1
|
Liu Z, Zhang Q, Zhang H, Yi Z, Ma H, Wang X, Wang J, Liu Y, Zheng Y, Fang W, Huang P, Liu X. Colorectal cancer microbiome programs DNA methylation of host cells by affecting methyl donor metabolism. Genome Med 2024; 16:77. [PMID: 38840170 PMCID: PMC11151592 DOI: 10.1186/s13073-024-01344-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 05/09/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) arises from complex interactions between host and environment, which include the gut and tissue microbiome. It is hypothesized that epigenetic regulation by gut microbiota is a fundamental interface by which commensal microbes dynamically influence intestinal biology. The aim of this study is to explore the interplay between gut and tissue microbiota and host DNA methylation in CRC. METHODS Metagenomic sequencing of fecal samples was performed on matched CRC patients (n = 18) and healthy controls (n = 18). Additionally, tissue microbiome was profiled with 16S rRNA gene sequencing on tumor (n = 24) and tumor-adjacent normal (n = 24) tissues of CRC patients, while host DNA methylation was assessed through whole-genome bisulfite sequencing (WGBS) in a subset of 13 individuals. RESULTS Our analysis revealed substantial alterations in the DNA methylome of CRC tissues compared to adjacent normal tissues. An extensive meta-analysis, incorporating publicly available and in-house data, identified significant shifts in microbial-derived methyl donor-related pathways between tumor and adjacent normal tissues. Of note, we observed a pronounced enrichment of microbial-associated CpGs within the promoter regions of genes in adjacent normal tissues, a phenomenon notably absent in tumor tissues. Furthermore, we established consistent and recurring associations between methylation patterns of tumor-related genes and specific bacterial taxa. CONCLUSIONS This study emphasizes the pivotal role of the gut microbiota and pathogenic bacteria in dynamically shaping DNA methylation patterns, impacting physiological homeostasis, and contributing to CRC tumorigenesis. These findings provide valuable insights into the intricate host-environment interactions in CRC development and offer potential avenues for therapeutic interventions in this disease.
Collapse
Affiliation(s)
- Zhi Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Qingqing Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hong Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhongyuan Yi
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Huihui Ma
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaoyi Wang
- Core Facility Center, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, China
| | - Jingjing Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215008, China
| | - Yang Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yi Zheng
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Ping Huang
- Department of Surgery, The Third Affiliated Hospital, Nanjing Medical University, Nanjing, 211166, China.
| | - Xingyin Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China.
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215008, China.
| |
Collapse
|
2
|
An J, Wang J, Kong S, Song S, Chen W, Yuan P, He Q, Chen Y, Li Y, Yang Y, Wang W, Li R, Yan L, Yan Z, Qiao J. GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad004. [PMID: 38862425 DOI: 10.1093/gpbjnl/qzad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been uniformed and integrated, which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and spermatogenesis. Here, we develop GametesOmics, a comprehensive database that integrates the data of gene expression, DNA methylation, and chromatin accessibility during oogenesis and spermatogenesis in humans and mice. GametesOmics provides a user-friendly website and various tools, including Search and Advanced Search for querying the expression and epigenetic modification(s) of each gene; Tools with Differentially expressed gene (DEG) analysis for identifying DEGs, Correlation analysis for demonstrating the genetic and epigenetic changes, Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors (TFs), and MethylView for studying the genomic distribution of epigenetic modifications. GametesOmics also provides Genome Browser and Ortholog for tracking and comparing gene expression, DNA methylation, and chromatin accessibility between humans and mice. GametesOmics offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development, and can be accessed at http://gametesomics.cn/.
Collapse
Affiliation(s)
- Jianting An
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jing Wang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Siming Kong
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shi Song
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Wei Chen
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Peng Yuan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Qilong He
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yidong Chen
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ye Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yi Yang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Wei Wang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rong Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Liying Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Zhiqiang Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100191, China
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Liu XS, Chen YL, Chen YX, Wu RM, Tan F, Wang YL, Liu ZY, Gao Y, Pei ZJ. Pan-cancer analysis reveals correlation between RAB3B expression and tumor heterogeneity, immune microenvironment, and prognosis in multiple cancers. Sci Rep 2024; 14:9881. [PMID: 38688977 PMCID: PMC11061125 DOI: 10.1038/s41598-024-60581-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: 01/03/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
RAB3B is essential for the transportation and secretion within cells. Its increased expression is linked to the development and progression of various malignancies. However, understanding of RAB3B's involvement in carcinogenesis is mostly limited to specific cancer subtypes. Hence, exploring RAB3B's regulatory roles and molecular mechanisms through comprehensive cancer datasets might offer innovative approaches for managing clinical cancer. To examine the potential involvement of RAB3B in the development of cancer, we analyzed data from various sources including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), cBioPortal, HPA, UALCAN, and tissue microarray (TAM). Using bioinformatics techniques, we examined the correlation between RAB3B expression and prognosis, tumor heterogeneity, methylation modifications, and immune microenvironment across different cancer types. Our findings indicate that elevated RAB3B expression can independently predict prognosis in many tumors and has moderate accuracy for diagnosing most cancers. In most cancer types, we identified RAB3B mutations that showed a significant correlation with tumor mutational burden (TMB), mutant-allele tumor heterogeneity (MATH), and microsatellite instability (MSI). Abnormal DNA methylation patterns were also observed in most cancers compared to normal tissues. Additionally, we found significant correlations between RAB3B expression, immune cell infiltration, and immune scores across various cancers. Through pan-cancer analysis, we observed significant differences in RAB3B expression levels between tumors and normal tissues, making it a potential primary factor for cancer diagnosis and prognosis. The IHC results revealed that the expression of RAB3B in six types of tumors was consistent with the results of the pan-cancer analysis of the database. Furthermore, RAB3B showed potential associations with tumor heterogeneity and immunity. Thus, RAB3B can be utilized as an auxiliary diagnostic marker for early tumor detection and a prognostic biomarker for various tumor types.
Collapse
Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan, 442000, Hubei, China
| | - Ya-Lan Chen
- Department of Gastroenterology, The Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, China
| | - Yu-Xuan Chen
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
| | - Rui-Min Wu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
| | - Fan Tan
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
| | - Ya-Lan Wang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China.
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
- Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan, 442000, Hubei, China.
| |
Collapse
|
5
|
Xu Y, Hong Z, Yu S, Huang R, Li K, Li M, Xie S, Zhu L. Fresh Insights Into SLC25A26: Potential New Therapeutic Target for Cancers: A Review. Oncol Rev 2024; 18:1379323. [PMID: 38745827 PMCID: PMC11091378 DOI: 10.3389/or.2024.1379323] [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: 01/31/2024] [Accepted: 04/02/2024] [Indexed: 05/16/2024] Open
Abstract
SLC25A26 is the only known human mitochondrial S-adenosylmethionine carrier encoding gene. Recent studies have shown that SLC25A26 is abnormally expressed in some cancers, such as cervical cancer, low-grade glioma, non-small cell lung cancer, and liver cancer, which suggests SLC25A26 can affect the occurrence and development of some cancers. This article in brief briefly reviewed mitochondrial S-adenosylmethionine carrier in different species and its encoding gene, focused on the association of SLC25A26 aberrant expression and some cancers as well as potential mechanisms, summarized its potential for cancer prognosis, and characteristics of mitochondrial diseases caused by SLC25A26 mutation. Finally, we provide a brief expectation that needs to be further investigated. We speculate that SLC25A26 will be a potential new therapeutic target for some cancers.
Collapse
Affiliation(s)
- Yangheng Xu
- Science and Engineering, National University of Defense Technology, Changsha, China
| | - Zhisheng Hong
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Sheng Yu
- Science and Engineering, National University of Defense Technology, Changsha, China
| | - Ronghan Huang
- Science and Engineering, National University of Defense Technology, Changsha, China
| | - Kunqi Li
- Science and Engineering, National University of Defense Technology, Changsha, China
| | - Ming Li
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Sisi Xie
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Lvyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| |
Collapse
|
6
|
Morgan AE, Mc Auley MT. Vascular dementia: From pathobiology to emerging perspectives. Ageing Res Rev 2024; 96:102278. [PMID: 38513772 DOI: 10.1016/j.arr.2024.102278] [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: 01/26/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024]
Abstract
Vascular dementia (VaD) is the second most common type of dementia. VaD is synonymous with ageing, and its symptoms place a significant burden on the health and wellbeing of older people. Despite the identification of a substantial number of risk factors for VaD, the pathological mechanisms underpinning this disease remain to be fully elucidated. Consequently, a biogerontological imperative exists to highlight the modifiable lifestyle factors which can mitigate against the risk of developing VaD. This review will critically examine some of the factors which have been revealed to modulate VaD risk. The survey commences by providing an overview of the putative mechanisms which are associated with the pathobiology of VaD. Next, the factors which influence the risk of developing VaD are examined. Finally, emerging treatment avenues including epigenetics, the gut microbiome, and pro-longevity pharmaceuticals are discussed. By drawing this key evidence together, it is our hope that it can be used to inform future experimental investigations in this field.
