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Wang D, Zhang Y, Li Q, Li Y, Li W, Zhang A, Xu J, Meng J, Tang L, Lyu S. Epigenetics: Mechanisms, potential roles, and therapeutic strategies in cancer progression. Genes Dis 2024; 11:101020. [PMID: 38988323 PMCID: PMC11233905 DOI: 10.1016/j.gendis.2023.04.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/20/2023] [Accepted: 04/14/2023] [Indexed: 07/12/2024] Open
Abstract
Mutations or abnormal expression of oncogenes and tumor suppressor genes are known to cause cancer. Recent studies have shown that epigenetic modifications are key drivers of cancer development and progression. Nevertheless, the mechanistic role of epigenetic dysregulation in the tumor microenvironment is not fully understood. Here, we reviewed the role of epigenetic modifications of cancer cells and non-cancer cells in the tumor microenvironment and recent research advances in cancer epigenetic drugs. In addition, we discussed the great potential of epigenetic combination therapies in the clinical treatment of cancer. However, there are still some challenges in the field of cancer epigenetics, such as epigenetic tumor heterogeneity, epigenetic drug heterogeneity, and crosstalk between epigenetics, proteomics, metabolomics, and other omics, which may be the focus and difficulty of cancer treatment in the future. In conclusion, epigenetic modifications in the tumor microenvironment are essential for future epigenetic drug development and the comprehensive treatment of cancer. Epigenetic combination therapy may be a novel strategy for the future clinical treatment of cancer.
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Affiliation(s)
- Dong Wang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yan Zhang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Qingbo Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wen Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ao Zhang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jingxuan Xu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jingyan Meng
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lin Tang
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shuhua Lyu
- Department of Pathology, Tianjin Union Medical Center, Tianjin 300121, China
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2
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Zhao X, Yang Y, Fu Y, Lv W, Xu D. DNA methylation detection is a significant biomarker for screening endometrial cancer in premenopausal women with abnormal uterine bleeding. Int J Gynecol Cancer 2024; 34:1165-1171. [PMID: 39043572 DOI: 10.1136/ijgc-2024-005723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
OBJECTIVE The aim of our study was to explore the value of DNA (CDO1m/CELF4m) methylation detection in exfoliated cervical cells collected for screening endometrial cancer in premenopausal women with abnormal uterine bleeding. METHODS A total of 296 premenopausal women with abnormal uterine bleeding admitted to the Department of Obstetrics and Gynecology at the Third Xiangya Hospital of Central South University from November 2021 to October 2022 were selected. Clinical characteristics, endometrial thickness measured by transvaginal ultrasound and serum CA125 were collected. Exfoliated cervical cells from the thinPrep cytogic test were collected for DNA (CDO1m/CELF4m) methylation testing. Endometrial tissue was collected under hysteroscopy for pathological diagnosis as the gold standard. A univariate logistic regression model was used to analyze risk factors for endometrial cancer. The receiver operating characteristic (ROC) curve and area under the curve (AUC) were used to measure the diagnostic efficacy of DNA methylation detection in endometrial cancer screening of women with abnormal uterine bleeding. RESULTS Univariate logistic regression analysis showed that age, body mass index (BMI) ≥25 kg/m2, endometrial thickness ≥11 mm, CDO1 methylation (CDO1mΔCt≤8.4), CELF4 methylation (CELF4mΔCt≤8.8), and dual gene methylation (CDO1mΔCt≤8.4 or CELF4mΔCt≤8.8) were independent risk factors for endometrial cancer in women with abnormal uterine bleeding. The odds ratio (OR) values (95% confidence interval (CI) were 0.87 (0.80-0.95), 4.76 (1.89-11.96), 8.41 (3.13-22.59), 64.49 (20.46-203.33), 12.79 (4.91-33.30), and 42.53 (11.90-152.04), respectively. Among these indicators, dual gene methylation had the higher sensitivity and specificity for endometrial cancer screening (85.7% and 87.6%). Moreover, dual gene methylation combined with BMI or endometrial thickness could further improve the screening efficiency of endometrial cancer in women with abnormal uterine bleeding. CONCLUSIONS In premenopausal women with abnormal uterine bleeding, the clinical efficacy of DNA (CDO1m/CELF4m) methylation detection in exfoliated cervical cells for endometrial cancer screening was better than that of other noninvasive clinical indicators. In addition, dual gene methylation combined with BMI or endometrial thickness was a good predictor of endometrial cancer screening.
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Affiliation(s)
- Xingping Zhao
- Gynecology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Jiangwan Research Institute, Central South University, Changsha, Hunan, China
- Postdoctoral Station of Clinical Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Yanfei Yang
- Gynecology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yinqin Fu
- Gynecology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Weigang Lv
- Gynecology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dabao Xu
- Gynecology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
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Zhang C, Zheng J, Liu J, Li Y, Xing G, Zhang S, Chen H, Wang J, Shao Z, Li Y, Jiang Z, Pan Y, Liu X, Xu P, Wu W. Pan-cancer analyses reveal the molecular and clinical characteristics of TET family members and suggests that TET3 maybe a potential therapeutic target. Front Pharmacol 2024; 15:1418456. [PMID: 39104395 PMCID: PMC11298443 DOI: 10.3389/fphar.2024.1418456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/28/2024] [Indexed: 08/07/2024] Open
Abstract
The Ten-Eleven Translocation (TET) family genes are implicated in a wide array of biological functions across various human cancers. Nonetheless, there is a scarcity of studies that comprehensively analyze the correlation between TET family members and the molecular phenotypes and clinical characteristics of different cancers. Leveraging updated public databases and employing several bioinformatics analysis methods, we assessed the expression levels, somatic variations, methylation levels, and prognostic values of TET family genes. Additionally, we explored the association between the expression of TET family genes and pathway activity, tumor microenvironment (TME), stemness score, immune subtype, clinical staging, and drug sensitivity in pan-cancer. Molecular biology and cytology experiments were conducted to validate the potential role of TET3 in tumor progression. Each TET family gene displayed distinct expression patterns across at least ten detected tumors. The frequency of Single Nucleotide Variant (SNV) in TET genes was found to be 91.24%, primarily comprising missense mutation types, with the main types of copy number variant (CNV) being heterozygous amplifications and deletions. TET1 gene exhibited high methylation levels, whereas TET2 and TET3 genes displayed hypomethylation in most cancers, which correlated closely with patient prognosis. Pathway activity analysis revealed the involvement of TET family genes in multiple signaling pathways, including cell cycle, apoptosis, DNA damage response, hormone AR, PI3K/AKT, and RTK. Furthermore, the expression levels of TET family genes were shown to impact the clinical staging of tumor patients, modulate the sensitivity of chemotherapy drugs, and thereby influence patient prognosis by participating in the regulation of the tumor microenvironment, cellular stemness potential, and immune subtype. Notably, TET3 was identified to promote cancer progression across various tumors, and its silencing was found to inhibit tumor malignancy and enhance chemotherapy sensitivity. These findings shed light on the role of TET family genes in cancer progression and offer insights for further research on TET3 as a potential therapeutic target for pan-cancer.
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Affiliation(s)
- Chunyan Zhang
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Jie Zheng
- Department of Pathology, Tianjin Fifth Central Hospital, Tianjin, China
| | - Jin Liu
- North China University of Science and Technology, Tangshan, Hebei, China
| | - Yanxia Li
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Guoqiang Xing
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
| | - Shupeng Zhang
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
| | - Hekai Chen
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
| | - Jian Wang
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
| | - Zhijiang Shao
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Yongyuan Li
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Zhongmin Jiang
- Department of Pathology, Tianjin Fifth Central Hospital, Tianjin, China
| | - Yingzi Pan
- Department of Ophthalmology, Peking University First Hospital, Beijing, China
| | - Xiaozhi Liu
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Ping Xu
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
- Department of Pharmacy, Tianjin Fifth Central Hospital, Tianjin, China
| | - Wenhan Wu
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
- Department of General Surgery, Peking University First Hospital, Beijing, China
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Ahmadi Asouri S, Aghadavood E, Mirzaei H, Abaspour A, Esmaeil Shahaboddin M. PIWI-interacting RNAs (PiRNAs) as emerging biomarkers and therapeutic targets in biliary tract cancers: A comprehensive review. Heliyon 2024; 10:e33767. [PMID: 39040379 PMCID: PMC11261894 DOI: 10.1016/j.heliyon.2024.e33767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 06/09/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Cancers affecting the biliary tract, such as gallbladder cancer and cholangiocarcinoma, make up a small percentage of adult gastrointestinal malignancies, but their incidence is on the rise. Due to the lack of dependable molecular biomarkers for diagnosis and prognosis, these cancers are often not detected until later stages and have limited treatment options. Piwi-interacting RNAs (piRNAs) are a type of small noncoding RNA that interacts with Piwi proteins and has been linked to various diseases, especially cancer. Manipulation of piRNA expression has the potential to serve as an important biomarker and target for therapy. This review uncovers the relationship between PIWI-interacting RNA (piRNA) and a variety of gastrointestinal cancers, including biliary tract cancer (BTC). It is evident that piRNAs have the ability to impact gene expression and regulate key genes and pathways related to the advancement of digestive cancers. Abnormal expression of piRNAs plays a significant role in the development and progression of digestive-related malignancies. The potential of piRNAs as potential biomarkers for diagnosis and prognosis, as well as therapeutic targets in BTC, is noteworthy. Nevertheless, there are obstacles and limitations that require further exploration to fully comprehend piRNAs' role in BTC and to devise effective diagnostic and therapeutic approaches using piRNAs. In summary, this review underscores the value of piRNAs as valuable biomarkers and promising targets for treating BTC, as we delve into the association between piRNAs and various gastrointestinal cancers, including BTC, and how piRNAs can impact gene expression and control essential pathways for digestive cancer advancement. The present research consists of a thorough evaluation presented in a storytelling style. The databases utilized to locate original sources were PubMed, MEDLINE, and Google Scholar, and the search was conducted using the designated keywords.
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Affiliation(s)
- Sahar Ahmadi Asouri
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Esmat Aghadavood
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Institute for Basic Sciences, Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Alireza Abaspour
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Esmaeil Shahaboddin
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Institute for Basic Sciences, Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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5
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Kita K, Gawinowska M, Chełmińska M, Niedoszytko M. The Role of Exhaled Breath Condensate in Chronic Inflammatory and Neoplastic Diseases of the Respiratory Tract. Int J Mol Sci 2024; 25:7395. [PMID: 39000502 PMCID: PMC11242091 DOI: 10.3390/ijms25137395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/16/2024] Open
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are among the most common chronic respiratory diseases. Chronic inflammation of the airways leads to an increased production of inflammatory markers by the effector cells of the respiratory tract and lung tissue. These biomarkers allow the assessment of physiological and pathological processes and responses to therapeutic interventions. Lung cancer, which is characterized by high mortality, is one of the most frequently diagnosed cancers worldwide. Current screening methods and tissue biopsies have limitations that highlight the need for rapid diagnosis, patient differentiation, and effective management and monitoring. One promising non-invasive diagnostic method for respiratory diseases is the assessment of exhaled breath condensate (EBC). EBC contains a mixture of volatile and non-volatile biomarkers such as cytokines, leukotrienes, oxidative stress markers, and molecular biomarkers, providing significant information about inflammatory and neoplastic states in the lungs. This article summarizes the research on the application and development of EBC assessment in diagnosing and monitoring respiratory diseases, focusing on asthma, COPD, and lung cancer. The process of collecting condensate, potential issues, and selected groups of markers for detailed disease assessment in the future are discussed. Further research may contribute to the development of more precise and personalized diagnostic and treatment methods.
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Affiliation(s)
- Karolina Kita
- Department of Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Marika Gawinowska
- Department of Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Marta Chełmińska
- Department of Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Marek Niedoszytko
- Department of Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
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6
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Kudo G, Hirao T, Harada R, Hirokawa T, Shigeta Y, Yoshino R. Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation. Sci Rep 2024; 14:13508. [PMID: 38866895 PMCID: PMC11169543 DOI: 10.1038/s41598-024-64236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
DNA methylation is an epigenetic mechanism that introduces a methyl group at the C5 position of cytosine. This reaction is catalyzed by DNA methyltransferases (DNMTs) and is essential for the regulation of gene transcription. The DNMT1 and DNMT3A or -3B family proteins are known targets for the inhibition of DNA hypermethylation in cancer cells. A selective non-nucleoside DNMT3A inhibitor was developed that mimics S-adenosyl-l-methionine and deoxycytidine; however, the mechanism of selectivity is unclear because the inhibitor-protein complex structure determination is absent. Therefore, we performed docking and molecular dynamics simulations to predict the structure of the complex formed by the association between DNMT3A and the selective inhibitor. Our simulations, binding free energy decomposition analysis, structural isoform comparison, and residue scanning showed that Arg688 of DNMT3A is involved in the interaction with this inhibitor, as evidenced by its significant contribution to the binding free energy. The presence of Asn1192 at the corresponding residues in DNMT1 results in a loss of affinity for the inhibitor, suggesting that the interactions mediated by Arg688 in DNMT3A are essential for selectivity. Our findings can be applied in the design of DNMT-selective inhibitors and methylation-specific drug optimization procedures.
