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Shore CJ, Villicaña S, El-Sayed Moustafa JS, Roberts AL, Gunn DA, Bataille V, Deloukas P, Spector TD, Small KS, Bell JT. Genetic effects on the skin methylome in healthy older twins. Am J Hum Genet 2024:S0002-9297(24)00254-4. [PMID: 39137780 DOI: 10.1016/j.ajhg.2024.07.010] [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: 12/05/2023] [Revised: 05/22/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Whole-skin DNA methylation variation has been implicated in several diseases, including melanoma, but its genetic basis has not yet been fully characterized. Using bulk skin tissue samples from 414 healthy female UK twins, we performed twin-based heritability and methylation quantitative trait loci (meQTL) analyses for >400,000 DNA methylation sites. We find that the human skin DNA methylome is on average less heritable than previously estimated in blood and other tissues (mean heritability: 10.02%). meQTL analysis identified local genetic effects influencing DNA methylation at 18.8% (76,442) of tested CpG sites, as well as 1,775 CpG sites associated with at least one distal genetic variant. As a functional follow-up, we performed skin expression QTL (eQTL) analyses in a partially overlapping sample of 604 female twins. Colocalization analysis identified over 3,500 shared genetic effects affecting thousands of CpG sites (10,067) and genes (4,475). Mediation analysis of putative colocalized gene-CpG pairs identified 114 genes with evidence for eQTL effects being mediated by DNA methylation in skin, including in genes implicating skin disease such as ALOX12 and CSPG4. We further explored the relevance of skin meQTLs to skin disease and found that skin meQTLs and CpGs under genetic influence were enriched for multiple skin-related genome-wide and epigenome-wide association signals, including for melanoma and psoriasis. Our findings give insights into the regulatory landscape of epigenomic variation in skin.
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Affiliation(s)
- Christopher J Shore
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Amy L Roberts
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Panos Deloukas
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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2
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Yang Y, Chen Y, Xu S, Guo X, Jia G, Ping J, Shu X, Zhao T, Yuan F, Wang G, Xie Y, Ci H, Liu H, Qi Y, Liu Y, Liu D, Li W, Ye F, Shu XO, Zheng W, Li L, Cai Q, Long J. Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk. Nat Commun 2024; 15:6071. [PMID: 39025880 PMCID: PMC11258330 DOI: 10.1038/s41467-024-50404-y] [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: 09/06/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
The relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging resources from the Genotype-Tissue Expression consortium, here we develop genetic models to predict DNA methylation at CpG sites across the genome for seven tissues and apply these models to genome-wide association study data of corresponding cancers, namely breast, colorectal, renal cell, lung, ovarian, prostate, and testicular germ cell cancers. At Bonferroni-corrected P < 0.05, we identify 4248 CpGs that are significantly associated with cancer risk, of which 95.4% (4052) are specific to a particular cancer type. Notably, 92 CpGs within 55 putative novel loci retain significant associations with cancer risk after conditioning on proximal signals identified by genome-wide association studies. Integrative multi-omics analyses reveal 854 CpG-gene-cancer trios, suggesting that DNA methylation at 309 distinct CpGs might influence cancer risk through regulating the expression of 205 unique cis-genes. These findings substantially advance our understanding of the interplay between genetics, epigenetics, and gene expression in cancer etiology.
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Affiliation(s)
- Yaohua Yang
- Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA.
| | - Yaxin Chen
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shuai Xu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Shu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tianying Zhao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fangcheng Yuan
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gang Wang
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yufang Xie
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hang Ci
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongmo Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yawen Qi
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongjun Liu
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Dan Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fei Ye
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Li Li
- Department of Family Medicine, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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3
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Fu M, Deng F, Chen J, Fu L, Lei J, Xu T, Chen Y, Zhou J, Gao Q, Ding H. Current data and future perspectives on DNA methylation in ovarian cancer (Review). Int J Oncol 2024; 64:62. [PMID: 38757340 PMCID: PMC11095605 DOI: 10.3892/ijo.2024.5650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Ovarian cancer (OC) represents the most prevalent malignancy of the female reproductive system. Its distinguishing features include a high aggressiveness, substantial morbidity and mortality, and a lack of apparent symptoms, which collectively pose significant challenges for early detection. Given that aberrant DNA methylation events leading to altered gene expression are characteristic of numerous tumor types, there has been extensive research into epigenetic mechanisms, particularly DNA methylation, in human cancers. In the context of OC, DNA methylation is often associated with the regulation of critical genes, such as BRCA1/2 and Ras‑association domain family 1A. Methylation modifications within the promoter regions of these genes not only contribute to the pathogenesis of OC, but also induce medication resistance and influence the prognosis of patients with OC. As such, a more in‑depth understanding of DNA methylation underpinning carcinogenesis could potentially facilitate the development of more effective therapeutic approaches for this intricate disease. The present review focuses on classical tumor suppressor genes, oncogenes, signaling pathways and associated microRNAs in an aim to elucidate the influence of DNA methylation on the development and progression of OC. The advantages and limitations of employing DNA methylation in the diagnosis, treatment and prevention of OC are also discussed. On the whole, the present literature review indicates that the DNA methylation of specific genes could potentially serve as a prognostic biomarker for OC and a therapeutic target for personalized treatment strategies. Further investigations in this field may yield more efficacious diagnostic and therapeutic alternatives for patients with OC.
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Affiliation(s)
- Mengyu Fu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Fengying Deng
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jie Chen
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Li Fu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jiahui Lei
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Ting Xu
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
- Department of Gynecology and Obstetrics, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu 215100, P.R. China
| | - Youguo Chen
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jinhua Zhou
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Qinqin Gao
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Hongmei Ding
- Institute for Fetology, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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Yang M, Wang M, Zhao X, Xu F, Liang S, Wang Y, Wang N, Sambou ML, Jiang Y, Dai J. DNA methylation marker identification and poly-methylation risk score in prediction of healthspan termination. Epigenomics 2024; 16:461-472. [PMID: 38482663 DOI: 10.2217/epi-2023-0343] [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] [Indexed: 03/23/2024] Open
Abstract
Aim: To elucidate the epigenetic consequences of DNA methylation in healthspan termination (HST), considering the current limited understanding. Materials & methods: Genetically predicted DNA methylation models were established (n = 2478). These models were applied to genome-wide association study data on HST. Then, a poly-methylation risk score (PMRS) was established in 241,008 individuals from the UK Biobank. Results: Of the 63,046 CpGs from the prediction models, 13 novel CpGs were associated with HST. Furthermore, people with high PMRSs showed higher HST risk (hazard ratio: 1.18; 95% CI: 1.13-1.25). Conclusion: The study indicates that DNA methylation may influence HST by regulating the expression of genes (e.g., PRMT6, CTSK). PMRSs have a promising application in discriminating subpopulations to facilitate early prevention.
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Affiliation(s)
- Meiqi Yang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Mei Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaoyu Zhao
- Department of Statistics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Feifei Xu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Shuang Liang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yifan Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Nanxi Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Muhammed Lamin Sambou
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yue Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Collaborative Innovation Center for Cancer Personalized Medicine & China International Cooperation Center for Environment & Human Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Collaborative Innovation Center for Cancer Personalized Medicine & China International Cooperation Center for Environment & Human Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
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5
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Skinner MK. Epigenetic biomarkers for disease susceptibility and preventative medicine. Cell Metab 2024; 36:263-277. [PMID: 38176413 DOI: 10.1016/j.cmet.2023.11.015] [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: 08/15/2023] [Revised: 10/11/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
The development of molecular biomarkers for disease makes it possible for preventative medicine approaches to be considered. Therefore, therapeutics, treatments, or clinical management can be used to delay or prevent disease development. The problem with genetic mutations as biomarkers is the low frequency with genome-wide association studies (GWASs), generally at best a 1% association of the patients with the disease. In contrast, epigenetic alterations have a high-frequency association of greater than 90%-95% of individuals with pathology in epigenome-wide association studies (EWASs). A wide variety of human diseases have been shown to have epigenetic biomarkers that are disease specific and that detect pathology susceptibility. This review is focused on the epigenetic biomarkers for disease susceptibility, and it distinct from the large literature on epigenetics of disease etiology or progression. The development of efficient epigenetic biomarkers for disease susceptibility will facilitate a paradigm shift from reactionary medicine to preventative medicine.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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Lu H, Wang Z, Cao B, Cong F, Wang X, Wei W. Dietary sources of branched-chain fatty acids and their biosynthesis, distribution, and nutritional properties. Food Chem 2024; 431:137158. [PMID: 37604010 DOI: 10.1016/j.foodchem.2023.137158] [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: 04/07/2023] [Revised: 08/05/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023]
Abstract
Branched-chain fatty acids (BCFAs) consist of a wide variety of fatty acids with alkyl branching of methyl group. The most common BCFAs are the types with one methyl group (mmBCFA) on the penultimate carbon (iBCFA) or the antepenultimate carbon (aiBCFA). Long-chain mmBCFAs are widely existing in animal fats, milks and are mostly derived from bacteria in the diet or animal digestive system. Recent studies show that BCFAs benefit human intestinal health and immune homeostasis, but the connection between their content, distribution in the human and their nutritional functions are not well established. In this paper, we reviewed BCFAs from various dietary sources focused on their molecular species. The BCFAs biosynthesis in bacteria, Caenorhabditis elegans, mammals and their distribution in human tissues are summarized. This paper also discusses the nutritional properties of BCFAs including influences on intestinal health, immunoregulatory effects, anti-carcinoma, and anti-obesity activities, by highlighting the most recent research progress.
