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Moulton C, Murri A, Benotti G, Fantini C, Duranti G, Ceci R, Grazioli E, Cerulli C, Sgrò P, Rossi C, Magno S, Di Luigi L, Caporossi D, Parisi A, Dimauro I. The impact of physical activity on promoter-specific methylation of genes involved in the redox-status and disease progression: A longitudinal study on post-surgery female breast cancer patients undergoing medical treatment. Redox Biol 2024; 70:103033. [PMID: 38211440 PMCID: PMC10821067 DOI: 10.1016/j.redox.2024.103033] [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: 11/13/2023] [Revised: 12/30/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
Most anticancer treatments act on oxidative-stress pathways by producing reactive oxygen species (ROS) to kill cancer cells, commonly resulting in consequential drug-induced systemic cytotoxicity. Physical activity (PA) has arisen as an integrative cancer therapy, having positive health effects, including in redox-homeostasis. Here, we investigated the impact of an online supervised PA program on promoter-specific DNA methylation, and corresponding gene expression/activity, in 3 antioxidants- (SOD1, SOD2, and CAT) and 3 breast cancer (BC)-related genes (BRCA1, L3MBTL1 and RASSF1A) in a population-based sample of women diagnosed with primary BC, undergoing medical treatment. We further examined mechanisms involved in methylating and demethylating pathways, predicted biological pathways and interactions of exercise-modulated molecules, and the functional relevance of modulated antioxidant markers on parameters related to aerobic capacity/endurance, physical fatigue and quality of life (QoL). PA maintained levels of SOD activity in blood plasma, and at the cellular level significantly increased SOD2 mRNA (≈+77 %), contrary to their depletion due to medical treatment. This change was inversely correlated with DNA methylation in SOD2 promoter (≈-20 %). Similarly, we found a significant effect of PA only on L3MBTL1 promoter methylation (≈-25 %), which was inversely correlated with its mRNA (≈+43 %). Finally, PA increased TET1 mRNA levels (≈+15 %) and decreased expression of DNMT3B mRNA (≈-28 %). Our results suggest that PA-modulated DNA methylation affects several signalling pathways/biological activities involved in the cellular oxidative stress response, chromatin organization/regulation, antioxidant activity and DNA/protein binding. These changes may positively impact clinical outcomes and improve the response to cancer treatment in post-surgery BC patients.
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Affiliation(s)
- Chantalle Moulton
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Arianna Murri
- Unit of Physical Exercise and Sport Sciences, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Gianmarco Benotti
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Cristina Fantini
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Guglielmo Duranti
- Unit of Biochemistry and Molecular Biology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Roberta Ceci
- Unit of Biochemistry and Molecular Biology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Elisa Grazioli
- Unit of Physical Exercise and Sport Sciences, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Claudia Cerulli
- Unit of Biochemistry and Molecular Biology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Paolo Sgrò
- Unit of Endocrinology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Cristina Rossi
- Center for Integrative Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Italy
| | - Stefano Magno
- Center for Integrative Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Italy
| | - Luigi Di Luigi
- Unit of Endocrinology, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Daniela Caporossi
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Attilio Parisi
- Unit of Physical Exercise and Sport Sciences, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy
| | - Ivan Dimauro
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy.
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Wu Q, Yu Y, Chen M, Long J, Yang X. A label-free fluorescence sensing strategy based on GlaI-assisted EXPAR for rapid and accurate quantification of human methyltranferase activity. Talanta 2024; 269:125456. [PMID: 38061202 DOI: 10.1016/j.talanta.2023.125456] [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: 04/25/2023] [Revised: 09/23/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
DNA methylation plays an important role in epigenetic modification. DNA methyltransferase (DNMT) is essential in the DNA methylation process, and its abnormal expression is closely related to cancer. In this study, we propose a novel biosensor platform (DS-GlaI-EXPAR) that combines hemi-methylated double-stranded DNA (dsDNA) as the substrate for DNMT1 with GlaI-assisted isothermal exponential amplification reaction (EXPAR) for rapid, simple, and sensitive detection of DNMT1 activity. The hemi-methylated dsDNA is fully methylated by DNMT1, and GlaI recognizes and cleaves the fully methylated sequence, generating terminal fragments that trigger EXPAR for efficient signal amplification. Whereas hemi-methylated dsDNA without DNMT1 will keep intact and cannot initiate EXPAR. DNMT1 activity can therefore be sensitively quantified by the real-time fluorescence signal of the DS-GlaI-EXPAR platform. The high-efficiency amplification of EXPAR and the recognition of GlaI enable the platform to overcome the inherent cumbersome and time-consuming shortcomings of traditional methods while meeting specificity and sensitivity. This DS-GlaI-EXPAR platform offers an impressively low limit of detection of 0.86 pg/μL and the entire detection process can be completed in a short time of 2.5 h in a single tube. Furthermore, DNMT1 activity detected by this platform in MCF-7 cells was significantly higher than that of HEK293 cells, and the inhibition of Apt. #9 was verified. This DNMT1 activity detection platform is very convenient and effective for the discovery of inhibitors and early cancer diagnosis.
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Affiliation(s)
- Qiaomin Wu
- Clinical Laboratory, Dongyang People's Hospital, Dongyang, Zhejiang, 322100, China; Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Mengqi Chen
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Jinyan Long
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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Wu H, Hu Y, Jiang C, Chen C. Global scientific trends in research of epigenetic response to exercise: A bibliometric analysis. Heliyon 2024; 10:e25644. [PMID: 38370173 PMCID: PMC10869857 DOI: 10.1016/j.heliyon.2024.e25644] [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: 11/02/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
The purpose of this work is to comprehensively understand the adaptive response of multiple epigenetic modifications on gene expression changes driven by exercise. Here, we retrieved literatures from publications in the PubMed and Web of Science Core Collection databases up to and including October 15, 2023. After screening with the exclusion criteria, 1910 publications were selected in total, comprising 1399 articles and 511 reviews. Specifically, a total of 512, 224, and 772 publications is involved in DNA methylation, histone modification, and noncoding RNAs, respectively. The correlations between publication number, authors, institutions, countries, references, and the characteristics of hotspots were explored by CiteSpace. Here, the USA (621 publications) ranked the world's most-influential countries, the University of California System (68 publications) was the most productive, and Tiago Fernandes (14 publications) had the most-published publications. A comprehensive keyword analysis revealed that cardiovascular disease, cancer, skeletal muscle development, and metabolic syndrome, and are the research hotspots. The detailed impact of exercise was further discussed in different aspects of these three categories of epigenetic modifications. Detailed analysis of epigenetic modifications in response to exercise, including DNA methylation, histone modification, and changes in noncoding RNAs, will offer valuable information to help researchers understand hotspots and emerging trends.
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Affiliation(s)
- Huijuan Wu
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
| | - Yue Hu
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
| | - Cai Jiang
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
| | - Cong Chen
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
- National-Local Joint Engineering Research Center of Rehabilitation Medicine Technology, Fujian University of Traditional Chinese Medicine, 350122 Fuzhou, Fujian, China
- Fujian Key Laboratory of Cognitive Rehabilitation, Fujian University of Traditional Chinese Medicine, 350122, Fuzhou, Fujian, China
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Guan C, Chen H, Chen H, Li S, Chen Y, Chen J, Dong Y, Zheng Z, Wang K, Pan C. Treatment of lung cancer by acupuncture combined with medicine based on pathophysiological mechanism: A review. Medicine (Baltimore) 2024; 103:e37229. [PMID: 38335396 PMCID: PMC10860975 DOI: 10.1097/md.0000000000037229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Lung cancer is one of the most frequently diagnosed cancers in the world. There are an estimated 2.2 million new cases and 1.79 million deaths each year. Over the past 2 decades, our understanding of disease biology, the use of predictive biomarkers, and improvements in therapeutic approaches have made significant progress and transformed the outcomes of many patients. Treatment is determined by the subtype and stage of the cancer; however, the effect of personalized treatment remains unsatisfactory. The use of Chinese medicines has attracted increasing attention worldwide. Chinese medicine treatment of lung cancer has few side effects, which can effectively prolong the survival expectation of patients and improve their quality of life, and has attracted increasing attention. Based on the pathophysiological mechanism of lung cancer reported in modern medical research, this article explores the efficacy and safety of acupuncture combined with medicine in the treatment of lung cancer.
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Affiliation(s)
- Chenguang Guan
- Heilongjiang Academy of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Hong Chen
- Heilongjiang Academy of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Haipeng Chen
- Cancer Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuhua Li
- North Hospital of Qiqihar First Hospital, Qiqihar, Heilongjiang Province, China
| | - Yuhan Chen
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingyu Chen
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yushan Dong
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Zhitao Zheng
- Qiqihar First Hospital South Hospital, Qiqihar, Heilongjiang Province, China
| | - Kaiwen Wang
- Qiqihar First Hospital South Hospital, Qiqihar, Heilongjiang Province, China
| | - Chuqiao Pan
- Qiqihar First Hospital South Hospital, Qiqihar, Heilongjiang Province, China
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Torresan S, de Scordilli M, Bortolot M, Di Nardo P, Foltran L, Fumagalli A, Guardascione M, Ongaro E, Puglisi F. Liquid biopsy in colorectal cancer: Onward and upward. Crit Rev Oncol Hematol 2024; 194:104242. [PMID: 38128627 DOI: 10.1016/j.critrevonc.2023.104242] [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: 10/05/2023] [Revised: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Colorectal cancer (CRC) remains a leading cause of cancer-related deaths worldwide. In recent years, liquid biopsy has emerged as one of the most interesting areas of research in oncology, leading to innovative trials and practical changes in all aspects of CRC management. RNAs and cell free DNA (cfDNA) methylation are emerging as promising biomarkers for early diagnosis. Post-surgical circulating tumour DNA (ctDNA) can aid in evaluating minimal residual disease and personalising adjuvant treatment. In rectal cancer, ctDNA could improve response assessment to neoadjuvant therapy and risk stratification, especially in the era of organ-preservation trials. In the advanced setting, ctDNA analysis offers the opportunity to monitor treatment response and identify driver and resistance mutations more comprehensively than traditional tissue analysis, providing prognostic and predictive information. The aim of this review is to provide a detailed overview of the clinical applications and future perspectives of liquid biopsy in CRC.