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Affiliation(s)
- Genki Kudo
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Takumi Hirao
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yasuteru Shigeta
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Ryunosuke Yoshino
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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Li Z, Yan H, Wang B, Wang H, Chen A, Zhu T, Liu J, Yu G, Kang M. High methylation of the same promoter of lncRNA ZNF582-AS1/ ZNF582 promotes malignant progression of esophageal cancer. Epigenomics 2024; 16:733-752. [PMID: 38869483 PMCID: PMC11318746 DOI: 10.1080/17501911.2024.2342229] [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: 11/13/2023] [Accepted: 04/09/2024] [Indexed: 06/14/2024] Open
Abstract
Aim: This study aimed to investigate the functions of ZNF582-AS1 and ZNF582 in esophageal cancer (EC). Materials & methods: Bioinformatics analysis, qRT-PCR and western blot were used to analyze the expression levels. Biological functions were evaluated using cell-counting kit 8, colony formation, Transwell assays and flow cytometry. FISH was used to detect subcellular localization, and methylation-specific PCR determined gene methylation levels. Animal experiments validated the impact on tumor progression. Results: ZNF582-AS1 and ZNF582 were highly methylated and downregulated in EC. Overexpression of ZNF582-AS1 up-regulated the expression of ZNF582, thereby inhibiting EC cell viability and metastasis, promoting apoptosis and inhibiting tumor growth. Conclusion: Low expression of ZNF582-AS1/ZNF582 mediated by DNA hypermethylation facilitates the malignant progression of EC.
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Affiliation(s)
- Zhupeng Li
- Second Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Hefang Yan
- Department of Endocrinology, Rheumatology & immunology, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Bin Wang
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Haiyong Wang
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Aixia Chen
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Ting Zhu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Jianjiang Liu
- Department of Radiotherapy, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Guangmao Yu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Mingqiang Kang
- Second Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
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8
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Akanyibah FA, Zhu Y, Wan A, Ocansey DKW, Xia Y, Fang AN, Mao F. Effects of DNA methylation and its application in inflammatory bowel disease (Review). Int J Mol Med 2024; 53:55. [PMID: 38695222 DOI: 10.3892/ijmm.2024.5379] [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: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is marked by persistent inflammation, and its development and progression are linked to environmental, genetic, immune system and gut microbial factors. DNA methylation (DNAm), as one of the protein modifications, is a crucial epigenetic process used by cells to control gene transcription. DNAm is one of the most common areas that has drawn increasing attention recently, with studies revealing that the interleukin (IL)‑23/IL‑12, wingless‑related integration site, IL‑6‑associated signal transducer and activator of transcription 3, suppressor of cytokine signaling 3 and apoptosis signaling pathways are involved in DNAm and in the pathogenesis of IBD. It has emerged that DNAm‑associated genes are involved in perpetuating the persistent inflammation that characterizes a number of diseases, including IBD, providing a novel therapeutic strategy for exploring their treatment. The present review discusses DNAm‑associated genes in the pathogenesis of IBD and summarizes their application as possible diagnostic, prognostic and therapeutic biomarkers in IBD. This may provide a reference for the particular form of IBD and its related methylation genes, aiding in clinical decision‑making and encouraging therapeutic alternatives.
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Affiliation(s)
- Francis Atim Akanyibah
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| | - Yi Zhu
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, P.R. China
| | - Aijun Wan
- Zhenjiang College, Zhenjiang, Jiangsu 212028, P.R. China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - An-Ning Fang
- Basic Medical School, Anhui Medical College, Hefei, Anhui 230061, P.R. China
| | - Fei Mao
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
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Ma T, Zhang Q, Zhang S, Yue D, Wang F, Ren Y, Zhang H, Wang Y, Wu Y, Liu LE, Yu F. Research progress of human key DNA and RNA methylation-related enzymes assay. Talanta 2024; 273:125872. [PMID: 38471421 DOI: 10.1016/j.talanta.2024.125872] [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: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Gene methylation-related enzymes (GMREs) are disfunction and aberrantly expressed in a variety of cancers, such as lung, gastric, and pancreatic cancers and have important implications for human health. Therefore,it is critical for early diagnosis and therapy of tumor to develop strategies that allow rapid and sensitive quantitative and qualitative detection of GMREs. With the development of modern analytical techniques and the application of various biosensors, there are numerous methods have been developed for analysis of GMREs. Therefore, this paper provides a systematic review of the strategies for level and activity assay of various GMREs including methyltransferases and demethylase. The detection methods mainly involve immunohistochemistry, colorimetry, fluorescence, chemiluminescence, electrochemistry, etc. Then, this review also addresses the coordinated role of various detection probes, novel nanomaterials, and signal amplification methods. The aim is to highlight potential challenges in the present field, to expand the analytical application of GMREs detection strategies, and to meet the urgent need for future disease diagnosis and intervention.
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Affiliation(s)
- Tiantian Ma
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Qiongwen Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuying Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Dan Yue
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fanting Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yujie Ren
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Hengmiao Zhang
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Yinuo Wang
- Zhengzhou Foreign Language School, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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10
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Tan L, Zhang H, Ding Y, Huang Y, Sun D. CRTAC1 identified as a promising diagnosis and prognostic biomarker in lung adenocarcinoma. Sci Rep 2024; 14:11223. [PMID: 38755183 PMCID: PMC11099150 DOI: 10.1038/s41598-024-61804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
CRTAC1, one of the pyroptosis-related genes, has been identified as a protective factor in certain kinds of cancer, such as gastric adenocarcinoma and bladder cancer. The study aimed to investigate the role of CRTAC1 in lung adenocarcinoma (LUAD). LUAD datasets were obtained from Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA), pyroptosis-related genes from GeneCard. Limma package used to find differentially expressed genes (DEGs), least absolute shrinkage and selection operator (LASSO) regression and weighted genes co-expression network analysis (WGCNA) to identify CRTAC1 as hub gene. CRTAC1 expression was confirmed in a real-world cohort using quantitative polymerase chain reaction (qPCR) and Western Blot (WB) analyses. Cellular experiments were conducted to investigate CRTAC1's potential oncogenic mechanisms. CRTAC1 mRNA expression was significantly lower in LUAD tissues (p < 0.05) and showed high accuracy in diagnosing LUAD. Reduced CRTAC1 expression was associated with a poor prognosis. Higher CRTAC1 expression correlated with increased immune cell infiltration. Individuals with high CRTAC1 expression showed increased drug sensitivity. Additionally, qPCR and WB analyses showed that CRTAC1 expression was lower in tumor tissue compared to adjacent normal tissue at both the RNA and protein levels. Upregulation of CRTAC1 significantly inhibited LUAD cell proliferation, invasion, and migration in cellular experiments. CRTAC1 has the potential to serve as a diagnostic and prognostic biomarker in LUAD.
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Affiliation(s)
- Lin Tan
- Tianjin Medical University Graduate School, Tianjin, China
- Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China
| | - Han Zhang
- Tianjin Medical University Graduate School, Tianjin, China
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Yun Ding
- Tianjin Medical University Graduate School, Tianjin, China
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Yangyun Huang
- Tianjin Medical University Graduate School, Tianjin, China
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Daqiang Sun
- Tianjin Chest Hospital, Tianjin University, Tianjin, China.
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11
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Shen J, Su J, Chu X, Yu X, Gao X. DNMT3A-mediated DNA methylation and transcription inhibition of FZD5 suppresses lung carcinogenesis. Heliyon 2024; 10:e29733. [PMID: 38707304 PMCID: PMC11066612 DOI: 10.1016/j.heliyon.2024.e29733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Background Based on the bioinformatics prediction, this study investigates the correlation between aberrant transcription factor Frizzled 5 (FZD5) expression and the establishment of non-small cell lung cancer (NSCLC). Methods A mouse model with regard to primary NSCLC was encouraged by intraperitoneal injection of urethane. Lentivirus-based FZD5 silencing was then administrated to examine its role in tumorigenesis in the mouse lung. Silencing of FZD5 was induced in two NSCLC cell lines to examine its function in the malignant behavior pertaining to cells in vitro. Quantitative methylation-specific PCR was employed to assess the DNA methylation level within the NSCLC cells. DNA methyltransferases (DNMTs) that administer FZD5 were assessed by chromatin immunoprecipitation assay. Consequently, overexpression of DNMT3A was introduced in mice and NSCLC cells to verify its regulation on FZD and its biological roles in NSCLC development. Results In NSCLC, FZD5 expression is elevated, and its knockdown reduced tumor incidence rate in the urethane-challenged mice. The FZD5 silencing also inhibited proliferation, migration, as well as invasion with regard to Calu-3 and NCI-H1299 cells in vitro. The aberrant upregulation with regard to FZD5 in NSCLC was due to at least partly by reduced promoter methylation level. DNMT3A, which bound to FZD5 promoter to suppress its transcription, was poorly expressed in NSCLC. Artificial upregulation of DNMT3A suppressed urethane-induced lung carcinogenesis in mice and suppressed the malignant phenotype pertaining to NSCLC cells in vitro. Conclusion This research demonstrates that the lack of DNA methylation level-induced activation of FZD5 is correlated with NSCLC's onset and progression.
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Affiliation(s)
- Jiqiao Shen
- Department of Respiratory and Critical Care Medicine, Minhang Hospital, Fudan University, Shanghai, 201100, China
| | - Jinchen Su
- School of Medicine, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Xiangling Chu
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200000, China
| | - Xin Yu
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200000, China
| | - Xiwen Gao
- Department of Respiratory and Critical Care Medicine, Minhang Hospital, Fudan University, Shanghai, 201100, China
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12
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Xie H, Wei L, Wang Q, Tang S, Gan J. Elevated serum homocysteine levels associated with poor recurrence-free and overall survival in patients with colorectal cancer. Sci Rep 2024; 14:10057. [PMID: 38698172 PMCID: PMC11066114 DOI: 10.1038/s41598-024-60855-4] [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: 11/16/2023] [Accepted: 04/29/2024] [Indexed: 05/05/2024] Open
Abstract
This study aimed to evaluate the significance of homocysteine (HCY) levels in predicting recurrence-free survival (RFS) and overall survival (OS) in colorectal cancer (CRC) patients. This retrospective study involved 1272 CRC patients. The risk of mortality increased with increasing HCY levels in CRC patients. The optimal HCY cutoff value in CRC patients was 15.2 μmol/L. The RFS (45.8% vs. 60.5%, p < 0.001) and OS (48.2% vs. 63.2%, p < 0.001) of patients with high HCY levels were significantly lower than those of patients with low HCY levels. Patients with high HCY levels were older, male, had large tumours, high carcinoembryonic antigen (CEA) levels, and long hospital stays, and incurred high hospitalisation costs. Multivariate analysis showed that when HCY levels exceeded 15.2 μmol/L, the risk of adverse RFS and OS increased by 55.7% and 61.4%, respectively. Subgroup analysis showed that HCY levels could supplement CEA levels and pathological staging. We constructed HCY-based prognostic nomograms, which demonstrated feasible discrimination and calibration values better than the traditional tumour, node, metastasis staging system for predicting RFS and OS. Elevated serum HCY levels were strongly associated with poor RFS and OS in CRC patients. HCY-based prognostic models are effective tools for a comprehensive evaluation of prognosis.
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Affiliation(s)
- Hailun Xie
- Department of Gastrointestinal Gland Surgery, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, Guangxi, People's Republic of China
| | - Lishuang Wei
- Department of Geriatric Respiratory Disease Ward, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Qiwen Wang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, Guangxi, People's Republic of China
| | - Shuangyi Tang
- Department of Pharmacy, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.
| | - Jialiang Gan
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China.
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Nanning, 530021, Guangxi, People's Republic of China.