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Affiliation(s)
- Huijia Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhen Wang
- Wilmar (Shanghai) Biotechnology Research & Development Center, Shanghai 200137, China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Bo Cao
- Wilmar (Shanghai) Biotechnology Research & Development Center, Shanghai 200137, China
| | - Fang Cong
- Wilmar (Shanghai) Biotechnology Research & Development Center, Shanghai 200137, China.
| | - Xingguo Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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Szymanski M, Wilczynski M, Pakiet A, Kaska L, Proczko-Stepaniak M, Bigda J, Sledzinski T, Mika A. Effect of Primary Versus Revisional One Anastomosis Gastric Bypass (OAGB) on Fatty Acid Profile. Obes Surg 2024; 34:77-85. [PMID: 37964164 PMCID: PMC10781856 DOI: 10.1007/s11695-023-06928-1] [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: 06/20/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
INTRODUCTION One anastomosis gastric bypass (OAGB) is one option of a revisional procedure for failed sleeve gastrectomy. Moreover, it can be used as a primary bariatric procedure, and is an effective surgery resulting in significant weight loss and the resolution or improvement of obesity-associated medical problems, accompanied by low perioperative complications. However, as with any therapy, OAGB has its limitations, including micronutrient deficiency or malnutrition. In our study, we compared the fatty acid (FA) profile in serum of patients after both primary OAGB (pOAGB) and revisional OAGB (rOAGB) to identify potential postsurgical FA alterations. METHODS This is a retrospective study on patients with obesity who underwent OAGB procedures (pOAGB n=68; rOAGB n=17), conducted from 2016 to 2018. In blood, we analyzed a series of biochemical parameters, and in the serum, the FA profile was determined using gas chromatography-mass spectrometry. RESULTS The percentage of excess BMI loss (% EBMIL) after pOAGB was 73.5 ± 2.47% in comparison to 45.9 ± 4.15% in the rOAGB group (p<0.001). In contrast to the lack of effect of rOAGB on most polyunsaturated FAs, in the pOAGB group, there was a decrease in eicosapentaenoic acid, and eicosatetraenoic and docosahexaenoic acid levels (p<0.001). We also found a decrease in very long-chain FAs (VLCFAs) and an increase in branched-chain FAs (BCFAs) after both types of OAGB procedure. CONCLUSIONS Both OAGB procedures improved the profile of most FAs, leading to a decrease in VLCFAs, which are considered harmful, and an improvement in BCFAs, which are considered to be beneficial. There is a need to further investigate the possibility of n-3 polyunsaturated FA supplementation after pOAGB, due to the large decrease in these FAs after pOAGB.
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Affiliation(s)
- Michal Szymanski
- Department of General, Endocrine, and Transplant Surgery, Medical University of Gdansk, ul. Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Maciej Wilczynski
- Department of General, Endocrine, and Transplant Surgery, Medical University of Gdansk, ul. Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Alicja Pakiet
- Department of Environmental Analysis, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Lukasz Kaska
- Department of General, Endocrine, and Transplant Surgery, Medical University of Gdansk, ul. Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Monika Proczko-Stepaniak
- Department of General, Endocrine, and Transplant Surgery, Medical University of Gdansk, ul. Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Justyna Bigda
- Department of General, Endocrine, and Transplant Surgery, Medical University of Gdansk, ul. Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, ul. Debinki 1, 80-211, Gdansk, Poland
| | - Adriana Mika
- Department of Environmental Analysis, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, ul. Debinki 1, 80-211, Gdansk, Poland.
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Sun Y, Zhu J, Yang Y, Zhang Z, Zhong H, Zeng G, Zhou D, Nowakowski RS, Long J, Wu C, Wu L. Identification of candidate DNA methylation biomarkers related to Alzheimer's disease risk by integrating genome and blood methylome data. Transl Psychiatry 2023; 13:387. [PMID: 38092781 PMCID: PMC10719322 DOI: 10.1038/s41398-023-02695-w] [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: 07/18/2022] [Revised: 11/16/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Alzheimer disease (AD) is a common neurodegenerative disease with a late onset. It is critical to identify novel blood-based DNA methylation biomarkers to better understand the extent of the molecular pathways affected in AD. Two sets of blood DNA methylation genetic prediction models developed using different reference panels and modelling strategies were leveraged to evaluate associations of genetically predicted DNA methylation levels with AD risk in 111,326 (46,828 proxy) cases and 677,663 controls. A total of 1,168 cytosine-phosphate-guanine (CpG) sites showed a significant association with AD risk at a false discovery rate (FDR) < 0.05. Methylation levels of 196 CpG sites were correlated with expression levels of 130 adjacent genes in blood. Overall, 52 CpG sites of 32 genes showed consistent association directions for the methylation-gene expression-AD risk, including nine genes (CNIH4, THUMPD3, SERPINB9, MTUS1, CISD1, FRAT2, CCDC88B, FES, and SSH2) firstly reported as AD risk genes. Nine of 32 genes were enriched in dementia and AD disease categories (P values ranged from 1.85 × 10-4 to 7.46 × 10-6), and 19 genes in a neurological disease network (score = 54) were also observed. Our findings improve the understanding of genetics and etiology for AD.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P. R. China
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Yaohua Yang
- Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, 22093, USA
| | - Zichen Zhang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Guanghua Zeng
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P. R. China
| | - Dan Zhou
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P.R. China
| | - Richard S Nowakowski
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, 32304, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA.
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9
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Kong L, Wang L, Wang Z, Xiao X, You Y, Wu H, Wu M, Liu P, Li L. Cytological DNA methylation for cervical cancer screening: a validation set. Front Oncol 2023; 13:1181982. [PMID: 37671063 PMCID: PMC10475939 DOI: 10.3389/fonc.2023.1181982] [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: 03/08/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023] Open
Abstract
Background In a previous training set with a case-controlled design, cutoff values for host EPB41L3 and JAM3 gene methylation were obtained for the detection of cervical intraepithelial neoplasia (CIN) 2 or more severe lesions (CIN2+). This validation trial was conducted to evaluate the role of DNA methylation in screening for CIN2+ by cervical cytology among unselected participants. Methods From June 1, 2019, to September 1, 2019, in our study center, we collected liquid-based samples from cervical swabs for methylation assays and hrHPV testing in eligible patients. The primary endpoint was the diagnostic accuracy of DNA methylation and hrHPV genotyping for CIN2+ according to confirmed histology results. Results Among 307 participants, compared with hrHPV testing, the methylation assay for CIN2+ had lower sensitivity (68.7% versus 86.1%, p=0.002) but higher specificity (96.7% versus 0.696, p<0.001). The methylation assay also had favorable sensitivity and specificity in patients with negative hrHPV testing (56.3% and 96.9%) and in patients with cervical adenocarcinoma (73.7% and 92.7%). DNA methylation had higher specificity than the hrHPV assay (100.0% versus 44.4%, p<0.001) for identifying residual CIN2+ in patients without residual lesions. Positive cervical DNA methylation was associated with a diagnostic probability of endometrial carcinoma (odds ratio 15.5 [95% confidence interval 4.1-58.6]) but not of ovarian epithelial carcinoma (1.4 [0.3-6.5]). Conclusions The host EPB41L3 and JAM3 gene methylation assay in cervical cytology had favorable diagnostic accuracy for CIN2+ and was highly specific for residual CIN2+ lesions The methylation assay is a promising triage tool in hrHPV+ women, or even an independent tool for cervical cancer screening. The methylation status in cervical cytology could also serve as a prognostic biomarker. Its role in detecting endometrial carcinomas is worthy of further exploration.
