital of Wuxi, Wuxi, China
| | - Bo Wang
- Anchordx Medical Co., Ltd, Guangzhou, China.
| | - Jian-Bing Fan
- Anchordx Medical Co., Ltd, Guangzhou, China.
- Department of Pathology, Southern Medical University, Guangzhou, China.
| | - Bin Ni
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
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15
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Wang Y, Douville C, Cohen JD, Mattox A, Curtis S, Silliman N, Popoli M, Ptak J, Dobbyn L, Nehme N, Dudley JC, Summers M, Zhang M, Ho-Pham LT, Tran BNH, Tran TS, Nguyen TV, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B. Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules. Proc Natl Acad Sci U S A 2023; 120:e2220704120. [PMID: 37014860 PMCID: PMC10104560 DOI: 10.1073/pnas.2220704120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/28/2023] [Indexed: 04/05/2023] Open
Abstract
The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.
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Affiliation(s)
- Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Joshua D. Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD21218
| | - Austin Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sam Curtis
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Pharmacology and Molecular Science, Johns Hopkins School of Medicine, Baltimore, MD21287
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Nadine Nehme
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Jonathan C. Dudley
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Mahmoud Summers
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ming Zhang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Lan T. Ho-Pham
- BioMedical Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City72510, Vietnam
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
| | - Bich N. H. Tran
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
| | - Thach S. Tran
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
- School of Biomedical Engineering, University of Technology, NSW2007, Australia
| | - Tuan V. Nguyen
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
- Centre for Health Technologies, University of Technology, NSW2007, Australia
- School of Population Health, University of New South Wales, NSW2003, Australia
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD21298
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
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16
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Analyses of P16 INK4a gene promoter methylation relative to molecular, demographic and clinical parameters characteristics in non-small cell lung cancer patients: A pilot study. Mol Biol Rep 2023; 50:971-979. [PMID: 36378420 DOI: 10.1007/s11033-022-07982-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND The aim of this study was to examine the methylation status of p16INK4a promoter region in non small cell lung cancer (NSCLC) patients and their associations with single nucleotide polymorphisms (SNPs) of the epidermal growth factor receptor (EGFR) gene, as well as with demographic or clinical characteristics. METHODS Formalin-fixed and paraffin-embedded (FFPE) DNA samples extracted from 22 NSCLC patients were analyzed with methylation-specific polymerase chain reaction (PCR) method to obtain promoter methylation profile. The same cohort was genotyped for - 216G > T, -191 C > A, and 181,946 C > T EGFR SNPs. RESULTS There was a significant association between methylated p16INK4a in patients prior therapy (p = 0.017) since a significantly higher frequency of methylated p16INK4a was detected in these patients (40.9%) in comparison to frequency in patients after therapy (31.8%). Also, a higher frequency of methylated p16INK4a was detected among patients with leucopenia (p = 0.056). No associations were observed between the methylation status of the p16INK4a promoter region and EGFR SNPs or other clinical and demographic data in this cohort. CONCLUSION High frequency of methylation of the p16INK4a gene promoter was observed in NSCLC patients prior therapy and with leucopenia that can indicate their significance related to advanced clinical stage.
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17
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Zheng C, Wang H, Liu Q, Han D, Xin Y, Lu W, Yan Z. Application effect of low-dose spiral CT on pulmonary nodules and its diagnostic value for benign and malignant nodules. Am J Transl Res 2023; 15:256-263. [PMID: 36777849 PMCID: PMC9908493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/05/2022] [Indexed: 02/14/2023]
Abstract
OBJECTIVE This study was designed to determine the application effect of low-dose computed tomography (LDCT) on detecting pulmonary nodules (PNs) and its diagnostic value for benign and malignant pulmonary nodules. METHODS Data of 432 patients with PNs admitted to Julu County Hospital between March 2018 and June 2021 in were collected and analysed retrospectively. All patients underwent LDCT and conventional-dose spiral computed tomography (CT). The detection rate and image characteristics of the two methods were compared, and the image quality and radiation dose of the two diagnostic methods were also compared. RESULTS No significant difference was found between LDCT and conventional-dose spiral CT in the detection rate of lung cancer (P>0.05). The area under the curve of conventional-dose CT was 0.932, with a specificity and sensitivity of 93.87% and 92.45%, and the area under the curve of LDCT was 0.902, with a specificity and sensitivity of 90.80% and 89.62%. The radiation dose consumed during LDCT was greatly less than that consumed by conventional-dose CT (P<0.05). Additionally, the two methods were not different in CT image quality and superior vena cava artifact (P>0.05). No notable difference was found between LDCT and conventional-dose CT in terms of the diagnosis rate of PNs in vascular aggregation sign, pleural indentation sign, lobulation sign and spiculation sign. CONCLUSION LDCT can clearly show the typical images of early lung cancer, with less effective radiation dose, and can thus contribute to a high detection rate, so it is worth popularizing.