Collapse
Affiliation(s)
- Amy Elizabeth Morgan
- School of Health and Sports Sciences, Hope Park, Liverpool Hope University, Liverpool L16 9JD, United Kingdom.
| | - Mark Tomás Mc Auley
- School of Science, Engineering and Environment, University of Salford Manchester, Salford M5 4NT, United Kingdom
| |
Collapse
|
7
|
Yeung-Luk BH, Wally A, Swaby C, Jauregui S, Lee E, Zhang R, Chen D, Luk SH, Upadya N, Tieng E, Wilmsen K, Sherman E, Sudhakar D, Luk M, Shrivastav AK, Cao S, Ghosh B, Christenson SA, Huang YJ, Ortega VE, Biswal S, Tang WY, Sidhaye VK. Epigenetic Reprogramming Drives Epithelial Disruption in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2024; 70:165-177. [PMID: 37976469 PMCID: PMC10914773 DOI: 10.1165/rcmb.2023-0147oc] [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: 04/25/2023] [Accepted: 11/17/2023] [Indexed: 11/19/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) remains a major public health challenge that contributes greatly to mortality and morbidity worldwide. Although it has long been recognized that the epithelium is altered in COPD, there has been little focus on targeting it to modify the disease course. Therefore, mechanisms that disrupt epithelial cell function in patients with COPD are poorly understood. In this study, we sought to determine whether epigenetic reprogramming of the cell-cell adhesion molecule E-cadherin, encoded by the CDH1 gene, disrupts epithelial integrity. By reducing these epigenetic marks, we can restore epithelial integrity and rescue alveolar airspace destruction. We used differentiated normal and COPD-derived primary human airway epithelial cells, genetically manipulated mouse tracheal epithelial cells, and mouse and human precision-cut lung slices to assess the effects of epigenetic reprogramming. We show that the loss of CDH1 in COPD is due to increased DNA methylation site at the CDH1 enhancer D through the downregulation of the ten-eleven translocase methylcytosine dioxygenase (TET) enzyme TET1. Increased DNA methylation at the enhancer D region decreases the enrichment of RNA polymerase II binding. Remarkably, treatment of human precision-cut slices derived from patients with COPD with the DNA demethylation agent 5-aza-2'-deoxycytidine decreased cell damage and reduced air space enlargement in the diseased tissue. Here, we present a novel mechanism that targets epigenetic modifications to reverse the tissue remodeling in human COPD lungs and serves as a proof of concept for developing a disease-modifying target.
Collapse
Affiliation(s)
| | - Ara Wally
- Department of Environmental Health and Engineering and
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Carter Swaby
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Sofia Jauregui
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Esther Lee
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Rachel Zhang
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Daniel Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Sean H. Luk
- Department of Environmental Health and Engineering and
| | - Nisha Upadya
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ethan Tieng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Kai Wilmsen
- Department of Environmental Health and Engineering and
| | - Ethan Sherman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Dheeksha Sudhakar
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Matthew Luk
- Department of Environmental Health and Engineering and
| | - Abhishek Kumar Shrivastav
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Shuo Cao
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | | | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Yvonne J. Huang
- Department of Medicine, University of Michigan, Ann Arbor, Michigan; and
| | | | - Shyam Biswal
- Department of Environmental Health and Engineering and
| | - Wan-yee Tang
- Department of Environmental Health and Engineering and
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Venkataramana K. Sidhaye
- Department of Environmental Health and Engineering and
- Department of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| |
Collapse
|
8
|
Wang P, Ning J, Chen W, Zou F, Yu W, Rao T, Cheng F. Comprehensive analysis indicated that NDE1 is a potential biomarker for pan-cancer and promotes bladder cancer progression. Cancer Med 2024; 13:e6931. [PMID: 38466053 PMCID: PMC10926885 DOI: 10.1002/cam4.6931] [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: 08/23/2023] [Revised: 11/08/2023] [Accepted: 12/31/2023] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND The nuclear distribution E homologue 1 (NDE1) is a crucial dynein binding partner. The NDE1 protein has the potential to disrupt the normal functioning of centrosomes, leading to a compromised ability to generate spindles and ensure precise separation of chromosomes during cell division. The potential consequences of this phenomenon include genomic instability, malignant transformation and the proliferation of neoplastic growths. However, studies examining the connection between NDE1 and cancer is still very rare. METHODS The expression level, prognostic impact, gene change, DNA methylation, protein interaction, mRNA m6A modification, ceRNA network, associated gene and function enrichment, and immune-related effects of NDE1 in pan-cancer were examined using a range of online analytic tools and the R software package. The CCK-8 test, transwell assay, scratch assay and colony formation assay were used to confirm the effects of NDE1 on the proliferation, invasion and metastasis of bladder cancer cells. RESULTS Numerous tumour types have elevated NDE1, which is linked to a bad prognosis. NDE1 is an excellent diagnostic tool for many different types of cancer. Numerous malignancies have been linked to genetic changes in NDE1. NDE1 was connected to TMB, MSI, several immunological checkpoint genes and immune cell infiltration. NDE1 is linked to a number of immunological subtypes. NDE1 could affect how well immunotherapy works to treat different types of cancer. NDE1 was mostly associated with cell cycle, chromosomal segregation, DNA replication and mitotic segregation, according to GO and KEGG analyses. NDE1 physically binds to PAFAH1B1 and DCTN1, respectively. The proliferation, invasion and metastasis of bladder cancer cells may be prevented by NDE1 knockdown. Furthermore, knockdown of NDE1 promoted the apoptosis of bladder cancer cells. CONCLUSION High expression of NDE1 is present in a variety of tumours, which is linked to a bad prognosis for cancer. Knockdown of NDE1 inhibited the proliferation, invasion and metastasis of bladder cancer cells, and promoted the apoptosis. For a number of malignancies, NDE1 may be a biomarker for immunotherapy and prognosis.
Collapse
Affiliation(s)
- Peihan Wang
- Department of Urology, Hubei International Scientific and Technological Cooperation Base of ImmunotherapyRenmin Hospital of Wuhan UniversityWuhanP.R. China
| | - Jinzhuo Ning
- Department of Urology, Hubei International Scientific and Technological Cooperation Base of ImmunotherapyRenmin Hospital of Wuhan UniversityWuhanP.R. China
| | - Wu Chen
- Department of Urology, Hubei International Scientific and Technological Cooperation Base of ImmunotherapyRenmin Hospital of Wuhan UniversityWuhanP.R. China
| | - Fan Zou
- Department of Urology, Hubei International Scientific and Technological Cooperation Base of ImmunotherapyRenmin Hospital of Wuhan UniversityWuhanP.R. China
| | - Weimin Yu
- Department of Urology, Hubei International Scientific and Technological Cooperation Base of ImmunotherapyRenmin Hospital of Wuhan UniversityWuhanP.R. China
| | - Ting Rao
- Department of Urology, Hubei International Scientific and Technological Cooperation Base of ImmunotherapyRenmin Hospital of Wuhan UniversityWuhanP.R. China
| | - Fan Cheng
- Department of Urology, Hubei International Scientific and Technological Cooperation Base of ImmunotherapyRenmin Hospital of Wuhan UniversityWuhanP.R. China
| |
Collapse
|
9
|
Li R, Zeng X, Lv M, Zhang R, Zhang S, Zhang T, Yu X, Li C, Jin L, Zhao C. First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne. Phys Chem Chem Phys 2024; 26:5558-5568. [PMID: 38284214 DOI: 10.1039/d3cp04726a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components.