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Affiliation(s)
- Linghua Kong
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Linhai Wang
- Department of Technology, Beijing OriginPoly Biotechnology CO., Ltd., Beijing, China
| | - Ziyun Wang
- Department of Technology, Beijing OriginPoly Biotechnology CO., Ltd., Beijing, China
| | - Xiaoping Xiao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Yan You
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Ming Wu
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Pei Liu
- Department of Technology, Beijing OriginPoly Biotechnology CO., Ltd., Beijing, China
| | - Lei Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Beijing, China
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10
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Matsas A, Stefanoudakis D, Troupis T, Kontzoglou K, Eleftheriades M, Christopoulos P, Panoskaltsis T, Stamoula E, Iliopoulos DC. Tumor Markers and Their Diagnostic Significance in Ovarian Cancer. Life (Basel) 2023; 13:1689. [PMID: 37629546 PMCID: PMC10455076 DOI: 10.3390/life13081689] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Ovarian cancer (OC) is characterized by silent progression and late-stage diagnosis. It is critical to detect and accurately diagnose the disease early to improve survival rates. Tumor markers have emerged as valuable tools in the diagnosis and management of OC, offering non-invasive and cost-effective options for screening, monitoring, and prognosis. PURPOSE This paper explores the diagnostic importance of various tumor markers including CA-125, CA15-3, CA 19-9, HE4,hCG, inhibin, AFP, and LDH, and their impact on disease monitoring and treatment response assessment. METHODS Article searches were performed on PubMed, Scopus, and Google Scholar. Keywords used for the searching process were "Ovarian cancer", "Cancer biomarkers", "Early detection", "Cancer diagnosis", "CA-125","CA 15-3","CA 19-9", "HE4","hCG", "inhibin", "AFP", "LDH", and others. RESULTS HE4, when combined with CA-125, shows improved sensitivity and specificity, particularly in early-stage detection. Additionally, hCG holds promise as a prognostic marker, aiding treatment response prediction and outcome assessment. Novel markers like microRNAs, DNA methylation patterns, and circulating tumor cells offer potential for enhanced diagnostic accuracy and personalized management. Integrating these markers into a comprehensive panel may improve sensitivity and specificity in ovarian cancer diagnosis. However, careful interpretation of tumor marker results is necessary, considering factors such as age, menopausal status, and comorbidities. Further research is needed to validate and refine diagnostic algorithms, optimizing the clinical significance of tumor markers in ovarian cancer management. In conclusion, tumor markers such as CA-125, CA15-3, CA 19-9, HE4, and hCG provide valuable insights into ovarian cancer diagnosis, monitoring, and prognosis, with the potential to enhance early detection.
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Affiliation(s)
- Alkis Matsas
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Stefanoudakis
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Theodore Troupis
- Department of Anatomy, Faculty of Health Sciences, Medical School, National and Kapodistrian University of Athens, MikrasAsias Str. 75, 11627 Athens, Greece
| | - Konstantinos Kontzoglou
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Makarios Eleftheriades
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Panagiotis Christopoulos
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Theodoros Panoskaltsis
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Eleni Stamoula
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, University Campus Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dimitrios C. Iliopoulos
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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11
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Duan Y, Zhang P, Zhang T, Zhou L, Yin R. Characterization of global research trends and prospects on platinum-resistant ovarian cancer: a bibliometric analysis. Front Oncol 2023; 13:1151871. [PMID: 37342181 PMCID: PMC10277726 DOI: 10.3389/fonc.2023.1151871] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/22/2023] [Indexed: 06/22/2023] Open
Abstract
Background In the last decades, growing attention has been focused on identifying effective therapeutic strategies in the orphan clinical setting of women with platinum-resistant ovarian cancer (PROC), generating thousands of original articles. However, the literature involving bibliometric analysis of PROC has not been published yet. Objective This study hopes to gain a better understanding of the hot spots and trends in PROC by conducting a bibliometric analysis, as well as identify potential new research directions. Methods We searched the Web of Science Core Collection (WOSCC) for PROC-related articles published between 1990 and 2022. CiteSpace 6.1.R2 and VOS viewer 1.6.18.0 were primarily utilized to evaluate the contribution and co-occurrence relationships of various countries and regions, institutes, and journals and to identify research hotspots and promising future trends in this research field. Results A total of 3,462 Web of Science publications were retrieved that were published in 671 academic journals by 1135 authors from 844 organizations in 75 countries and regions. The United States was the leading contributor in this field, and the University of Texas MD Anderson Cancer Center was the most productive institution. Gynecologic Oncology was the most productive journal, while the Journal of Clinical Oncology was the most cited and influential. Co-citation cluster labels revealed the characteristics of seven major clusters, including synthetic lethality, salvage treatment, human ovarian-carcinoma cell line, PARP inhibitor resistance, antitumor complexes, folate receptor, and targeting platinum-resistant disease. Keywords and references burst detection indicated that biomarkers, genetic and phenotypic changes, immunotherapy, and targeted therapy were the most recent and most significant aspects of PROC research. Conclusion This study conducted a comprehensive review of PROC research using bibliometric and visual techniques. Understanding the immunological landscape of PROC and identifying the population that can benefit from immunotherapy, especially in combination with other therapeutic options (such as chemotherapy and targeted therapy), will continue to be the focal point of research.
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Affiliation(s)
- Yuanqiong Duan
- Department of Obstetrics and Gynecology, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Peixuan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Tianyue Zhang
- Department of Obstetrics and Gynecology, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lu Zhou
- Department of Obstetrics and Gynecology, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Rutie Yin
- Department of Obstetrics and Gynecology, West China Second Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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12
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Ding H, Yu JH, Ge G, Ma YY, Wang JC, Zhang J, Liu J. RASAL2 Deficiency Attenuates Hepatic Steatosis by Promoting Hepatic VLDL Secretion via the AKT/TET1/MTTP Axis. J Clin Transl Hepatol 2023; 11:261-272. [PMID: 36643045 PMCID: PMC9817063 DOI: 10.14218/jcth.2022.00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND AIMS RAS protein activator like 2 (RASAL2) is a newly discovered metabolic regulator involved in energy homeostasis and adipogenesis. However, whether RASAL2 is involved in hepatic lipid metabolism remains undetermined. This study explored the function of RASAL2 and elucidated its potential mechanisms in nonalcoholic fatty liver disease (NAFLD). METHODS NAFLD models were established either by feeding mice a high-fat diet or by incubation of hepatocytes with 1 mM free fatty acids (oleic acid:palmitic acid=2:1). Pathological changes were observed by hematoxylin and eosin staining. Lipid accumulation was assessed by Oil Red O staining, BODIPY493/503 staining, and triglyceride quantification. The in vivo secretion rate of very low-density lipoprotein was determined by intravenous injection of tyloxapol. Gene regulation was analyzed by chromatin immunoprecipitation assays and hydroxymethylated DNA immunoprecipitation combined with real-time polymerase chain reaction. RESULTS RASAL2 deficiency ameliorated hepatic steatosis both in vivo and in vitro. Mechanistically, RASAL2 deficiency upregulated hepatic TET1 expression by activating the AKT signaling pathway and thereby promoted MTTP expression by DNA hydroxymethylation, leading to increased production and secretion of very low-density lipoprotein, which is the major carrier of triglycerides exported from the liver to distal tissues. CONCLUSIONS Our study reports the first evidence that RASAL2 deficiency ameliorates hepatic steatosis by regulating lipid metabolism through the AKT/TET1/MTTP axis. These findings will help understand the pathogenesis of NAFLD and highlight the potency of RASAL2 as a new molecular target for NAFLD.