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13
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Guo DZ, Huang A, Wang YC, Zhou S, Wang H, Xing XL, Zhang SY, Cheng JW, Xie KH, Yang QC, Ma CC, Li Q, Chen Y, Su ZX, Fan J, Liu R, Liu XL, Zhou J, Yang XR. Early detection and prognosis evaluation for hepatocellular carcinoma by circulating tumour DNA methylation: A multicentre cohort study. Clin Transl Med 2024; 14:e1652. [PMID: 38741204 DOI: 10.1002/ctm2.1652] [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: 01/27/2024] [Revised: 03/07/2024] [Accepted: 03/21/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Early diagnosis of hepatocellular carcinoma (HCC) can significantly improve patient survival. We aimed to develop a blood-based assay to aid in the diagnosis, detection and prognostic evaluation of HCC. METHODS A three-phase multicentre study was conducted to screen, optimise and validate HCC-specific differentially methylated regions (DMRs) using next-generation sequencing and quantitative methylation-specific PCR (qMSP). RESULTS Genome-wide methylation profiling was conducted to identify DMRs distinguishing HCC tumours from peritumoural tissues and healthy plasmas. The twenty most effective DMRs were verified and incorporated into a multilocus qMSP assay (HepaAiQ). The HepaAiQ model was trained to separate 293 HCC patients (Barcelona Clinic Liver Cancer (BCLC) stage 0/A, 224) from 266 controls including chronic hepatitis B (CHB) or liver cirrhosis (LC) (CHB/LC, 96), benign hepatic lesions (BHL, 23), and healthy controls (HC, 147). The model achieved an area under the curve (AUC) of 0.944 with a sensitivity of 86.0% in HCC and a specificity of 92.1% in controls. Blind validation of the HepaAiQ model in a cohort of 523 participants resulted in an AUC of 0.940 with a sensitivity of 84.4% in 205 HCC cases (BCLC stage 0/A, 167) and a specificity of 90.3% in 318 controls (CHB/LC, 100; BHL, 102; HC, 116). When evaluated in an independent test set, the HepaAiQ model exhibited a sensitivity of 70.8% in 65 HCC patients at BCLC stage 0/A and a specificity of 89.5% in 124 patients with CHB/LC. Moreover, HepaAiQ model was assessed in paired pre- and postoperative plasma samples from 103 HCC patients and correlated with 2-year patient outcomes. Patients with high postoperative HepaAiQ score showed a higher recurrence risk (Hazard ratio, 3.33, p < .001). CONCLUSIONS HepaAiQ, a noninvasive qMSP assay, was developed to accurately measure HCC-specific DMRs and shows great potential for the diagnosis, detection and prognosis of HCC, benefiting at-risk populations.
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Affiliation(s)
- De-Zhen Guo
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Ao Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Ying-Chao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | | | - Hui Wang
- Singlera Genomics Ltd., Shanghai, China
| | - Xiang-Lei Xing
- Biliary Tract Surgery Department IV, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Shi-Yu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Jian-Wen Cheng
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | | | | | | | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Chen
- XiangYa Medical Laboratory, Central South University, Changsha, Hunan, China
| | - Zhi-Xi Su
- Singlera Genomics Ltd., Shanghai, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Rui Liu
- Singlera Genomics Ltd., Shanghai, China
| | - Xiao-Long Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Xin-Rong Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
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14
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Zhou S, Cheng C, Liao YX, Wang L, Zeng JM, Zhou FF, Zhang XQ, Yang T. Epigenetic regulation of FOXI2 promotes clear cell renal cell carcinoma progression. Heliyon 2024; 10:e29218. [PMID: 38628758 PMCID: PMC11016964 DOI: 10.1016/j.heliyon.2024.e29218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
In recent decades, substantial advancements in epigenetics have unveiled a profound understanding of its mechanisms in tumorigenesis and have offered promising strategies for epigenetic therapy in cancer patients. In our study, through bioinformatics analysis, we discovered a significant downregulation and hypermethylation of FOXI2 in clear cell renal cell carcinoma (ccRCC), while the expression in chromophobe cell carcinoma (chRCC) exhibited the opposite trend. Moreover, we established a strong correlation between FOXI2 expression levels and the prognosis of ccRCC. Gene enrichment analysis and cell function experiments unequivocally demonstrate that FOXI2 possesses the capability to induce cell cycle arrest and inhibit cell proliferation. Our research findings demonstrate that the expression of FOXI2 in ccRCC is under the regulation of promoter hypermethylation. Furthermore, in vitro experiments have conclusively shown that the overexpression of FOXI2 induces cell cycle arrest and inhibits cell proliferation.
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Affiliation(s)
- Shuai Zhou
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Cong Cheng
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Yi xiang Liao
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Li Wang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Jin min Zeng
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Fang fang Zhou
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Xiu qin Zhang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Tao Yang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
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15
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Zhao J, Liu Z, Yang K, Shen S, Peng J. DNA methylation regulator-based molecular subtyping and tumor microenvironment characterization in hepatocellular carcinoma. Front Immunol 2024; 15:1333923. [PMID: 38736884 PMCID: PMC11082416 DOI: 10.3389/fimmu.2024.1333923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Backgroud Although recent studies have reported the regulation of the immune response in hepatocellular carcinoma (HCC) through DNA methylation, the comprehensive impact methylation modifications on tumor microenvironment characteristics and immunotherapy efficacy has not been fully elucidated. Methods In this research, we conducted a comprehensive assessment of the patterns of DNA methylation regulators and the profiles of the tumor microenvironment (TME) in HCC, focusing on 21 specific DNA methylation regulators. We subsequently developed a unique scoring system, a DNA methylation score (DMscore), to assess the individual DNA methylation modifications among the three distinct methylation patterns for differentially expressed genes (DEGs). Results Three distinct methylation modification patterns were identified with distinct TME infiltration characteristics. We demonstrated that the DMscore could predict patient subtype, TME infiltration, and patient prognosis. A low DMscore, characterized by an elevated tumor mutation burden (TMB), hepatitis B virus (HBV)/hepatitis C virus (HCV) infection, and immune activation, indicates an inflamed tumor microenvironment phenotype with a 5-year survival rate of 7.8%. Moreover, a low DMscore appeared to increase the efficacy of immunotherapy in the anti-CTLA-4/PD-1/PD-L1 cohort. Conclusions In brief, this research has enhanced our understanding of the correlation between modifications in DNA methylation patterns and the profile of the tumor microenvironment in individuals diagnosed with HCC. The DMscore may serve as an alternative biomarker for survival and efficacy of immunotherapy in patients with HCC.
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Affiliation(s)
- Junsheng Zhao
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengtao Liu
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Keda Yang
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Sijia Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan (Hangzhou) Hospital Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jing Peng
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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16
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Yan LJ, Y. Lau AT, Xu YM. The regulation of microRNAs on chemoresistance in triple-negative breast cancer: a recent update. Epigenomics 2024; 16:571-587. [PMID: 38639712 PMCID: PMC11160456 DOI: 10.2217/epi-2023-0430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/07/2024] [Indexed: 04/20/2024] Open
Abstract
Triple-negative breast cancer (TNBC) has negative expressions of ER, PR and HER2. Due to the insensitivity to both endocrine therapy and HER2-targeted therapy, the main treatment method for TNBC is cytotoxic chemotherapy. However, the curative effect of chemotherapy is limited because of the existence of acquired or intrinsic multidrug resistance. MicroRNAs (miRNAs) are frequently dysregulated in malignant tumors and involved in tumor occurrence and progression. Interestingly, growing studies show that miRNAs are involved in chemoresistance in TNBC. Thus, targeting dysregulated miRNAs could be a plausible way for better treatment of TNBC. Here, we present the updated knowledge of miRNAs associated with chemoresistance in TNBC, which may be helpful for the early diagnosis, prognosis and treatment of this life-threatening disease.
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Affiliation(s)
- Li-Jun Yan
- Laboratory of Cancer Biology & Epigenetics, Department of Cell Biology & Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology & Epigenetics, Department of Cell Biology & Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology & Epigenetics, Department of Cell Biology & Genetics, Shantou University Medical College, Shantou, 515041, China
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17
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Qi JH, Huang SL, Jin SZ. Novel milestones for early esophageal carcinoma: From bench to bed. World J Gastrointest Oncol 2024; 16:1104-1118. [PMID: 38660637 PMCID: PMC11037034 DOI: 10.4251/wjgo.v16.i4.1104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/28/2024] [Accepted: 02/26/2024] [Indexed: 04/10/2024] Open
Abstract
Esophageal cancer (EC) is the seventh most common cancer worldwide, and esophageal squamous cell carcinoma (ESCC) accounts for the majority of cases of EC. To effectively diagnose and treat ESCC and improve patient prognosis, timely diagnosis in the initial phase of the illness is necessary. This article offers a detailed summary of the latest advancements and emerging technologies in the timely identification of ECs. Molecular biology and epigenetics approaches involve the use of molecular mechanisms combined with fluorescence quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology (next-generation sequencing), and digital PCR technology to study endogenous or exogenous biomolecular changes in the human body and provide a decision-making basis for the diagnosis, treatment, and prognosis of diseases. The investigation of the microbiome is a swiftly progressing area in human cancer research, and microorganisms with complex functions are potential components of the tumor microenvironment. The intratumoral microbiota was also found to be connected to tumor progression. The application of endoscopy as a crucial technique for the early identification of ESCC has been essential, and with ongoing advancements in technology, endoscopy has continuously improved. With the advancement of artificial intelligence (AI) technology, the utilization of AI in the detection of gastrointestinal tumors has become increasingly prevalent. The implementation of AI can effectively resolve the discrepancies among observers, improve the detection rate, assist in predicting the depth of invasion and differentiation status, guide the pericancerous margins, and aid in a more accurate diagnosis of ESCC.
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Affiliation(s)
- Ji-Han Qi
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang Province, China
| | - Shi-Ling Huang
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang Province, China
| | - Shi-Zhu Jin
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang Province, China
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18
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Da W, Song Z, Liu X, Wang Y, Wang S, Ma J. The role of TET2 in solid tumors and its therapeutic potential: a comprehensive review. Clin Transl Oncol 2024:10.1007/s12094-024-03478-5. [PMID: 38598002 DOI: 10.1007/s12094-024-03478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]
Abstract
Indeed, tumors are a significant health concern worldwide, and understanding the underlying mechanisms of tumor development is crucial for effective prevention and treatment. Epigenetics, which refers to changes in gene expression that are not caused by alterations in the DNA sequence itself, plays a critical role in the entire process of tumor development. It goes without saying that the effect of methylation on tumors is a significant aspect of epigenetics. Among the methylation modifications, DNA methylation is an important part, which plays a regulatory role in tumor-related genes. Ten-eleven translocation 2 (TET2) is a highly influential protein involved in the modification of DNA methylation. Its primary role is associated with the suppression of tumor development, making it a significant player in cancer research. However, TET2 is frequently mentioned in hematological diseases, its role in solid tumors has received little attention. Studying the changes of TET2 in solid tumors and the regulatory mechanism will facilitate its investigation as a clinical target for targeted therapy and may also provide directions for clinical treatment of malignant tumors.
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Affiliation(s)
- Wenxin Da
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Ziyu Song
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Xiaodong Liu
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Yahui Wang
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Shengjun Wang
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China
| | - Jie Ma
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Xuefu Road No. 301, Zhenjiang, 212013, China.
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Tan Z, Li H, Huang Y, Fu S, Wang H, Wang J. Multi-omics landscape analysis reveals the pan-cancer association of arginine biosynthesis genes with tumor immune evasion and therapy resistance. Heliyon 2024; 10:e26804. [PMID: 38468956 PMCID: PMC10925990 DOI: 10.1016/j.heliyon.2024.e26804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Background The metabolism of arginine, a conditionally essential amino acid, plays a crucial role in cancer progression and prognosis. However, a more detailed understanding of the influence of arginine biosynthesis genes in cancer is currently unavailable. Methods We performed an integrative multi-omics analysis using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to determine the characteristics of these genes across multiple cancer types. To measure the overall activity of arginine biosynthesis genes in cancer, we calculated arginine biosynthesis scores based on gene expression. Results Our results indicated that the arginine biosynthesis score was negatively correlated with immune-related pathways, immune infiltration, immune checkpoint expression, and patient prognosis, and single-cell data further clarified that patients with high arginine biosynthesis scores showed a reduced proportion of T and B cells in an immune desert tumor microenvironment and were insensitive to immunotherapy. We also identified several potential drugs through the Cancer Therapeutic Response Portal (CTRP) and Genomics of Drug Sensitivity in Cancer (GDSC) databases that could target arginine biosynthesis genes and potentially improve the response rate to immunotherapy in patients with a high arginine biosynthesis fraction. Conclusion Overall, our analyses emphasize that arginine biosynthesis genes are associated with immune evasion in several cancers. Targeting these genes may facilitate more effective immunotherapy.
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Affiliation(s)
- Zhiyong Tan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Urological disease clinical medical center of Yunnan province, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming 650101, Yunnan, China
| | - Haihao Li
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Urological disease clinical medical center of Yunnan province, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming 650101, Yunnan, China
| | - Yinglong Huang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Urological disease clinical medical center of Yunnan province, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming 650101, Yunnan, China
| | - Shi Fu
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Urological disease clinical medical center of Yunnan province, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming 650101, Yunnan, China
| | - Haifeng Wang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Urological disease clinical medical center of Yunnan province, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming 650101, Yunnan, China
| | - Jiansong Wang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Urological disease clinical medical center of Yunnan province, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming, 650101, Yunnan, China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, The Second Affiliated Hospital of Kunming Medical University, No. 347, Dianmian Street, Wuhua District, Kunming 650101, Yunnan, China
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Duan C, Yan Z, Wu C, Zhou X, Bao W. DNA methylation characteristics associated with chemotherapy resistance in epithelial ovarian cancer. Heliyon 2024; 10:e27212. [PMID: 38468944 PMCID: PMC10926131 DOI: 10.1016/j.heliyon.2024.e27212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Objective The high mortality rate of epithelial ovarian cancer (EOC) is often attributed to the frequent development of chemoresistance. DNA methylation is a predictive biomarker for chemoresistance. Methods This study utilized DNA methylation profiles and relevant information from GEO and TCGA to identify different methylated CpG sites (DMCs) between chemoresistant and chemosensitive patients. Subsequently, we constructed chemoresistance risk models with DMCs. The genes corresponding to candidate DMCs in chemoresistance risk models were further analyzed to identify different methylated gene symbols (DMGs) associated with chemoresistance. The DMGs that showed a strong correlation with the corresponding DMCs were analyzed through immunohistochemistry. Results Compared to chemosensitive EOC patients, chemoresistant patients showed 423 hypermethylated CpGs and 1445 hypomethylated CpGs. The chemoresistance risk models based on DMCs have shown the improved predictive ability for chemoresistance in EOC (AUC = 65.0-76.2%). The methylations of cg25510164, cg13154880, cg15362155 and cg08665359 were strongly associated with decreased risk of chemoresistance. Conversely, the methylation of cg08872590 and cg14739437 significantly increased the risk. We identified 13 DMGs, from 47 DMCs corresponding genes, between chemosensitive and chemoresistant samples. Among the DMGs, the expression levels of DDR2 and OPCML exhibited strong correlations with the corresponding DMCs. DDR2 and OPCML both showed enhanced expression in chemoresistant ovarian microarray tissue. Conclusions Hypomethylated CpGs may play a significant role in DNA methylation associated with chemoresistance in EOC. The epigenetic modification of DDR2 could have important implications for the development of chemoresistance. Our study provides valuable insights for future research on DNA methylation in the chemoresistance of EOC.