Collapse
Affiliation(s)
- Ruirui Li
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Xia Zeng
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Mengdan Lv
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Ruiying Zhang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Shengrui Zhang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Tianlei Zhang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Xiaohu Yu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Chen Li
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| |
Collapse
|
10
|
Takeda Y, Kimura F, Takasawa S. Possible Molecular Mechanisms of Hypertension Induced by Sleep Apnea Syndrome/Intermittent Hypoxia. Life (Basel) 2024; 14:157. [PMID: 38276286 PMCID: PMC10821044 DOI: 10.3390/life14010157] [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: 12/19/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Intermittent hypoxia (IH) is a central characteristic of sleep apnea syndrome (SAS), and it subjects cells in the body to repetitive apnea, chronic hypoxia, oxygen desaturation, and hypercapnia. Since SAS is linked to various serious cardiovascular complications, especially hypertension, many studies have been conducted to elucidate the mechanism of hypertension induced by SAS/IH. Hypertension in SAS is associated with numerous cardiovascular disorders. As hypertension is the most common complication of SAS, cell and animal models to study SAS/IH have developed and provided lots of hints for elucidating the molecular mechanisms of hypertension induced by IH. However, the detailed mechanisms are obscure and under investigation. This review outlines the molecular mechanisms of hypertension in IH, which include the regulation systems of reactive oxygen species (ROS) that activate the renin-angiotensin system (RAS) and catecholamine biosynthesis in the sympathetic nervous system, resulting in hypertension. And hypoxia-inducible factors (HIFs), Endotheline 1 (ET-1), and inflammatory factors are also mentioned. In addition, we will discuss the influences of SAS/IH in cardiovascular dysfunction and the relationship of microRNA (miRNA)s to regulate the key molecules in each mechanism, which has become more apparent in recent years. These findings provide insight into the pathogenesis of SAS and help in the development of future treatments.
Collapse
Affiliation(s)
- Yoshinori Takeda
- Department of Biochemistry, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Japan;
- Department of Obstetrics and Gynecology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8522, Japan;
| | - Fuminori Kimura
- Department of Obstetrics and Gynecology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8522, Japan;
| | - Shin Takasawa
- Department of Biochemistry, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Japan;
| |
Collapse
|
11
|
Luo J, Zhu WC, Chen QX, Yang CF, Huang BJ, Zhang SJ. A prognostic model based on DNA methylation-related gene expression for predicting overall survival in hepatocellular carcinoma. Front Oncol 2024; 13:1171932. [PMID: 38304027 PMCID: PMC10830715 DOI: 10.3389/fonc.2023.1171932] [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: 05/02/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) continues to increase in morbidity and mortality among all types of cancer. DNA methylation, an important epigenetic modification, is associated with cancer occurrence and progression. The objective of this study was to establish a model based on DNA methylation risk scores for identifying new potential therapeutic targets in HCC and preventing cancer progression. Methods Transcriptomic, clinical, and DNA methylation data on 374 tumor tissues and 50 adjacent normal tissues were downloaded from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma database. The gene expression profiles of the GSE54236 liver cancer dataset, which contains data on 161 liver tissue samples, were obtained from the Gene Expression Omnibus database. We analyzed the relationship between DNA methylation and gene expression levels after identifying the differentially methylated and expressed genes. Then, we developed and validated a risk score model based on the DNA methylation-driven genes. A tissue array consisting of 30 human hepatocellular carcinoma samples and adjacent normal tissues was used to assess the protein and mRNA expression levels of the marker genes by immunohistochemistry and qRT-PCR, respectively. Results Three methylation-related differential genes were identified in our study: GLS, MEX3B, and GNA14. The results revealed that their DNA methylation levels were negatively correlated with local gene expression regulation. The gene methylation levels correlated strongly with the prognosis of patients with liver cancer. This was confirmed by qRT-PCR and immunohistochemical verification of the expression of these genes or proteins in tumors and adjacent tissues. These results revealed the relationship between the level of relevant gene methylation and the prognosis of patients with liver cancer as well as the underlying cellular and biological mechanisms. This allows our gene signature to provide more accurate and appropriate predictions for clinical applications. Conclusion Through bioinformatics analysis and experimental validation, we obtained three DNA methylation marker: GLS, MEX3B, and GNA14. This helps to predict the prognosis and may be a potential therapeutic target for HCC patients.
Collapse
Affiliation(s)
- Jin Luo
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Traditional Chinese Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Wan-Cui Zhu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qiu-Xia Chen
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chang-Fu Yang
- Department of Oncology, The People’s Hospital of Gaozhou, Gaozhou, China
| | - Bi-Jun Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shi-Jun Zhang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
12
|
Li K, Qi L, Tang G, Xu H, Li Z, Fan B, Li Z, Li Y. Epigenetic Regulation in Urothelial Carcinoma. Curr Mol Med 2024; 24:85-97. [PMID: 36545729 DOI: 10.2174/1566524023666221221094432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022]
Abstract
Urothelial carcinoma (UC) is a common malignancy that remains a clinical challenge: Non-muscle-invasive urothelial carcinoma (NMIUC) has a high rate of recurrence and risk of progression, while muscle-invasive urothelial carcinoma (MIUC) has a high mortality. Although some new treatments, such as immunotherapies, have shown potential effects on some patients, most cases of advanced UC remain incurable. While treatments based on epigenetic mechanisms, whether combined with traditional platinum-based chemotherapy or emerging immunotherapy, show therapeutic advantages. With the advancement of sequencing and bioinformatics, the study of epigenomics, containing DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA, is increasingly linked with the occurrence and progression of UC. Since the epigenetics of UC is a constantly developing field of medicine, this review aims to summarize the latest research on epigenetic regulation of UC, generalize the mechanism of epigenetics in UC, and reveal the potential epigenetic therapies in the clinical setting, in order to provide some new clues on the discovery of new drugs based on the epigenetics.
Collapse
Affiliation(s)
- Ke Li
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Lin Qi
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Guyu Tang
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Haozhe Xu
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhi Li
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Bo Fan
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhongbei Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Yuan Li
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, China
| |
Collapse
|
13
|
Morgan AE, Salcedo-Sora JE, Mc Auley MT. A new mathematical model of folate homeostasis in E. coli highlights the potential importance of the folinic acid futile cycle in cell growth. Biosystems 2024; 235:105088. [PMID: 38000545 DOI: 10.1016/j.biosystems.2023.105088] [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: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Folate (vitamin B9) plays a central role in one-carbon metabolism in prokaryotes and eukaryotes. This pathway mediates the transfer of one-carbon units, playing a crucial role in nucleotide synthesis, methylation, and amino acid homeostasis. The folinic acid futile cycle adds a layer of intrigue to this pathway, due to its associations with metabolism, cell growth, and dormancy. It also introduces additional complexity to folate metabolism. A logical way to deal with such complexity is to examine it by using mathematical modelling. This work describes the construction and analysis of a model of folate metabolism, which includes the folinic acid futile cycle. This model was tested under three in silico growth conditions. Model simulations revealed: 1) the folate cycle behaved as a stable biochemical system in three growth states (slow, standard, and rapid); 2) the initial concentration of serine had the greatest impact on metabolite concentrations; 3) 5-formyltetrahydrofolate cyclo-ligase (5-FCL) activity had a significant impact on the levels of the 7 products that carry the one-carbon donated from folates, and the redox couple NADP/NADPH; this was particularly evident in the rapid growth state; 4) 5-FCL may be vital to the survival of the cells by maintaining low levels of homocysteine, as high levels can induce toxicity; and 5) the antifolate therapeutic trimethoprim had a greater impact on folate metabolism with higher nutrient availability. These results highlight the important role of 5-FCL in intracellular folate homeostasis and mass generation under different metabolic scenarios.
Collapse
Affiliation(s)
- Amy E Morgan
- School of Health & Sport Sciences, Hope Park, Liverpool Hope University, Liverpool, L16 9JD, UK.
| | - J Enrique Salcedo-Sora
- Liverpool Shared Research Facilities, GeneMill, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Mark T Mc Auley
- School of Science, Engineering and Environment, University of Salford, Manchester, M5 4NT, UK
| |
Collapse
|
14
|
Zhang Q, Xiao X, Zheng J, Li M, Yu M, Ping F, Wang T, Wang X. DNA methylation regulates pancreatic gene expression and links maternal high-fat diet to the offspring glucose metabolism. J Nutr Biochem 2024; 123:109490. [PMID: 37865384 DOI: 10.1016/j.jnutbio.2023.109490] [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: 07/06/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/23/2023]
Abstract
Maternal high-fat diet (HFD) is related to an increased risk of glucose metabolism disorders throughout the whole life of offspring. The pancreas is a glucose homeostasis regulator. Accumulating evidence has revealed that maternal HFD affects offspring pancreas structure and function. However, the potential mechanism remains unclear. In this study, the mouse dam was fed with HFD or control diet (CD) during prepregnancy, pregnancy and lactation. The pancreatic insulin secretion function and islet genome methylome of offspring were analyzed. Pancreatic islet specific gene methylation was detected by using MeDIP qPCR. The results showed that body weight, blood glucose after oral glucose loads, fasting serum insulin, and HOMA-IR index values were significantly higher in male 12-week-old offspring from HFD dams than in the offspring from CD dams. Maternal HFD induced insulin secretion defects in male offspring. Compared with that in maternal CD group, methylation of the Abcc8 and Kcnj11 genes was increased in maternal HFD group in male offspring pancreatic islets. Furthermore, the expression levels of Abcc8 and Kcnj11 were downregulated by intrauterine exposure to a maternal HFD. In summary, maternal HFD results in a long-term functional disorder of the pancreas that is involved in insulin secretion-related gene DNA hypermethylation.