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Affiliation(s)
- Hao Ding
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiang-Hong Yu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ge Ge
- Department of Dermatology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Yan-Yun Ma
- Human Phenome Institute, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Six-sector Industrial Research Institute, Fudan University, Shanghai, China
| | - Jiu-Cun Wang
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Jun Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Correspondence to: Jie Liu and Jun Zhang, Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China. ORCID: https://orcid.org/0000-0002-7638-187X (JL), https://orcid.org/0000-0002-9330-6070 (JZ). Tel: +86-21-52888236 (JL), +86-21-52888237 (JZ), Fax: +86-21-52888236, E-mail: (JL) and
| | - Jie Liu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Correspondence to: Jie Liu and Jun Zhang, Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China. ORCID: https://orcid.org/0000-0002-7638-187X (JL), https://orcid.org/0000-0002-9330-6070 (JZ). Tel: +86-21-52888236 (JL), +86-21-52888237 (JZ), Fax: +86-21-52888236, E-mail: (JL) and
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13
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Martínez-Montoro JI, Núñez-Sánchez MÁ, Martinez-Sanchez MA, Balaguer-Román A, Fernández-Ruiz VE, Ferrer-Gómez M, Sledzinski T, Frutos MD, Fernández-García JC, Mika A, Ramos-Molina B. Hepatic and serum branched-chain fatty acid profile in patients with nonalcoholic fatty liver disease: A case-control study. Obesity (Silver Spring) 2023; 31:1064-1074. [PMID: 36876627 DOI: 10.1002/oby.23711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/05/2022] [Accepted: 12/18/2022] [Indexed: 03/07/2023]
Abstract
OBJECTIVE Alterations in the hepatic lipidome are a crucial factor involved in the pathophysiology of nonalcoholic fatty liver disease (NAFLD). The aim of this study was to evaluate the serum and hepatic profile of branched-chain fatty acids (BCFAs) in patients with different stages of NAFLD. METHODS This was a case-control study performed in 27 patients without NAFLD, 49 patients with nonalcoholic fatty liver, and 17 patients with nonalcoholic steatohepatitis, defined by liver biopsies. Serum and hepatic levels of BCFAs were analyzed by gas chromatography-mass spectrometry. The hepatic expression of genes involved in the endogenous synthesis of BCFAs was analyzed by real-time quantitative polymerase chain reaction (RT-qPCR). RESULTS A significant increase in hepatic BCFAs was found in subjects with NAFLD compared with those without NAFLD; no differences were observed in serum BCFAs between study groups. Trimethyl BCFAs, iso-BCFAs, and anteiso-BCFAs were increased in subjects with NAFLD (either nonalcoholic fatty liver or nonalcoholic steatohepatitis) compared with those without NAFLD. Correlation analysis showed a relationship between hepatic BCFAs and the histopathological diagnosis of NAFLD, as well as other histological and biochemical parameters related to this disease. Gene expression analysis in liver showed that the mRNA levels of BCAT1, BCAT2, and BCKDHA were upregulated in patients with NAFLD. CONCLUSIONS These results suggest that the increased production of liver BCFAs might be related to NAFLD development and progression.
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Affiliation(s)
- José Ignacio Martínez-Montoro
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga (IBIMA), Faculty of Medicine, University of Málaga, Málaga, Spain
| | | | | | - Andrés Balaguer-Román
- Obesity and Metabolism Research Laboratory, Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
- Department of General and Digestive System Surgery, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - Virginia E Fernández-Ruiz
- Obesity and Metabolism Research Laboratory, Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
- Department of Endocrinology and Nutrition, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - Mercedes Ferrer-Gómez
- Obesity and Metabolism Research Laboratory, Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
- Department of Endocrinology and Nutrition, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - María Dolores Frutos
- Department of General and Digestive System Surgery, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - José Carlos Fernández-García
- Department of Endocrinology and Nutrition, Regional University Hospital of Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Faculty of Medicine, University of Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBERObn), Instituto de Salud Carlos III, Madrid, Spain
| | - Adriana Mika
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Bruno Ramos-Molina
- Obesity and Metabolism Research Laboratory, Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
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14
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Xu Z, Zhang L, Wang M, Huang Y, Zhang M, Li S, Wang L, Li K, Hou Y. A novel subtype to predict prognosis and treatment response with DNA driver methylation-transcription in ovarian cancer. Epigenomics 2022; 14:1073-1088. [PMID: 36200265 DOI: 10.2217/epi-2022-0206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To identify a novel subtype with DNA driver methylation-transcriptomic multiomics and predict prognosis and therapy response in serous ovarian cancer (SOC). Methods: SOC cohorts with both mRNA and methylation were collected, and DNA driver methylation (DNAme) was identified with the MithSig method. A novel prognostic subtype was developed by integrating the information on DNAme and prognosis-regulated DNAme-associated mRNA by similarity network fusion. Results: 43 overlapped DNAme were identified in three independent cohorts. SOC patients were categorized into three distinct subtypes by integrated multiomics. There were differences in prognosis, tumor microenvironment and response to therapy among the subtypes. Conclusion: This study identified 43 DNAmes and proposes a novel subtype toward personalized chemotherapy and immunotherapy for SOC patients based on multiomics.
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Affiliation(s)
- Zhenyi Xu
- Department of Epidemiology & Biostatistics, School of Public Health, Harbin Medical University, Harbin, 150086, China
| | - Liuchao Zhang
- Department of Epidemiology & Biostatistics, School of Public Health, Harbin Medical University, Harbin, 150086, China
| | - Meng Wang
- Department of Epidemiology & Biostatistics, School of Public Health, Harbin Medical University, Harbin, 150086, China
| | - Yue Huang
- Department of Epidemiology & Biostatistics, School of Public Health, Harbin Medical University, Harbin, 150086, China
| | - Min Zhang
- Department of Epidemiology & Biostatistics, School of Public Health, Harbin Medical University, Harbin, 150086, China
| | - Shuang Li
- Department of Epidemiology & Biostatistics, School of Public Health, Harbin Medical University, Harbin, 150086, China
| | - Liuying Wang
- Department of Epidemiology & Biostatistics, School of Public Health, Harbin Medical University, Harbin, 150086, China
| | - Kang Li
- Department of Epidemiology & Biostatistics, School of Public Health, Harbin Medical University, Harbin, 150086, China
| | - Yan Hou
- Department of Biostatistics, Peking University, Beijing, 100000, China
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15
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Integrative multi-omic analysis identifies genetically influenced DNA methylation biomarkers for breast and prostate cancers. Commun Biol 2022; 5:594. [PMID: 35710732 PMCID: PMC9203749 DOI: 10.1038/s42003-022-03540-4] [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: 11/25/2021] [Accepted: 05/30/2022] [Indexed: 12/02/2022] Open
Abstract
Aberrant DNA methylation has emerged as a hallmark in several cancers and contributes to risk, oncogenesis, progression, and prognosis. In this study, we performed imputation-based and conventional methylome-wide association analyses for breast cancer (BrCa) and prostate cancer (PrCa). The imputation-based approach identified DNA methylation at cytosine-phosphate-guanine sites (CpGs) associated with BrCa and PrCa risk utilising genome-wide association summary statistics (NBrCa = 228,951, NPrCa = 140,254) and prebuilt methylation prediction models, while the conventional approach identified CpG associations utilising TCGA and GEO experimental methylation data (NBrCa = 621, NPrCa = 241). Enrichment analysis of the association results implicated 77 and 81 genetically influenced CpGs for BrCa and PrCa, respectively. Furthermore, analysis of differential gene expression around these CpGs suggests a genome-epigenome-transcriptome mechanistic relationship. Conditional analyses identified multiple independent secondary SNP associations (Pcond < 0.05) around 28 BrCa and 22 PrCa CpGs. Cross-cancer analysis identified eight common CpGs, including a strong therapeutic target in SREBF1 (17p11.2)—a key player in lipid metabolism. These findings highlight the utility of integrative analysis of multi-omic cancer data to identify robust biomarkers and understand their regulatory effects on cancer risk. Methylome-wide association studies identify genetically-influenced CpGs associated with breast and prostate cancer risk and (epi)genome-transcriptome mechanistic relationships, with lipid metabolism genes implicated as potential therapeutic targets.
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16
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Fixing the GAP: the role of RhoGAPs in cancer. Eur J Cell Biol 2022; 101:151209. [DOI: 10.1016/j.ejcb.2022.151209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/29/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
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17
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Barrett JE, Jones A, Evans I, Reisel D, Herzog C, Chindera K, Kristiansen M, Leavy OC, Manchanda R, Bjørge L, Zikan M, Cibula D, Widschwendter M. The DNA methylome of cervical cells can predict the presence of ovarian cancer. Nat Commun 2022; 13:448. [PMID: 35105887 PMCID: PMC8807742 DOI: 10.1038/s41467-021-26615-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 10/04/2021] [Indexed: 02/03/2023] Open
Abstract
The vast majority of epithelial ovarian cancer arises from tissues that are embryologically derived from the Müllerian Duct. Here, we demonstrate that a DNA methylation signature in easy-to-access Müllerian Duct-derived cervical cells from women with and without ovarian cancer (i.e. referred to as the Women's risk IDentification for Ovarian Cancer index or WID-OC-index) is capable of identifying women with an ovarian cancer in the absence of tumour DNA with an AUC of 0.76 and women with an endometrial cancer with an AUC of 0.81. This and the observation that the cervical cell WID-OC-index mimics the epigenetic program of those cells at risk of becoming cancerous in BRCA1/2 germline mutation carriers (i.e. mammary epithelium, fallopian tube fimbriae, prostate) further suggest that the epigenetic misprogramming of cervical cells is an indicator for cancer predisposition. This concept has the potential to advance the field of risk-stratified cancer screening and prevention.