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Affiliation(s)
- Sara Torresan
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Marco de Scordilli
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy.
| | - Martina Bortolot
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Paola Di Nardo
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Luisa Foltran
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Arianna Fumagalli
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Michela Guardascione
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Elena Ongaro
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Fabio Puglisi
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy; Department of Medicine, University of Udine, 33100 Udine, Italy
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Cardoso GC, Ganzella FADO, Miniskiskosky G, da Cunha RS, Ramos EADS. Digital methylation-specific PCR: New applications for liquid biopsy. Biomol Concepts 2024; 15:bmc-2022-0041. [PMID: 38345545 DOI: 10.1515/bmc-2022-0041] [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: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
Epigenetic analysis is a fundamental part of understanding pathophysiological processes with potential applications in diagnosis, prognosis, and assessment of disease susceptibility. Epigenetic changes have been widely studied in chronic obstructive pulmonary disease (COPD), but currently, there is no molecular marker used to improve the treatment of patients. Furthermore, this progressive disease is a risk factor for the development of more severe COVID-19. Methylation-specific polymerase chain reaction (MSP-PCR) plays an important role in the analysis of DNA methylation profiles, and it is one of the most widely used techniques. In this context, the combination of MSP-PCR with emerging PCR technologies, such as digital PCR (dPCR), results in more accurate analyses of the DNA methylation profile of the genes under study. In this study, we propose the application of the MSP-dPCR technique to evaluate the methylation profile of the ADAM33 gene from saliva samples and lung tissue biopsies of patients with COPD and COVID-19. MSP-dPCR generated a measurable prediction of gene methylation rate, with the potential application of this combined technology for diagnostic and prognostic purposes. It has also proven to be a powerful tool for liquid biopsy applications.
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Affiliation(s)
- Gabriela Casani Cardoso
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | | | - Guilherme Miniskiskosky
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | - Regiane Stafim da Cunha
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | - Edneia Amancio de Souza Ramos
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
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Chang L, Wang D, Han Y, Diao Z, Chen Y, Li J, Zhang R. External quality assessment for detection of colorectal cancer by Septin9 DNA methylation in clinical laboratories. Clin Chim Acta 2024; 552:117663. [PMID: 38008152 DOI: 10.1016/j.cca.2023.117663] [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: 06/25/2023] [Revised: 10/28/2023] [Accepted: 11/15/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND AND AIMS The incidence and mortality rate of colorectal cancer (CRC) are increasing worldwide. Septin9 methylated (mSEPT9) DNA in circulation can be used as a non-invasive detection method to assist in the early diagnosis of CRC; however, the detection methods and procedures are complicated. This study aimed to evaluate the ability of clinical laboratories to detect Septin9 methylation in plasma cell-free DNA (cfDNA). MATERIALS AND METHODS We prepared a sample panel consisting of positive and negative Septin9 methylation cells and CRC cells. Three positive samples with different methylation levels, one negative sample and one duplicate sample, two samples containing interference, three different CRC cell samples, and a fictitious case report were included. The panel was distributed to 59 laboratories for mSEPT9 analysis, result comparison, and scoring. RESULTS The sample panel, validated by National Medical Products Administration (NMPA)-approved tests and targeted bisulfite sequencing, met expectations and could be used for external quality assessment (EQA). Among the 59 laboratories, 55 (93.22%) correctly reported the mSEPT9 results for all samples, while four (6.79%) reported 15 false negatives and were considered improvable. All false negatives originated from four laboratories using laboratory-developed tests (LDTs), with three failing to detect weakly positive samples, samples containing interference, and samples from different CRC cells, and one reported erroneous results on all positive samples. CONCLUSION Our results illustrated that the detection of mSEPT9 in cfDNA is satisfactory in China. EQA is indispensable because it can help improve the diagnostic capability and quality management of the laboratories, and provide suggestions for the problems existing in mSEPT9 detection.
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Affiliation(s)
- Lu Chang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China.
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Ghosh A, Himaja A, Biswas S, Kulkarni O, Ghosh B. Advances in the Delivery and Development of Epigenetic Therapeutics for the Treatment of Cancer. Mol Pharm 2023; 20:5981-6009. [PMID: 37899551 DOI: 10.1021/acs.molpharmaceut.3c00610] [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: 10/31/2023]
Abstract
Gene expression at the transcriptional level is altered by epigenetic modifications such as DNA methylation, histone methylation, and acetylation, which can upregulate, downregulate, or entirely silence genes. Pathological dysregulation of epigenetic processes can result in the development of cancer, neurological problems, metabolic disorders, and cardiovascular diseases. It is of promising therapeutic interest to find medications that target these epigenetic alterations. Despite the enormous amount of work that has been done in this area, very few molecules have been approved for clinical purposes. This article provides a comprehensive review of recent advances in epigenetic therapeutics for cancer, with a specific focus on emerging delivery and development strategies. Various delivery systems, including pro-drugs, conjugated molecules, nanoparticles (NPs), and liposomes, as well as remedial strategies such as combination therapies, and epigenetic editing, are being investigated to improve the efficacy and specificity of epigenetic drugs (epi-drugs). Furthermore, the challenges associated with available epi-drugs and the limitations of their translation into clinics have been discussed. Target selection, isoform selectivity, physiochemical properties of synthesized molecules, drug screening, and scalability of epi-drugs from preclinical to clinical fields are the major shortcomings that are addressed. This Review discusses novel strategies for the identification of new biomarkers, exploration of the medicinal chemistry of epigenetic modifiers, optimization of the dosage regimen, and design of proper clinical trials that will lead to better utilization of epigenetic modifiers over conventional therapies. The integration of these approaches holds great potential for improving the efficacy and precision of epigenetic treatments, ultimately benefiting cancer patients.
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Affiliation(s)
- Aparajita Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
- Pharmacology Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
| | - Ambati Himaja
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
| | - Swati Biswas
- Nanomedicine Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
| | - Onkar Kulkarni
- Pharmacology Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
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Foster C, Mamaeva O, Shrestha S, Hidalgo B. Epigenetic age in African American adolescents with type 2 diabetes: A cross-sectional case-control study protocol. Health Sci Rep 2023; 6:e1747. [PMID: 38078300 PMCID: PMC10702396 DOI: 10.1002/hsr2.1747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 02/12/2024] Open
Abstract
Background and Aims Type 2 diabetes (T2D) is a disease caused by a relative insulin deficiency compared to the significant insulin requirement needed by the body to achieve glycemic control. T2D in adolescence appears to be increasing in prevalence over the past several decades, necessitating studies to understand for the onset of the disease to occur early in the lifespan. Given the high burden of disease, specifically in young African American adolescents, our study chose to focus initially on feasibility of recruitment of this population. Methods Data was collected at a single study center at Children's of Alabama. The protocol was completed as part of routine care or at a study visit. The study team was able to leverage the Electronic Medical Record to prescreen eligible patients to discuss the study. A variety of times of day were utilized to improve likely of success with reaching potential participants. Inclusion criteria for patients with T2D was focused on the adolescent population (ages 12-18 years), with no history of an obesity syndrome. DNA methylation age will be calculated using the EPIC 850K array. Statistical analysis will be done using linear regression analysis, adjusting for covariates. Conclusions This study's aim was to screen and enroll young African American adolescents for a study investigating epigenetic aging and T2D. Our study found that more direct contact (face-to-face- or phone call) improve success of recruitment. Leveraging the electronic medical record also helped improve success with pre-screening participants. Challenges included recruiting participants who might come from long distances to a tertiary care center. Consolidating appointments helped improve the success of reaching these participants. Other challenges included frequent address changes and changed phone numbers. Close attention to the barriers as well as the successes will aid in understanding effective strategies for this important population.
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Affiliation(s)
- Christy Foster
- Division of Pediatric EndocrinologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Olga Mamaeva
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Sadeep Shrestha
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Bertha Hidalgo
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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10
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Yuan Y, Ye F, Wu JH, Fu XY, Huang ZX, Zhang T. Early screening of nasopharyngeal carcinoma. Head Neck 2023; 45:2700-2709. [PMID: 37552128 DOI: 10.1002/hed.27466] [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: 01/10/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 08/09/2023] Open
Abstract
The low positive predictive value (PPV) of early screening of nasopharyngeal carcinoma (NPC) is the problems that need to be solved urgently. The combination of cell-free DNA (cfDNA) methylation testing and Epstein-Barr virus (EBV) serological testing is the key to solve this problem. This paper reviews recent advances in early screening for NPC and cfDNA methylation, with future perspectives. Pubmed was searched for the literature related to early screening of NPC and cfDNA methylation in the past 5 years. The results of these studies were summarized. Despite these efforts, the PPV is still low (10%). Previous studies have shown that cfDNA methylation analysis has good specificity and accuracy across a variety of tumors. The combination of cfDNA methylation and EBV detection helps to improve the PPV for early screening of NPC. The combination of cfDNA methylation and EBV serological testing is key to addressing the low PPV of NPC early screening.
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Affiliation(s)
- Yue Yuan
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Otolaryngology Head and Neck Surgery, Zhongshan City People's Hospital, Zhongshan City, Guangdong Province, China
| | - Fei Ye
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Otolaryngology Head and Neck Surgery, Zhongshan City People's Hospital, Zhongshan City, Guangdong Province, China
- Department of Otolaryngology Head and Neck Surgery, Huangpu Hospital, Zhongshan City, Guangdong Province, China
| | - Jian-Hui Wu
- Department of Otolaryngology Head and Neck Surgery, Zhongshan City People's Hospital, Zhongshan City, Guangdong Province, China
| | - Xiao-Yan Fu
- Department of Pediatric Otolaryngology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhong-Xi Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Tao Zhang
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, China
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11
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Funderburk K, Bang-Christensen SR, Miller BF, Tan H, Margolin G, Petrykowska HM, Baugher C, Farney SK, Grimm SA, Jameel N, Holland DO, Altman NS, Elnitski L. Evaluating Stacked Methylation Markers for Blood-Based Multicancer Detection. Cancers (Basel) 2023; 15:4826. [PMID: 37835520 PMCID: PMC10571530 DOI: 10.3390/cancers15194826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/16/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The ability to detect several types of cancer using a non-invasive, blood-based test holds the potential to revolutionize oncology screening. We mined tumor methylation array data from the Cancer Genome Atlas (TCGA) covering 14 cancer types and identified two novel, broadly-occurring methylation markers at TLX1 and GALR1. To evaluate their performance as a generalized blood-based screening approach, along with our previously reported methylation biomarker, ZNF154, we rigorously assessed each marker individually or combined. Utilizing TCGA methylation data and applying logistic regression models within each individual cancer type, we found that the three-marker combination significantly increased the average area under the ROC curve (AUC) across the 14 tumor types compared to single markers (p = 1.158 × 10-10; Friedman test). Furthermore, we simulated dilutions of tumor DNA into healthy blood cell DNA and demonstrated increased AUC of combined markers across all dilution levels. Finally, we evaluated assay performance in bisulfite sequenced DNA from patient tumors and plasma, including early-stage samples. When combining all three markers, the assay correctly identified nine out of nine lung cancer plasma samples. In patient plasma from hepatocellular carcinoma, ZNF154 alone yielded the highest combined sensitivity and specificity values averaging 68% and 72%, whereas multiple markers could achieve higher sensitivity or specificity, but not both. Altogether, this study presents a comprehensive pipeline for the identification, testing, and validation of multi-cancer methylation biomarkers with a considerable potential for detecting a broad range of cancer types in patient blood samples.