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18
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Blood-based DNA methylation signatures in cancer: A systematic review. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166583. [PMID: 36270476 DOI: 10.1016/j.bbadis.2022.166583] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
DNA methylation profiles are in dynamic equilibrium via the initiation of methylation, maintenance of methylation and demethylation, which control gene expression and chromosome stability. Changes in DNA methylation patterns play important roles in carcinogenesis and primarily manifests as hypomethylation of the entire genome and the hypermethylation of individual loci. These changes may be reflected in blood-based DNA, which provides a non-invasive means for cancer monitoring. Previous blood-based DNA detection objects primarily included circulating tumor DNA/cell-free DNA (ctDNA/cfDNA), circulating tumor cells (CTCs) and exosomes. Researchers gradually found that methylation changes in peripheral blood mononuclear cells (PBMCs) also reflected the presence of tumors. Blood-based DNA methylation is widely used in early diagnosis, prognosis prediction, dynamic monitoring after treatment and other fields of clinical research on cancer. The reversible methylation of genes also makes them important therapeutic targets. The present paper summarizes the changes in DNA methylation in cancer based on existing research and focuses on the characteristics of the detection objects of blood-based DNA, including ctDNA/cfDNA, CTCs, exosomes and PBMCs, and their application in clinical research.
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19
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Ibrahim J, Peeters M, Van Camp G, Op de Beeck K. Methylation biomarkers for early cancer detection and diagnosis: Current and future perspectives. Eur J Cancer 2023; 178:91-113. [PMID: 36427394 DOI: 10.1016/j.ejca.2022.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 10/17/2022] [Indexed: 11/25/2022]
Abstract
The increase in recent scientific studies on cancer biomarkers has brought great new insights into the field. Moreover, novel technological breakthroughs such as long read sequencing and microarrays have enabled high throughput profiling of many biomarkers, while advances in bioinformatic tools have made the possibility of developing highly reliable and accurate biomarkers a reality. These changes triggered renewed interest in biomarker research and provided tremendous opportunities for enhancing cancer management and improving early disease detection. DNA methylation alterations are known to accompany and contribute to carcinogenesis, making them promising biomarkers for cancer, namely due to their stability, frequency and accessibility in bodily fluids. The advent of newer minimally invasive experimental methods such as liquid biopsies provide the perfect setting for methylation-based biomarker development and application. Despite their huge potential, accurate and robust biomarkers for the conclusive diagnosis of most cancer types are still not routinely used, hence a strong need for sustained research in this field is still needed. This review provides a brief exposition of current methylation biomarkers for cancer diagnosis and early detection, including markers already in clinical use as well as various upcoming ones. It also outlines how recent big data and novel technologies will revolutionise the next generation of cancer tests in supplementing or replacing currently existing invasive techniques.
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Affiliation(s)
- Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium; Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium.
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20
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Li P, Liu S, Du L, Mohseni G, Zhang Y, Wang C. Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer. Clin Epigenetics 2022; 14:118. [PMID: 36153611 PMCID: PMC9509651 DOI: 10.1186/s13148-022-01337-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/16/2022] [Indexed: 11/27/2022] Open
Abstract
Lung cancer (LC) is the main cause of cancer-related mortality. Most LC patients are diagnosed in an advanced stage when the symptoms are obvious, and the prognosis is quite poor. Although low-dose computed tomography (LDCT) is a routine clinical examination for early detection of LC, the false-positive rate is over 90%. As one of the intensely studied epigenetic modifications, DNA methylation plays a key role in various diseases, including cancer and other diseases. Hypermethylation in tumor suppressor genes or hypomethylation in oncogenes is an important event in tumorigenesis. Remarkably, DNA methylation usually occurs in the very early stage of malignant tumors. Thus, DNA methylation analysis may provide some useful information about the early detection of LC. In recent years, liquid biopsy has developed rapidly. Liquid biopsy can detect and monitor both primary and metastatic malignant tumors and can reflect tumor heterogeneity. Moreover, it is a minimally invasive procedure, and it causes less pain for patients. This review summarized various liquid biopsies based on DNA methylation for LC. At first, we briefly discussed some emerging technologies for DNA methylation analysis. Subsequently, we outlined cell-free DNA (cfDNA), sputum, bronchoalveolar lavage fluid, bronchial aspirates, and bronchial washings DNA methylation-based liquid biopsy for the early detection of LC. Finally, the prognostic value of DNA methylation in cfDNA and sputum and the diagnostic value of other DNA methylation-based liquid biopsies for LC were also analyzed.
