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Peng S, Zhang X, Wu Y. Potential applications of DNA methylation testing technology in female tumors and screening methods. Biochim Biophys Acta Rev Cancer 2023; 1878:188941. [PMID: 37329994 DOI: 10.1016/j.bbcan.2023.188941] [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: 04/21/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
DNA methylation is a common epigenetic modification, and the current commonly used methods for DNA methylation detection include methylation-specific PCR, methylation-sensitive restriction endonuclease-PCR, and methylation-specific sequencing. DNA methylation plays an important role in genomic and epigenomic studies, and combining DNA methylation with other epigenetic modifications, such as histone modifications, may lead to better DNA methylation. DNA methylation also plays an important role in the development of disease, and analyzing changes in individual DNA methylation patterns can provide individualized diagnostic and therapeutic solutions. Liquid biopsy techniques are also increasingly well established in clinical practice and may provide new methods for early cancer screening. It is important to find new screening methods that are easy to perform, minimally invasive, patient-friendly, and affordable. DNA methylation mechanisms are thought to have an important role in cancer and have potential applications in the diagnosis and treatment of female tumors. This review discussed early detection targets and screening methods for common female tumors such as breast, ovarian, and cervical cancers and discussed advances in the study of DNA methylation in these tumors. Although existing screening, diagnostic, and treatment modalities exist, the high morbidity and mortality rates of these tumors remain challenging.
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Affiliation(s)
- Shixuan Peng
- Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China
| | - Xinwen Zhang
- Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China
| | - Yongjun Wu
- Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China.
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2
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Nam AR, Heo M, Lee KH, Kim JY, Won SH, Cho JY. The landscape of PBMC methylome in canine mammary tumors reveals the epigenetic regulation of immune marker genes and its potential application in predicting tumor malignancy. BMC Genomics 2023; 24:403. [PMID: 37460953 DOI: 10.1186/s12864-023-09471-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Genome-wide dysregulation of CpG methylation accompanies tumor progression and characteristic states of cancer cells, prompting a rationale for biomarker development. Understanding how the archetypic epigenetic modification determines systemic contributions of immune cell types is the key to further clinical benefits. RESULTS In this study, we characterized the differential DNA methylome landscapes of peripheral blood mononuclear cells (PBMCs) from 76 canines using methylated CpG-binding domain sequencing (MBD-seq). Through gene set enrichment analysis, we discovered that genes involved in the growth and differentiation of T- and B-cells are highly methylated in tumor PBMCs. We also revealed the increased methylation at single CpG resolution and reversed expression in representative marker genes regulating immune cell proliferation (BACH2, SH2D1A, TXK, UHRF1). Furthermore, we utilized the PBMC methylome to effectively differentiate between benign and malignant tumors and the presence of mammary gland tumors through a machine-learning approach. CONCLUSIONS This research contributes to a better knowledge of the comprehensive epigenetic regulation of circulating immune cells responding to tumors and suggests a new framework for identifying benign and malignant cancers using genome-wide methylome.
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Affiliation(s)
- A-Reum Nam
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Heo
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ji-Yoon Kim
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung-Ho Won
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea.
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea.
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
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3
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Manoochehri M, Borhani N, Gerhäuser C, Assenov Y, Schönung M, Hielscher T, Christensen BC, Lee MK, Gröne HJ, Lipka DB, Brüning T, Brauch H, Ko YD, Hamann U. DNA methylation biomarkers for noninvasive detection of triple-negative breast cancer using liquid biopsy. Int J Cancer 2023; 152:1025-1035. [PMID: 36305646 DOI: 10.1002/ijc.34337] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/06/2022] [Accepted: 09/20/2022] [Indexed: 01/06/2023]
Abstract
Noninvasive detection of aberrant DNA methylation could provide invaluable biomarkers for earlier detection of triple-negative breast cancer (TNBC) which could help clinicians with easier and more efficient treatment options. We evaluated genome-wide DNA methylation data derived from TNBC and normal breast tissues, peripheral blood of TNBC cases and controls and reference samples of sorted blood and mammary cells. Differentially methylated regions (DMRs) between TNBC and normal breast tissues were stringently selected, verified and externally validated. A machine-learning algorithm was applied to select the top DMRs, which then were evaluated on plasma-derived circulating cell-free DNA (cfDNA) samples of TNBC patients and healthy controls. We identified 23 DMRs accounting for the methylation profile of blood cells and reference mammary cells and then selected six top DMRs for cfDNA analysis. We quantified un-/methylated copies of these DMRs by droplet digital PCR analysis in a plasma test set from TNBC patients and healthy controls and confirmed our findings obtained on tissues. Differential cfDNA methylation was confirmed in an independent validation set of plasma samples. A methylation score combining signatures of the top three DMRs overlapping with the SPAG6, LINC10606 and TBCD/ZNF750 genes had the best capability to discriminate TNBC patients from controls (AUC = 0.78 in the test set and AUC = 0.74 in validation set). Our findings demonstrate the usefulness of cfDNA-based methylation signatures as noninvasive liquid biopsy markers for the diagnosis of TNBC.