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Affiliation(s)
- James E Barrett
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Kantaraja Chindera
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Mark Kristiansen
- UCL Genomics, Zayed Centre for Research into Rare Disease in Children, University College London, London, WC1N 1DZ, UK
| | - Olivia C Leavy
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- Department of Non-communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Ranjit Manchanda
- Department of Gynaecological Oncology, Barts Health NHS Trust, Royal London Hospital, London, E1 1BB, UK
- Centre for Prevention, Detection & Diagnosis, Wolfson Institute of Population Health, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Health Services Research, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Line Bjørge
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Michal Zikan
- Hospital Na Bulovce, Prague, Czech Republic
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Cibula
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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18
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Zhang S, Zhang J, Zhang Q, Liang Y, Du Y, Wang G. Identification of Prognostic Biomarkers for Bladder Cancer Based on DNA Methylation Profile. Front Cell Dev Biol 2022; 9:817086. [PMID: 35174173 PMCID: PMC8841402 DOI: 10.3389/fcell.2021.817086] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022] Open
Abstract
Background: DNA methylation is an important epigenetic modification, which plays an important role in regulating gene expression at the transcriptional level. In tumor research, it has been found that the change of DNA methylation leads to the abnormality of gene structure and function, which can provide early warning for tumorigenesis. Our study aims to explore the relationship between the occurrence and development of tumor and the level of DNA methylation. Moreover, this study will provide a set of prognostic biomarkers, which can more accurately predict the survival and health of patients after treatment. Methods: Datasets of bladder cancer patients and control samples were collected from TCGA database, differential analysis was employed to obtain genes with differential DNA methylation levels between tumor samples and normal samples. Then the protein-protein interaction network was constructed, and the potential tumor markers were further obtained by extracting Hub genes from subnet. Cox proportional hazard regression model and survival analysis were used to construct the prognostic model and screen out the prognostic markers of bladder cancer, so as to provide reference for tumor prognosis monitoring and improvement of treatment plan. Results: In this study, we found that DNA methylation was indeed related with the occurrence of bladder cancer. Genes with differential DNA methylation could serve as potential biomarkers for bladder cancer. Through univariate and multivariate Cox proportional hazard regression analysis, we concluded that FASLG and PRKCZ can be used as prognostic biomarkers for bladder cancer. Patients can be classified into high or low risk group by using this two-gene prognostic model. By detecting the methylation status of these genes, we can evaluate the survival of patients. Conclusion: The analysis in our study indicates that the methylation status of tumor-related genes can be used as prognostic biomarkers of bladder cancer.
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Affiliation(s)
- Shumei Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Jingyu Zhang
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qichao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yingjian Liang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Youwen Du
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
- *Correspondence: Guohua Wang,
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Zhu J, Yang Y, Kisiel JB, Mahoney DW, Michaud DS, Guo X, Taylor WR, Shu XO, Shu X, Liu D, Li B, Tao R, Cai Q, Zheng W, Long J, Wu L. Integrating Genome and Methylome Data to Identify Candidate DNA Methylation Biomarkers for Pancreatic Cancer Risk. Cancer Epidemiol Biomarkers Prev 2021; 30:2079-2087. [PMID: 34497089 PMCID: PMC8568683 DOI: 10.1158/1055-9965.epi-21-0400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/20/2021] [Accepted: 08/21/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The role of methylation in pancreatic cancer risk remains unclear. We integrated genome and methylome data to identify CpG sites (CpG) with the genetically predicted methylation to be associated with pancreatic cancer risk. We also studied gene expression to understand the identified associations. METHODS Using genetic data and white blood cell methylation data from 1,595 subjects of European descent, we built genetic models to predict DNA methylation levels. After internal and external validation, we applied prediction models with satisfactory performance to the genetic data of 8,280 pancreatic cancer cases and 6,728 controls of European ancestry to investigate the associations of predicted methylation with pancreatic cancer risk. For associated CpGs, we compared their measured levels in pancreatic tumor versus benign tissue. RESULTS We identified 45 CpGs at nine loci showing an association with pancreatic cancer risk, including 15 CpGs showing an association independent from identified risk variants. We observed significant correlations between predicted methylation of 16 of the 45 CpGs and predicted expression of eight adjacent genes, of which six genes showed associations with pancreatic cancer risk. Of the 45 CpGs, we were able to compare measured methylation of 16 in pancreatic tumor versus benign pancreatic tissue. Of them, six showed differentiated methylation. CONCLUSIONS We identified methylation biomarker candidates associated with pancreatic cancer using genetic instruments and added additional insights into the role of methylation in regulating gene expression in pancreatic cancer development. IMPACT A comprehensive study using genetic instruments identifies 45 CpG sites at nine genomic loci for pancreatic cancer risk.
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Affiliation(s)
- Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Dominique S Michaud
- Department of Public Health and Community Medicine, Tufts University Medical School, Boston, Massachusetts
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Duo Liu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii.
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20
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Jareid M, Snapkov I, Holden M, Busund LTR, Lund E, Nøst TH. The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort. PLoS One 2021; 16:e0256442. [PMID: 34449791 PMCID: PMC8396762 DOI: 10.1371/journal.pone.0256442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/06/2021] [Indexed: 11/22/2022] Open
Abstract
Epithelial ovarian cancer (EOC) has a 5-year relative survival of 50%, partly because markers of early-stage disease are not available in current clinical diagnostics. The aim of the present study was to investigate whether EOC is associated with transcriptional profiles in blood collected up to 7 years before diagnosis. For this, we used RNA-stabilized whole blood, which contains circulating immune cells, from a sample of EOC cases from the population-based Norwegian Women and Cancer (NOWAC) postgenome cohort. We explored case-control differences in gene expression in all EOC (66 case-control pairs), as well as associations between gene expression and metastatic EOC (56 pairs), serous EOC (45 pairs, 44 of which were metastatic), and interval from blood sample collection to diagnosis (≤3 or >3 years; 34 and 31 pairs, respectively). Lastly, we assessed differential expression of genes associated with EOC in published functional genomics studies that used blood samples collected from newly diagnosed women. After adjustment for multiple testing, this nested case-control study revealed no significant case-control differences in gene expression in all EOC (false discovery rate q>0.96). With the exception of a few probes, the log2 fold change values obtained in gene-wise linear models were below ±0.2. P-values were lowest in analyses of metastatic EOC (80% of which were serous EOC). No common transcriptional profile was indicated by interval to diagnosis; when comparing the 100 genes with the lowest p-values in gene-wise tests in samples collected ≤3 and >3 years before EOC diagnosis, no overlap in these genes was observed. Among 86 genes linked to ovarian cancer in previous publications, our data contained expression values for 42, and of these, tests of LIME1, GPR162, STAB1, and SKAP1, resulted in unadjusted p<0.05. Although limited by sample size, our findings indicated less variation in blood gene expression between women with similar tumor characteristics.
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Affiliation(s)
- Mie Jareid
- Faculty of Health Sciences, Department of Community Medicine, UiT – The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Igor Snapkov
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | | | - Lill-Tove Rasmussen Busund
- Faculty of Health Sciences, Department of Medical Biology, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Eiliv Lund
- Faculty of Health Sciences, Department of Community Medicine, UiT – The Arctic University of Norway, Tromsø, Norway
- Cancer Registry of Norway, Oslo, Norway
| | - Therese Haugdahl Nøst
- Faculty of Health Sciences, Department of Community Medicine, UiT – The Arctic University of Norway, Tromsø, Norway
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21
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Wu L, Zhu J, Liu D, Sun Y, Wu C. An integrative multiomics analysis identifies putative causal genes for COVID-19 severity. Genet Med 2021; 23:2076-2086. [PMID: 34183789 PMCID: PMC8237048 DOI: 10.1038/s41436-021-01243-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Purpose It is critical to identify putative causal targets for SARS coronavirus 2, which may guide drug repurposing options to reduce the public health burden of COVID-19. Methods We applied complementary methods and multiphased design to pinpoint the most likely causal genes for COVID-19 severity. First, we applied cross-methylome omnibus (CMO) test and leveraged data from the COVID-19 Host Genetics Initiative (HGI) comparing 9,986 hospitalized COVID-19 patients and 1,877,672 population controls. Second, we evaluated associations using the complementary S-PrediXcan method and leveraging blood and lung tissue gene expression prediction models. Third, we assessed associations of the identified genes with another COVID-19 phenotype, comparing very severe respiratory confirmed COVID versus population controls. Finally, we applied a fine-mapping method, fine-mapping of gene sets (FOGS), to prioritize putative causal genes. Results Through analyses of the COVID-19 HGI using complementary CMO and S-PrediXcan methods along with fine-mapping, XCR1, CCR2, SACM1L, OAS3, NSF, WNT3, NAPSA, and IFNAR2 are identified as putative causal genes for COVID-19 severity. Conclusion We identified eight genes at five genomic loci as putative causal genes for COVID-19 severity.
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Affiliation(s)
- Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA.