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Comprehensive Analysis of DNA Methylation and Transcriptome to Identify PD-1-Negative Prognostic Methylated Signature in Endometrial Carcinoma. DISEASE MARKERS 2022; 2022:3085289. [PMID: 35634444 PMCID: PMC9133896 DOI: 10.1155/2022/3085289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 11/23/2022]
Abstract
Background Epigenetic mechanism plays an important role in endometrial carcinoma (EC). This study was designed to analyze the epigenetic mechanism between DNA methylation-driven genes (DEDGs) and drugs targeting DEDGs and to develop a DEDG score model for predicting the prognosis of EC. Methods Expression profile and methylation profile data of PD-1-negative EC samples were obtained from TCGA. To obtain intersected DEDGs, differentially expressed genes (DEGs) and differentially methylated genes from tumor tissues and normal tissues were analyzed by limma. A linear discriminant classification model was constructed using the gene expression profile of DMDGs, methylation profile of TSS1500, TSS200, and gene body regions. Principal component analysis (PCA) and ROC analysis were conducted. The protein-drug interactions analysis of DMDGs was performed using Network Analyst 3.0 tool. Lasso Cox regression analysis was used to screen prognostic DNA methylation driving gene and to build a risk score model. The ROC curve and Kaplan-Meier survival curve were plotted to evaluate the model prediction capability. Results A total of 96 DMDGs were screened from the three regions, distributed on 22 chromosomes, with consistent methylation patterns in different gene regions. Both the expression profile and methylation profile of the three regions can neatly distinguish tumor samples from normal ones, with a high classifying performance. A gene signature, which consisted of ELFN1-AS1 and ZNF132, could classify EC patients into a high-risk group and low-risk group. Prognosis of the high-risk group was significantly worse than that of the low-risk group. The risk model showed a high performance in predicting the prognosis of EC. Conclusion We successfully established a risk score system with two DMDGs, which showed a high prediction accuracy of EC prognosis.
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Vo TTL, Nguyen TN, Nguyen TT, Pham ATD, Vuong DL, Ta VT, Ho VS. SHOX2 methylation in Vietnamese patients with lung cancer. Mol Biol Rep 2022; 49:3413-3421. [PMID: 35088378 DOI: 10.1007/s11033-022-07172-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND DNA methylation on cytosine in the CpG dinucleotides is one of the most common epigenetic perturbations taking place during cancer initiation, progression, occurrence and resistance therapy. DNA methylation seems to be sufficiently stable epigenetic modification to be utilized as a cancer biomarker in in vitro diagnostic (IVD) settings. Nowadays, the SHOX2 methylation (mSHOX2) is one of the most valuable DNA methylation biomarkers of lung cancer that is the leading cause of cancer death. It is being continuously validated across ethnicities, lifestyles and lifespan. This study focused on characteristics of mSHOX2 in Vietnamese patients with lung cancer since a lack of investigation and evidence of its utility in this country. METHODS The probe and primer sets were designed according to the MethyLight method for quantitative assessment of the mSHOX2 in 214 formalin-fixed paraffin-embedded (FFPE) lung tissues and 57 plasma samples. RESULTS mSHOX2 in FFPE tissues allowed discriminating benign and malignant lung diseases with 60% (95% CI 50.7-68.8%) sensitivity and 90.4% (95% CI 82.6-95.5%) specificity. Importantly, based on mSHOX2 in plasma, lung cancer could be detected with 83.3% (95% CI 65.3-94.4%) sensitivity and 92.6% (95% CI 75.7-99.1%) specificity, respectively. There were insignificant associations between mSHOX2 with age, cancer stage, EGFR mutation and serum CEA, CYFRA21-1 concentrations except for that gender. CONCLUSION Our study indicated that mSHOX2 was satisfactory for distinguishing malignant from benign lung tissue and noninvasively detecting lung cancer.