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Affiliation(s)
- Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Nasim Borhani
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clarissa Gerhäuser
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yassen Assenov
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maximilian Schönung
- Section Translational Cancer Epigenomics, Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Hielscher
- Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire, USA
| | | | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Thomas Brüning
- Institute for Prevention & Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,iFIT Cluster of Excellence, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Tübingen, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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Shoukat I, Mueller CR. Searching for DNA methylation in patients triple-negative breast cancer: a liquid biopsy approach. Expert Rev Mol Diagn 2023; 23:41-51. [PMID: 36715539 DOI: 10.1080/14737159.2023.2173579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Liquid biopsies are proving to have diagnostic and prognostic value in many different cancers, and in breast cancer they have the potential to improve outcomes by providing valuable information throughout a patient's cancer journey. However, patients with triple negative breast cancer (TNBC) have received little benefit from such liquid biopsies due to underlying limitations in the discovery and utility of robust biomarkers. Here, we examine the development of DNA methylation-based liquid biopsy assays for breast cancer and how they pertain to TNBC. AREAS COVERED We conducted a systematic review of liquid biopsy assays for breast cancer and analyzed their relevance in TNBC. We show that the utility of DNA mutation-based assays is poor for TNBC due to the low mutational frequencies across the genome in this subtype. We offer a detailed review of mDETECT - a liquid biopsy specifically designed for assessing tumor burden in TNBC patients. EXPERT OPINION DNA methylation are foundational and robust events that occur in cancer evolution and may differentiate almost all forms of cancer, including TNBC. Longitudinal patient monitoring using DNA methylation-based liquid biopsies offers great potential for improving the detection and management of TNBC.
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Affiliation(s)
- Irsa Shoukat
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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Herrgott GA, Asmaro KP, Wells M, Sabedot TS, Malta TM, Mosella MS, Nelson K, Scarpace L, Barnholtz-Sloan JS, Sloan AE, Selman WR, deCarvalho AC, Poisson LM, Mukherjee A, Robin AM, Lee IY, Snyder J, Walbert T, Rosenblum M, Mikkelsen T, Bhan A, Craig J, Kalkanis S, Rock J, Noushmehr H, Castro AV. Detection of Tumor-specific DNA Methylation Markers in the Blood of Patients with Pituitary Neuroendocrine Tumors. Neuro Oncol 2022; 24:1126-1139. [PMID: 35212383 PMCID: PMC9248407 DOI: 10.1093/neuonc/noac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background DNA methylation abnormalities are pervasive in pituitary neuroendocrine tumors (PitNETs). The feasibility to detect methylome alterations in circulating cell-free DNA (cfDNA) has been reported for several central nervous system (CNS) tumors but not across PitNETs. The aim of the study was to use the liquid biopsy (LB) approach to detect PitNET-specific methylation signatures to differentiate these tumors from other sellar diseases. Methods We profiled the cfDNA methylome (EPIC array) of 59 serum and 41 plasma LB specimens from patients with PitNETs and other CNS diseases (sellar tumors and other pituitary non-neoplastic diseases, lower-grade gliomas, and skull-base meningiomas) or nontumor conditions, grouped as non-PitNET. Results Our results indicated that despite quantitative and qualitative differences between serum and plasma cfDNA composition, both sources of LB showed that patients with PitNETs presented a distinct methylome landscape compared to non-PitNETs. In addition, LB methylomes captured epigenetic features reported in PitNET tissue and provided information about cell-type composition. Using LB-derived PitNETs-specific signatures as input to develop machine-learning predictive models, we generated scores that distinguished PitNETs from non-PitNETs conditions, including sellar tumor and non-neoplastic pituitary diseases, with accuracies above ~93% in independent cohort sets. Conclusions Our results underpin the potential application of methylation-based LB profiling as a noninvasive approach to identify clinically relevant epigenetic markers to diagnose and potentially impact the prognostication and management of patients with PitNETs.