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Affiliation(s)
| | | | - Cailiang Wu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Xuexin Zhou
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Wei Bao
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
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Ahmadi S, Surmava S, Kvaratskhelia D, Gogolashvili A, Kvaratskhelia E, Abzianidze E, Kankava K. Association Between Multiple Single Nucleotide Polymorphisms in Folate Metabolism Pathway and Breast Cancer Risk in Georgian Women: A Case-Control Study. Clin Med Insights Oncol 2024; 18:11795549241233693. [PMID: 38433849 PMCID: PMC10908228 DOI: 10.1177/11795549241233693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Background The folate metabolism pathway plays an integral part in DNA synthesis, methylation, and repair. Methylenetetrahydrofolate reductase (MTHFR) and methylenetetrahydrofolate dehydrogenase (MTHFD1) are both enzymes that are involved in this pathway, and the single nucleotide polymorphisms (SNPs) in genes coding for them have modulatory effects on DNA expression. This study aimed to investigate the relationship between MTHFR C677T (rs1801133) and MTHFD1 G1958A (rs2236225) polymorphisms and the risk of developing breast cancer in Georgian women. Methods A case-control study was performed examining the MTHFR C677T and MTHFD1 G1958A SNP in breast cancer-confirmed cases and healthy matched controls. Real time-polymerase chain reaction (PCR) was used to genotype SNPs. The case individuals' pathology reports were obtained following surgeries for cancer characteristic data. Statistical analysis was performed to investigate the significance of the acquired data. Results Statistical analysis of MTHFR C677T SNP revealed that the CT genotype increased the risk of breast cancer by 2.17 folds in the over-dominant model. Statistical analysis of MTHFD1 G1958A SNP showed that the GA genotype increased the risk of breast cancer by 4.12 folds in the codominant model and 2.41 folds in the over-dominant model. No statistically significant link was found between genotypes and lymph node status, however, patients with the CT genotype had higher percentages of proliferative activity. Conclusions Breast cancer seems to have a statistically significant association with the CT genotype in MTHFR C677T and the GA genotype in MTHFD1 G1958A in Georgian women.
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Affiliation(s)
- Saba Ahmadi
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Sandro Surmava
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Davit Kvaratskhelia
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Ana Gogolashvili
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Eka Kvaratskhelia
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
- V. Bakhutashvili Institute of Medical Biotechnology, Tbilisi State Medical University, Tbilisi, Georgia
| | - Elene Abzianidze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
- Ivane Beritashvili Center Of Experimental Biomedicine, Tbilisi, Georgia
| | - Ketevani Kankava
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
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Yu F, Zhao LX, Chu S. TCHH as a Novel Prognostic Biomarker for Patients with Gastric Cancer by Bioinformatics Analysis. Clin Exp Gastroenterol 2024; 17:61-74. [PMID: 38434179 PMCID: PMC10906726 DOI: 10.2147/ceg.s451676] [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: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 03/05/2024] Open
Abstract
Background This study aims to investigate the clinicopathological significance and prognostic value of Trichohyalin (TCHH) in gastric cancer patients through bioinformatics analysis. Materials and Methods Data on TCHH expression and clinicopathological information were sourced from The Cancer Genome Atlas (TCGA). The Wilcoxon signed-rank test was used for evaluating the correlation between TCHH mRNA expression levels and clinicopathological features. The predictive significance of TCHH mRNA expression for overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in patients with gastric cancer was assessed using Cox regression models. Furthermore, measures of immune cell infiltration in gastric cancer were made, and studies of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were also carried out to investigate the possible roles of TCHH in patients with gastric cancer. Results Compared to normal tissues, gastric cancer had a considerably higher expression of TCHH mRNA (P < 0.05). Wilcoxon analysis revealed a significant association between TCHH mRNA expression and the pathologic M stage (P = 0.017). High TPMT mRNA levels were also correlated with worse OS, DFS, and PFI in gastric cancer patients (both P < 0.05). TCHH showed significant negative correlations with the levels of NK CD56dim infiltration (r = -0.157, p = 0.002), Th17 cells infiltration (r = -0.235, P < 0.001), and Th2 infiltration (r = -0.195, P < 0.001). Furthermore, enrichment analysis indicated potential involvement in intermediate filament cytoskeleton organization, DNA methylation in gamete generation, cell-cell recognition, and G protein-coupled peptide receptor (GPCRs) activity. Conclusion The level of TCHH mRNA may serve as a novel prognostic biomarker for gastric cancer patients.
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Affiliation(s)
- Fu Yu
- Department of Medical Oncology, Mingguang People’s Hospital of Anhui Province in China, Chuzhou, 239400, People’s Republic of China
| | - Li Xia Zhao
- Department of Radiation Oncology, Jieshou People’s Hospital of Anhui Province in China, Fuyang, 236500, People’s Republic of China
| | - Shangqi Chu
- Department of Medical Oncology, Nantong Haimen District People’s Hospital, Nantong, Jiangsu Province, 226100, People’s Republic of China
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Yoshioka S, Arakawa Y, Hasegawa M, Kato S, Hashimoto H, Mori S, Ueda H, Watanabe M. Twin study: genotype-dependent epigenetic factors affecting free thyroxine levels in the normal range. Epigenomics 2024; 16:147-158. [PMID: 38264851 DOI: 10.2217/epi-2023-0372] [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: 01/25/2024] Open
Abstract
Aim: To explore the clinical application of DNA methylation affecting thyroid function, we evaluated the association of DNA methylation with free thyroxine (FT4) and TSH measurements in monozygotic twins. Materials & methods: Discordant pairs for FT4 or TSH levels were examined for the relationship between the within-pair difference of each measurement and the DNA methylation levels using epigenome-wide association studies. The contribution of polymorphisms to the methylation sensitivity was also examined. Results: We found two CpG sites significantly associated with FT4 levels, and also some CpG sites showing significant differences in their methylation levels within FT4-discordant pairs depending on the polymorphism in EPHB2. Conclusion: The FT4 level may be associated with a combination of methylation and polymorphisms in the EPHB2 gene.
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Affiliation(s)
- Saki Yoshioka
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Yuya Arakawa
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
- Center for Twin Research, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Mika Hasegawa
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Shiho Kato
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Hinako Hashimoto
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Saho Mori
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Hiromichi Ueda
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
| | - Mikio Watanabe
- Department of Clinical Laboratory & Biomedical Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
- Center for Twin Research, Osaka University Graduate School of Medicine, Yamadaoka 1-7, Suita, Osaka, 565-0871, Japan
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Tang Q, Wang S, Li H, Liu J, Hu X, Zhao D, Di M. Integrated multi-omics analyses reveal the TM4SF family genes with prognostic and therapeutic relevance in hepatocellular carcinoma. Aging (Albany NY) 2024; 16:593-616. [PMID: 38206300 PMCID: PMC10817404 DOI: 10.18632/aging.205398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/16/2023] [Indexed: 01/12/2024]
Abstract
TM4SF family members (TM4SFs) have been shown to be aberrantly expressed in multiple types of cancer. However, a comprehensive investigation of the TM4SFs has yet to be performed in LIHC. The study comprehensively investigated the expression and prognostic value of TM4SFs. Then, a TM4SFs-based risk model and nomogram were constructed for prognostic prediction. Finally, functional loss of TM4SFs was performed to verify the potential role of TM4SFs in LIHC. We found that TM4SFs were significantly up-regulated in LIHC. High expression and hypomethylation of TM4SFs were associated with poor prognosis of LIHC patients. Then, a TM4SFs-based risk model was constructed that could effectively classify LIHC patients into high and low-risk groups. In addition, we constructed a prognostic nomogram that could predict the long-term survival of LIHC patients. Based on immune infiltration analysis, high-risk patients had a relatively higher immune status than low-risk patients. Moreover, the prediction module could predict patient responses to immunotherapy and chemotherapy. Finally, loss-of-function studies showed that TM4SF4 knockdown could substantially suppress the growth, migratory, and invasive abilities of LIHC cells. Targeting TM4SFs will contribute to effective immunotherapy strategies and improve the prognosis of liver cancer patients.
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Affiliation(s)
- Qiang Tang
- Department of Gastrointestinal Surgery, Shiyan Taihe Hospital, Hubei University of Medicine, Hubei Province, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Shurui Wang
- School of Nursing, Peking Union Medical College, Beijing, China
| | - Huimin Li
- Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Junzhi Liu
- Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xin Hu
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dong Zhao
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Maojun Di
- Department of Gastrointestinal Surgery, Shiyan Taihe Hospital, Hubei University of Medicine, Hubei Province, China
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25
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Feng Q, Duan H, Zhou X, Wang Y, Zhang J, Zhang H, Chen G, Bao X. DNA Methyltransferase 3A: A Significant Target for the Discovery of Inhibitors as Potent Anticancer Drugs. Mini Rev Med Chem 2024; 24:507-520. [PMID: 37642180 DOI: 10.2174/1389557523666230825100246] [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: 04/20/2023] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
DNA methyltransferase (DNMT) is a conserved family of Cytosine methylases, which plays a crucial role in the regulation of Epigenetics. They have been considered promising therapeutic targets for cancer. Among the DNMT family, mutations in the DNMT3A subtype are particularly important in hematologic malignancies. The development of specific DNMT3A subtype inhibitors to validate the therapeutic potential of DNMT3A in certain diseases is a significant task. In this review, we summarized the small molecule inhibitors of DNMT3A discovered in recent years and their inhibitory activities, and classified them based on their inhibitory mechanisms.
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Affiliation(s)
- Qixun Feng
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Honggao Duan
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinglong Zhou
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuning Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jinda Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Haoge Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Guoliang Chen
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xuefei Bao
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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26
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Sanjai C, Hakkimane SS, Guru BR, Gaonkar SL. A comprehensive review on anticancer evaluation techniques. Bioorg Chem 2024; 142:106973. [PMID: 37984104 DOI: 10.1016/j.bioorg.2023.106973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The development of effective anticancer strategies and the improvement of our understanding of cancer need analytical tools. Utilizing a variety of analytical approaches while investigating anti-cancer medicines gives us a thorough understanding of the traits and mechanisms concerned to cancer cells, which enables us to develop potent treatments to combat them. The importance of anticancer research may be attributed to various analytical techniques that contributes to the identification of therapeutic targets and the assessment of medication efficacy, which are crucial things in expanding our understanding of cancer biology. The study looks at methods that are often used in cancer research, including cell viability assays, clonogenic assay, flow cytometry, 2D electrophoresis, microarray, immunofluorescence, western blot caspase activation assay, bioinformatics, etc. The fundamentals, applications, and how each technique analytical advances our understanding of cancer are briefly reviewed.
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Affiliation(s)
- Chetana Sanjai
- Department of Biotechnology, Manipal Institute of Technology Bengaluru, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushruta S Hakkimane
- Department of Biotechnology, Manipal Institute of Technology Bengaluru, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Bharath Raja Guru
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Santosh L Gaonkar
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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27
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Crisalli AM, Chen YT, Cai A, Li D, Cho BP. Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts. Nucleic Acids Res 2023; 51:12043-12053. [PMID: 37953358 PMCID: PMC10711442 DOI: 10.1093/nar/gkad1038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/27/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5'-CTTCTC#G*NCCTCATTC-3'], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3' flanking pyrimidine were better bypassed when the 5' base was 5mC, whereas sequences with a 3' purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.