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Affiliation(s)
- Thi Thuong Lan Vo
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam.
| | - Thuy Ngan Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Thu Trang Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Anh Thuy Duong Pham
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Dieu Linh Vuong
- Pathology and Molecular Biology Center, Vietnam National Cancer Hospital, Hanoi, Vietnam
| | - Van To Ta
- Pathology and Molecular Biology Center, Vietnam National Cancer Hospital, Hanoi, Vietnam
| | - Van Son Ho
- Department of Chemistry, 175 Hospital, Ho Chi Minh City, Vietnam
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Cai Y, He Q, Liu W, Liang Q, Peng B, Li J, Zhang W, Kang F, Hong Q, Yan Y, Peng J, Xu Z, Bai N. Comprehensive analysis of the potential cuproptosis-related biomarker LIAS that regulates prognosis and immunotherapy of pan-cancers. Front Oncol 2022; 12:952129. [PMID: 35982953 PMCID: PMC9379260 DOI: 10.3389/fonc.2022.952129] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/11/2022] [Indexed: 12/14/2022] Open
Abstract
Lipoic acid synthetase (LIAS) has been demonstrated to play a crucial role in the progression of cancer. Exploring the underlying mechanisms and biological functions of LIAS could have potential therapeutic guidance for cancer treatment. Our study has explored the expression levels and prognostic values of LIAS in pan-cancer through several bioinformatics platforms, including TIMER2.0, Gene Expression Profiling Interactive Analysis, version 2 (GEPIA2.0), and Human Protein Atlas (HPA). We found that a high LIAS expression was related to the good prognosis in patients with kidney renal clear cell carcinoma (KIRC), rectum adenocarcinoma (READ), breast cancer, and ovarian cancer. Inversely, a high LIAS expression showed unfavorable prognosis in lung cancer patients. In addition, the genetic alteration, methylation levels, and immune analysis of LIAS in pan-cancer have been evaluated. To elucidate the underlying molecular mechanism of LIAS, we conduct the single-cell sequencing to implicate that LIAS expression was related to hypoxia, angiogenesis, and DNA repair. Thus, these comprehensive pan-cancer analyses have conveyed that LIAS could be potentially significant in the progression of various cancers. Moreover, the LIAS expression could predict the efficacy of immunotherapy in cancer patients.
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Affiliation(s)
- Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Qingchun He
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, China
- Department of Emergency, Xiangya Changde Hospital, Changde, China
| | - Wei Liu
- Department of Orthopedic Surgery, The Second Hospital University of South China, Hengyang, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Jianbo Li
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Wenqin Zhang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Fanhua Kang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Qianhui Hong
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Jinwu Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Xiangya Changde Hospital, Changde, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Ning Bai, ; Jinwu Peng,
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Xiangya Changde Hospital, Changde, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ning Bai
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Ning Bai, ; Jinwu Peng,
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Zhou X, Lu X, Wu H, Liu J, Huang H. Diagnostic performance of SHOX2 promoter methylation as biomarker for lung cancer identification: A meta-analysis update. Thorac Cancer 2021; 12:3327-3332. [PMID: 34741433 PMCID: PMC8671898 DOI: 10.1111/1759-7714.14206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 12/16/2022] Open
Abstract
Objective To evaluate the diagnostic performance of short state homeobox 2 (SHOX2) promoter methylation as biomarker for lung cancer identification through aggregating the open published data. Methods We did an electronic search in Pubmed, EMBASE, Ovid, Web of Science, Google Scholar, and the China National Knowledge Infrastructure (CNKI) to identify the publications related to SHOX2 promoter methylation and lung cancer. The diagnostic performance of sensitivity (SEN), specificity (SPE), odds ratio (DOR), and summary receiver operating characteristic (SROC) cure were aggregated by fixed or random effect model. Fagan's nomogram was used to investigate the post‐test diagnostic probability. Deek's funnel plot and line regression test was applied to evaluate the publication bias. Results In total, 18 clinical studies about SHOX2 promoter methylation and lung cancer were included in the meta‐analysis. The combined diagnostic SEN, SPE, DOR were 0.63 (95% CI = 0.54–0.70), 0.91 (95% CI = 0.87–0.94), and 16.84 (95% CI = 11.18–25.36) in random effect model respectively. The pooled area under the curve (AUC) of SROC was 0.88 (95% CI = 0.84–0.90). The post‐test probability of lung cancer was 88% and 29% when SHOX2 methylated and unmethylated in humoral components given a pre‐test probability of 50%. Deek's funnel plot and regression test indicated no publication bias (p = 0.62). Conclusion SHOX2 promoter methylation in humoral components may be a potential biomarker for lung cancer diagnosis with relative high diagnostic specificity.
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Affiliation(s)
- Xiaoxi Zhou
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
| | - Xiaoling Lu
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
| | - Haiyan Wu
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
| | - Juan Liu
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
| | - He Huang
- Department of Respiratory, Zhejiang Hospital, Hangzhou, China
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