Collapse
Affiliation(s)
- Qian Zhang
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinhua Xiao
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
| | - Jia Zheng
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Li
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Miao Yu
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fan Ping
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tong Wang
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaojing Wang
- Key Laboratory of Endocrinology, Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
15
|
Wan B, Zhang W, Deng X, Lu Y, Zhang Z, Yang Y. Molecular Expression and Prognostic Implications of Krüppel-Like Factor 3 (KLF3) in Clear Cell Renal Cell Carcinoma. Crit Rev Eukaryot Gene Expr 2024; 34:45-59. [PMID: 38073441 DOI: 10.1615/critreveukaryotgeneexpr.2023049010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
A major subtype of renal cancer is clear cell renal cell carcinoma (ccRCC). Krüppel-like factor 3 (KLF3) dysfunction is also revealed leading to poor prognosis in multiple cancer types. However, dysregulation and molecular dynamics of KLF3 underlying ccRCC progression still remains elusive. Here KLF3 gene and protein expressions in ccRCC were explored using data cohorts from The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), Clinical Proteomic Tumor Analysis Consortium (CPTAC) and verified them in our patient cohort. Correlations of KLF3 expression with clinicopathological features, epigenetic modification, and immune microenvironment characteristics were further investigated. KLF3 was significantly down-regulated expressed in ccRCC tissues compared to adjacent normal controls. Adverse pathological parameters and poor prognosis were associated with lower expression of KLF3. Mechanically, KLF3 regulation was mainly attributed to CpG island methylation. KLF3-high expression subgroup was significantly enriched in cell signaling pathways most associated with EMT markers, angiogenesis, inflammatory response, apoptosis, TGF-β, degradation of ECM, G2M checkpoint, and PI3K-AKT-mTOR. Based on GDSC database, KLF3 upregulation was identified to be associated with higher sensitivities towards PI3K-Akt-mTOR pathway inhibitors such as PI-103, PIK-93, and OSI-027. In addition, patients with down-regulated KLF3 expressions were found more sensitive towards Trametinib, Cetuximab, and Erlotinib. Collectively, our findings suggest that KLF3 may act as a suitable biomarker for prognosis prediction, tumor microenvironment (TME) phenotype identification, thereby helping ccRCC patients to make better therapeutic decisions.
Collapse
Affiliation(s)
- Bin Wan
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Wensheng Zhang
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Xinxi Deng
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Yigang Lu
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Zhuo Zhang
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Yang Yang
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| |
Collapse
|
16
|
Gao J, Feng Y, Yang Y, Shi Y, Liu J, Lin H, Zhang L. Identification of Key DNA methylation sites related to differentially expressed genes in Lung squamous cell carcinoma. Comput Biol Med 2023; 167:107615. [PMID: 37918267 DOI: 10.1016/j.compbiomed.2023.107615] [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: 08/25/2023] [Revised: 09/24/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Changes in DNA methylation level at some CpG locus are closely associated with the occurrence of lung squamous cell carcinoma (LUSC). However, its specific regulatory mechanism is still unclear. Therefore, it is necessary to systematically identify and analyze those key CpG sites whose DNA methylation levels are closely related to the differential expression of up- and down-regulated genes in LUSC. Due to the dispersion of DNA methylation sites in different regions of genome, to study the correlation between gene expression level and DNA methylation, we divided gene into 6 non-overlapping functional regions and proposed a two-step correlation analysis method to identify differential DNA methylation sites and matched differential expression genes. As a results, we obtained 39 key CpG sites scattered in 27 genes. Through comparative analysis of LUSC-normal sample pairs, we found that these sites and genes can accurately cluster LUSC samples and normal samples. Finally, we used these sites and genes to distinguish LUSC from normal samples. The results suggest that they can be used as effective biomarkers for identifying LUSC. In addition, the proposed two-step correlation analysis method can also be extended to the identification of biomarkers of other cancers and diseases.
Collapse
Affiliation(s)
- Jie Gao
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Yongxian Feng
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Yan Yang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Yuetong Shi
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Junjie Liu
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hao Lin
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Lirong Zhang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| |
Collapse
|
17
|
Pan D, Su M, Xu D, Wang Y, Gao H, Smith JD, Sun J, Wang X, Yan Q, Song G, Lu Y, Feng W, Wang S, Sun G. Exploring the Interplay Between Vitamin B 12-related Biomarkers, DNA Methylation, and Gene-Nutrition Interaction in Esophageal Precancerous Lesions. Arch Med Res 2023; 54:102889. [PMID: 37738887 DOI: 10.1016/j.arcmed.2023.102889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/29/2023] [Accepted: 08/31/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND Vitamin B12 depletion has been suggested to be associated with esophageal precancerous lesions (EPL). However, the potential mechanisms remain unclear. AIMS This study aims to evaluate the role of vitamin B12 and its regulated epigenetic modification in EPL and provide preliminary information on the identification of potential molecular biomarkers for the early prediction of EPL. METHODS We collected information and samples from the Early Diagnosis and Early Treatment Project of Esophageal Cancer database from 200 EPL cases and 200 matched controls. Vitamin B12, one-carbon metabolism biomarkers, genetic polymorphism of TCN2 C776G, and DNA methylation were compared. Preliminarily identified candidate promoters of differentially methylated CpG positions were further verified by targeted bisulfite sequencing. RESULTS EPL cases had significantly lower serum levels of vitamin B12 and transcobalamin II, and higher serum levels of homocysteine and 5-methyltetrahydrofolate than controls. The TCN2 C776G polymorphism was found to be associated with susceptibility to EPL and may interact with vitamin B12 nutritional status to influence the risk of EPL in male subjects. In addition, global hypomethylation related to vitamin B12 depletion was observed in EPL cases, along with region-specific hypermethylation of UGT2B15 and FGFR2 promoters. CONCLUSIONS This study suggests that vitamin B12 depletion may be associated with aberrant DNA methylation and increased risk of EPL through the one-carbon metabolism pathway, presents that the TCN2 C776G polymorphism may interact with vitamin B12 nutritional status to affect EPL risk in males, and also identifies specific locations in the UGT2B15 and FGFR2 promoters with potential as promising molecular biomarkers.
Collapse
Affiliation(s)
- Da Pan
- Key Laboratory of Environmental Medicine and Engineering of the Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, PR China
| | - Ming Su
- Huai'an District Center for Disease Control and Prevention, Huai'an, PR China
| | - Dengfeng Xu
- Key Laboratory of Environmental Medicine and Engineering of the Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, PR China
| | - Yuanyuan Wang
- Key Laboratory of Environmental Medicine and Engineering of the Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, PR China
| | - Han Gao
- Department of Biomedical Engineering, University Medical Center Groningen/University of Groningen, The Netherlands; Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | | | - Jihan Sun
- Key Laboratory of Environmental Medicine and Engineering of the Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, PR China
| | - Xin Wang
- Huai'an District Center for Disease Control and Prevention, Huai'an, PR China
| | - Qingyang Yan
- Huai'an District Center for Disease Control and Prevention, Huai'an, PR China
| | - Guang Song
- Huai'an District Center for Disease Control and Prevention, Huai'an, PR China
| | - Yifei Lu
- Key Laboratory of Environmental Medicine and Engineering of the Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, PR China
| | - Wuqiong Feng
- Huai'an District Center for Disease Control and Prevention, Huai'an, PR China
| | - Shaokang Wang
- Key Laboratory of Environmental Medicine and Engineering of the Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, PR China; School of Medicine, Xizang Minzu University, Xianyang, PR China
| | - Guiju Sun
- Key Laboratory of Environmental Medicine and Engineering of the Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, PR China.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Dai S, Li F, Xu S, Hu J, Gao L. The important role of miR-1-3p in cancers. J Transl Med 2023; 21:769. [PMID: 37907984 PMCID: PMC10617136 DOI: 10.1186/s12967-023-04649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/22/2023] [Indexed: 11/02/2023] Open
Abstract
Cancer is a malignant tumor that seriously threatens human life and health. At present, the main treatment methods include surgical resection, chemotherapy, radiotherapy, and immunotherapy. However, the mechanism of tumor occurrence and development is complex, and it produces resistance to some traditional treatment methods, leading to treatment failure and a high mortality rate for patients. Therefore, exploring the molecular mechanisms of tumor occurrence, development, and drug resistance is a very important task. MiRNAs are a type of non-coding small RNA that regulate a series of biological effects by binding to the 3'-UTR of the target mRNA, degrading the mRNA, or inhibiting its translation. MiR-1-3p is an important member of them, which is abnormally expressed in various tumors and closely related to the occurrence and development of tumors. This article introduces miR-1-3p from multiple aspects, including its production and regulation, role in tumor occurrence and development, clinical significance, role in drug resistance, and approaches for targeting miR-1-3p. Intended to provide readers with a comprehensive understanding of the important role of miR-1-3p in tumors.