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Affiliation(s)
- Karen Funderburk
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara R. Bang-Christensen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brendan F. Miller
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hua Tan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gennady Margolin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanna M. Petrykowska
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Catherine Baugher
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - S. Katie Farney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara A. Grimm
- Integrative Bioinformatics Support Group, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, Durham, NC 27709, USA
| | - Nader Jameel
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David O. Holland
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naomi S. Altman
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Albogami S. Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia. Pharmgenomics Pers Med 2023; 16:859-882. [PMID: 37731406 PMCID: PMC10508282 DOI: 10.2147/pgpm.s427977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023] Open
Abstract
Purpose According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with diabetes mellitus. To our knowledge, no research has addressed the potential of noncoding RNA as a diagnostic and/or management biomarker for patients with type 2 diabetes mellitus (T2DM) living in high-altitude areas. This study aimed to identify molecular biomarkers influencing patients with T2DM living in high-altitude areas by analyzing lncRNA and mRNA. Patients and Methods RNA sequencing and bioinformatics analyses were used to identify significantly expressed lncRNAs and mRNAs in T2DM and healthy control groups. Coding potential was analyzed using coding-noncoding indices, the coding potential calculator, and PFAM, and the lncRNA function was predicted using Pearson's correlation. Differentially expressed transcripts between the groups were identified, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify the biological functions of both lncRNAs and mRNAs. Results We assembled 1766 lncRNAs in the T2DM group, of which 582 were novel. This study identified three lncRNA target genes (KLF2, CREBBP, and REL) and seven mRNAs (PIK3CD, PIK3R5, IL6R, TYK2, ZAP70, LAMTOR4, and SSH2) significantly enriched in important pathways, playing a role in the progression of T2DM. Conclusion To the best of our knowledge, this comprehensive study is the first to explore the applicability of certain lncRNAs as diagnostic or management biomarkers for T2DM in females in Taif City, Saudi Arabia through the genome-wide identification of lncRNA and mRNA profiling using RNA seq and bioinformatics analysis. Our findings could help in the early diagnosis of T2DM and in designing effective therapeutic targets.
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Affiliation(s)
- Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi Arabia
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13
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Maleknia M, Ahmadirad N, Golab F, Katebi Y, Haj Mohamad Ebrahim Ketabforoush A. DNA Methylation in Cancer: Epigenetic View of Dietary and Lifestyle Factors. Epigenet Insights 2023; 16:25168657231199893. [PMID: 37720354 PMCID: PMC10504848 DOI: 10.1177/25168657231199893] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/22/2023] [Indexed: 09/19/2023] Open
Abstract
Background Alterations in DNA methylation play an important role in cancer development and progression. Dietary nutrients and lifestyle behaviors can influence DNA methylation patterns and thereby modulate cancer risk. Introduction To comprehensively review available evidence on how dietary and lifestyle factors impact DNA methylation and contribute to carcinogenesis through epigenetic mechanisms. Materials and methods A literature search was conducted using PubMed to identify relevant studies published between 2005 and 2022 that examined relationships between dietary/lifestyle factors and DNA methylation in cancer. Studies investigating the effects of dietary components (eg, micronutrients, phytochemicals), physical activity, smoking, and obesity on global and gene-specific DNA methylation changes in animal and human cancer models were included. Data on specific dietary/lifestyle exposures, cancer types, DNA methylation targets and underlying mechanisms were extracted. Results Multiple dietary and lifestyle factors were found to influence DNA methylation patterns through effects on DNA methyltransferase activity, methyl donor availability, and generation of oxidative stress. Altered methylation of specific genes regulating cell proliferation, apoptosis, and inflammation were linked to cancer development and progression. Conclusion Dietary and lifestyle interventions aimed at modulating DNA methylation have potential for both cancer prevention and treatment through epigenetic mechanisms. Further research is needed to identify actionable targets for nutrition and lifestyle-based epigenetic therapies.
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Affiliation(s)
- Mohsen Maleknia
- Noorgene Genetic & Clinical Laboratory, Molecular Research Center, Ahvaz, Iran
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Nooshin Ahmadirad
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Fereshteh Golab
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Yasmina Katebi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Chakraborty S, Ramasubbu K, Banerjee M, Balaji MP, Vinayagam Y, V DR. A systematic review on the molecular and clinical association between Human Papillomavirus and Human Immunodeficiency Virus co-infection in Head, Neck and Oral squamous cell carcinoma. Rev Med Virol 2023; 33:e2462. [PMID: 37280764 DOI: 10.1002/rmv.2462] [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: 03/27/2023] [Revised: 04/27/2023] [Accepted: 05/23/2023] [Indexed: 06/08/2023]
Abstract
Head and neck cancer, one of the most commonly prevalent malignancies globally is a complex category of tumours that comprises cancers of the oral cavity, pharynx, and larynx. A specific subgroup of such cancers has been found with some unique chromosomal, therapeutic, and epidemiologic traits with the possibility of affecting via co-infection. About 25% of all head and neck cancers in the population are human papillomavirus infection (HPV)-associated, typically developing in the oropharynx, which comprises the tonsils. In the period of efficient combined antiviral treatment, HPV-positive oral cancers are also becoming a significant contributor to illness and fatality for Human Immunodeficiency Virus (HIV)-infected persons. Although the prevalence and historical background of oral HPV transmission are not thoroughly understood, it seems likely that oral HPV transmission is relatively frequent in HIV-infected people when compared to the overall population. Therefore, there is a need to understand the mechanisms leading to this co-infection, as there is very little research related to that. Hence, this study mainly focus on the therapeutical and biomedical analysis of HPV and HIV co-infection in the above-mentioned cancer, including oral squamous cell carcinoma.
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Affiliation(s)
- Shreya Chakraborty
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kanagavalli Ramasubbu
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Manosi Banerjee
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Menaka Priya Balaji
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Yamini Vinayagam
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Devi Rajeswari V
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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15
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Yi JM, Kang T, Han YK, Park HY, Yang JH, Bae J, Suh J, Kim T, Kim J, Cui Y, Suzuki H, Kumegawa K, Kim SJ, Zhao Y, Park IJ, Hong S, Chung J, Lee S. Human Neuralized is a novel tumour suppressor targeting Wnt/β-catenin signalling in colon cancer. EMBO Rep 2023; 24:e56335. [PMID: 37341560 PMCID: PMC10398657 DOI: 10.15252/embr.202256335] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
While there is growing evidence that many epigenetically silenced genes in cancer are tumour suppressor candidates, their significance in cancer biology remains unclear. Here, we identify human Neuralized (NEURL), which acts as a novel tumour suppressor targeting oncogenic Wnt/β-catenin signalling in human cancers. The expression of NEURL is epigenetically regulated and markedly suppressed in human colorectal cancer. We, therefore, considered NEURL to be a bona fide tumour suppressor in colorectal cancer and demonstrate that this tumour suppressive function depends on NEURL-mediated oncogenic β-catenin degradation. We find that NEURL acts as an E3 ubiquitin ligase, interacting directly with oncogenic β-catenin, and reducing its cytoplasmic levels in a GSK3β- and β-TrCP-independent manner, indicating that NEURL-β-catenin interactions can lead to a disruption of the canonical Wnt/β-catenin pathway. This study suggests that NEURL is a therapeutic target against human cancers and that it acts by regulating oncogenic Wnt/β-catenin signalling.
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Affiliation(s)
- Joo Mi Yi
- Department of Microbiology and Immunology, College of MedicineInje UniversityBusanSouth Korea
| | - Tae‐Hong Kang
- Department of Biological ScienceDong‐A UniversityBusanSouth Korea
| | - Yu Kyeong Han
- Department of Microbiology and Immunology, College of MedicineInje UniversityBusanSouth Korea
| | - Ha Young Park
- Department of Pathology, College of MedicineInje UniversityBusanSouth Korea
| | - Ju Hwan Yang
- Department of Physiology and Convergence Medical Science, Institute of Health SciencesGyeongsang National University Medical SchoolJinjuSouth Korea
| | - Jin‐Han Bae
- Department of Integrated Biological Science, College of Natural SciencesPusan National UniversityBusanSouth Korea
| | - Jung‐Soo Suh
- Department of Integrated Biological Science, College of Natural SciencesPusan National UniversityBusanSouth Korea
| | - Tae‐Jin Kim
- Department of Integrated Biological Science, College of Natural SciencesPusan National UniversityBusanSouth Korea
| | - Joong‐Gook Kim
- Research CenterDongnam Institute of Radiological and Medical SciencesBusanSouth Korea
| | - Yan‐Hong Cui
- Department of Life Science, Research Institute for Natural SciencesHanyang UniversitySeoulSouth Korea
- Section of Dermatology, Department of MedicineUniversity of ChicagoChicagoILUSA
| | - Hiromu Suzuki
- Department of Molecular BiologySapporo Medical University School of MedicineSapporoJapan
| | - Kohei Kumegawa
- Cancer Cell Diversity Project, NEXT‐Ganken ProgramJapanese Foundation for Cancer ResearchTokyoJapan
| | - Sung Joo Kim
- Department of Pathology, Kyung Hee University Hospital at GangdongKyung Hee University School of MedicineSeoulSouth Korea
| | - Yi Zhao
- Institute for Translation Medicine, Qingdao UniversityQingdaoChina
| | - In Ja Park
- Department of Colon and Rectal Surgery, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulSouth Korea
| | - Seung‐Mo Hong
- Department of Pathology, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulSouth Korea
| | - Joon‐Yong Chung
- Molecular Imaging Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Su‐Jae Lee
- Fibrosis & Cancer Targeting BiotechnologySeoulSouth Korea
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16
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Qin T, Li S, Henry LE, Chou E, Cavalcante RG, Garb BF, D'Silva NJ, Rozek LS, Sartor MA. Whole-genome CpG-resolution DNA Methylation Profiling of HNSCC Reveals Distinct Mechanisms of Carcinogenesis for Fine-scale HPV+ Cancer Subtypes. CANCER RESEARCH COMMUNICATIONS 2023; 3:1701-1715. [PMID: 37654626 PMCID: PMC10467604 DOI: 10.1158/2767-9764.crc-23-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/24/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
DNA methylation is a vital early step in carcinogenesis. Most findings of aberrant DNA methylation in head and neck squamous cell carcinomas (HNSCC) are array based with limited coverage and resolution, and mainly explored by human papillomavirus (HPV) status, ignoring the high heterogeneity of this disease. In this study, we performed whole-genome bisulfite sequencing on a well-studied HNSCC cohort (n = 36) and investigated the methylation changes between fine-scaled HNSCC subtypes in relation to genomic instability, repetitive elements, gene expression, and key carcinogenic pathways. The previously observed hypermethylation phenotype in HPV-positive (HPV+) tumors compared with HPV-negative tumors was robustly present in the immune-strong (IMU) HPV+ subtype but absent in the highly keratinized (KRT) HPV+ subtype. Methylation levels of IMU tumors were significantly higher in repetitive elements, and methylation showed a significant correlation with genomic stability, consistent with the IMU subtype having more genomic stability and better prognosis. Expression quantitative trait methylation (cis-eQTM) analysis revealed extensive functionally-relevant differences, and differential methylation pathway analysis recapitulated gene expression pathway differences between subtypes. Consistent with their characteristics, KRT and HPV-negative tumors had high regulatory potential for multiple regulators of keratinocyte differentiation, which positively correlated with an expression-based keratinization score. Together, our findings revealed distinct mechanisms of carcinogenesis between subtypes in HPV+ HNSCC and uncovered previously ignored epigenomic differences and clinical implications, illustrating the importance of fine-scale subtype analysis in cancer. Significance This study revealed that the previously observed hypermethylation of HPV(+) HNSCC is due solely to the IMU subtype, illustrating the importance of fine-scale subtype analysis in such a heterogeneous disease. Particularly, IMU has significantly higher methylation of transposable elements, which can be tested as a prognosis biomarker in future translational studies.