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Duo Liu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA.,Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanfa Sun
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA.,College of Life Science, Longyan University, Longyan, Fujian, P. R. China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, P.R. China.,Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University, Longyan, Fujian, P.R. China
| | - Chong Wu
- Department of Statistics, Florida State University, Tallahassee, FL, USA.
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22
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Abstract
The G84E germline mutation of HOXB13 predisposes to prostate cancer and is clinically tested for familial cancer care. We investigated the HOXB locus to define a potentially broader contribution to prostate cancer heritability. We sought HOXB locus germline variants altering prostate cancer risk in three European-ancestry case-control study populations (combined 7812 cases and 5047 controls): the International Consortium for Prostate Cancer Genetics Study; the Nashville Familial Prostate Cancer Study; and the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Multiple rare genetic variants had concordant and strong risk effects in these study populations and exceeded genome-wide significance. Independent risk signals were best detected by sentinel variants rs559612720 within SKAP1 (OR = 8.1, P = 2E-9) and rs138213197 (G84E) within HOXB13 (OR = 5.6, P = 2E-11), separated by 567 kb. Half of carriers inherited both risk alleles, while others inherited either alone. Under mutual adjustment, the variants separately carried 3.6- and 3.1-fold risk, respectively, while joint inheritance carried 11.3-fold risk. These risks were further accentuated among men meeting criteria for hereditary prostate cancer, and further still for those with early-onset or aggressive disease. Among hereditary prostate cancer cases diagnosed under age 60 and with aggressive disease, joint inheritance carried a risk of OR = 27.7 relative to controls, P = 2E-8. The HOXB sentinel variant pair more fully captured genetic risk for prostate cancer within the study populations than either variant alone.
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23
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Brasil S, Neves CJ, Rijoff T, Falcão M, Valadão G, Videira PA, Dos Reis Ferreira V. Artificial Intelligence in Epigenetic Studies: Shedding Light on Rare Diseases. Front Mol Biosci 2021; 8:648012. [PMID: 34026829 PMCID: PMC8131862 DOI: 10.3389/fmolb.2021.648012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/09/2021] [Indexed: 12/29/2022] Open
Abstract
More than 7,000 rare diseases (RDs) exist worldwide, affecting approximately 350 million people, out of which only 5% have treatment. The development of novel genome sequencing techniques has accelerated the discovery and diagnosis in RDs. However, most patients remain undiagnosed. Epigenetics has emerged as a promise for diagnosis and therapies in common disorders (e.g., cancer) with several epimarkers and epidrugs already approved and used in clinical practice. Hence, it may also become an opportunity to uncover new disease mechanisms and therapeutic targets in RDs. In this “big data” age, the amount of information generated, collected, and managed in (bio)medicine is increasing, leading to the need for its rapid and efficient collection, analysis, and characterization. Artificial intelligence (AI), particularly deep learning, is already being successfully applied to analyze genomic information in basic research, diagnosis, and drug discovery and is gaining momentum in the epigenetic field. The application of deep learning to epigenomic studies in RDs could significantly boost discovery and therapy development. This review aims to collect and summarize the application of AI tools in the epigenomic field of RDs. The lower number of studies found, specific for RDs, indicate that this is a field open to expansion, following the results obtained for other more common disorders.
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Affiliation(s)
- Sandra Brasil
- Portuguese Association for CDG, Lisbon, Portugal.,CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
| | - Cátia José Neves
- Portuguese Association for CDG, Lisbon, Portugal.,CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
| | - Tatiana Rijoff
- Portuguese Association for CDG, Lisbon, Portugal.,CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
| | - Marta Falcão
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Gonçalo Valadão
- Instituto de Telecomunicações, Lisbon, Portugal.,Departamento de Ciências e Tecnologias, Autónoma Techlab - Universidade Autónoma de Lisboa, Lisbon, Portugal.,Electronics, Telecommunications and Computers Engineering Department, Instituto Superior de Engenharia de Lisboa, Lisbon, Portugal
| | - Paula A Videira
- Portuguese Association for CDG, Lisbon, Portugal.,CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal.,UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Vanessa Dos Reis Ferreira
- Portuguese Association for CDG, Lisbon, Portugal.,CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
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24
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Shang C, Li Y, Wu Z, Han Q, Zhu Y, He T, Guo H. The Prognostic Value of DNA Methylation, Post-Translational Modifications and Correlated with Immune Infiltrates in Gynecologic Cancers. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:39-53. [PMID: 33488112 PMCID: PMC7814251 DOI: 10.2147/pgpm.s293399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/26/2020] [Indexed: 11/23/2022]
Abstract
Background To depict the prognostic landscape of gynecological cancers from the perspective of DNA methylation, alternative splicing (AS) and polyadenylation (APA) events and investigate their correlation with immune infiltrates. Methods Methylation and RNA-seq data and corresponding clinical information regarding gynecologic cancers were used to explore the relationships between changes in DNA methylation, AS and APA events and gynecologic cancer prognosis. QRT-PCR and multiple bioinformatics tools were employed to construct a gene interaction network and explore immune infiltrates. Results Only the mRNA levels of CIRBP and INPP5K were simultaneously significantly decreased in gynecologic cancers and negatively associated with overall survival, which verified by qrt-PCR. We also identified that CIRBP or INPP5K DNA methylation, AS and APA events are prognostic indicators of gynecologic cancers. The activation of T cells might be the main signaling pathway by which these genes modulate cancer progression. CIRBP/INPP5K expression is positively associated with immune infiltration and is a major risk factor of survival, especially among uterine corpus endometrial carcinoma (UCEC) patients. Conclusion According to these findings, the DNA methylation, AS and APA events of CIRBP and INPP5K may serve as important prognostic biomarkers and targets in gynecological cancers by modulating T cell infiltration.
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Affiliation(s)
- Chunliang Shang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Yuan Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Zhangxin Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Qin Han
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Yuan Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Tianhui He
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Hongyan Guo
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, People's Republic of China
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25
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Dong T, Ma X, Sheng N, Qi X, Chu Y, Song Q, Zou B, Zhou G. Point-of-care DNA testing by automatically and sequentially performing extraction, amplification and identification in a closed-type cassette. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 327:128919. [PMID: 32963421 PMCID: PMC7497388 DOI: 10.1016/j.snb.2020.128919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 05/06/2023]
Abstract
Nucleic acid detection is important for clinical diagnostics; however, it is challenging to perform genetic testing at the point-of-care due to the tedious steps involved in DNA extraction and the risk of cross-contamination from amplicons. To achieve a fully-automated and contamination-free nucleic acid detection, we propose a closed-type cassette system which enables the following steps to be operated automatically and sequentially: sample preparation based on magnetic beads, target amplification using multiplex polymerase chain reaction, and colorimetric detection of amplicons using a serial invasive reaction coupled with the aggregation of gold nanoparticle probes. The cassette was designed to be round and closed, and 10 targets in a sample could be simultaneously detected by the naked eye or using a spectrophotometer in the system. In addition, a cassette-driven device was fabricated to transfer reagents between wells, to control the temperature of each reaction, and to sense the colour in the detection wells. The cassette system was sensitive enough to detect 10 genotypes at 5 single nucleotide polymorphism sites related to the anticoagulant's usage, by using a 0.5 μL blood sample. The accuracy of the system was evaluated by detecting 12 whole blood samples, and the results obtained were consistent with those obtained using pyrosequencing. The cassette is airtight and the whole system is fully automatic; the only manual operation is the addition of the sample to the cassette, performing point-of-care genetic testing in a sample-in/answer-out way.
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Affiliation(s)
- Tianhui Dong
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Nan Sheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Qinxin Song
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Guohua Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, China
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26
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Reid BM, Fridley BL. DNA Methylation in Ovarian Cancer Susceptibility. Cancers (Basel) 2020; 13:E108. [PMID: 33396385 PMCID: PMC7795210 DOI: 10.3390/cancers13010108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic alterations are somatically acquired over the lifetime and during neoplastic transformation but may also be inherited as widespread 'constitutional' alterations in normal tissues that can cause cancer predisposition. Epithelial ovarian cancer (EOC) has an established genetic susceptibility and mounting epidemiological evidence demonstrates that DNA methylation (DNAm) intermediates as well as independently contributes to risk. Targeted studies of known EOC susceptibility genes (CSGs) indicate rare, constitutional BRCA1 promoter methylation increases familial and sporadic EOC risk. Blood-based epigenome-wide association studies (EWAS) for EOC have detected a total of 2846 differentially methylated probes (DMPs) with 71 genes replicated across studies despite significant heterogeneity. While EWAS detect both symptomatic and etiologic DMPs, adjustments and analytic techniques may enrich risk associations, as evidenced by the detection of dysregulated methylation of BNC2-a known CSG identified by genome-wide associations studies (GWAS). Integrative genetic-epigenetic approaches have mapped methylation quantitative trait loci (meQTL) to EOC risk, revealing DNAm variations that are associated with nine GWAS loci and, further, one novel risk locus. Increasing efforts to mapping epigenome variation across populations and cell types will be key to decoding both the genomic and epigenomic causal pathways to EOC.