Collapse
Affiliation(s)
- Shangming Dai
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Fengjiao Li
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Shuoguo Xu
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Jinda Hu
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Lichen Gao
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China.
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China.
| |
Collapse
|
20
|
Liang K, Guo Z, Zhang S, Chen D, Zou R, Weng Y, Peng C, Xu Z, Zhang J, Liu X, Pang X, Ji Y, Liao D, Lai M, Peng H, Ke Y, Wang Z, Wang Y. GPR37 expression as a prognostic marker in gliomas: a bioinformatics-based analysis. Aging (Albany NY) 2023; 15:10146-10167. [PMID: 37837549 PMCID: PMC10599758 DOI: 10.18632/aging.205063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/21/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Gliomas are the most frequently diagnosed primary brain tumors, and are associated with multiple molecular aberrations during their development and progression. GPR37 is an orphan G protein-coupled receptor (GPCR) that is implicated in different physiological pathways in the brain, and has been linked to various malignancies. The aim of this study was to explore the relationship between GPR37 gene expression and the clinicopathological factors, patient prognosis, tumor-infiltrating immune cell signature GSEA and methylation levels in glioma. METHODS We explored the diagnostic value, clinical relevance, and molecular function of GPR37 in glioma using TCGA, STRING, cBioPortal, Tumor Immunity Estimation Resource (TIMER) database and MethSurv databases. Besides, the "ssGSEA" algorithm was conducted to estimate immune cells infiltration abundance, with 'ggplot2' package visualizing the results. Immunohistochemical staining of clinical samples were used to verify the speculations of bioinformatics analysis. RESULTS GPR37 expression was significantly higher in the glioma tissues compared to the normal brain tissues, and was linked to poor prognosis. Functional annotation of GPR37 showed enrichment of ether lipid metabolism, fat digestion and absorption, and histidine metabolism. In addition, GSEA showed that GPR37 was positively correlated to the positive regulation of macrophage derived foam cell differentiation, negative regulation of T cell receptor signaling pathway, neuroactive ligand receptor interaction, calcium signaling pathway, and negatively associated with immunoglobulin complex, immunoglobulin complex circulating, ribosome and spliceosome mediated by circulating immunoglobulin etc. TIMER2.0 and ssGSEA showed that GPR37 expression was significantly associated with the infiltration of T cells, CD8 T cell, eosinophils, macrophages, neutrophils, NK CD56dim cells, NK cells, plasmacytoid DCs (pDCs), T helper cells and T effector memory (Tem) cells. In addition, high GPR37 expression was positively correlated with increased infiltration of M2 macrophages, which in turn was associated with poor prognosis. Furthermore, GPR37 was positively correlated with various immune checkpoints (ICPs). Finally, hypomethylation of the GPR37 promoter was associated with its high expression levels and poor prognosis in glioma. CONCLUSION GPR37 had diagnostic and prognostic value in glioma. The possible biological mechanisms of GPR37 provide novel insights into the clinical diagnosis and treatment of glioma.
Collapse
Affiliation(s)
- Kairong Liang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhaoxiong Guo
- Science and Technology Innovation Center, Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Shizhen Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Danmin Chen
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Renheng Zou
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yuhao Weng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Chengxiang Peng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhichao Xu
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Jingbai Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Xiaorui Liu
- Department of Pharmacy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Xiao Pang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Degui Liao
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Miaoling Lai
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Huaidong Peng
- Department of Pharmacy, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yanbin Ke
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Zhaotao Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| |
Collapse
|
21
|
Patnaik E, Madu C, Lu Y. Epigenetic Modulators as Therapeutic Agents in Cancer. Int J Mol Sci 2023; 24:14964. [PMID: 37834411 PMCID: PMC10573652 DOI: 10.3390/ijms241914964] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Epigenetics play a crucial role in gene regulation and cellular processes. Most importantly, its dysregulation can contribute to the development of tumors. Epigenetic modifications, such as DNA methylation and histone acetylation, are reversible processes that can be utilized as targets for therapeutic intervention. DNA methylation inhibitors disrupt DNA methylation patterns by inhibiting DNA methyltransferases. Such inhibitors can restore normal gene expression patterns, and they can be effective against various forms of cancer. Histone deacetylase inhibitors increase histone acetylation levels, leading to altered gene expressions. Like DNA methylation inhibitors, histone methyltransferase inhibitors target molecules involved in histone methylation. Bromodomain and extra-terminal domain inhibitors target proteins involved in gene expression. They can be effective by inhibiting oncogene expression and inducing anti-proliferative effects seen in cancer. Understanding epigenetic modifications and utilizing epigenetic inhibitors will offer new possibilities for cancer research.
Collapse
Affiliation(s)
- Eshaan Patnaik
- Department of Biology, Memphis University School, Memphis, TN 38119, USA;
| | - Chikezie Madu
- Departments of Biological Sciences, University of Memphis, Memphis, TN 38152, USA;
| | - Yi Lu
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| |
Collapse
|
22
|
Zhang C, Wu S. Hypomethylation of CD3D promoter induces immune cell infiltration and supports malignant phenotypes in uveal melanoma. FASEB J 2023; 37:e23128. [PMID: 37651092 DOI: 10.1096/fj.202300505rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
Alterations in DNA methylation in malignant diseases have been heralded as promising targets for diagnostic, prognostic, and predictive values. This study was based on epigenetic alterations and immune cell infiltration analysis to investigate the mechanism of CD3D methylation in uveal melanoma (UM). Bioinformatics analysis was performed on transcriptome data, 450 K methylation data, and clinical information of UM patients from the TCGA database. Stromal and immune cell infiltration was evaluated by calculating the StromalScore and ImmuneScore of UM samples. UM samples were divided into high and low StromalScore and ImmuneScore groups, followed by differential and enrichment analyses. PPI network construction and correlation analysis was used to identify the core prognosis-related genes. The bioinformatics analysis results were confirmed in UM cell experiments. StromalScore and ImmuneScore were significantly associated with the prognosis of UM patients. CD3D, IRF1, CCL3, and FN1 were identified as core genes driven by methylation that affected the prognosis of UM patients. CD3D expression showed the highest correlation with its methylation and was closely related to the four key immune cells in UM development. CD3D was hypomethylated and abundantly expressed in UM cells, while silencing of CD3D inhibited the proliferation, migration, and invasion of UM cells in vitro. In summary, this study identifies hypomethylation of CD3D promoter in UM, which was associated with immune cell infiltration of UM.