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Affiliation(s)
- Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shiting Li
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Leanne E. Henry
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Elysia Chou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Raymond G. Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Bailey F. Garb
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Nisha J. D'Silva
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Laura S. Rozek
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
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17
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Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare RP, Banday S, Mishra AK, Das G, Malonia SK. Next-Generation Sequencing Technology: Current Trends and Advancements. BIOLOGY 2023; 12:997. [PMID: 37508427 PMCID: PMC10376292 DOI: 10.3390/biology12070997] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.
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Affiliation(s)
- Heena Satam
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Kandarp Joshi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Upasana Mangrolia
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sanober Waghoo
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Gulnaz Zaidi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Shravani Rawool
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Ritesh P. Thakare
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Shahid Banday
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Alok K. Mishra
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Gautam Das
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sunil K. Malonia
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
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18
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Zhu L, Wang J, Zhang Y, Xiang X, Liu K, Wei J, Li Z, Shao D, Li B, Ma Z, Qiu Y. A Porcine DNMT1 Variant: Molecular Cloning and Generation of Specific Polyclonal Antibody. Genes (Basel) 2023; 14:1324. [PMID: 37510229 PMCID: PMC10379332 DOI: 10.3390/genes14071324] [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: 06/12/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
DNA methyltransferase 1 (DNMT1), the first-identified DNA methyltransferase in mammals, has been well studied in the control of embryo development and somatic homeostasis in mice and humans. Accumulating reports have demonstrated that DNMT1 plays an important role in the regulation of differentiation and the activation of immune cells. However, little is known about the effects of porcine DNMT1 on such functional regulation, especially the regulation of the biological functions of immune cells. In this study, we report the cloning of DNMT1 (4833 bp in length) from porcine alveolar macrophages (PAMs). According to the sequence of the cloned DNMT1 gene, the deduced protein sequence contains a total of 1611 amino acids with a 2 amino acid insertion, a 1 amino acid deletion, and 12 single amino acid mutations in comparison to the reported DNMT1 protein. A polyclonal antibody based on a synthetic peptide was generated to study the expression of the porcine DNMT1. The polyclonal antibody only recognized the cloned porcine DNMT1 and not the previously reported protein due to a single amino acid difference in the antigenic peptide region. However, the polyclonal antibody recognized the endogenous DNMT1 in several porcine cells (PAM, PK15, ST, and PIEC) and the cells of other species (HEK-293T, Marc-145, MDBK, and MDCK cells). Moreover, our results demonstrated that all the detected tissues of piglet express DNMT1, which is the same as that in porcine alveolar macrophages. In summary, we have identified a porcine DNMT1 variant with sequence and expression analyses.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yafeng Qiu
- Correspondence: ; Tel.: +86-21-34293635; Fax: +86-21-54081818
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19
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Wang XK, Zhang XD, Luo K, Yu L, Huang S, Liu ZY, Li RF. Comprehensive analysis of candidate signatures of long non-coding RNA LINC01116 and related protein-coding genes in patients with hepatocellular carcinoma. BMC Gastroenterol 2023; 23:216. [PMID: 37340445 DOI: 10.1186/s12876-023-02827-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 05/19/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a long-term malignancy that causes high morbidities and mortalities worldwide. Notably, long non-coding RNAs (LncRNAs) have been identified as candidate targets for malignancy treatments. METHODS LncRNA LINC01116 and its Pearson-correlated genes (PCGs) were identified and analyzed in HCC patients. The diagnostic and prognostic value of the lncRNA was evaluated using data from The Cancer Genome Atlas (TCGA). Further, we explored the target drugs of LINC01116 for clinical application. Relationships between immune infiltration and PCGs, methylation and PCGs were explored. The diagnostic potentials were then validated by Oncomine cohorts. RESULTS LINC01116 and the PCG OLFML2B are differentially and highly expressed in tumor tissues (both P ≤ 0.050). We found that LINC01116, TMSB15A, PLAU, OLFML2B, and MRC2 have diagnostic potentials (all AUC ≥ 0.700, all P ≤ 0.050) while LINC01116 and TMSB15A have prognostic significance (both adjusted P ≤ 0.050). LINC01116 was enriched in the vascular endothelial growth factor (VEGF) receptor signaling pathway, mesenchyme morphogenesis, etc. After that, candidate target drugs with potential clinical significance were identified: Thiamine, Cromolyn, Rilmenidine, Chlorhexidine, Sulindac_sulfone, Chloropyrazine, and Meprylcaine. Analysis of immune infiltration revealed that MRC2, OLFML2B, PLAU, and TMSB15A are negatively associated with the purity but positively associated with the specific cell types (all P < 0.050). Analysis of promoter methylation demonstrated that MRC2, OLFML2B, and PLAU have differential and high methylation levels in primary tumors (all P < 0.050). Validation results of the differential expressions and diagnostic potential of OLFML2B (Oncomine) were consistent with those obtained in the TCGA cohort (P < 0.050, AUC > 0.700). CONCLUSIONS Differentially expressed LINC01116 could be a candidate diagnostic and an independent prognostic signature in HCC. Besides, its target drugs may work for HCC therapy via the VEGF receptor signaling pathway. Differentially expressed OLFML2B could be a diagnostic signature involved in HCC via immune infiltrates.
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Affiliation(s)
- Xiang-Kun Wang
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province, Zhengzhou, 450052, P. R. China
| | - Xu-Dong Zhang
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province, Zhengzhou, 450052, P. R. China
| | - Kai Luo
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province, Zhengzhou, 450052, P. R. China
| | - Long Yu
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province, Zhengzhou, 450052, P. R. China
| | - Shuai Huang
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province, Zhengzhou, 450052, P. R. China
| | - Zhong-Yuan Liu
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province, Zhengzhou, 450052, P. R. China
| | - Ren-Feng Li
- Departments of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Province, Zhengzhou, 450052, P. R. China.
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20
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Ying W. Phenomic Studies on Diseases: Potential and Challenges. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:285-299. [PMID: 36714223 PMCID: PMC9867904 DOI: 10.1007/s43657-022-00089-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 01/23/2023]
Abstract
The rapid development of such research field as multi-omics and artificial intelligence (AI) has made it possible to acquire and analyze the multi-dimensional big data of human phenomes. Increasing evidence has indicated that phenomics can provide a revolutionary strategy and approach for discovering new risk factors, diagnostic biomarkers and precision therapies of diseases, which holds profound advantages over conventional approaches for realizing precision medicine: first, the big data of patients' phenomes can provide remarkably richer information than that of the genomes; second, phenomic studies on diseases may expose the correlations among cross-scale and multi-dimensional phenomic parameters as well as the mechanisms underlying the correlations; and third, phenomics-based studies are big data-driven studies, which can significantly enhance the possibility and efficiency for generating novel discoveries. However, phenomic studies on human diseases are still in early developmental stage, which are facing multiple major challenges and tasks: first, there is significant deficiency in analytical and modeling approaches for analyzing the multi-dimensional data of human phenomes; second, it is crucial to establish universal standards for acquirement and management of phenomic data of patients; third, new methods and devices for acquirement of phenomic data of patients under clinical settings should be developed; fourth, it is of significance to establish the regulatory and ethical guidelines for phenomic studies on diseases; and fifth, it is important to develop effective international cooperation. It is expected that phenomic studies on diseases would profoundly and comprehensively enhance our capacity in prevention, diagnosis and treatment of diseases.
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Affiliation(s)
- Weihai Ying
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030 China
- Collaborative Innovation Center for Genetics and Development, Shanghai, 200043 China
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21
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Jiang X, Li Z, Mehmood A, Wang H, Wang Q, Chu Y, Mao X, Zhao J, Jiang M, Zhao B, Lin G, Wang E, Wei D. A Self-attention Graph Convolutional Network for Precision Multi-tumor Early Diagnostics with DNA Methylation Data. Interdiscip Sci 2023:10.1007/s12539-023-00563-1. [PMID: 37247186 DOI: 10.1007/s12539-023-00563-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 05/30/2023]
Abstract
DNA methylation-based precision tumor early diagnostics is emerging as state-of-the-art technology that could capture early cancer signs 3 ~ 5 years in advance, even for clinically homogenous groups. Presently, the sensitivity of early detection for many tumors is ~ 30%, which needs significant improvement. Nevertheless, based on the genome-wide DNA methylation data, one could comprehensively characterize tumors' entire molecular genetic landscape and their subtle differences. Therefore, novel high-performance methods must be modeled by considering unbiased information using excessively available DNA methylation data. To fill this gap, we have designed a computational model involving a self-attention graph convolutional network and multi-class classification support vector machine to identify the 11 most common cancers using DNA methylation data. The self-attention graph convolutional network automatically learns key methylation sites in a data-driven way. Then, multi-tumor early diagnostics is realized by training a multi-class classification support vector machine based on the selected methylation sites. We evaluated our model's performance through several data sets of experiments, and our results demonstrate the effectiveness of the selected key methylation sites, which are highly relevant for blood diagnosis. The pipeline of the self-attention graph convolutional network based computational framework.
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Affiliation(s)
- Xue Jiang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiqi Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Aamir Mehmood
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Heng Wang
- International School of Cosmetics, School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Qiankun Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyi Chu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xueying Mao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Zhao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingming Jiang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bowen Zhao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guanning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Edwin Wang
- Department of Biochemistry and Molecular Biology, Medical Genetics, and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Canada.
| | - Dongqing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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22
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Yue C, Qian Y, Wang C, Chen J, Wang J, Wang Z, Wan X, Cao S, Zhu J, Tao Q, Yan M, Liu Q. TRIM29 acts as a potential senescence suppressor with epigenetic activation in nasopharyngeal carcinoma. Cancer Sci 2023. [PMID: 37248790 PMCID: PMC10394149 DOI: 10.1111/cas.15852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/31/2023] Open
Abstract
Epigenetic alterations marked by DNA methylation are frequent events during the early development of nasopharyngeal carcinoma (NPC). We identified that TRIM29 is hypomethylated and overexpressed in NPC cell lines and tissues. TRIM29 silencing not only limited the growth of NPC cells in vitro and in vivo, but also induced cellular senescence, along with reactive oxygen species (ROS) accumulation. Mechanistically, we found that TRIM29 interacted with voltage-dependent anion-selective channel 1 (VDAC1) to activate mitophagy clearing up damaged mitochondria, which are the major source of ROS. In patients with NPC, high levels of TRIM29 expression are associated with an advanced clinical stage. Moreover, we detected hypomethylation of TRIM29 in patient nasopharyngeal swab DNA. Our findings indicate that TRIM29 depends on VDAC1 to induce mitophagy and prevents cellular senescence by decreasing ROS. Detection of aberrantly methylated TRIM29 in the nasopharyngeal swab DNA could be a promising strategy for the early detection of NPC.