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Affiliation(s)
- Alicia M Crisalli
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Ang Cai
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Bongsup P Cho
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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28
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Liu X, Li X, Wang L, Yu K, Wu D, Tao P, Li Y. Pan‑cancer analysis identified ARHGAP23 as a potential biomarker for pancreatic adenocarcinoma. Mol Clin Oncol 2023; 19:100. [PMID: 38022849 PMCID: PMC10666083 DOI: 10.3892/mco.2023.2696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Rho GTPASE-activating protein 23 (ARHGAP23) is known to activate RHO-GTPase and has an important role in the infiltration and metastasis of tumors. Although previous studies suggested its involvement in certain human cancers, its role in pan-cancer remains unclear. In the present study, the expression, prognosis and potential functions of ARHGAP23 in pan-cancer were evaluated through various public databases such as Human Protein Atlas, Tumor IMmune Estimation Resource, Gene Set Co-Expression Analysis, Gene Expression Profiling Interactive Analysis, cBio Cancer Genomics Portal, Tumor-Immune System Interactions Database (TISIDB) and others. Through these data combined with a variety of biological information analysis methods, the potential role of ARHGAP23 as a carcinogenic gene was explored in the present study. The present analysis revealed that ARHGAP23 expressed abnormalities in >10 tumors, which was associated with differences in prognosis. Furthermore, the findings of the present study indicated that ARHGAP23 is associated with DNA methylation and multiple immune cell infiltrations in these tumors. ARHGAP23 expression was related to clinical prognosis, DNA methylation and immune infiltration. These findings support the potential of ARHGAP23 as a prognostic biomarker and a molecular target for cancer treatment.
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Affiliation(s)
- Xiaolong Liu
- The First School of Clinical Medical, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xin Li
- The General Surgery Department, Lanzhou University Second Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Ling Wang
- Department of Pathology, Lanzhou, Gansu 730000, P.R. China
| | - Kaihua Yu
- The First School of Clinical Medical, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Dean Wu
- The First School of Clinical Medical, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Pengxian Tao
- Cadre Ward of General Surgery Department, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Yulan Li
- The First School of Clinical Medical, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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Li W, Zou C. NXNL2 Promotes Colon Cancer Proliferation and Metastasis by Regulating AKT Pathway. Appl Biochem Biotechnol 2023; 195:7685-7696. [PMID: 37084033 DOI: 10.1007/s12010-023-04513-x] [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] [Accepted: 04/11/2023] [Indexed: 04/22/2023]
Abstract
This study aimed to explore the role of nucleoredoxin-like 2 (NXNL2) in colon cancer (CC). The GEPIA and UALCAN databases were analyzed to explore genes involved in the prognosis of CC patients. DLD1 cells were treated with the DNA methylation inhibitor 5-azacitidine to validate the above findings. The methyltransferase DNMT (DNA methylation) was further knocked down by shRNA, then the expression of NXNL2 was assessed by qPCR. The role of NXNL2 on cell proliferation and metastasis was examined using corresponding assays. NXNL2 was found to exhibit the greatest impact on the prognosis of CC patients. High NXNL2 correlated with poor survival outcomes of CC. The expression of NXNL2 was regulated by DNA methylation. NXNL2 promoted CC cell proliferation and metastasis. Also, NXNL2 promoted the AKT pathway activity. In conclusion, NXNL2 could affect the cancer cell proliferation and metastasis, and has a poor survival prognosis in CC.
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Affiliation(s)
- Wenqin Li
- Department of Gastroenterology, the Second Clinical Medical college, Yangtze University, No. 60 Jingzhong Road, Jingzhou, 434020, Hubei, China
| | - Chuanxin Zou
- Department of Gastroenterology, the Second Clinical Medical college, Yangtze University, No. 60 Jingzhong Road, Jingzhou, 434020, Hubei, China.
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30
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Qi B, Sun Y, Lv Y, Hu P, Ma Y, Gao W, Li S, Zhang X, Jin X, Liou Y, Liu P, Liu S. Hypermethylated CDO1 and CELF4 in cytological specimens as triage strategy biomarkers in endometrial malignant lesions. Front Oncol 2023; 13:1289366. [PMID: 38107069 PMCID: PMC10722236 DOI: 10.3389/fonc.2023.1289366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Objective Developing a non-invasive and reliable triage test for endometrial malignant lesions is an important goal, as it could help to reduce the number of invasive diagnostic procedures required and improve patient survival. We aimed to estimate the diagnostic value of DNA methylation levels in cervical cytological samples of endometrial cancer (EC) and endometrial atypical hyperplasia (AH). Methods A total of 607 women who had indications for endometrial biopsy in the Department of Obstetrics and Gynecology of Cangzhou Central Hospital from October 2022 to April 2023 were enrolled in this study. The cervical exfoliated cells were collected for gene methylation before endometrial biopsy. Clinical information, tumor biomarkers, and endometrial thickness (ET) of transvaginal ultrasonography (TVS) were also collected. With endometrial histopathology as the gold standard, multivariate unconditional logistic regression was applied to analyze the risk factors of endometrial malignant lesions. The role of cysteine dioxygenase type 1 (CDO1) and CUGBP Elav-like family member 4 (CELF4) gene methylation as a triage strategy biomarker in endometrial malignant lesions was specifically explored. Results Multivariate logistic regression analysis showed that premenopausal ET ≥ 11 mm or postmenopausal ET ≥ 5 mm, CDO1 ΔCt ≤ 8.4, or CELF4 ΔCt ≤ 8.8 were the risk factors for AH and EC, with odds ratios (ORs) (95%CI) of 5.03 (1.83-13.82) and 6.92 (1.10-43.44), respectively (p-values < 0.05). The sensitivity and specificity of CDO1/CELF4 dual-gene methylation assay for AH and EC reached 84.9% (95%CI: 75.3%-94.5%) and 86.6% (95%CI: 83.8%-89.5%), respectively. ET combined with DNA methylation detection further improved the specificity to (94.9%, 95%CI: 93.1%-96.8%). Conclusion The accuracy of cervical cytology DNA methylation is superior to that of other clinical indicators in the non-invasive examination of endometrial malignant lesions. DNA methylation combined with TVS can further improve the specificity and is a promising biomarker triage strategy in women with suspected endometrial lesions.
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Affiliation(s)
- Bingli Qi
- Department of Gynecologic Oncology and Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Ye Sun
- Department of Gynecologic Oncology and Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Yaohua Lv
- Department of Gynecologic Oncology and Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Pei Hu
- Department of Gynecologic Oncology and Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Yanli Ma
- Department of Pharmacy, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Wenying Gao
- Department of Gynecologic Oncology and Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Shumei Li
- Department of Gynecologic Oncology and Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Xin Zhang
- Department of Gynecologic Oncology and Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Xitong Jin
- Department of Medical Laboratory, Beijing Origin-Poly Bio-Tec Co., Ltd., Beijing, China
| | - Yuligh Liou
- Department of Medical Laboratory, Beijing Origin-Poly Bio-Tec Co., Ltd., Beijing, China
| | - Pei Liu
- Department of Medical Laboratory, Beijing Origin-Poly Bio-Tec Co., Ltd., Beijing, China
| | - Shikai Liu
- Department of Gynecologic Oncology and Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
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Park JW, Lee K, Kim EE, Kim SI, Park SH. Brain Tumor Classification by Methylation Profile. J Korean Med Sci 2023; 38:e356. [PMID: 37935168 PMCID: PMC10627723 DOI: 10.3346/jkms.2023.38.e356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/12/2023] [Indexed: 11/09/2023] Open
Abstract
The goal of the methylation classifier in brain tumor classification is to accurately classify tumors based on their methylation profiles. Accurate brain tumor diagnosis is the first step for healthcare professionals to predict tumor prognosis and establish personalized treatment plans for patients. The methylation classifier can be used to perform classification on tumor samples with diagnostic difficulties due to ambiguous histology or mismatch between histopathology and molecular signatures, i.e., not otherwise specified (NOS) cases or not elsewhere classified (NEC) cases, aiding in pathological decision-making. Here, the authors elucidate upon the application of a methylation classifier as a tool to mitigate the inherent complexities associated with the pathological evaluation of brain tumors, even when pathologists are experts in histopathological diagnosis and have access to enough molecular genetic information. Also, it should be emphasized that methylome cannot classify all types of brain tumors, and it often produces erroneous matches even with high matching scores, so, excessive trust is prohibited. The primary issue is the considerable difficulty in obtaining reference data regarding the methylation profile of each type of brain tumor. This challenge is further amplified when dealing with recently identified novel types or subtypes of brain tumors, as such data are not readily accessible through open databases or authors of publications. An additional obstacle arises from the fact that methylation classifiers are primarily research-based, leading to the unavailability of charging patients. It is important to note that the application of methylation classifiers may require specialized laboratory techniques and expertise in DNA methylation analysis.
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Affiliation(s)
- Jin Woo Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Kwanghoon Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Eric Eunshik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Seong-Ik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Institute of Neuroscience, Seoul National University College of Medicine, Seoul, Korea.
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Peter RM, Chou PJ, Shannar A, Patel K, Pan Y, Dave PD, Xu J, Sarwar MS, Kong ANT. An Update on Potential Molecular Biomarkers of Dietary Phytochemicals Targeting Lung Cancer Interception and Prevention. Pharm Res 2023; 40:2699-2714. [PMID: 37726406 DOI: 10.1007/s11095-023-03595-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023]
Abstract
Since ancient times, dietary phytochemicals are known for their medicinal properties. They are broadly classified into polyphenols, terpenoids, alkaloids, phytosterols, and organosulfur compounds. Currently, there is considerable interest in their potential health effects against various diseases, including lung cancer. Lung cancer is the leading cause of cancer deaths with an average of five-year survival rate of lung cancer patients limited to just 14%. Identifying potential early molecular biomarkers of pre-malignant lung cancer cells may provide a strong basis to develop early cancer detection and interception methods. In this review, we will discuss molecular changes, including genetic alterations, inflammation, signal transduction pathways, redox imbalance, epigenetic and proteomic signatures associated with initiation and progression of lung carcinoma. We will also highlight molecular targets of phytochemicals during lung cancer development. These targets mainly consist of cellular signaling pathways, epigenetic regulators and metabolic reprogramming. With growing interest in natural products research, translation of these compounds into new cancer prevention approaches to medical care will be urgently needed. In this context, we will also discuss the overall pharmacokinetic challenges of phytochemicals in translating to humans. Lastly, we will discuss clinical trials of phytochemicals in lung cancer patients.
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Affiliation(s)
- Rebecca Mary Peter
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Pochung Jordan Chou
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Ahmad Shannar
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Komal Patel
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Yuxin Pan
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Parv Dushyant Dave
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jiawei Xu
- Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Md Shahid Sarwar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Ah-Ng Tony Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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Qadir Nanakali NM, Maleki Dana P, Sadoughi F, Asemi Z, Sharifi M, Asemi R, Yousefi B. The role of dietary polyphenols in alternating DNA methylation in cancer. Crit Rev Food Sci Nutr 2023; 63:12256-12269. [PMID: 35848113 DOI: 10.1080/10408398.2022.2100313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Natural products such as curcumin, quercetin, and resveratrol have been shown to have antitumor effectsand several studies have examined their role in treating cancer, either alone or in combination with other chemotherapeutic drugs. These compounds are capable of affecting different cancer-related mechanisms, such as proliferation, inflammation, invasion, and metastasis. Along with all of the benefits of these agents, affecting epigenetic processes is one of the most important aspects of their impact. Epigenetic modifications can be categorized into three main processes that include DNA methylation, histone modification, and regulation of small non-coding RNAs. Therefore, targeting DNA methylation can be used as a cancer treatment strategy by identifying or developing methylation modulators. Herein, we take a look into the studies investigating the role of natural products (e.g. curcumin, resveratrol, epigallocatechin gallate (EGCG), and quercetin) in alternating the DNA methylation status of various cancer cells. We discuss how these compounds reduce the expression of enzymes mediating the methylation of tumor suppressor genes and thereby, increasing the expression of tumor suppressors while reactivating antitumor signaling pathways.
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Affiliation(s)
- Nadir Mustafa Qadir Nanakali
- Department of Biomedical Science, College of Science, Cihan University-Erbil, Kurdistan Region, Erbil, Iraq
- Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Erbil, Iraq
| | - Parisa Maleki Dana
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Fatemeh Sadoughi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Mehran Sharifi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Reza Asemi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Liu T, Li ZZ, Sun L, Yang K, Chen JM, Han XY, Qi LM, Zhou XG, Wang P. Upregulated CANT1 is correlated with poor prognosis in hepatocellular carcinoma. BMC Cancer 2023; 23:1007. [PMID: 37858061 PMCID: PMC10588055 DOI: 10.1186/s12885-023-11463-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND CANT1, as calcium-activated protein nucleotidase 1, is a kind of phosphatase. It is overexpressed in some tumors and related to poor prognosis, but few studies explore its function and carcinogenic mechanism in hepatocellular carcinoma (HCC). METHODS The expression of CANT1 mRNA and protein was analyzed by the Cancer Genome Atlas (TCGA) database and immunohistochemistry(IHC) staining. The relationship between CANT1 expression and clinicopathology was evaluated by various public databases. The receiver operating characteristic (ROC) curve was used to assess the diagnostic accuracy of CANT1 by the area under curve (AUC). Univariate, multivariate Cox regression and Kaplan-Meier curves were applied to evaluate the predictive value of CANT1 on the prognosis of HCC. Methsurv was used to analyze gene changes and DNA methylation, and its impact on prognosis. The enrichment analysis of DEGs associated with CANT1 revealed the biological process of CANT1 based on Gene Set Enrichment Analysis (GSEA). The relationship between immune cell infiltration level and CANT1 expression in HCC was investigated using the single-sample GSEA (ssGSEA) method and the Tumor Immune Estimation Resource (TIMER) database. Finally, the association between CANT1 and immune checkpoints and drug sensitivity was also analyzed. RESULTS CANT1 was highly expressed in 22 cancers, including HCC, and CANT1 overexpression in HCC was confirmed by IHC. The expression of CANT1 was correlated with clinical features, such as histologic grade. Highly expressed CANT1 caused poor overall survival (OS) of HCC patients. Univariate and multivariate regression analysis suggested that CANT1 was an independent prognostic marker. Of the 31 DNA methylation at CpG sites, three CpG sites were associated with the prognosis of HCC. GSEA indicated that CANT1 was mainly involved in the cell cycle, DNA replication, and etc. Moreover, CANT1 expression was correlated with immune cell infiltration and independently associated with the prognosis of HCC patients. Finally, CANT1 expression was correlated with most immune checkpoints and drug sensitivity. CONCLUSION CANT1 may be a latent oncogene of HCC, and associated with immune cells and immune checkpoints, which may assist in HCC treatment.