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Affiliation(s)
- Brett M. Reid
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Brooke L. Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
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27
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Chen YX, Rong Y, Jiang F, Chen JB, Duan YY, Dong SS, Zhu DL, Chen H, Yang TL, Dai Z, Guo Y. An integrative multi-omics network-based approach identifies key regulators for breast cancer. Comput Struct Biotechnol J 2020; 18:2826-2835. [PMID: 33133424 PMCID: PMC7585874 DOI: 10.1016/j.csbj.2020.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/13/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Although genome-wide association studies (GWASs) have successfully identified thousands of risk variants for human complex diseases, understanding the biological function and molecular mechanisms of the associated SNPs involved in complex diseases is challenging. Here we developed a framework named integrative multi-omics network-based approach (IMNA), aiming to identify potential key genes in regulatory networks by integrating molecular interactions across multiple biological scales, including GWAS signals, gene expression-based signatures, chromatin interactions and protein interactions from the network topology. We applied this approach to breast cancer, and prioritized key genes involved in regulatory networks. We also developed an abnormal gene expression score (AGES) signature based on the gene expression deviation of the top 20 rank-ordered genes in breast cancer. The AGES values are associated with genetic variants, tumor properties and patient survival outcomes. Among the top 20 genes, RNASEH2A was identified as a new candidate gene for breast cancer. Thus, our integrative network-based approach provides a genetic-driven framework to unveil tissue-specific interactions from multiple biological scales and reveal potential key regulatory genes for breast cancer. This approach can also be applied in other complex diseases such as ovarian cancer to unravel underlying mechanisms and help for developing therapeutic targets.
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Affiliation(s)
- Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China.,Research Institute of Xi'an Jiaotong University, Zhejiang Province 311215, PR China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China.,Research Institute of Xi'an Jiaotong University, Zhejiang Province 311215, PR China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, PR China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
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28
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Wu L, Yang Y, Guo X, Shu XO, Cai Q, Shu X, Li B, Tao R, Wu C, Nikas JB, Sun Y, Zhu J, Roobol MJ, Giles GG, Brenner H, John EM, Clements J, Grindedal EM, Park JY, Stanford JL, Kote-Jarai Z, Haiman CA, Eeles RA, Zheng W, Long J. An integrative multi-omics analysis to identify candidate DNA methylation biomarkers related to prostate cancer risk. Nat Commun 2020; 11:3905. [PMID: 32764609 PMCID: PMC7413371 DOI: 10.1038/s41467-020-17673-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/28/2020] [Indexed: 12/21/2022] Open
Abstract
It remains elusive whether some of the associations identified in genome-wide association studies of prostate cancer (PrCa) may be due to regulatory effects of genetic variants on CpG sites, which may further influence expression of PrCa target genes. To search for CpG sites associated with PrCa risk, here we establish genetic models to predict methylation (N = 1,595) and conduct association analyses with PrCa risk (79,194 cases and 61,112 controls). We identify 759 CpG sites showing an association, including 15 located at novel loci. Among those 759 CpG sites, methylation of 42 is associated with expression of 28 adjacent genes. Among 22 genes, 18 show an association with PrCa risk. Overall, 25 CpG sites show consistent association directions for the methylation-gene expression-PrCa pathway. We identify DNA methylation biomarkers associated with PrCa, and our findings suggest that specific CpG sites may influence PrCa via regulating expression of candidate PrCa target genes.
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Affiliation(s)
- Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA.
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chong Wu
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Jason B Nikas
- Research & Development, Genomix Inc, Minneapolis, MN, USA
| | - Yanfa Sun
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
- College of Life Science, Longyan University, Longyan, Fujian, P. R. China
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Monique J Roobol
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, 207 Bouverie St, Melbourne, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, 615 St Kilda Rd, Melbourne, VIC, 3004, Australia
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Esther M John
- Department of Medicine (Oncology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Judith Clements
- Australian Prostate Cancer Research Centre-QLD, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
| | | | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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Paço A, de Bessa Garcia SA, Freitas R. Methylation in HOX Clusters and Its Applications in Cancer Therapy. Cells 2020; 9:cells9071613. [PMID: 32635388 PMCID: PMC7408435 DOI: 10.3390/cells9071613] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 02/08/2023] Open
Abstract
HOX genes are commonly known for their role in embryonic development, defining the positional identity of most structures along the anterior–posterior axis. In postembryonic life, HOX gene aberrant expression can affect several processes involved in tumorigenesis such as proliferation, apoptosis, migration and invasion. Epigenetic modifications are implicated in gene expression deregulation, and it is accepted that methylation events affecting HOX gene expression play crucial roles in tumorigenesis. In fact, specific methylation profiles in the HOX gene sequence or in HOX-associated histones are recognized as potential biomarkers in several cancers, helping in the prediction of disease outcomes and adding information for decisions regarding the patient’s treatment. The methylation of some HOX genes can be associated with chemotherapy resistance, and its identification may suggest the use of other treatment options. The use of epigenetic drugs affecting generalized or specific DNA methylation profiles, an approach that now deserves much attention, seems likely to be a promising weapon in cancer therapy in the near future. In this review, we summarize these topics, focusing particularly on how the regulation of epigenetic processes may be used in cancer therapy.
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Affiliation(s)
- Ana Paço
- Centre Bio: Bioindustries, Biorefineries and Bioproducts, BLC3 Association—Technology and Innovation Campus, 3405-169 Oliveira do Hospital, Portugal;
| | | | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal;
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Correspondence:
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30
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Xu J, Sram RJ, Cebulska-Wasilewska A, Miloradov MV, Sardas S, Au WW. Challenge-comet assay, a functional and genomic biomarker for precision risk assessment and disease prevention among exposed workers. Toxicol Appl Pharmacol 2020; 397:115011. [PMID: 32305282 DOI: 10.1016/j.taap.2020.115011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 02/05/2023]
Abstract
Advancements in genomic technologies have ushered application of innovative changes into biomedical sciences and clinical medicine. Consequently, these changes have created enormous opportunities to implement precision population/occupational disease prevention and target-specific disease intervention (or personalized medicine). To capture the opportunities, however, it is necessary is to develop novel, especially genomic-based, biomarkers which can provide precise and individualized health risk assessment. In this review, development of the Challenge-comet assay is used as an example to demonstrate how assays need to be validated for its sensitivity, specificity, and functional and quantitative features, and how assays can be used to provide individualized health risk assessment for precision prevention and intervention. Other examples of genomic-based novel biomarkers will also be discussed. Furthermore, no biomarkers can be used alone therefore their integrated usage with other biomarkers and with personal data bases will be discussed.
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Affiliation(s)
- Jianzhen Xu
- Shantou University Medical College, Shantou, China
| | - Radim J Sram
- Institute of Experimental Medicine AS, CR, Prague, Czech Republic
| | | | | | - Semra Sardas
- Istinye University, Zeytinburnu, Istanbul, Turkey
| | - William W Au
- University of Medicine, Pharmacy, Sciences and Technology, Targu Mures, Romania; University of Texas Medical Branch, Galveston, TX, USA.
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31
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Liu Y, Ding Y, Nie Y, Yang M. EMP1 Promotes the Proliferation and Invasion of Ovarian Cancer Cells Through Activating the MAPK Pathway. Onco Targets Ther 2020; 13:2047-2055. [PMID: 32210572 PMCID: PMC7071728 DOI: 10.2147/ott.s240028] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
Introduction Epithelial membrane protein 1 (EMP1), a member of the EMP family, is overexpressed in a large number of tumors and is thought to be a cellular connexin on the cell membrane and is involved in proliferation, invasion, metastasis of tumor cells, and epithelial-mesenchymal transition (EMT). Nevertheless, its biomedical function in ovarian cancer is still unclear. Methods EMP1 was detected in ovarian cancer cell lines by whole transcriptome resequencing. The mRNA of EMP1 was examined by qRT-PCR. The relationship between expression of EMP1 and clinical classification, metastasis, and shortened survival time in ovarian cancer specimens was analysed by immunohistochemical (IHC). The mechanism of EMP1 enhanced proliferation and invasion of ovarian cancer cells was determined by siRNA interference, colony formation, migration and invasion experiments, and Western blot. Results EMP1 was up-regulated in ovarian cancer cell lines and ovarian cancer tissues in comparison with non-cancerous ovarian specimens. High expression of EMP1 in ovarian cancer specimens was obviously related to high clinical classification, metastasis, and shortened survival time. High expressed EMP1 facilitates cell proliferation, invasion and EMT in ovarian cancer cells. Over-expressed EMP1 increased the protein levels of RAS/RAF/MAPK/c-JUN. Conclusion Over-expressed EMP1 in ovarian cancer promotes tumor cell proliferation, invasion, and EMT by the MAPK signaling pathway.