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Affiliation(s)
- Caifeng Yue
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Laboratory Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, China
| | - Yuanmin Qian
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Chang Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Jiewei Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Jing Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Zifeng Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Xiangbo Wan
- Gastrointestinal Institute, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sumei Cao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Jingde Zhu
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, China
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - Min Yan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Quentin Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
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23
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Bao J, Ding K, Zhu Y. An electrochemical biosensor for detecting DNA methylation based on AuNPs/rGO/g-C 3N 4 nanocomposite. Anal Biochem 2023; 673:115180. [PMID: 37146956 DOI: 10.1016/j.ab.2023.115180] [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: 02/25/2023] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/07/2023]
Abstract
DNA methylation as a ubiquitously regulation is closely associated with cell proliferation and differentiation. Growing data shows that aberrant methylation contributes to disease incidence, especially in tumorigenesis. The approach for identifying DNA methylation usually depends on treatment of sodium bisulfite, which is time-consuming and conversion-insufficient. Here, with a special biosensor, we establish an alternative approach for detecting DNA methylation. The biosensor is consisted of two parts, which are gold electrode and nanocomposite (AuNPs/rGO/g-C3N4). Nanocomposite was fabricated by three components, which are gold nanoparticles (AuNPs), reduced graphene oxide (rGO) and graphite carbon nitride (g-C3N4). For methylated DNA detection, the target DNA was captured by probe DNA immobilized on the gold electrode surface through thiolating process and subjected to hybrid with anti-methylated cytosine conjugated to nanocomposite. When the methylated cytosines in target DNA were recognized by anti-methylated cytosine, a change of electrochemical signals will be observed. With different size of target DNAs, the concentration and methylation level were tested. It is shown that in short size methylated DNA fragment, the linear range and LOD of concentration is 10-7M-10-15M and 0.74 fM respectively; in longer size methylated DNA, the linear range of methylation proportion and LOD of copy number is 3%-84% and 103 respectively. Also, this approach has a high sensitivity and specificity as well as anti-disturbing ability.
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Affiliation(s)
- Junming Bao
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Kejian Ding
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China.
| | - Yunfeng Zhu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China.
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24
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Li M, Zhu C, Xue Y, Miao C, He R, Li W, Zhang B, Yu W, Huang X, Lv M, Xu Y, Huang Q. A DNA methylation signature for the prediction of tumour recurrence in stage II colorectal cancer. Br J Cancer 2023; 128:1681-1689. [PMID: 36828869 PMCID: PMC10133253 DOI: 10.1038/s41416-023-02155-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND A major challenge in stage II colorectal carcinoma is to identify patients with increased risk of recurrence. Biomarkers that distinguish patients with poor prognosis from patients without recurrence are currently lacking. This study aims to develop a robust DNA methylation classifier that allows the prediction of recurrence and chemotherapy benefit in patients with stage II colorectal cancer. We performed a genome-wide DNA methylation capture sequencing in 243 stage II colorectal carcinoma samples and identified a relapse-specific DNA methylation signature consisting of eight CpG sites. METHODS Two hundred and forty-three patients with stage II CRC were enrolled in this study. In order to select differential methylation sites among recurrence and non-recurrence stage II CRC samples, DNA methylation profiles of 62 tumour samples including 31 recurrence and 31 nonrecurrence samples were analysed using the Agilent SureSelectXT Human Methyl-Seq, a comprehensive target enrichment system to analyse CpG methylation. Pyrosequencing was applied to quantify the methylation level of candidate DNA methylation sites in 243 patients. Least absolute shrinkage and selection operator (LASSO) method was employed to build the disease recurrence prediction classifier. RESULTS We identified a relapse-related DNA methylation signature consisting of eight CpG sites in stage II CRC by DNA methylation capture sequencing. The classifier showed significantly higher prognostic accuracy than any clinicopathological risk factors. The Kaplan-Meier survival curve showed an association of high-risk score with poor prognosis. In multivariate analysis, the signature was the most significant prognosis factor, with an HR of 2.80 (95% CI, 1.71-4.58, P < 0.001). The signature could identify patients who are suitable candidates for adjuvant chemotherapy. CONCLUSIONS An eight-CpG DNA methylation signature is a reliable prognostic and predictive tool for disease recurrence in patients with stage II CRC.
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Affiliation(s)
- Min Li
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Congcong Zhu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China
| | - Ying Xue
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Changhong Miao
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Ruiping He
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Baolong Zhang
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Minzhi Lv
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Department of Biostatistics, Clinical Research Unit, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China.
| | - Qihong Huang
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Shanghai Respiratory Research Institute, 180 Fenglin Road, 200032, Shanghai, P. R. China.
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25
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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26
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Wang W, Zhu X, Zhang X, Lei C, Zeng Z, Lan X, Cui W, Wang F, Xu S, Zhou J, Wu X, Deng H, Li X, Fan J, Ding Y, Huang Z, Liang L. Recurrence risk assessment for stage III colorectal cancer based on five methylation biomarkers in plasma cell-free DNA. J Pathol 2023; 259:376-387. [PMID: 36573552 DOI: 10.1002/path.6047] [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: 06/18/2022] [Revised: 11/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
For stage III colorectal cancer (CRC) patients with a high risk of recurrence, intensified adjuvant chemotherapy can improve overall survival. We aimed to develop a circulating tumor DNA (ctDNA) methylation marker model for predicting the relapse risk of stage III CRC patients. Differentially methylated markers identified between 53 normal mucosa samples and 165 CRC tissue samples, as well as between plasma samples from 75 stage I/II (early-stage) CRC patients and 55 stage IV (late-stage) CRC patients, were analyzed using Student's t-tests. The overlapping methylation markers shared by plasma and tissue samples were used to establish a methylation marker model to evaluate the tumor burden in the peripheral blood of CRC patients using the random forest method. This model was verified in the validation cohort (n = 44) and then applied to predict recurrence risk in 50 stage III CRC patients and monitor the clinical disease course in serial samples from four CRC patients. We built a five-marker-based ctDNA methylation model that had high sensitivity (84.21%) and specificity (84%) in identifying late-stage CRC in a validation cohort containing 24 stage I/II CRC patients and 20 stage IV CRC patients. The model achieved high sensitivity (87.5%) and specificity (94.12%) in predicting tumor relapse in an independent cohort of 50 stage III CRC patients and could be an independent recurrence risk factor for stage III patients [Hazard ratio (HR), 60.4; 95% confidence interval (CI): 7.68-397; p = 9.73e-5]. Analysis of serial blood samples of CRC showed that the model could monitor disease relapse earlier than imaging examination and serum carcinoembryonic antigen (CEA) and so may provide an opportunity for the early adjustment of therapeutic strategies. Moreover, the model could potentially monitor the clinical course and treatment response dynamically. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Wei Wang
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Department of Pathology, General Hospital of Southern Theater Command, People's Liberation Army of China, Guangzhou, PR China
| | - Xiaohui Zhu
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Xuecong Zhang
- Department of Bioinformatics, School of Basic Medicine, Southern Medical University, Guangzhou, PR China
| | - Chengyong Lei
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Zhicheng Zeng
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Xiaoliang Lan
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Wenzhi Cui
- Department of Pathology, General Hospital of Southern Theater Command, People's Liberation Army of China, Guangzhou, PR China
| | - Feifei Wang
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Shaowan Xu
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Juan Zhou
- Department of Oncology, General Hospital of Southern Theater Command, People's Liberation Army of China, Guangzhou, PR China
| | - Xuehui Wu
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Haijun Deng
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Xia Li
- AnchorDx Medical Co., Ltd., Guangzhou, PR China
| | - Jianbing Fan
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,AnchorDx Medical Co., Ltd., Guangzhou, PR China
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Zhongxi Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, PR China
| | - Li Liang
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
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Tang X, Mo Z, Chang C, Qian X. Group-shrinkage feature selection with a spatial network for mining DNA methylation data. Comput Biol Med 2023; 154:106573. [PMID: 36706568 DOI: 10.1016/j.compbiomed.2023.106573] [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: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
Abstract
Identifying disease-related biomarkers from high-dimensional DNA methylation data helps in reducing early screening costs and inferring pathogenesis mechanisms. Good discovery results have been achieved through spatial correlation methods of methylation sites, group-based regularization, and network constraints. However, these methods still have some key limitations as they cannot exclude isolated differential sites and only consider adjacent site ordering. Therefore, we propose a group-shrinkage feature selection algorithm to encourage the selection of clustered sites and discourage the selection of isolated differential sites. Specifically, a network-guided group-shrinkage strategy is developed to penalize weakly-correlated isolated methylation sites through a network structure constraint. The spatial network is constructed based on spatial correlation information of DNA methylation sites, where this information accounts for the uneven site distribution. The experimental simulations and applications demonstrated that the proposed method outperforms the advanced regularization methods, especially in rejecting isolated methylation sites; hence this study provides an efficient and clinical-valuable method for biomarker candidate discovery in DNA methylation data. Additionally, the proposed method exhibits enhanced reliability due to introducing biological prior knowledge into a regularization-based feature selection framework and could promote more research in the integration between biological prior knowledge and classical feature selection methods, thus facilitating their clinical application. Our source codes will be released at https://github.com/SJTUBME-QianLab/Group-shrinkage-Spatial-Network once this manuscript is accepted for publication.
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Affiliation(s)
- Xinlu Tang
- Medical Image and Health Informatics Lab, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhanfeng Mo
- School of Computer Science and Engineering, Nanyang Technological University, Singapore.
| | - Cheng Chang
- Department of Nuclear Medicine, Shanghai, Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Xiaohua Qian
- Medical Image and Health Informatics Lab, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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Hill C, Duffy S, Coulter T, Maxwell AP, McKnight AJ. Harnessing Genomic Analysis to Explore the Role of Telomeres in the Pathogenesis and Progression of Diabetic Kidney Disease. Genes (Basel) 2023; 14:609. [PMID: 36980881 PMCID: PMC10048490 DOI: 10.3390/genes14030609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
The prevalence of diabetes is increasing globally, and this trend is predicted to continue for future decades. Research is needed to uncover new ways to manage diabetes and its co-morbidities. A significant secondary complication of diabetes is kidney disease, which can ultimately result in the need for renal replacement therapy, via dialysis or transplantation. Diabetic kidney disease presents a substantial burden to patients, their families and global healthcare services. This review highlights studies that have harnessed genomic, epigenomic and functional prediction tools to uncover novel genes and pathways associated with DKD that are useful for the identification of therapeutic targets or novel biomarkers for risk stratification. Telomere length regulation is a specific pathway gaining attention recently because of its association with DKD. Researchers are employing both observational and genetics-based studies to identify telomere-related genes associated with kidney function decline in diabetes. Studies have also uncovered novel functions for telomere-related genes beyond the immediate regulation of telomere length, such as transcriptional regulation and inflammation. This review summarises studies that have revealed the potential to harness therapeutics that modulate telomere length, or the associated epigenetic modifications, for the treatment of DKD, to potentially slow renal function decline and reduce the global burden of this disease.