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Affiliation(s)
- Ting Liu
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China
| | - Zhi-Zhao Li
- Department of Cardiovascular medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China
| | - Lei Sun
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China
| | - Kun Yang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China
| | - Jia-Min Chen
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China
| | - Xiao-Yi Han
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China
| | - Li-Ming Qi
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China
| | - Xin-Gang Zhou
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China.
| | - Peng Wang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, China.
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Pei B, Zhao G, Geng Z, Wang Y, Wang M, Wang X, Xiong S, Zheng M. Identifying potential DNA methylation markers for the detection of esophageal cancer in plasma. Front Genet 2023; 14:1222617. [PMID: 37867599 PMCID: PMC10586502 DOI: 10.3389/fgene.2023.1222617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023] Open
Abstract
Background: Esophageal cancer (EC) is a leading cause of cancer-related deaths in China, with the 5-year survival rate reaching less than 30%, because most cases were diagnosed and treated at the advanced stage. However, there is still a lack of low-cost, efficient, and accurate non-invasive methods for the early detection of EC at present. Methods: A total of 48 EC plasma and 101 control plasma samples were collected in a training cohort from 1 January 2021 to 31 December 2021, and seven cancer-related DNA methylation markers (ELMO1, ZNF582, FAM19A4, PAX1, C13orf18, JAM3 and TERT) were tested in these samples to select potential markers. In total, 20 EC, 10 gastric cancer (GC), 10 colorectal cancer (CRC), and 20 control plasma samples were collected in a validation cohort to evaluate the two-gene panel. Results: ZNF582, FAM19A4, JAM3, or TERT methylation in plasma was shown to significantly distinguish EC and control subjects (p < 0.05), and the combination of ZNF582 and FAM19A4 methylation was the two-gene panel that exhibited the best performance for the detection of EC with 60.4% sensitivity (95% CI: 45.3%-73.9%) and 83.2% specificity (95% CI: 74.1%-89.6%) in the training cohort. The performance of this two-gene panel showed no significant difference between different age and gender groups. When the two-gene panel was combined with CEA, the sensitivity for EC detection was further improved to 71.1%. In the validation cohort, the sensitivity of the two-gene panel for detecting EC, GC, and CRC was 60.0%, 30.0%, and 30.0%, respectively, with a specificity of 90.0%. Conclusion: The identified methylation marker panel provided a potential non-invasive strategy for EC detection, but further validation should be performed in more clinical centers.
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Affiliation(s)
- Bing Pei
- The Suqian Clinical College of Xuzhou Medical University, Suqian, China
- Department of Clinical Laboratory, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Guodong Zhao
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
- Department of R&D, Suzhou VersaBio Technologies Co Ltd., Kunshan, China
| | - Zhixin Geng
- Department of Clinical Laboratory, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Yue Wang
- Department of R&D, Suzhou VersaBio Technologies Co Ltd., Kunshan, China
| | - Menglin Wang
- Department of Clinical Laboratory, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Xiaomei Wang
- Department of R&D, Suzhou VersaBio Technologies Co Ltd., Kunshan, China
| | - Shangmin Xiong
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, China
- Department of R&D, Suzhou VersaBio Technologies Co Ltd., Kunshan, China
| | - Minxue Zheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
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Pitaksalee R, Parmar R, Hodgett R, Emery P, Ponchel F. DNA Hypomethylation in the TNF-Alpha Gene Predicts Rheumatoid Arthritis Classification in Patients with Early Inflammatory Symptoms. Cells 2023; 12:2376. [PMID: 37830590 PMCID: PMC10571942 DOI: 10.3390/cells12192376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023] Open
Abstract
Biomarkers for the classification of rheumatoid arthritis (RA), and particularly for anti-citrullinated peptide antibody (ACPA)-negative patients, remain an important hurdle for the early initiation of treatment. Taking advantage of DNA-methylation patterns specific to early RA, quantitative methylation-specific qPCR (qMSP) offers a robust technology for the development of biomarkers. We developed assays and established their value as RA classification biomarkers. METHODS DNA-methylation data were screened to select candidate CpGs to design qMSP assays. Eight assays were developed and tested on two early inflammatory arthritis cohorts. Logistic regression and bootstrapping were used to demonstrate the added value of the qMSP assays. RESULT Differentially methylated CpG data were screened for candidate CpG, thereby meeting the qMSP assay requirements. The top CpG candidate was in the TNF gene, for which we successfully developed a qMSP assay. Significantly lower DNA-methylation levels were observed in RA (p < 4 × 10-9), with a high predictive value (OR < 0.54/AUC < 0.198) in both cohorts (n = 127/n = 157). Regression using both datasets showed improved accuracy = 87.7% and AUC = 0.944 over the model using only clinical variables (accuracy = 85.2%, AUC = 0.917). Similar data were obtained in ACPA-negative patients (n = 167, accuracy = 82.6%, AUC = 0.930) compared to the clinical variable model (accuracy = 79.5%, AUC = 0.892). Bootstrapping using 2000 datasets confirmed that the AUCs for the clinical+TNF-qMSP model had significant added value in both analyses. CONCLUSION The qMSP technology is robust and can successfully be developed with a high specificity of the TNF qMSP assay for RA in patients with early inflammatory arthritis. It should assist classification in ACPA-negative patients, providing a means of reducing time to diagnosis and treatment.
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Affiliation(s)
- Rujiraporn Pitaksalee
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Rekha Parmar
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Richard Hodgett
- Leeds University Business School, University of Leeds, Leeds LS2 9JT, UK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds LS2 9JT, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds LS1 9LF, UK
| | - Frederique Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds LS2 9JT, UK
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Zhang X, Yang L, Deng Y, Huang Z, Huang H, Wu Y, He B, Hu F. Single-cell RNA-Seq and bulk RNA-Seq reveal reliable diagnostic and prognostic biomarkers for CRC. J Cancer Res Clin Oncol 2023; 149:9805-9821. [PMID: 37247080 DOI: 10.1007/s00432-023-04882-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/19/2023] [Indexed: 05/30/2023]
Abstract
PURPOSE The potential role of epithelium-specific genes through the adenoma-carcinoma sequence in the development of colorectal cancer (CRC) remains unknown. Therefore, we integrated single-cell RNA sequencing and bulk RNA sequencing data to select diagnosis and prognosis biomarkers for CRC. METHODS The CRC scRNA-seq dataset was used to describe the cellular landscape of normal intestinal mucosa, adenoma and CRC and to further select epithelium-specific clusters. Differentially expressed genes (DEGs) of epithelium-specific clusters were identified between intestinal lesion and normal mucosa in the scRNA-seq data throughout the adenoma-carcinoma sequence. Diagnostic biomarkers and prognostic biomarker (the risk score) for CRC were selected in the bulk RNA-seq dataset based on DEGs shared by the adenoma epithelium-specific cluster and the CRC epithelium-specific cluster (shared-DEGs). RESULTS Among the 1063 shared-DEGs, we selected 38 gene expression biomarkers and 3 methylation biomarkers that had promising diagnostic power in plasma. Multivariate Cox regression identified 174 shared-DEGs as prognostic genes for CRC. We combined 1000 times LASSO-Cox regression and two-way stepwise regression to select 10 prognostic shared-DEGs to construct the risk score in the CRC meta-dataset. In the external validation dataset, the 1- and 5-year AUCs of the risk score were higher than those of stage, the pyroptosis-related genes (PRG) score and the cuproptosis-related genes (CRG) score. In addition, the risk score was closely associated with the immune infiltration of CRC. CONCLUSION The combined analysis of the scRNA-seq dataset and the bulk RNA-seq dataset in this study provides reliable biomarkers for the diagnosis and prognosis of CRC.
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Affiliation(s)
- Xing Zhang
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China
| | - Longkun Yang
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China
| | - Ying Deng
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China
| | - Zhicong Huang
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China
| | - Hao Huang
- Department of Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen University Medical School, Shenzhen, 518061, Guangdong Province, People's Republic of China
| | - Yuying Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Baochang He
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China.
| | - Fulan Hu
- Department of Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen University Medical School, Shenzhen, 518061, Guangdong Province, People's Republic of China.
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Wei HF, Zhang RF, Zhao YC, Tong XS. SERPINB7 as a prognostic biomarker in cervical cancer: Association with immune infiltration and facilitation of the malignant phenotype. Heliyon 2023; 9:e20184. [PMID: 37809412 PMCID: PMC10559959 DOI: 10.1016/j.heliyon.2023.e20184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Purpose The purpose of this study was to investigate the expression patterns, predictive significance, and roles in the immune microenvironment of Serpin Family-B Member 7 (SERPINB7) in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). Methods The expression of SERPINB7 and its prognostic relevance were evaluated using RNA-seq data from The Cancer Genome Atlas. SERPINB7 regulation of CESC cell growth and metastasis was investigated using MTT, scratch, and Transwell assays. In vivo effects of SERPINB7 were examined in xenograft model mice and differentially expressed genes (DEGs) associated with SERPINB7 were identified to explore its functional role in oncogenesis. Associations between SERPINB7 levels, chemosensitivity, and immune infiltration were assessed, and mutations and methylation of SERPINB7 were evaluated using the cBioPortal and MethSurv databases, respectively. Results SERPINB7 was up-regulated in CESC samples as well as in other tumors, and patients with higher SERPINB7A mRNA levels exhibited shorter overall survival. The area under the curve for the use of SERPINB7 in CESC diagnosis was above 0.9, and the gene was shown to regulate tumor cell proliferation and metastasis in vitro and in vivo. Overall, 398 DEGs enriched in key CESC progression-related signaling pathways were identified. SERPINB7 expression was additionally correlated with intratumoral immune infiltration and immune checkpoint activity. Patients expressing higher SERPINB7 levels exhibited distinct chemosensitivity profiles, and methylation of the SERPINB7 gene was linked to CESC patient prognostic outcomes. Conclusion SERPINB7 was found to be a crucial regulator of CESC progression, prognosis, and the tumor immune microenvironment, highlighting its potential as a diagnostic and prognostic biomarker and target for CESC immunotherapy.
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Affiliation(s)
- Hua-Fang Wei
- Department of Internal Medicine-1, Jilin Cancer Hospital, Changchun, Jilin, People's Republic of China
| | - Rui-Feng Zhang
- Department of Internal Medicine-1, Jilin Cancer Hospital, Changchun, Jilin, People's Republic of China
- Department of Radiation Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Yue-Chen Zhao
- Department of Radiation Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Xian-Shuang Tong
- Department of Internal Medicine-1, Jilin Cancer Hospital, Changchun, Jilin, People's Republic of China
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Wen R, Zhou L, Jiang S, Fan H, Zheng K, Yu Y, Gao X, Hao L, Lou Z, Yu G, Yang F, Zhang W. DSTN Hypomethylation Promotes Radiotherapy Resistance of Rectal Cancer by Activating the Wnt/β-Catenin Signaling Pathway. Int J Radiat Oncol Biol Phys 2023; 117:198-210. [PMID: 37019366 DOI: 10.1016/j.ijrobp.2023.03.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023]
Abstract
PURPOSE Although surgical resection combined with neoadjuvant radiation therapy can reduce the local recurrence rate of rectal cancer, not all patients benefit from neoadjuvant radiation therapy. Therefore, screening for patients with rectal cancer who are sensitive or resistant to radiation therapy has great clinical significance. METHODS AND MATERIALS Patients with rectal cancer were selected according to postoperative tumor regression grade, and tumor samples were taken for detection. Differential genes between radiation-resistant and radiation-sensitive tissues were screened and validated by Illumina Infinium MethylationEPIC BeadChip, proteomics, Agena MassARRAY methylation, reverse transcription quantitative real-time polymerase chain reaction, and immunohistochemistry. In vitro and in vivo functional experiments verified the role of DSTN. Protein coimmunoprecipitation, western blot, and immunofluorescence were used to investigate the mechanisms of DSTN-related radiation resistance. RESULTS DSTN was found to be highly expressed (P < .05) and hypomethylated (P < .01) in rectal cancer tissues resistant to neoadjuvant radiation therapy. Follow-up data confirmed that patients with high expression of DSTN in neoadjuvant radiation therapy-resistant rectal cancer tissues had shorter disease-free survival (P < .05). DSTN expression increased after methyltransferase inhibitor inhibition of DNA methylation in colorectal cancer cells (P < .05). In vitro and in vivo experiments showed that knockdown of DSTN promoted the sensitivity of colorectal cancer cells to radiation therapy, and overexpression of DSTN promoted the resistance of colorectal cancer cells to radiation (P < .05). The Wnt/β-catenin signaling pathway was activated in colorectal cancer cells overexpressing DSTN. β-catenin was highly expressed in radiation therapy-resistant tissues, and there was a linear correlation between the expression of DSTN and β-catenin (P < .0001). Further studies showed that DSTN can bind to β-catenin and increase its stability. CONCLUSIONS The degree of DNA methylation and the expression level of DSTN can be used as biomarkers to predict the sensitivity of neoadjuvant radiation therapy for rectal cancer. DSTN and β-catenin are also expected to become a reference for the selection of neoadjuvant radiation therapy.