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Affiliation(s)
- Yang Liu
- Department of Obstetrics and Gynecology, Second Xiangya Hospital of Central South University, Changsha 410083, People's Republic of China
| | - Yiling Ding
- Department of Obstetrics and Gynecology, Second Xiangya Hospital of Central South University, Changsha 410083, People's Republic of China
| | - Yanting Nie
- Department of Obstetrics and Gynecology, Second Xiangya Hospital of Central South University, Changsha 410083, People's Republic of China
| | - Mengyuan Yang
- Department of Obstetrics and Gynecology, Second Xiangya Hospital of Central South University, Changsha 410083, People's Republic of China
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32
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Novel Epigenetic Biomarkers in Pregnancy-Related Disorders and Cancers. Cells 2019; 8:cells8111459. [PMID: 31752198 PMCID: PMC6912400 DOI: 10.3390/cells8111459] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/08/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
As the majority of cancers and gestational diseases are prognostically stage- and grade-dependent, the ultimate goal of ongoing studies in precision medicine is to provide early and timely diagnosis of such disorders. These studies have enabled the development of various new diagnostic biomarkers, such as free circulating nucleic acids, and detection of their epigenetic changes. Recently, extracellular vesicles including exosomes, microvesicles, oncosomes, and apoptotic bodies have been recognized as powerful diagnostic tools. Extracellular vesicles carry specific proteins, lipids, DNAs, mRNAs, and miRNAs of the cells that produced them, thus reflecting the function of these cells. It is believed that exosomes, in particular, may be the optimal biomarkers of pathological pregnancies and cancers, especially those that are frequently diagnosed at an advanced stage, such as ovarian cancer. In the present review, we survey and critically appraise novel epigenetic biomarkers related to free circulating nucleic acids and extracellular vesicles, focusing especially on their status in trophoblasts (pregnancy) and neoplastic cells (cancers).
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33
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Zhou D, Sun Y, Jia Y, Liu D, Wang J, Chen X, Zhang Y, Ma X. Bioinformatics and functional analyses of key genes in smoking-associated lung adenocarcinoma. Oncol Lett 2019; 18:3613-3622. [PMID: 31516576 PMCID: PMC6732981 DOI: 10.3892/ol.2019.10733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/12/2019] [Indexed: 12/16/2022] Open
Abstract
Smoking is one of the most important factors associated with the development of lung cancer. However, the signaling pathways and driver genes in smoking-associated lung adenocarcinoma remain unknown. The present study analyzed 433 samples of smoking-associated lung adenocarcinoma and 75 samples of non-smoking lung adenocarcinoma from the Cancer Genome Atlas database. Gene Ontology (GO) analysis was performed using the Database for Annotation, Visualization and Integrated Discovery and the ggplot2 R/Bioconductor package. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed using the R packages RSQLite and org.Hs.eg.db. Multivariate Cox regression analysis was performed to screen factors associated with patient survival. Kaplan-Meier and receiver operating characteristic curves were used to analyze the potential clinical significance of the identified biomarkers as molecular prognostic markers for the five-year overall survival time. A total of 373 differentially expressed genes (DEGs; |log2-fold change|≥2.0 and P<0.01) were identified, of which 71 were downregulated and 302 were upregulated. These DEGs were associated with 28 significant GO functions and 11 significant KEGG pathways (false discovery rate <0.05). Two hundred thirty-eight proteins were associated with the 373 differentially expressed genes, and a protein-protein interaction network was constructed. Multivariate regression analysis revealed that 7 mRNAs, cytochrome P450 family 17 subfamily A member 1, PKHD1 like 1, retinoid isomerohydrolase RPE65, neurotensin receptor 1, fetuin B, insulin-like growth factor binding protein 1 and glucose-6-phosphatase catalytic subunit, significantly distinguished between non-smoking and smoking-associated adenocarcinomas. Kaplan-Meier analysis demonstrated that patients in the 7 mRNAs-high-risk group had a significantly worse prognosis than those of the low-risk group. The data obtained in the current study suggested that these genes may serve as potential novel prognostic biomarkers of smoking-associated lung adenocarcinoma.
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Affiliation(s)
- Dajie Zhou
- Central Laboratory, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China.,Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Yilin Sun
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yanfei Jia
- Central Laboratory, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Duanrui Liu
- Central Laboratory, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Jing Wang
- Central Laboratory, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Xiaowei Chen
- Central Laboratory, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Yujie Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Xiaoli Ma
- Central Laboratory, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
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Wu L, Shu X, Bao J, Guo X, Kote-Jarai Z, Haiman CA, Eeles RA, Zheng W. Analysis of Over 140,000 European Descendants Identifies Genetically Predicted Blood Protein Biomarkers Associated with Prostate Cancer Risk. Cancer Res 2019; 79:4592-4598. [PMID: 31337649 DOI: 10.1158/0008-5472.can-18-3997] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/21/2019] [Accepted: 07/17/2019] [Indexed: 12/24/2022]
Abstract
Several blood protein biomarkers have been associated with prostate cancer risk. However, most studies assessed only a small number of biomarkers and/or included a small sample size. To identify novel protein biomarkers of prostate cancer risk, we studied 79,194 cases and 61,112 controls of European ancestry, included in the PRACTICAL/ELLIPSE consortia, using genetic instruments of protein quantitative trait loci for 1,478 plasma proteins. A total of 31 proteins were associated with prostate cancer risk including proteins encoded by GSTP1, whose methylation level was shown previously to be associated with prostate cancer risk, and MSMB, SPINT2, IGF2R, and CTSS, which were previously implicated as potential target genes of prostate cancer risk variants identified in genome-wide association studies. A total of 18 proteins inversely correlated and 13 positively correlated with prostate cancer risk. For 28 of the identified proteins, gene somatic changes of short indels, splice site, nonsense, or missense mutations were detected in patients with prostate cancer in The Cancer Genome Atlas. Pathway enrichment analysis showed that relevant genes were significantly enriched in cancer-related pathways. In conclusion, this study identifies 31 candidates of protein biomarkers for prostate cancer risk and provides new insights into the biology and genetics of prostate tumorigenesis. SIGNIFICANCE: Integration of genomics and proteomics data identifies biomarkers associated with prostate cancer risk.
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Affiliation(s)
- Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii.,Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, California
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
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Markowska A, Kaysiewicz J, Markowska J, Huczyński A. Doxycycline, salinomycin, monensin and ivermectin repositioned as cancer drugs. Bioorg Med Chem Lett 2019; 29:1549-1554. [PMID: 31054863 DOI: 10.1016/j.bmcl.2019.04.045] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 01/24/2023]
Abstract
Chemotherapy is one of the standard methods for the treatment of malignant tumors. It aims to cause lethal damage to cellular structures, mainly DNA. Noteworthy, in recent years discoveries of novel anticancer agents from well-known antibiotics have opened up new treatment pathways for several cancer diseases. The aim of this review article is to describe new applications for the following antibiotics: doxycycline (DOX), salinomycin (SAL), monensin (MON) and ivermectin (IVR) as they are known to show anti-tumor activity, but have not yet been introduced into standard oncological therapy. To date, these agents have been used for the treatment of a broad-spectrum of bacterial and parasitic infectious diseases and are widely available, which is why they were selected. The data presented here clearly show that the antibiotics mentioned above should be recognised in the near future as novel agents able to eradicate cancer cells and cancer stem cells (CSCs) across several cancer types.
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Affiliation(s)
- Anna Markowska
- Department of Perinatology and Women's Diseases, Poznan University of Medical Sciences, Polna 33, 60-545 Poznan, Poland
| | | | - Janina Markowska
- Department of Oncology, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569 Poznan, Poland
| | - Adam Huczyński
- Department of Bioorganic Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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Teng F, Wang P, Yang L, Ma Y, Day L. Quantification of Fatty Acids in Human, Cow, Buffalo, Goat, Yak, and Camel Milk Using an Improved One-Step GC-FID Method. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-0852-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Yan Y, Wang Z, Wang X, Wang Y, Xiang J, Kothapalli KS, Brenna JT. Branched chain fatty acids positional distribution in human milk fat and common human food fats and uptake in human intestinal cells. J Funct Foods 2017. [DOI: 10.1016/j.jff.2016.12.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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