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Affiliation(s)
- Claire Hill
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Seamus Duffy
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Tiernan Coulter
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Alexander Peter Maxwell
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast BT9 7AB, UK
| | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
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WDR74 rs11231247 contributes to the susceptibility and prognosis of non-small cell lung cancer. Pathol Res Pract 2023; 242:154318. [PMID: 36701849 DOI: 10.1016/j.prp.2023.154318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/03/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
OBJECTIVES WD repeat-containing protein 74 (WDR74) has been linked with the development of lung cancer. This study aims to investigate the relationship between WDR74 rs11231247 and non-small cell lung cancer (NSCLC) susceptibility and the prognosis of NSCLC patients. METHODS UALCAN, MethPrimer, ensembl and Pancan meQTL databases were used for bioinformatics analysis. The case-control study included 462 NSCLC patients and 462 health controls. WDR74 rs11231247 genotype was determined by PCR-RFLP. Logistic regression model was used to calculate odds ratio (OR) and 95% confidence interval (95% CI) for analyzing the association of WDR74 SNP with the risk of NSCLC. Log-rank test and Cox regression analysis were used to evaluate the effect of WDR74 genetic variation on the prognosis of NSCLC. RESULTS Compared with normal tissues, WDR74 expression level was higher and methylation level was lower in LUAD tissues. There were two CpG islands presented in the promoter of WDR74. And rs11231247 was in the second CpG island. We then discovered that rs11231247 CC and CT were more likely modified by methylation. LUAD case-control study demonstrated that rs11231247 CC genotype was associated with NSCLC risk with OR (95%CI) of 5.29 (2.59-10.79). Stratified analysis showed that rs11231247 T > C polymorphism could increase NSCLC risk in younger subjects (age≤58) (OR = 1.64, 95%CI = 1.06-2.54, P = 0.027). Survival analysis and Cox regression analysis showed rs11231247 CC genotype contributed to a poor prognosis of NSCLC patients (MST=21, HR=2.09, 95%CI=1.17-3.75). CONCLUSION WDR74 rs11231247 polymorphism affected the risk and prognosis of NSCLC.
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Circulating Tumor DNA Methylation Biomarkers for Characterization and Determination of the Cancer Origin in Malignant Liver Tumors. Cancers (Basel) 2023; 15:cancers15030859. [PMID: 36765815 PMCID: PMC9913861 DOI: 10.3390/cancers15030859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Malignant liver tumors include primary malignant liver tumors and liver metastases. They are among the most common malignancies worldwide. The disease has a poor prognosis and poor overall survival, especially with liver metastases. Therefore, early detection and differentiation between malignant liver tumors are critical for patient treatment selection. The detection of cancer and the prediction of its origin is possible with a DNA methylation profile of the tumor DNA compared to that of normal cells, which reflects tissue differentiation and malignant transformation. New technologies enable the characterization of the tumor methylome in circulating tumor DNA (ctDNA), providing a variety of new ctDNA methylation biomarkers, which can provide additional information to clinical decision-making. Our review of the literature provides insight into methylation changes in ctDNA from patients with common malignant liver tumors and can serve as a starting point for further research.
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Jung A, Munõz-López Á, Buchmuller BC, Banerjee S, Summerer D. Imaging-Based In Situ Analysis of 5-Methylcytosine at Low Repetitive Single Gene Loci with Transcription-Activator-Like Effector Probes. ACS Chem Biol 2023; 18:230-236. [PMID: 36693632 PMCID: PMC9942090 DOI: 10.1021/acschembio.2c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Transcription-activator-like effectors (TALEs) are programmable DNA binding proteins that can be used for sequence-specific, imaging-based analysis of cellular 5-methylcytosine. However, this has so far been limited to highly repetitive satellite DNA. To expand this approach to the analysis of coding single gene loci, we here explore a number of signal amplification strategies for increasing imaging sensitivity with TALEs. We develop a straightforward amplification protocol and employ it to target the MUC4 gene, which features only a small cluster of repeat sequences. This offers high sensitivity imaging of MUC4, and in costaining experiments with pairs of one TALE selective for unmethylated cytosine and one universal control TALE enables analyzing methylation changes in the target independently of changes in target accessibility. These advancements offer prospects for 5-methylcytosine analysis at coding, nonrepetitive gene loci by the use of designed TALE probe collections.
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Affiliation(s)
- Anne Jung
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Álvaro Munõz-López
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany,International
Max Planck Research School of Living Matter, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Benjamin C. Buchmuller
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany,International
Max Planck Research School of Living Matter, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Sudakshina Banerjee
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany,International
Max Planck Research School of Living Matter, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Daniel Summerer
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany,International
Max Planck Research School of Living Matter, Otto-Hahn-Str. 11, 44227 Dortmund, Germany,
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Wang EJ, Haddad AF, Young JS, Morshed RA, Wu JPH, Salha DM, Butowski N, Aghi MK. Recent advances in the molecular prognostication of meningiomas. Front Oncol 2023; 12:910199. [PMID: 36686824 PMCID: PMC9845914 DOI: 10.3389/fonc.2022.910199] [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: 04/01/2022] [Accepted: 11/17/2022] [Indexed: 01/05/2023] Open
Abstract
Meningiomas are the most common primary intracranial neoplasm. While traditionally viewed as benign, meningiomas are associated with significant patient morbidity, and certain meningioma subgroups display more aggressive and malignant behavior with higher rates of recurrence. Historically, the risk stratification of meningioma recurrence has been primarily associated with the World Health Organization histopathological grade and surgical extent of resection. However, a growing body of literature has highlighted the value of utilizing molecular characteristics to assess meningioma aggressiveness and recurrence risk. In this review, we discuss preclinical and clinical evidence surrounding the use of molecular classification schemes for meningioma prognostication. We also highlight how molecular data may inform meningioma treatment strategies and future directions.
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Affiliation(s)
- Elaina J. Wang
- Department of Neurological Surgery, Brown University, Rhode Island Hospital, Providence, RI, United States
| | - Alexander F. Haddad
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Jacob S. Young
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Ramin A. Morshed
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Joshua P. H. Wu
- Department of Neurological Surgery, Brown University, Rhode Island Hospital, Providence, RI, United States
| | - Diana M. Salha
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Nicholas Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Manish K. Aghi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States,*Correspondence: Manish K. Aghi,
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P14.5 functions to inhibit cell migration and can be used as a prognostic marker in hepatocellular carcinoma. Genes Genomics 2023; 45:83-91. [PMID: 36434386 DOI: 10.1007/s13258-022-01331-z] [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: 04/24/2022] [Accepted: 10/14/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common primary liver malignancy with a high mortality rate. P14.5 is a member of the highly conserved YER057c/YIL051c/YjgF subfamily and is highly expressed in the liver. However, its low expression is associated with carcinogenesis in HCC. OBJECTIVE This study aimed to investigate the role and prognostic significance of P14.5 in HCC. METHODS The clinical significance of P14.5 in HCC was examined using ONCOMINE, UALCAN, Human Protein Atlas, and Kaplan-Meier plotter. The DNA methylation profile of the P14.5 promoter was examined in 103 HCC and paired precancerous tissues; the HCC cell lines HepG2, MHCC-97L, SMMC-7721, SK-Hep-1, and Huh7; and the normal hepatic cell line HL-7702 via MALDI-TOF mass spectrometry. In addition, in vitro experiments were performed to examine the effects of P14.5 overexpression on the proliferation and migration of SMMC-7721 cells. RESULTS Low expression of P14.5 was correlated with shorter overall survival (OS) and disease-free survival (DFS) in HCC. Based on the results of MALDI-TOF mass spectrometry, no difference was observed in the methylation level between HCC cells and normal human hepatic cells and between HCC and paired precancerous tissues. Additionally, P14.5 overexpression promoted the proliferation and inhibited the migration of SMMC7721 cells in vitro. CONCLUSIONS P14.5 may serve as a prognostic biomarker in HCC and plays a role in the migration and proliferation of HCC cells. Low expression of P14.5 during hepatocarcinogenesis is not attributed to DNA methylation.
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Okada Y, Peng F, Perea J, Corchete L, Bujanda L, Li W, Goel A. Genome-wide methylation profiling identifies a novel gene signature for patients with synchronous colorectal cancer. Br J Cancer 2023; 128:112-120. [PMID: 36319845 PMCID: PMC9814149 DOI: 10.1038/s41416-022-02033-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND There are no robust tools for the diagnosis of synchronous colorectal cancer (SyCRC). Herein, we developed the first methylation signature to identify and characterise patients with SyCRC. METHODS For biomarker discovery, we analysed the genome-wide methylation profiles of 16 SyCRC and 18 solitary colorectal cancer (SoCRC) specimens. We thereafter established a methylation signature risk-scoring model to identify SyCRC in an independent cohort of 38 SyCRC and 42 SoCRC patients. In addition, we evaluated the prognostic value of the identified methylation profile. RESULTS We identified six differentially methylated CpG probes/sites that distinguished SyCRC from SoCRC. In the validation cohort, we developed a methylation panel that identified patients with SyCRC from not only larger tumour (AUC = 0.91) but also the paired remaining tumour (AUC = 0.93). Moreover, high risk scores of our panel were associated with the development of metachronous CRC among patients with SyCRC (AUC = 0.87) and emerged as an independent predictor for relapse-free survival (hazard ratio = 2.72; 95% CI = 1.12-6.61). Furthermore, the risk stratification model which combined with clinical risk factors was a diagnostic predictor of recurrence (AUC = 0.90). CONCLUSIONS Our novel six-gene methylation panel robustly identifies patients with SyCRC, which has the clinical potential to improve the diagnosis and management of patients with CRC.
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Affiliation(s)
- Yasuyuki Okada
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Gastroenterology and Oncology, Tokushima University Graduate School, Tokushima, Japan
| | - Fuduan Peng
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - José Perea
- Molecular Medicine Unit. Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
- Surgery Department, Vithas Arturo Soria University Hospital and School of Medicine, European University of Madrid, Madrid, Spain
| | - Luis Corchete
- Hematology Department, University Hospital of Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Cancer Research Center (CiC-IBMCC, CSIC/USAL), Center for Biomedical Research in Network of Cancer (CIBERONC), Salamanca, Spain
| | - Luis Bujanda
- Gastroenterology Department, Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Wei Li
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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Fan Y, S Chan A, Zhu J, Yi Leung S, Fan X. A Bayesian model for identifying cancer subtypes from paired methylation profiles. Brief Bioinform 2022; 24:6961790. [PMID: 36575828 PMCID: PMC9851340 DOI: 10.1093/bib/bbac568] [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: 07/29/2022] [Revised: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 12/29/2022] Open
Abstract
Aberrant DNA methylation is the most common molecular lesion that is crucial for the occurrence and development of cancer, but has thus far been underappreciated as a clinical tool for cancer classification, diagnosis or as a guide for therapeutic decisions. Partly, this has been due to a lack of proven algorithms that can use methylation data to stratify patients into clinically relevant risk groups and subtypes that are of prognostic importance. Here, we proposed a novel Bayesian model to capture the methylation signatures of different subtypes from paired normal and tumor methylation array data. Application of our model to synthetic and empirical data showed high clustering accuracy, and was able to identify the possible epigenetic cause of a cancer subtype.