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Affiliation(s)
- Rongbo Wen
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Leqi Zhou
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Siyuan Jiang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Hao Fan
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Kuo Zheng
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yue Yu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xianhua Gao
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Liqiang Hao
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Zheng Lou
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Guanyu Yu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China.
| | - Fu Yang
- Department of Medical Genetics, Naval Medical University, Shanghai, China.
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China.
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Ma S, Wang Z, Li C, Liu Z, Zhang X, Li L, An F, Qiao X. CEACAM1 as a molecular target in oral cancer. Aging (Albany NY) 2023; 15:8137-8154. [PMID: 37589542 PMCID: PMC10497000 DOI: 10.18632/aging.204960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/24/2023] [Indexed: 08/18/2023]
Abstract
OBJECTIVE The majority of oral cancer is caused by malignant transformation of squamous cells in surface of the oral mucosa. However, the relationship between CEACAM1 and oral cancer is unclear. METHODS GSE23558 and GSE25099 profiles were downloaded from gene expression omnibus (GEO). Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. Construction and analysis of protein-protein interaction (PPI) Network. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG), gene set enrichment analysis (GSEA), gene expression heatmap, immune infiltration analysis, comparative toxicogenomics database (CTD) were performed. TargetScan screened miRNAs that regulated central DEGs. Western blotting (WB) experiment was performed. RESULTS 1269 DEGs were identified. According to GO analysis, they were mainly enriched in same protein binding, signal receptor binding, cell surface, epithelial cell development. KEGG analysis showed that they were mainly enriched in cancer pathways, PI3K Akt signaling pathway, TNF signaling pathway, NF kappa B signaling pathway, TGF beta signaling pathway. PPI network showed that 11 genes (CDCA8, CCNA2, MELK, KIF2C, CDC45, HMMR, TPX2, CENPF, CDK1, CEP55, CEACAM1) were obtained. Gene expression heatmap showed that CEP55 and MELK were highly expressed in oral cancer samples. CEACAM1 was lowly expressed in oral cancer samples. CEACAM1, CEP55 and MELK were involved in tumor, inflammation, necrosis, and proliferation. Western blotting (WB) showed that CEACAM1 in oral cancer samples was lower than that in normal samples, after CEACAM1 knockdown, it was lower than that in oral cancer samples. CONCLUSION CEACAM1 is lowly expressed in oral cancer, the lower CEACAM1, the worse prognosis.
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Affiliation(s)
- Sai Ma
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Zhonghua Wang
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Chao Li
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Zhenli Liu
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Xuan Zhang
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Liheng Li
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Feng An
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Xiaoli Qiao
- Department of Central Sterile Supply, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
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Li X, Ma Z, Mei L. Comprehensive analysis of UBE2C expression and its potential roles and mechanisms in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:7397-7407. [PMID: 37580802 PMCID: PMC10457065 DOI: 10.18632/aging.204792] [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: 09/01/2022] [Accepted: 05/01/2023] [Indexed: 08/16/2023]
Abstract
Hepatocellular carcinoma (HCC) ranks one of the most common and lethal cancers all over the world. Previous studies suggest that ubiquitin-conjugating enzyme E2C (UBE2C) serves as an oncogene in human cancers. However, its expression, diagnosis, prognosis and potential mechanisms in HCC remain largely unknown. In this study, the expression of UBE2C in HCC was first analyzed by comprehensive bioinformatic analysis. ROC curve analysis and survival analysis were employed to assess the diagnostic and prognostic roles of UBE2C in HCC. UBE2C promoter methylation level and upstream regulatory miRNAs of UBE2C in HCC were explored. The present work demonstrated that UBE2C was significantly upregulated in HCC compared with normal controls. We also found significant diagnostic and prognostic values of UBE2C in HCC. Promoter methylation of UBE2C was obviously decreased in HCC and was negatively correlated with UBE2C mRNA expression. 10 miRNAs were predicted to potentially bind to UBE2C. In vitro assay and bioinformatic correlation analysis together revealed that hsa-miR-193b-3p might be another key upstream regulatory mechanism of UBE2C in HCC. In conclusion, UBE2C is overexpressed in HCC and may serve as a key diagnostic/prognostic biomarker for patients with HCC.
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Affiliation(s)
- Xiao Li
- Department of Emergency, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 317000, China
| | - Zhaosheng Ma
- Department of Oncological Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 317000, China
| | - Linhang Mei
- Department of Oncological Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 317000, China
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Ma C, Xi S, Sun H, Zhang M, Pei Y. Identifying the oncogenic roles of FAP in human cancers based on systematic analysis. Aging (Albany NY) 2023; 15:7056-7083. [PMID: 37490719 PMCID: PMC10415543 DOI: 10.18632/aging.204892] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/22/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND Fibroblast activation protein-α (FAP) is a specific marker of cancer-associated fibroblasts (CAFs) and plays a crucial role in tumor development. However, the biological processes underlying FAP expression in tumor progression and tumor immunity have not been fully elucidated. METHODS We utilized RNA-seq data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) to perform differential analysis of FAP expression in tumor tissues and matched-normal tissues. The relationship between FAP expression and clinical prognosis, DNA methylation, and tumor-infiltrating immune cells in pan-cancer was assessed using R Studio (version 4.2.1). Additionally, we employed gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) to investigate the biological functions and pathways associated with FAP expression. RESULTS FAP exhibits high expression in most malignancies, albeit to a lesser extent in CESC, KICH, UCEC, SKCM, THCA, and UCS. Furthermore, FAP is either positively or negatively associated with the prognosis of several malignancies. In seven types of cancer, FAP expression is positively correlated with DNA methylation. CIBERSORT analysis revealed an inverse correlation between FAP expression and T cells, B cells, monocytes, and NK cells, while it exhibited a positive correlation with M0, M1, and M2 macrophages. Enrichment analysis further demonstrated that FAP modulates the cell cycle, epithelial-mesenchymal transition (EMT) process, angiogenesis, and immune-related functions and pathways. CONCLUSION Our findings indicate a close relationship between FAP expression and tumorigenesis as well as tumor immunity. FAP has the potential to serve as a diagnostic, prognostic, and immunotherapy marker.
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Affiliation(s)
- Chao Ma
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, Shandong, China
| | - Shuaishuai Xi
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, Shandong, China
- Department of Vascular Surgery, Weifang Yidu Central Hospital, Weifang 262500, Shandong, China
| | - He Sun
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, Shandong, China
| | - Meng Zhang
- Department of Vascular Surgery, Weifang Yidu Central Hospital, Weifang 262500, Shandong, China
| | - Yuanmin Pei
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, Shandong, China
- Department of Vascular Surgery, Weifang Yidu Central Hospital, Weifang 262500, Shandong, China
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Fan C, Ma Q, Wu X, Dai X, Peng Q, Cai H. Detection of DNA Methylation in Gene Loci ASTN1, DLX1, ITGA4, RXFP3, SOX17, and ZNF671 for Diagnosis of Cervical Cancer. Cancer Manag Res 2023; 15:635-644. [PMID: 37457377 PMCID: PMC10349600 DOI: 10.2147/cmar.s417877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Objective To evaluate the diagnostic value of DNA methylation detection of multiple gene loci in cervical cancer. Methods A total of 61 cases requiring cervical biopsy were selected from the outpatient clinic of Maternal and Child Health Hospital of Hubei Province between January 2018 and December 2019. The patients were divided into four groups based on histopathologic diagnosis: cervical cancer (CC) group, high-grade squamous intraepithelial lesion (HSIL) group, low-grade squamous intraepithelial lesion (LSIL) group, and control group. HPV examination, liquid-based cytology examination, and DNA methylation detection at multiple gene sites were performed. The positive rate of DNA methylation, sensitivity, specificity, area under the curve (AUC), and other efficacy indexes were calculated to evaluate the diagnostic value of DNA methylation detection at multiple gene loci in cervical cancer. Results The positive rates of DNA methylation in CC, HSIL, LSIL, and control groups were 100%, 88%, 83% and 17%, respectively. The ZNF671 gene had the highest positive rate among the cervical lesion group, with rates of 57%, 76%, and 100% in LSIL, HSIL, and CC groups respectively. The combination of DNA methylation detection at multiple gene loci showed the highest diagnostic efficacy for HSIL and cervical cancer, with AUC value of 0.850 (95% CI:0.746-0.954), a Youden index of 0.654, and a sensitivity and specificity of 85% and 85.4%, respectively. The diagnostic efficacy of the combined detection was significantly higher than that of HPV examination and liquid-based cytology examination (P < 0.05). Conclusion DNA methylation detection at multiple gene loci is highly effective and diagnostic tool for cervical cancer, and has potential application value in clinical practice.
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Affiliation(s)
- Chunli Fan
- Department of Scientific Research and Teaching Management Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Quanfu Ma
- Department of Scientific Research and Teaching Management Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Xufeng Wu
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Xuan Dai
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Qiuzi Peng
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Hongning Cai
- Department of Scientific Research and Teaching Management Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
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Wu S, Yang F, Chao S, Wang B, Wang W, Li H, Yu L, He L, Li X, Sun L, Qin S. Altered DNA methylome profiles of blood leukocytes in Chinese patients with mild cognitive impairment and Alzheimer's disease. Front Genet 2023; 14:1175864. [PMID: 37388929 PMCID: PMC10300350 DOI: 10.3389/fgene.2023.1175864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Objective: DNA methylation plays a potential role in the pathogenesis of Alzheimer's disease (AD). However, little is known about the global changes of blood leukocyte DNA methylome profiles from Chinese patients with mild cognitive impairment (MCI) and with AD, or the specific DNA methylation-based signatures associated with MCI and AD. In this study, we sought to dissect the characteristics of blood DNA methylome profiles in MCI- and AD-affected Chinese patients with the aim of identifying novel DNA methylation biomarkers for AD. Methods: In this study, we profiled the DNA methylome of peripheral blood leukocytes from 20 MCI- and 20 AD-affected Chinese patients and 20 cognitively healthy controls (CHCs) with the Infinium Methylation EPIC BeadChip array. Results: We identified significant alterations of the methylome profiles in MCI and AD blood leukocytes. A total of 2,582 and 20,829 CpG sites were significantly and differentially methylated in AD and MCI compared with CHCs (adjusted p < 0.05), respectively. Furthermore, 441 differentially methylated positions (DMPs), aligning to 213 unique genes, were overlapped by the three comparative groups of AD versus CHCs, MCI versus CHCs, and AD versus MCI, of which 6 and 5 DMPs were continuously hypermethylated and hypomethylated in MCI and AD relative to CHCs (adjusted p < 0.05), respectively, such as FLNC cg20186636 and AFAP1 cg06758191. The DMPs with an area under the curve >0.900, such as cg18771300, showed high potency for predicting MCI and AD. In addition, gene ontology and pathway enrichment results showed that these overlapping genes were mainly involved in neurotransmitter transport, GABAergic synaptic transmission, signal release from synapse, neurotransmitter secretion, and the regulation of neurotransmitter levels. Furthermore, tissue expression enrichment analysis revealed a subset of potentially cerebral cortex-enriched genes associated with MCI and AD, including SYT7, SYN3, and KCNT1. Conclusion: This study revealed a number of potential biomarkers for MCI and AD, also highlighted the presence of epigenetically dysregulated gene networks that may engage in the underlying pathological events resulting in the onset of cognitive impairment and AD progression. Collectively, this study provides prospective cues for developing therapeutic strategies to improve cognitive impairment and AD course.