Collapse
Affiliation(s)
- Chao Zhang
- Department of Strabismus and Pediatric Ophthalmology, the Second Hospital of Jilin University, Changchun, P.R. China
| | - Shuai Wu
- Department of Orbital Disease and Ocular Plastic Surgery, the Second Hospital of Jilin University, Changchun, P.R. China
| |
Collapse
|
23
|
Li L, Li F, Xu Z, Li L, Hu H, Li Y, Yu S, Wang M, Gao L. Identification and validation of SERPINE1 as a prognostic and immunological biomarker in pan-cancer and in ccRCC. Front Pharmacol 2023; 14:1213891. [PMID: 37680718 PMCID: PMC10482042 DOI: 10.3389/fphar.2023.1213891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
Background: SERPINE1, a serine protease inhibitor involved in the regulation of the plasminogen activation system, was recently identified as a cancer-related gene. However, its clinical significance and potential mechanisms in pan-cancer remain obscure. Methods: In pan-cancer multi-omics data from public datasets, including The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx), and online web tools were used to analyze the expression of SERPINE1 in different cancers and its correlation with prognosis, genetic alteration, DNA promoter methylation, biological processes, immunoregulator expression levels, immune cell infiltration into tumor, tumor mutation burden (TMB), microsatellite instability (MSI), immunotherapy response and drug sensitivity. Further, two single-cell databases, Tumor Immune Single-cell Hub 2 (TISCH2) and CancerSEA, were used to explore the expression and potential roles of SERPINE1 at a single-cell level. The aberrant expression of SERPINE1 was further verified in clear cell renal cell carcinoma (ccRCC) through qRT-PCR of clinical patient samples, validation in independent cohorts using The Gene Expression Omnibus (GEO) database, and proteomic validation using the Clinical Proteomic Tumor Analysis Consortium (CPTAC) database. Results: The expression of SERPINE1 was dysregulated in cancers and enriched in endothelial cells and fibroblasts. Copy number amplification and low DNA promoter methylation could be partly responsible for high SERPINE1 expression. High SERPINE1 expression was associated with poor prognosis in 21 cancers. The results of gene set enrichment analysis (GSEA) indicated SERPINE1 involvement in the immune response and tumor malignancy. SERPINE1 expression was also associated with the expression of several immunoregulators and immune cell infiltration and could play an immunosuppression role. Besides, SERPINE1 was found to be related with TMB, MSI, immunotherapy response and sensitivity to several drugs in cancers. Finally, the high expression of SERPINE1 in ccRCC was verified using qRT-PCR performed on patient samples, six independent GEO cohorts, and proteomic data from the CPTAC database. Conclusion: The findings of the present study revealed that SERPINE1 exhibits aberrant expression in various types of cancers and is associated with cancer immunity and tumor malignancy, providing novel insights for individualized cancer treatment.
Collapse
Affiliation(s)
- Lingqin Li
- Department of Operating Room, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, HangZhou, China
| | - Fan Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhehao Xu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liyang Li
- University of New South Wales, School of Medicine, Sydney, NSW, Australia
| | - Haiyi Hu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shicheng Yu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mingchao Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Gao
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
24
|
Yang Y, Liang J, Zhao J, Wang X, Feng D, Xu H, Shen Y, Zhang Y, Dai J, Wang Z, Wei Q, Liu Z. The multi-omics analyses of acsl1 reveal its translational significance as a tumor microenvironmental and prognostic biomarker in clear cell renal cell carcinoma. Diagn Pathol 2023; 18:96. [PMID: 37608295 PMCID: PMC10463412 DOI: 10.1186/s13000-023-01384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of kidney cancer. Dysregulation of long-chain acyl-CoA synthetase 1 (ACSL1) is strongly implicated in undesirable results in varieties of cancers. Nevertheless, the dysregulation and associated multi-omics characteristics of ACSL1 in ccRCC remain elusive. METHODS We probed the mRNA and protein profiles of ACSL1 in RCC using data from the Cancer Genome Atlas, Gene Expression Omnibus, the Human Protein Atlas (HPA), and Clinical Proteomic Tumor Analysis Consortium (CPTAC) and verified them in our patient cohort and RCC cell lines. Correlations between ACSL1 expression and clinicopathological features, epigenetic modification and immune microenvironment characteristics were analyzed to reveal the multi-omics profile associated with ACSL1. RESULTS ACSL1 was down-regulated in ccRCC tissues compared to adjacent normal tissues. Lower expression of ACSL1 was linked to unfavorable pathological parameters and prognosis. The dysregulation of ACSL1 was greatly ascribed to CpG island-associated methylation modification. The ACSL1 high-expression subgroup had enriched fatty acid metabolism-related pathways and high expression of ferroptosis-related genes. In contrast, the ACSL1 low-expression subgroup exhibited higher immune and microenvironment scores, elevated expression of immune checkpoints PDCD1, CTLA4, LAG3, and TIGIT, and higher TIDE scores. Using data from the GDSC database, we corroborated that down-regulation of ACSL1 was associated with higher sensitivity towards Erlotinib, Pazopanib, and PI3K-Akt-mTOR-targeted therapeutic strategies. CONCLUSION Taken together, our findings point to ACSL1 as a biomarker for prognostic prediction of ccRCC, identifying the tumor microenvironment (TME) phenotype, and even contributing to treatment decision-making in ccRCC patients.
Collapse
Affiliation(s)
- Yang Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, No. 48, Taling South Road, Xunyang District, Jiujiang City, 332000, Jiangxi Province, China
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junjie Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyuan Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dechao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hang Xu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yu Shen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yaowen Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jindong Dai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhipeng Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- , No.37 Guoxue Alley, Wuhou District, Chengdu City, Sichuan Province, PR China.
| | - Zhenhua Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- , No.37 Guoxue Alley, Wuhou District, Chengdu City, Sichuan Province, PR China.
| |
Collapse
|
25
|
Mc Auley MT. An evolutionary perspective of lifespan and epigenetic inheritance. Exp Gerontol 2023; 179:112256. [PMID: 37460026 DOI: 10.1016/j.exger.2023.112256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
In the last decade epigenetics has come to the fore as a discipline which is central to biogerontology. Age associated epigenetic changes are routinely linked with pathologies, including cardiovascular disease, cancer, and Alzheimer's disease; moreover, epigenetic clocks are capable of correlating biological age with chronological age in many species including humans. Recent intriguing empirical observations also suggest that inherited epigenetic effects could influence lifespan/longevity in a variety of organisms. If this is the case, an imperative exists to reconcile lifespan/longevity associated inherited epigenetic processes with the evolution of ageing. This review will critically evaluate inherited epigenetic effects from an evolutionary perspective. The overarching aim is to integrate the evidence which suggests epigenetic inheritance modulates lifespan/longevity with the main evolutionary theories of ageing.
Collapse
|
26
|
Li Y, Wu H, Guo Y, Wei C, Guan L, Ju W, Lian F. Cangfu Daotan Wan alleviates polycystic ovary syndrome with phlegm-dampness syndrome via disruption of the PKP3/ERCC1/MAPK axis. J Ovarian Res 2023; 16:134. [PMID: 37420272 DOI: 10.1186/s13048-023-01200-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND/AIM Cangfu Daotan Wan (CFDTW) has been widely used for polycystic ovary syndrome (PCOS) patients in the type of stagnation of phlegm and dampness. In this study, we aimed to evaluate the mechanism underlying the therapeutic effect of CFDTW on PCOS with phlegm-dampness syndrome (PDS). METHODS In silico analysis was adopted to identify CFDTW potential targets and the downstream pathways in the treatment of PCOS. Expression of PKP3 was examined in the ovarian granulosa cells from PCOS patients with PDS and rat PCOS models induced by dehydroepiandrosterone (DHEA). PKP3/ERCC1 was overexpressed or underexpressed or combined with CFDTW treatment in ovarian granulosa cells to assay the effect of CFDTW on ovarian granulosa cell functions via the PKP3/MAPK/ERCC1 axis. RESULTS Clinical samples and ovarian granulosa cells of rat models were characterized by hypomethylated PKP3 promoter and upregulated PKP3 expression. CFDTW reduced PKP3 expression by enhancing the methylation of PKP3 promoter, leading to proliferation of ovarian granulosa cells, increasing S and G2/M phase-arrested cells, and arresting their apoptosis. PKP3 augmented ERCC1 expression by activating the MAPK pathway. In addition, CFDTW facilitated the proliferation of ovarian granulosa cells and repressed their apoptosis by regulating PKP3/MAPK/ERCC1 axis. CONCLUSION Taken together, this study illuminates how CFDTW confers therapeutic effects on PCOS patients with PDS, which may offer a novel theranostic marker in PCOS.