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Affiliation(s)
- Yetian Fan
- School of Mathematics and Statistics, Liaoning University, Shenyang, 110036, China,Department of Statistics, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong SAR, China
| | - April S Chan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jun Zhu
- Sema4, Stamford, CT, 06902, USA,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xiaodan Fan
- Corresponding author: Xiaodan Fan, Department of Statistics, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong SAR, China. E-mail:
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Yi W, Qiao T, Yang Z, Hu L, Sun M, Fan H, Xu Y, Lv Z. The regulation role and diagnostic value of fibrinogen-like protein 1 revealed by pan-cancer analysis. Mater Today Bio 2022; 17:100470. [PMID: 36345363 PMCID: PMC9636576 DOI: 10.1016/j.mtbio.2022.100470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/07/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Although the role of fibrinogen-like protein 1 (FGL1) in tumorigenesis is well known, a pan-cancer analysis of FGL1 lacks. We used bioinformatics techniques to analyze cancer data from publicly available datasets from The Cancer Genome Atlas, UALCAN, TIMER, Gene Expression Profiling Interactive Analysis, cBioPortal, Search Tool for the Retrieval of Interacting Genes, and DAVID. FGL1 expression was significantly regulated in various common tumors than in normal tissues; it was increased in lung adenocarcinoma and decreased in colon adenocarcinoma. Cox regression analysis demonstrated that the upregulation of FGL1 expression was correlated with poor overall survival (OS) and disease-free survival (DFS) in stomach adenocarcinoma, brain low-grade glioma, cervical squamous cell carcinoma, and endocervical adenocarcinoma. Decreased FGL1 methylation levels were observed in majority of tumor types. FGL1 expression was significantly associated with the levels of immune cell subtypes and immune checkpoint genes. Deep deletion was the most common genetic mutation in FGL1 that led to frame-shift mutations, which was closely associated with poor progression-free interval, disease-specific survival, and OS in patients with FGL1 mutations. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that FGL1-related genes participate in diverse pathways. Ubiquitin-mediated proteolysis is significantly correlated to the function of FGL1, which was identified for the first time in the present study. This pan-cancer study provides a deep understanding of the functions of FGL1 in progression of many tumors and demonstrates that FGL1 may be a potential biomarker for the diagnosis, prognosis, and immune infiltration in cancer.
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Affiliation(s)
- Wanwan Yi
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Yanchang Middle Road 301, Shanghai, 200072, China
| | - Tingting Qiao
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Yanchang Middle Road 301, Shanghai, 200072, China
| | - Ziyu Yang
- Department of Integrated Chinese and Western Medicine, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, 200438, China
| | - Lei Hu
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, 200438, China
| | - Mingming Sun
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, 200438, China
| | - Hengwei Fan
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, 200438, China
- Corresponding author.
| | - Yanping Xu
- School of Life Sciences and Technology, Tongji University, No.1239 SiPing Road, Yangpu District, Shanghai, 200092, China
- Corresponding author.
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Yanchang Middle Road 301, Shanghai, 200072, China
- Corresponding author.
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Excavation of Molecular Subtypes of Endometrial Cancer Based on DNA Methylation. Genes (Basel) 2022; 13:genes13112106. [DOI: 10.3390/genes13112106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Tumor heterogeneity makes the diagnosis and treatment of endometrial cancer difficult. As an important modulator of gene expression, DNA methylation can affect tumor heterogeneity and, therefore, provide effective information for clinical treatment. In this study, we explored specific prognostic clusters based on 482 examples of endometrial cancer methylation data in the TCGA database. By analyzing 4870 CpG clusters, we distinguished three clusters with different prognostics. Differences in DNA methylation levels are associated with differences in age, grade, clinical pathological staging, and prognosis. Subsequently, we screened out 264 specific hypermethylation and hypomethylation sites and constructed a prognostic model for Bayesian network classification, which corresponded to the classification of the test set to the classification results of the train set. Since the tumor microenvironment plays a key role in determining immunotherapy responses, we conducted relevant analyses based on clusters separated from DNA methylation data to determine the immune function of each cluster. We also predicted their sensitivity to chemotherapy drugs. Specific classifications of DNA methylation may help to address the heterogeneity of previously existing molecular clusters of endometrial cancer, as well as to develop more effective, individualized treatments.
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Ambroa-Conde A, Girón-Santamaría L, Mosquera-Miguel A, Phillips C, Casares de Cal M, Gómez-Tato A, Álvarez-Dios J, de la Puente M, Ruiz-Ramírez J, Lareu M, Freire-Aradas A. Epigenetic age estimation in saliva and in buccal cells. Forensic Sci Int Genet 2022; 61:102770. [DOI: 10.1016/j.fsigen.2022.102770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/04/2022]
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Li N, Zhu X, Nian W, Li Y, Sun Y, Yuan G, Zhang Z, Yang W, Xu J, Lizaso A, Li B, Zhang Z, Wu L, Zhang Y. Blood-based DNA methylation profiling for the detection of ovarian cancer. Gynecol Oncol 2022; 167:295-305. [PMID: 36096974 DOI: 10.1016/j.ygyno.2022.07.008] [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: 02/27/2022] [Revised: 06/15/2022] [Accepted: 07/09/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Ovarian cancer is a fatal gynecological cancer due to the lack of effective screening strategies at early stage. This study explored the utility of DNA methylation profiling of blood samples for the detection of ovarian cancer. METHODS Targeted bisulfite sequencing was performed on tissue (n = 152) and blood samples (n = 373) obtained from healthy women, women with benign ovarian tumors, or malignant epithelial ovarian tumors. Based on the tissue-derived differentially-methylated regions, a supervised machine learning algorithm was implemented and cross-validated using the blood-derived DNA methylation profiles of the training cohort (n = 178) to predict and classify each blood sample as malignant or non-malignant. The model was further evaluated using an independent test cohort (n = 184). RESULTS Comparison of the DNA methylation profiles of normal/benign and malignant tumor samples identified 1272 differentially-methylated regions, with 49.4% hypermethylated regions and 50.6% hypomethylated regions. Five-fold cross-validation of the model using the training dataset yielded an area under the curve of 0.94. Using the test dataset, the model accurately predicted non-malignancy in 96.2% of healthy women (n = 53) and 93.5% of women with benign tumors (n = 46). For patients with malignant tumors, the model accurately predicted malignancy in 44.4% of stage I-II (n = 9), 86.4% of stage III (n = 59), 100.0% of stage IV tumors (n = 6), and 81.8% of tumors with unknown stage (n = 11). Overall, the model yielded a predictive accuracy of 89.5%. CONCLUSIONS Our study demonstrates the potential clinical application of blood-based DNA methylation profiling for the detection of ovarian cancer.
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Affiliation(s)
- Ning Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Xin Zhu
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China; Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha 410008, China
| | - Weiqi Nian
- Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yifan Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Yangchun Sun
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Guangwen Yuan
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Zhenjing Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wenqing Yang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China; Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha 410008, China
| | - Jiayue Xu
- Burning Rock Biotech, Guangzhou 510300, China
| | | | - Bingsi Li
- Burning Rock Biotech, Guangzhou 510300, China
| | | | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.
| | - Yu Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China; Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China.
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Comprehensive Analysis of GDF10 Methylation Site-Associated Genes as Prognostic Markers for Endometrial Cancer. JOURNAL OF ONCOLOGY 2022; 2022:7117083. [PMID: 36262352 PMCID: PMC9576415 DOI: 10.1155/2022/7117083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022]
Abstract
Growth differentiation factor-10 (GDF10) with its methylation trait has recently been found to play a crucial regulatory and communication role in cancers. This investigation aims to identify GDF10 methylation site-associated genes that are closely associated with endometrial cancer (EC) patients' survival based on normal and UCEC samples from the UCSC Xena database. Our study revealed for the first time that EC exhibited significantly higher levels of GDF10 promoter methylation in comparison with normal tissues. Multiple differentiated methylation sites, which have prognostic value due to their apparent survival differences, were found in the GDF10 promoter region. We performed weighted gene coexpression network analysis (WGCNA) on EC tissues and paraneoplastic tissues while using these differentially methylated sites as phenotypes for selecting the most correlated key modules and their internal genes. To obtain a gene set, the key module genes and differentially expressed genes (DEGs) of EC were intersected. The least absolute shrinkage and selection operator (LASSO) regression along with multivariate Cox regression were performed from the gene set and we screened out the key genes B4GALNT3, DNAJC22, and GREB1. Finally, a prognostic model was validated for effectiveness based on these genes. Additionally, Kaplan-Meier analysis and time-dependent receiver operating characteristics (ROC) were applied to assess and verify the model, and they showed good prognosis prediction. Moreover, the differences in risk scores were statistically significant with age, tumor stage, and grade. They may be related to the immune infiltration of tumors as well. In conclusion, based on the methylation-related genes associated with GDF10, we developed a prognosis model for EC patients. It might provide a fresh view for further research and treatment of EC.
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Yao Y, Liu K, Wu Y, Zhou J, Jin H, Zhang Y, Zhu Y. Comprehensive landscape of the functions and prognostic value of RNA binding proteins in uterine corpus endometrial carcinoma. Front Mol Biosci 2022; 9:962412. [PMID: 36262474 PMCID: PMC9574853 DOI: 10.3389/fmolb.2022.962412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/14/2022] [Indexed: 12/24/2022] Open
Abstract
Background: The dysregulation of RNA binding proteins (RBPs) is involved in tumorigenesis and progression. However, information on the overall function of RNA binding proteins in Uterine Corpus Endometrial Carcinoma (UCEC) remains to be studied. This study aimed to explore Uterine Corpus Endometrial Carcinoma-associated molecular mechanisms and develop an RNA-binding protein-associated prognostic model. Methods: Differently expressed RNA binding proteins were identified between Uterine Corpus Endometrial Carcinoma tumor tissues and normal tissues by R packages (DESeq2, edgeR) from The Cancer Genome Atlas (TCGA) database. Hub RBPs were subsequently identified by univariate and multivariate Cox regression analyses. The cBioPortal platform, R packages (ggplot2), Human Protein Atlas (HPA), and TIMER online database were used to explore the molecular mechanisms of Uterine Corpus Endometrial Carcinoma. Kaplan-Meier (K-M), Area Under Curve (AUC), and the consistency index (c-index) were used to test the performance of our model. Results: We identified 128 differently expressed RNA binding proteins between Uterine Corpus Endometrial Carcinoma tumor tissues and normal tissues. Seven RNA binding proteins genes (NOP10, RBPMS, ATXN1, SBDS, POP5, CD3EAP, ZC3H12C) were screened as prognostic hub genes and used to construct a prognostic model. Such a model may be able to predict patient prognosis and acquire the best possible treatment. Further analysis indicated that, based on our model, the patients in the high-risk subgroup had poor overall survival (OS) compared to those in the low-risk subgroup. We also established a nomogram based on seven RNA binding proteins. This nomogram could inform individualized diagnostic and therapeutic strategies for Uterine Corpus Endometrial Carcinoma. Conclusion: Our work focused on systematically analyzing a large cohort of Uterine Corpus Endometrial Carcinoma patients in the The Cancer Genome Atlas database. We subsequently constructed a robust prognostic model based on seven RNA binding proteins that may soon inform individualized diagnosis and treatment.