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Affiliation(s)
- Grayson A Herrgott
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
| | - Karam P Asmaro
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
| | - Michael Wells
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
| | - Thais S Sabedot
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
| | - Tathiane M Malta
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
| | - Maritza S Mosella
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
| | - Kevin Nelson
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Lisa Scarpace
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Jill S Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 2103 Cornell Rd, Cleveland, Ohio 44106 USA
| | - Andrew E Sloan
- Department of Neurological Surgery, University Hospitals of Cleveland, 11100 Euclid Ave., Cleveland, OH 44106 USA (EAS).,Case Comprehensive Cancer Center, 10900 Euclid Ave., Cleveland, OH 44106 USA (EAS)
| | - Warren R Selman
- Department of Neurological Surgery, University Hospitals of Cleveland, 11100 Euclid Ave., Cleveland, OH 44106 USA (EAS)
| | - Ana C deCarvalho
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Laila M Poisson
- Department of Biostatistics, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI, 48202 USA
| | - Abir Mukherjee
- Department of Pathology, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI, 48202 USA
| | - Adam M Robin
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Ian Y Lee
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - James Snyder
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
| | - Tobias Walbert
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Mark Rosenblum
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Tom Mikkelsen
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Arti Bhan
- Department of Endocrinology, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI, 48202 USA
| | - John Craig
- Department of Otolaryngology, Co-director of the Skull Base, Pituitary and Endoscopy Center
| | - Steven Kalkanis
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Jack Rock
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
| | - Ana Valeria Castro
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, 2799 West Grand Boulevard, Detroit, MI 48202 USA.,Department of Neurosurgery, Omics Laboratory, 2799 West Grand Boulevard, Henry Ford Health System, Detroit, MI 48202 USA
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Cucchiara F, Scarpitta R, Crucitta S, Scatena C, Arici R, Naccarato AG, Fogli S, Danesi R, Del Re M. Diagnosis and treatment monitoring in breast cancer: how liquid biopsy can support patient management. Pharmacogenomics 2022; 23:119-134. [PMID: 35006002 DOI: 10.2217/pgs-2021-0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Imaging and tissue biopsies represent the current gold standard for breast cancer diagnosis and patient management. However, these practices are time-consuming, expensive and require invasive procedures. Moreover, tissue biopsies do not capture spatial and temporal tumor heterogeneity. Conversely, liquid biopsy, which includes circulating tumor cells, circulating free nucleic acids and extracellular vesicles, is minimally invasive, easy to perform and can be repeated during a patient's follow-up. Increasing evidence also suggests that liquid biopsy can be used to efficiently screen and diagnose tumors at an early stage, and to monitor changes in the tumor molecular profile. In the present review, clinical applications and prospects are discussed.
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Affiliation(s)
- Federico Cucchiara
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Rosa Scarpitta
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Cristian Scatena
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Roberta Arici
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Antonio Giuseppe Naccarato
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Stefano Fogli
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
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Liu T, Guo L, Liu G, Hu X, Li X, Zhang J, Dai Z, Yu P, Jiang M, Wang J, Zhang J. Molecular Characterization of the Clinical and Tumor Immune Microenvironment Signature of 5-methylcytosine-Related Regulators in non-small Cell Lung Cancer. Front Cell Dev Biol 2021; 9:779367. [PMID: 34858994 PMCID: PMC8632062 DOI: 10.3389/fcell.2021.779367] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Background: DNA methylation is an important epigenetic modification, among which 5-methylcytosine methylation (5mC) is generally associated with tumorigenesis. Nonetheless, the potential roles of 5mC regulators in the tumor microenvironment (TME) remain unclear. Methods: The 5mC modification patterns of 1,374 lung adenocarcinoma samples were analyzed systematically. The correlation between the 5mC modification and tumor microenvironment cell infiltration was further assessed. The 5mCscore was developed to evaluate tumor mutation burden, immune check-point inhibitor response, and the clinical prognosis of individual tumors. Results: Three 5mC modification patterns were established based on the clinical characteristics of 21 5mC regulators. According to the differential expression of 5mC regulators, three distinct 5mC gene cluster were also identified, which showed distinct TME immune cell infiltration patterns and clinical prognoses. The 5mCscore was constructed to evaluate the tumor mutation burden, immune check-point inhibitor response, and prognosis characteristics. We found that patients with a low 5mCscore had significant immune cell infiltration and increased clinical benefit. Conclusion: This study indicated that the 5mC modification is involved in regulating TME infiltration remodeling. Targeting 5mC modification regulators might be a novel strategy to treat lung cancer.
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Affiliation(s)
- Taisheng Liu
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Liyi Guo
- The Sixth People's Hospital of Huizhou City, Huiyang Hospital Affiliated to Southern Medical University, Huizhou, China
| | - Guihong Liu
- Department of Radiation Oncology, DongGuan Tungwah Hospital, Dongguan, China
| | - Xiaoshan Hu
- Department of Internal Medicine of Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiaoning Li
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jinye Zhang
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Zili Dai
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
| | - Peng Yu
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
| | - Ming Jiang
- Department of Breast Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Wang
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
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