Collapse
Affiliation(s)
- Yuan Li
- Department of Reproduction and Genetics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42, Wenhua West Road, Jinan, 250011, Shandong Province, P. R. China
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, P. R. China
| | - Haicui Wu
- Department of Reproduction and Genetics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42, Wenhua West Road, Jinan, 250011, Shandong Province, P. R. China
| | - Ying Guo
- Department of Reproduction and Genetics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42, Wenhua West Road, Jinan, 250011, Shandong Province, P. R. China
| | - Chaofeng Wei
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, P. R. China
| | - Lu Guan
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, P. R. China
| | - Wenhan Ju
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, P. R. China
| | - Fang Lian
- Department of Reproduction and Genetics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42, Wenhua West Road, Jinan, 250011, Shandong Province, P. R. China.
| |
Collapse
|
27
|
Song L, Zeng R, Yang K, Liu W, Xu Z, Kang F. The biological significance of cuproptosis-key gene MTF1 in pan-cancer and its inhibitory effects on ROS-mediated cell death of liver hepatocellular carcinoma. Discov Oncol 2023; 14:113. [PMID: 37380924 DOI: 10.1007/s12672-023-00738-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/25/2023] [Indexed: 06/30/2023] Open
Abstract
Metal regulatory transcription factor 1 (MTF1) has been reported to be correlated with several human diseases, especially like cancers. Exploring the underlying mechanisms and biological functions of MTF1 could provide novel strategies for clinical diagnosis and therapy of cancers. In this study, we conducted the comprehensive analysis to evaluate the profiles of MTF1 in pan-cancer. For example, TIMER2.0, TNMplot and GEPIA2.0 were employed to analyze the expression values of MTF1 in pan-cancer. The methylation levels of MTF1 were evaluated via UALCAN and DiseaseMeth version 2.0 databases. The mutation profiles of MTF1 in pan-cancers were analyzed using cBioPortal. GEPIA2.0, Kaplan-Meier plotter and cBioPortal were also used to explore the roles of MTF1 in cancer prognosis. We found that high MTF1 expression was related to poor prognosis of liver hepatocellular carcinoma (LIHC) and brain lower grade glioma (LGG). Also, high expression level of MTF1 was associated with good prognosis of kidney renal clear cell carcinoma (KIRC), lung cancer, ovarian cancer and breast cancer. We investigated the genetic alteration and methylation levels of MTF1 between the primary tumor and normal tissues. The relationship between MTF1 expression and several immune cells was analyzed, including T cell CD8 + and dendritic cells (DC). Mechanically, MTF1-interacted molecules might participate in the regulation of metabolism-related pathways, such as peptidyl-serine phosphorylation, negative regulation of cellular amide metabolic process and peptidyl-threonine phosphorylation. Single cell sequencing indicated that MTF1 was associated with angiogenesis, DNA repair and cell invasion. In addition, in vitro experiment indicated knockdown of MTF1 resulted in the suppressed cell proliferation, increased reactive oxygen species (ROS) and promoted cell death in LIHC cells HepG2 and Huh7. Taken together, this pan-cancer analysis of MTF1 has implicated that MTF1 could play an essential role in the progression of various human cancers.
Collapse
Affiliation(s)
- Liying Song
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rong Zeng
- General Surgery Department, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Keda Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Liu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Department of Orthopedic Surgery, The Second Hospital University of South China, Hengyang, Hunan, China.
| | - Zhijie Xu
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, Xiangya Changde Hospital, Changde, Hunan, China
| | - Fanhua Kang
- Department of Pathology, Xiangya Changde Hospital, Changde, Hunan, China.
| |
Collapse
|
28
|
Helenius G, Lillsunde-Larsson G, Bergengren L. Molecular triage of cervical screening samples in women 55-59 years of age: a pilot study. Infect Agent Cancer 2023; 18:31. [PMID: 37221548 DOI: 10.1186/s13027-023-00510-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND With HPV screening the specificity of screening positives has decreased, even with a cytological triage test. Increases in colposcopies and detection of benign or low-grade dysplasia are reported, not least in older women. These results highlight the necessity to find other triage tests in HPV screening strategies, so that women can be more accurately selected for colposcopy, thus minimizing the clinically irrelevant findings. METHODS The study included 55- to 59-year-old women who exited the screening with normal cytology, but later in a follow-up test were positive for the HPV genotypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 and had a cervical cone biopsy done. To model a screening situation with hrHPV-positive women, three different triage strategies, namely, cytology, genotyping and methylation, were performed. The study considered the effect of direct referral to colposcopy for HPV genotypes 16, 18, 31, 33, 45, 52 and 58, and methylation for FAM19A4 and hsa-mir124-2 and/or any form of abnormal cytology. RESULTS Seven out of 49 women aged 55-59 years with hrHPV had a cone biopsy with high-grade squamous intraepithelial lesion. No triage method found all cases, and when comparing positive and negative predictive value and false negative rate, cytology showed better results than genotyping and methylation. CONCLUSION This study does not support a switch in triage strategies from cytology to hrHPV genotyping and methylation for women above 55 years of age yet, but demonstrates the need for more evidence on molecular triage strategies.
Collapse
Affiliation(s)
- Gisela Helenius
- School of Health Sciences, Örebro University, Örebro, Sweden
| | - Gabriella Lillsunde-Larsson
- School of Health Sciences, Örebro University, Örebro, Sweden
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Lovisa Bergengren
- Department of Women's Health, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Zou R, Zhong X, Liang K, Zhi C, Chen D, Xu Z, Zhang J, Liao D, Lai M, Weng Y, Peng H, Pang X, Ji Y, Ke Y, Zhang H, Wang Z, Wang Y. Elevated LILRB1 expression predicts poor prognosis and is associated with tumor immune infiltration in patients with glioma. BMC Cancer 2023; 23:403. [PMID: 37142967 PMCID: PMC10161664 DOI: 10.1186/s12885-023-10906-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/29/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Leukocyte immunoglobulin-like receptor subfamily B1 (LILRB1) is regarded as an inhibitory molecule. However, the importance of LILRB1 expression in glioma has not yet been determined. This investigation examined the immunological signature, clinicopathological importance and prognostic value of LILRB1 expression in glioma. METHODS We used data from the UCSC XENA database, the Cancer Genome Atlas (TCGA) database, the Chinese Glioma Genome Atlas (CGGA) database, the STRING database, the MEXPRESS database and our clinical glioma samples to perform bioinformatic analysis and used vitro experiments to examine the predictive value and potential biological roles of LILRB1 in glioma. RESULTS Higher LILRB1 expression was considerably present in the higher WHO grade glioma group and was linked to a poorer prognosis in patients with glioma. Gene set enrichment analysis (GSEA) revealed that LILRB1 was positively correlated with the JAK/STAT signaling pathway. LILRB1 combined with tumor mutational burden (TMB) and microsatellite instability (MSI) may be a promising indicator for the effectiveness of immunotherapy in patients with glioma. Increased LILRB1 expression was positively linked with the hypomethylation, M2 macrophage infiltration, immune checkpoints (ICPs) and M2 macrophage makers. Univariate and multivariate Cox regression analyses determined that increased LILRB1 expression was a standalone causal factor for glioma. Vitro experiments determined that LILRB1 positively enhanced the proliferation, migration and invasion in glioma cells. MRI images demonstrated that higher LILRB1 expression was related with larger tumor volume in patients with glioma. CONCLUSION Dysregulation of LILRB1 in glioma is correlated with immune infiltration and is a standalone causal factor for glioma.
Collapse
Affiliation(s)
- Renheng Zou
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Xunlong Zhong
- Science and Technology Innovation Center, Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
- Department of Pharmacy, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Kairong Liang
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Cheng Zhi
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Danmin Chen
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Zhichao Xu
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Jingbai Zhang
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Degui Liao
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Miaoling Lai
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yuhao Weng
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Huaidong Peng
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiao Pang
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yanbin Ke
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Hongri Zhang
- Department of Neurosurgery, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, Henan, China.