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Affiliation(s)
- Shaochang Wu
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, China
| | - Fan Yang
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Shan Chao
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Bo Wang
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wuqian Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - He Li
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, China
| | - Limei Yu
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Liya Sun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
- Shanghai Mental Health Center, Editorial Office, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
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Li L, Diao S, Chen Z, Zhang J, Chen W, Wang T, Chen X, Zhao Y, Xu T, Huang C, Li J. DNMT3a-mediated methylation of TCF21/hnRNPA1 aggravates hepatic fibrosis by regulating the NF-κB signaling pathway. Pharmacol Res 2023; 193:106808. [PMID: 37268177 DOI: 10.1016/j.phrs.2023.106808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 05/28/2023] [Accepted: 05/28/2023] [Indexed: 06/04/2023]
Abstract
Hepatic fibrosis is caused by liver damage as a consequence of wound healing response. Recent studies have shown that hepatic fibrosis could be effectively reversed, partly through regression of activated hepatic stellate cells (HSCs). Transcription factor 21 (TCF21), a member of the basic helix-loop-helix (bHLH) transcription factor, is involved in epithelial-mesenchymal transformation in various diseases. However, the mechanism by which TCF21 regulates epithelial-mesenchymal transformation in hepatic fibrosis has not been elucidated. In this research, we found that hnRNPA1, the downstream binding protein of TCF21, accelerates hepatic fibrosis reversal by inhibiting the NF-κB signaling pathway. Furthermore, the combination of DNMT3a with TCF21 promoter results in TCF21 hypermethylation. Our results suggest that DNMT3a regulation of TCF21 is a significant event in reversing hepatic fibrosis. In conclusion, this research identifies a novel signaling axis, DNMT3a-TCF21-hnRNPA1, that regulates HSCs activation and hepatic fibrosis reversal, providing a novel treatment strategy for hepatic fibrosis. The clinical trial was registered in the Research Registry (researchregistry9079).
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Affiliation(s)
- Liangyun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Shaoxi Diao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Zixiang Chen
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Jintong Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Wei Chen
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Tianqi Wang
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Xin Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Yuxin Zhao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University.
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University.
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Lv R, Liu X, Zhang Y, Dong N, Wang X, He Y, Yue H, Yin Q. Pathophysiological mechanisms and therapeutic approaches in obstructive sleep apnea syndrome. Signal Transduct Target Ther 2023; 8:218. [PMID: 37230968 DOI: 10.1038/s41392-023-01496-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Obstructive sleep apnea syndrome (OSAS) is a common breathing disorder in sleep in which the airways narrow or collapse during sleep, causing obstructive sleep apnea. The prevalence of OSAS continues to rise worldwide, particularly in middle-aged and elderly individuals. The mechanism of upper airway collapse is incompletely understood but is associated with several factors, including obesity, craniofacial changes, altered muscle function in the upper airway, pharyngeal neuropathy, and fluid shifts to the neck. The main characteristics of OSAS are recurrent pauses in respiration, which lead to intermittent hypoxia (IH) and hypercapnia, accompanied by blood oxygen desaturation and arousal during sleep, which sharply increases the risk of several diseases. This paper first briefly describes the epidemiology, incidence, and pathophysiological mechanisms of OSAS. Next, the alterations in relevant signaling pathways induced by IH are systematically reviewed and discussed. For example, IH can induce gut microbiota (GM) dysbiosis, impair the intestinal barrier, and alter intestinal metabolites. These mechanisms ultimately lead to secondary oxidative stress, systemic inflammation, and sympathetic activation. We then summarize the effects of IH on disease pathogenesis, including cardiocerebrovascular disorders, neurological disorders, metabolic diseases, cancer, reproductive disorders, and COVID-19. Finally, different therapeutic strategies for OSAS caused by different causes are proposed. Multidisciplinary approaches and shared decision-making are necessary for the successful treatment of OSAS in the future, but more randomized controlled trials are needed for further evaluation to define what treatments are best for specific OSAS patients.
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Affiliation(s)
- Renjun Lv
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Xueying Liu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Yue Zhang
- Department of Geriatrics, the 2nd Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Na Dong
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Xiao Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Yao He
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Hongmei Yue
- Department of Pulmonary and Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
| | - Qingqing Yin
- Department of Geriatric Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China.
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Li J, Zhou X, Li L, Ji L, Li J, Qu Y, Wang Z, Zhao Y, Zhang J, Liang F, Liu J, Gu W, Yang R, Ma F, Dai L. The association between CTSZ methylation in peripheral blood and breast cancer in Chinese women. Front Oncol 2023; 13:1148635. [PMID: 37274256 PMCID: PMC10233099 DOI: 10.3389/fonc.2023.1148635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023] Open
Abstract
Purpose Previous studies have shown that DNA methylation in peripheral blood may be associated with breast cancer (BC). To explore the association between the methylation level of the Cathepsin Z (CTSZ) gene in peripheral blood and BC, we conducted a case-control study in the Chinese population. Methods Peripheral blood samples were collected from 567 BC cases, 635 healthy controls, and 303 benign breast disease (BBD) cases. DNA extraction and bisulfite-specific PCR amplification were performed for all samples. The methylation levels of seven sites of the CTSZ gene were quantitatively determined by Mass spectrometry. The odds ratios (ORs) of CpG sites were evaluated for BC risk using per 10% reduction and quartiles analyses by logistic regression. Results Our analysis showed that five out of the seven CpG sites exhibited significant associations with hypomethylation of CTSZ and BC, compared to healthy controls. The highest OR was for Q2 of CTSZ_CpG_1 (OR: 1.62, P=0.006), particularly for early-stage breast cancer in the case of per 10% reduction of CTSZ_CpG_1 (OR: 1.20, P=0.003). We also found that per 10% reduction of CTSZ_CpG_5 (OR: 1.39, P=0.004) and CTSZ_CpG_7,8 (OR: 1.35, P=0.005) were associated with increased BC risk. Our study also revealed that four out of seven CpG sites were linked to increased BC risk in women under 50 years of age, compared to healthy controls. The highest OR was for per 10% reduction of CTSZ_CpG_1 (OR: 1.47, P<0.001). Additionally, we found that BC exhibited lower methylation levels than BBD at CTSZ_CpG_4 (OR for Q1: 2.18, P<0.001) and CTSZ_CpG_7,8 (OR for Q1: 2.01, P=0.001). Furthermore, we observed a correlation between methylation levels and tumor stage, ER, and HER2 status in BC patients. Conclusion Overall, our findings suggest that altered CTSZ methylation levels in peripheral blood may be associated with breast cancer, particularly in young women, and may serve as a potential biomarker for early-stage BC.
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Affiliation(s)
- Jinyu Li
- School of Basic Medical Sciences & The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiajie Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Longtao Ji
- BGI College, Zhengzhou University, Zhengzhou, Henan, China
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaqi Li
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Yunhui Qu
- Department of Clinical Laboratory in the First Affiliated Hospital & Key Clinical Laboratory of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhi Wang
- BGI College, Zhengzhou University, Zhengzhou, Henan, China
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Yutong Zhao
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Feifei Liang
- BGI College, Zhengzhou University, Zhengzhou, Henan, China
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Jingjing Liu
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liping Dai
- School of Basic Medical Sciences & The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
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48
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Zhou S, Ou H, Wu Y, Qi D, Pei X, Yu X, Hu X, Wu E. Targeting tumor endothelial cells with methyltransferase inhibitors: Mechanisms of action and the potential of combination therapy. Pharmacol Ther 2023:108434. [PMID: 37172786 DOI: 10.1016/j.pharmthera.2023.108434] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
Tumor endothelial cells (TECs) reside in the inner lining of blood vessels and represent a promising target for targeted cancer therapy. DNA methylation is a chemical process that involves the transfer of a methyl group to a specific base in the DNA strand, catalyzed by DNA methyltransferase (DNMT). DNMT inhibitors (DNMTis) can inhibit the activity of DNMTs, thereby preventing the transfer of methyl groups from s-adenosyl methionine (SAM) to cytosine. Currently, the most viable therapy for TECs is the development of DNMTis to release cancer suppressor genes from their repressed state. In this review, we first outline the characteristics of TECs and describe the development of tumor blood vessels and TECs. Abnormal DNA methylation is closely linked to tumor initiation, progression, and cell carcinogenesis, as evidenced by numerous studies. Therefore, we summarize the role of DNA methylation and DNA methyltransferase and the therapeutic potential of four types of DNMTi in targeting TECs. Finally, we discuss the accomplishments, challenges, and opportunities associated with combination therapy with DNMTis for TECs.
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Affiliation(s)
- Shu Zhou
- State Key Laboratory of Biosensing, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Hailong Ou
- State Key Laboratory of Biosensing, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Yatao Wu
- State Key Laboratory of Biosensing, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Dan Qi
- Texas A & M University Schools of Medicine and Pharmacy, College Station, TX 77843, USA
| | - Xiaming Pei
- Department of Urology, Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, Hunan 410013, China
| | - Xiaohui Yu
- Department of Urology, Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, Hunan 410013, China
| | - Xiaoxiao Hu
- State Key Laboratory of Biosensing, College of Biology, Hunan University, Changsha, Hunan 410082, China; Research Institute of Hunan University in Chongqing, Chongqing 401120, China.
| | - Erxi Wu
- Department of Neurosurgery, Neuroscience Institute, Baylor Scott & White Health, Temple, TX 78508, USA; Texas A & M University Schools of Medicine and Pharmacy, College Station, TX 77843, USA; LIVESTRONG Cancer Institutes, Department of Oncology, Dell Medical School, the University of Texas at Austin, Austin, TX 78712, USA.
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49
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Hou X, Ma B, Liu M, Zhao Y, Chai B, Pan J, Wang P, Li D, Liu S, Song F. The transcriptional risk scores for kidney renal clear cell carcinoma using XGBoost and multiple omics data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:11676-11687. [PMID: 37501415 DOI: 10.3934/mbe.2023519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Most kidney cancers are kidney renal clear cell carcinoma (KIRC) that is a main cause of cancer-related deaths. Polygenic risk score (PRS) is a weighted linear combination of phenotypic related alleles on the genome that can be used to assess KIRC risk. However, standalone SNP data as input to the PRS model may not provide satisfactory result. Therefore, Transcriptional risk scores (TRS) based on multi-omics data and machine learning models were proposed to assess the risk of KIRC. First, we collected four types of multi-omics data (DNA methylation, miRNA, mRNA and lncRNA) of KIRC patients from the TCGA database. Subsequently, a novel TRS method utilizing multiple omics data and XGBoost model was developed. Finally, we performed prevalence analysis and prognosis prediction to evaluate the utility of the TRS generated by our method. Our TRS methods exhibited better predictive performance than the linear models and other machine learning models. Furthermore, the prediction accuracy of combined TRS model was higher than that of single-omics TRS model. The KM curves showed that TRS was a valid prognostic indicator for cancer staging. Our proposed method extended the current definition of TRS from standalone SNP data to multi-omics data and was superior to the linear models and other machine learning models, which may provide a useful implement for diagnostic and prognostic prediction of KIRC.
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Affiliation(s)
- Xiaoyu Hou
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Baoshan Ma
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Ming Liu
- Physical Department of Science and Technology, Dalian University, Dalian 116622, China
| | - Yuxuan Zhao
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Bingjie Chai
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Jianqiao Pan
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Pengcheng Wang
- Department of Mechanical Engineering, University of Houston, Houston 77204, USA
| | - Di Li
- Department of Neuro Intervention, Dalian Medical University affiliated Dalian Municipal Central Hospital, Dalian 116033, China
| | - Shuxin Liu
- Department of Nephrology, Dalian Medical University affiliated Dalian Municipal Central Hospital, Dalian 116033, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
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50
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Qi C, Lei L, Hu J, Ou S. Establishment and validation of a novel integrin-based prognostic gene signature that sub-classifies gliomas and effectively predicts immunosuppressive microenvironment. Cell Cycle 2023; 22:1259-1283. [PMID: 37096960 DOI: 10.1080/15384101.2023.2205204] [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: 04/26/2023] Open
Abstract
The integrin family members play a key role in cancer immunomodulation and prognosis. We comprehensively analyzed the expression patterns and clinical significance of integrin family-related genes in gliomas. A total of 2293 gliomas from the Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA) and Gliovis platform were enrolled for analyses. Twenty-six integrin coding genes showed different expression patterns between glioma and normal brain tissues. We screened an integrin family-related gene signature (ITGA5, ITGA9, ITGAE, ITGB7 and ITGB8) that showed independent prognostic value and sub-classified gliomas into different prognostic and molecular clusters, further composed an integrin-based risk score model associated with glioma malignant clinical features, overall survival (OS), and immune microenvironment alterations. Besides, glioma patients with high-risk scores showed chemotherapeutic resistance and more immune cells infiltration as well as high immune checkpoints expression. Concurrently, we also revealed that high-risk score group presented resistance to T cell-mediated cancer killing process and lower rates of response to immune checkpoint blockade (ICB) treatment. In conclusion, our study identified a valuable integrin gene signature that predicted gliomas OS effectively, and sub-classified them into different phenotypes and accompanied with immunological changes, possibly acted as a biomarker for ICB treatment.
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Affiliation(s)
- Chunxiao Qi
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
- Department of Neurosurgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Lei Lei
- Department of Rheumatology and Immunology, Dalian Municipal Central Hospital Affiliated of Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Jinqu Hu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Shaowu Ou
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
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