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Affiliation(s)
- Yong Yao
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, Anhui, China
| | - Kangping Liu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, Anhui, China
| | - Yuxuan Wu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, Anhui, China
| | - Jieyu Zhou
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, Anhui, China
| | - Heyue Jin
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, Anhui, China
| | - Yimin Zhang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, Anhui, China
| | - Yumin Zhu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, Anhui, China
- *Correspondence: Yumin Zhu,
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Ballesteros M, Gil-Lluís P, Ejarque M, Diaz-Perdigones C, Martinez-Guasch L, Fernández-Veledo S, Vendrell J, Megía A. DNA Methylation in Gestational Diabetes and its Predictive Value for Postpartum Glucose Disturbances. J Clin Endocrinol Metab 2022; 107:2748-2757. [PMID: 35914803 PMCID: PMC9516049 DOI: 10.1210/clinem/dgac462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 11/21/2022]
Abstract
CONTEXT DNA methylation in the diagnosis of gestational diabetes. OBJECTIVE To assess the value of DNA methylation in the diagnosis of gestational diabetes (GDM) and in the prediction of maternal postpartum glucose disturbances. METHODS Two-stage observational study performed between July 2006 and December 2010, at University Hospital. Forty-eight randomly selected pregnant women formed the discovery cohort (24 with GDM and 24 controls) and 252 pregnant women (94 with GDM and 158 controls) formed the replication cohort. GDM women were re-evaluated 4 years postpartum. The main outcome measures were GDM, type 2 diabetes or prediabetes at 4 years postpartum. RESULTS We identified 3 CpG sites related to LINC00917, TRAPPC9, and LEF1 that were differentially methylated in women with GDM and abnormal glucose tolerance; and sites associated with LINC00917 and TRAPPC9 were independently associated with an abnormal glucose tolerance status 4 years postpartum after controlling for clinical variables. Moreover, the site associated with LINC00917 and the combination of the 3 sites had the highest predictive values. CONCLUSION Our results suggest that some of these sites may be implicated in the development of GDM and postpartum abnormal glucose tolerance.
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Affiliation(s)
- Mónica Ballesteros
- Mónica Ballesteros, Rovira i Virgili University, 43005, Tarragona, Spain.
| | - Pilar Gil-Lluís
- Department of Endocrinology and Nutrition, University Hospital of Tortosa Verge de la Cinta, Tarragona, Spain
| | - Miriam Ejarque
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition. Research Unit. University Hospital of Tarragona Joan XXIII-Institut d´Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
| | - Cristina Diaz-Perdigones
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition. Research Unit. University Hospital of Tarragona Joan XXIII-Institut d´Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
| | - Laia Martinez-Guasch
- Department of Medicine and Surgery, Rovira i Virgili University, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition. Research Unit. University Hospital of Tarragona Joan XXIII-Institut d´Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
| | - Sonia Fernández-Veledo
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition. Research Unit. University Hospital of Tarragona Joan XXIII-Institut d´Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
| | - Joan Vendrell
- Correspondence: Joan Vendrell, PhD, MD, Hospital Universitari de Tarragona Joan XXIII, Dr. Mallafre Guasch, 4, 43005 Tarragona, Spain.
| | - Ana Megía
- Ana Megia, PhD, MD, Hospital Universitari de Tarragona Joan XXIII, Dr. Mallafre Guasch, 4, 43005 Tarragona, Spain.
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Sensitive GlaI digestion and terminal transferase PCR for DNA methylation detection. Talanta 2022; 247:123616. [DOI: 10.1016/j.talanta.2022.123616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/30/2022]
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A sensing strategy combining T7 promoter-contained DNA probe with CRISPR/Cas13a for detection of bacteria and human methyltransferase. Anal Chim Acta 2022; 1227:340266. [DOI: 10.1016/j.aca.2022.340266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/03/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022]
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Hu R, Zhou XJ, Li W. Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis. J Comput Biol 2022; 29:769-781. [PMID: 35671506 PMCID: PMC9419965 DOI: 10.1089/cmb.2022.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Developing cancer prognostic models using multiomics data is a major goal of precision oncology. DNA methylation provides promising prognostic biomarkers, which have been used to predict survival and treatment response in solid tumor or plasma samples. This review article presents an overview of recently published computational analyses on DNA methylation for cancer prognosis. To address the challenges of survival analysis with high-dimensional methylation data, various feature selection methods have been applied to screen a subset of informative markers. Using candidate markers associated with survival, prognostic models either predict risk scores or stratify patients into subtypes. The model's discriminatory power can be assessed by multiple evaluation metrics. Finally, we discuss the limitations of existing studies and present the prospects of applying machine learning algorithms to fully exploit the prognostic value of DNA methylation.
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Affiliation(s)
- Ran Hu
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
- Bioinformatics Interdepartmental Graduate Program, University of California at Los Angeles, Los Angeles, California, USA
- Institute for Quantitative & Computational Biosciences, University of California at Los Angeles, Los Angeles, California, USA
| | - Xianghong Jasmine Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
- Institute for Quantitative & Computational Biosciences, University of California at Los Angeles, Los Angeles, California, USA
| | - Wenyuan Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
- Institute for Quantitative & Computational Biosciences, University of California at Los Angeles, Los Angeles, California, USA
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Prognostic and therapeutic prediction by screening signature combinations from transcriptome-methylome interactions in oral squamous cell carcinoma. Sci Rep 2022; 12:11400. [PMID: 35794182 PMCID: PMC9259703 DOI: 10.1038/s41598-022-15534-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/24/2022] [Indexed: 02/05/2023] Open
Abstract
DNA methylation pattern in oral squamous cell carcinoma (OSCC) remains poorly described. This study aimed to perform a genome-wide integrated analysis of the transcriptome and methylome and assess the efficacy of their prognostic signature model in patients with OSCC. We analyzed transcriptome and methylome data from 391 OSCC samples and 41 adjacent normal samples. A total of 8074 differentially expressed genes (DEGs) and 10,084 differentially expressed CpGs (DMCpGs) were identified. Then 241 DEGs with DMCpGs were identified. According to the prognostic analysis, the prognostic signature of methylation-related differentially expressed genes (mrDEGPS) was established. mrDEGPS consisted of seven prognostic methylation-related genes, including ESRRG, CCNA1, SLC20A1, COL6A6, FCGBP, CDKN2A, and ZNF43. mrDEGPS was a significant stratification factor of survival (P < 0.00001) irrespective of the clinical stage. The immune effector components, including B cells, CD4+ T cells, and CD8+ T cells, were decreased in the tumor environment of patients with high mrDEGPS. Immune checkpoint expressions, including CTLA-4, PD-1, LAG3, LGALS9, HAVCR2, and TIGHT, were comprehensively elevated (P < 0.001). The estimated half-maximal inhibitory concentration difference between low- and high-risk patients was inconsistent among chemotherapeutic drugs. In conclusion, the transcriptome–methylome interaction pattern in OSCC is complex. mrDEGPS can predict patient survival and responses to immunotherapy and chemotherapy and facilitate clinical decision-making in patients with OSCC.
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Epigenetic insights in the diagnosis, prognosis, and treatment selection in CRC, an updated review. Mol Biol Rep 2022; 49:10013-10022. [PMID: 35727475 DOI: 10.1007/s11033-022-07569-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 05/05/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND/AIM The gradual accumulation of genetic and epigenetic alterations can lead to the development of colorectal cancer. In the last decade much research has been done to discover how methylation as an epigenetic alteration leads to carcinogenesis. While Methylation is a biological process, it can influence gene expression by affecting the promoter activity. This article reviews the role of methylation in critical pathways in CRC. METHODS In this study using appropriate keywords, all research and review articles related to the role of methylation on different cancers were collected and analyzed. Also, existing information on methylation detection methods and therapeutic sensitivity or resistance due to DNA methylation were reviewed. RESULTS The results of this survey revealed that while Methylation is a biological process, it can influence gene expression by affecting the promoter activity. Promoter methylation is associated with up or downregulation of genes involved in critical pathways, including cell cycle, DNA repair, and cell adherence. Hence promoter methylation can be used as a molecular tool for early diagnosis, improving treatment, and predicting treatment resistance. CONCLUSION Current knowledge on potential methylation biomarkers for diagnosis and prognoses of CRC has also been discussed. Our survey proposes that a multi-biomarker panel is more efficient than a single biomarker in the early diagnosis of CRC.
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High-throughput sample processing for methylation analysis in an automated, enclosed environment. SLAS Technol 2022; 27:172-179. [DOI: 10.1016/j.slast.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Methylation Heterogeneity and Gene Expression of SPG20 in Solid Tumors. Genes (Basel) 2022; 13:genes13050861. [PMID: 35627246 PMCID: PMC9140344 DOI: 10.3390/genes13050861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/31/2022] Open
Abstract
Introduction. The downregulation of the Spastic Paraplegia-20 (SPG20) gene is correlated with a rare autosomal recessive disorder called Troyer Syndrome. Only in recent years has SPG20 been studied and partially characterized in cancer. SPG20 has been shown to be hypermethylated in colorectal cancer, gastric cancer, non-Hodgkin’s lymphoma and hepatocellular carcinoma. In this study, we analyze the methylation status and the gene expression of SPG20 in different tumors of various histological origins. Methods. We analyzed the data generated through Infinium Human Methylation 450 BeadChip arrays and RNA-seq approaches extrapolated from The Cancer Genome Atlas (TCGA) database. The statistics were performed with R 4.0.4. Results. We aimed to assess whether the hypermethylation of this target gene was a common characteristic among different tumors and if there was a correlation between the m-values and the gene expression in paired tumor versus solid tissue normal. Overall, our analysis highlighted that SPG20 open sea upstream the TSS is altogether hypermethylated, and the tumor tissues display a higher methylation heterogeneity compared to the solid tissue normal. The gene expression evidences a reproducible, higher gene expression in normal tissues. Conclusion. Our research, based on data mining from TCGA, evidences that colon and liver tumors display a consistent methylation heterogeneity compared to their normal counterparts. This parallels a downregulation of SPG20 gene expression in tumor samples and suggests a role for this multifunctional protein in the control of tumor progression.
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Chang L, Li J, Zhang R. Liquid biopsy for early diagnosis of non-small cell lung carcinoma: recent research and detection technologies. Biochim Biophys Acta Rev Cancer 2022; 1877:188729. [DOI: 10.1016/j.bbcan.2022.188729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/14/2022] [Accepted: 04/10/2022] [Indexed: 02/07/2023]
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