| | - Zhaotao Wang
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
| |
Collapse
|
31
|
Li X, Liu D, Dai Z, You Y, Chen Y, Lei C, Lv Y, Wang Y. Intraperitoneal 5-Azacytidine Alleviates Nerve Injury-Induced Pain in Rats by Modulating DNA Methylation. Mol Neurobiol 2023; 60:2186-2199. [PMID: 36627549 DOI: 10.1007/s12035-022-03196-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
To investigate the role of DNA methylation in modulating chronic neuropathic pain (NPP), identify possible target genes of DNA methylation involved in this process, and preliminarily confirm the medicinal value of the DNA methyltransferases (DNMTs) inhibitor 5-azacytidine (5-AZA) in NPP by targeting gene methylation. Two rat NPP models, chronic constriction injury (CCI) and spinal nerve ligation (SNL), were used. The DNA methylation profiles in the lumbar spinal cord were assayed using an Arraystar Rat RefSeq Promoter Array. The underlying genes with differential methylation were then identified and submitted to Gene Ontology and pathway analysis. Methyl-DNA immunoprecipitation quantitative PCR (MeDIP-qPCR) and quantitative reverse transcription-PCR (RT-qPCR) were used to confirm gene methylation and expression. The protective function of 5-AZA in NPP and gene expression were evaluated via behavioral assays and RT-qPCR, respectively. Analysis of the DNA methylation patterns in the lumbar spinal cord indicated that 1205 differentially methylated fragments in CCI rats were located within DNA promoter regions, including 638 hypermethylated fragments and 567 hypomethylated fragments. The methylation levels of Grm4, Htr4, Adrb2, Kcnf1, Gad2, and Pparg, which are associated with long-term potentiation (LTP) and glutamatergic synapse pathways, were increased with a corresponding decrease in their mRNA expression, in the spinal cords of CCI rats. Moreover, we found that the intraperitoneal injection of 5-AZA (4 mg/kg) attenuated CCI- or SNL-induced mechanical allodynia and thermal hyperalgesia. Finally, the mRNA expression of hypermethylated genes such as Grm4, Htr4, Adrb2, Kcnf1, and Gad2 was reversed after 5-AZA treatment. CCI induced widespread methylation changes in the DNA promoter regions in the lumbar spinal cord. Intraperitoneal 5-AZA alleviated hyperalgesia in CCI and SNL rats, an effect accompanied by the reversed expression of hypermethylated genes. Thus, DNA methylation inhibition represents a promising epigenetic strategy for protection against chronic NPP following nerve injury. Our study lays a theoretical foundation for 5-AZA to become a clinical targeted drug.
Collapse
Affiliation(s)
- Xuan Li
- Department of Anesthesiology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong, China
| | - DeZhao Liu
- Department of Anesthesiology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong, China
| | - ZhiSen Dai
- Department of Anesthesiology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - YiSheng You
- Department of Anesthesiology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Yan Chen
- Department of Anesthesiology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - ChenXing Lei
- Department of Anesthesiology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong, China
| | - YouYou Lv
- Department of Anesthesiology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong, China
| | - Ying Wang
- Department of Anesthesiology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong, China. .,Department of Anesthesiology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China.
| |
Collapse
|
32
|
Ultrasensitive photoelectrochemical biosensor for DNA 5-methylcytosine analysis based on co-sensitization strategy combined with bridged DNA nanoprobe. Talanta 2023; 254:124140. [PMID: 36463802 DOI: 10.1016/j.talanta.2022.124140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Altered DNA methylation in the form of 5-methylcytosine (5-mC) patterns is correlated with disease diagnosis, prognosis, and treatment response. Therefore, accurate analysis of 5-mC is of great significance for the diagnosis of diseases. Here, an efficient enhanced photoelectrochemical (PEC) biosensor was designed for the quantitative analysis of DNA 5-mC based on a cascaded energy level aligned co-sensitization strategy coupling with the bridged DNA nanoprobe (BDN). Firstly, Au nanoparticle/graphite phase carbon nitride/titanium dioxide (AuNPs/g-C3N4@TiO2) nanocomposite was synthesized through in situ growth of AuNPs on g-C3N4@TiO2 surface as a matrix to provide a stable background signal. Next, BDN with a high mass transfer rate synthesized from a pair of DNA tetrahedral as nanomechanical handles was used as a capture probe to bind to the target sequence. The polydopamine nanosphere was applied to load with CdTe QDs (PDANS-CdTe QDs) as a photocurrent label of 5-mC antibodies. When the 5-mC existed, a large number of PDANS-Ab-CdTe QDs were introduced to the electrode surface, the formed CdTe QDs/AuNPs/g-C3N4@TiO2 co-sensitive structure could effectively enhance the electron transfer capability and photocurrent response rate due to the effective cascade energy level arrangement, leading to a significantly enhanced photocurrent signal. The proposed PEC biosensor manifested a wide range from 10-17 M to 10-7 M and a detection limit of 2.2 aM. Meanwhile, the excellent performance indicated the practicability of the designed strategy, thus being capable of the clinical diagnosis of 5-mC.
Collapse
|
33
|
Ye J, Wu J, Liu B. Therapeutic strategies of dual-target small molecules to overcome drug resistance in cancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188866. [PMID: 36842765 DOI: 10.1016/j.bbcan.2023.188866] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/12/2023] [Accepted: 01/31/2023] [Indexed: 02/28/2023]
Abstract
Despite some advances in targeted therapeutics of human cancers, curative cancer treatment still remains a tremendous challenge due to the occurrence of drug resistance. A variety of underlying resistance mechanisms to targeted cancer drugs have recently revealed that the dual-target therapeutic strategy would be an attractive avenue. Compared to drug combination strategies, one agent simultaneously modulating two druggable targets generally shows fewer adverse reactions and lower toxicity. As a consequence, the dual-target small molecule has been extensively explored to overcome drug resistance in cancer therapy. Thus, in this review, we focus on summarizing drug resistance mechanisms of cancer cells, such as enhanced drug efflux, deregulated cell death, DNA damage repair, and epigenetic alterations. Based upon the resistance mechanisms, we further discuss the current therapeutic strategies of dual-target small molecules to overcome drug resistance, which will shed new light on exploiting more intricate mechanisms and relevant dual-target drugs for future cancer therapeutics.
Collapse
Affiliation(s)
- Jing Ye
- State Key Laboratory of Biotherapy and Cancer Center and Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junhao Wu
- State Key Laboratory of Biotherapy and Cancer Center and Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center and Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
34
|
Wang XY, Zhang LN. RNA binding protein SAMD4: current knowledge and future perspectives. Cell Biosci 2023; 13:21. [PMID: 36732864 PMCID: PMC9893680 DOI: 10.1186/s13578-023-00968-x] [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: 08/09/2022] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
SAMD4 protein family is a class of novel RNA-binding proteins that can mediate post-transcriptional regulation and translation repression in eukaryotes, which are highly conserved from yeast to humans during evolution. In mammalian cells, SAMD4 protein family consists of two members including SAMD4A/Smaug1 and SAMD4B/Smaug2, both of which contain common SAM domain that can specifically bind to different target mRNAs through stem-loop structures, also known as Smaug recognition elements (SREs), and regulate the mRNA stability, degradation and translation. In addition, SAMD4 can form the cytoplasmic mRNA silencing foci and regulate the translation of SRE-containing mRNAs in neurons. SAMD4 also can form the cytosolic membrane-less organelles (MLOs), termed as Smaug1 bodies, and regulate mitochondrial function. Importantly, many studies have identified that SAMD4 family members are involved in various pathological processes including myopathy, bone development, neural development, and cancer occurrence and progression. In this review, we mainly summarize the structural characteristics, biological functions and molecular regulatory mechanisms of SAMD4 protein family members, which will provide a basis for further research and clinical application of SAMD4 protein family.
Collapse
Affiliation(s)
- Xin-Ya Wang
- grid.28703.3e0000 0000 9040 3743Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, 100124 Beijing, People’s Republic of China
| | - Li-Na Zhang
- grid.28703.3e0000 0000 9040 3743Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, 100124 Beijing, People’s Republic of China
| |
Collapse
|
35
|
Pan RH, Zhang X, Chen ZP, Liu YJ. Arachidonate lipoxygenases 5 is a novel prognostic biomarker and correlates with high tumor immune infiltration in low-grade glioma. Front Genet 2023; 14:1027690. [PMID: 36777735 PMCID: PMC9911666 DOI: 10.3389/fgene.2023.1027690] [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: 08/25/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Objective: To investigate the prognostic value of arachidonate lipoxygenases 5 (ALOX5) expression and methylation, and explore the immune functions of arachidonate lipoxygenases 5 expression in low-grade glioma (LGG). Materials and Methods: Using efficient bioinformatics approaches, the differential expression of arachidonate lipoxygenases 5 and the association of its expression with clinicopathological characteristics were evaluated. Then, we analyzed the prognostic significance of arachidonate lipoxygenases 5 expression and its methylation level followed by immune cell infiltration analysis. The functional enrichment analysis was conducted to determine the possible regulatory pathways of arachidonate lipoxygenases 5 in low-grade glioma. Finally, the drug sensitivity analysis was performed to explore the correlation between arachidonate lipoxygenases 5 expression and chemotherapeutic drugs. Results: arachidonate lipoxygenases 5 mRNA expression was increased in low-grade glioma and its expression had a notable relation with age and subtype (p < 0.05). The elevated mRNA level of arachidonate lipoxygenases 5 could independently predict the disease-specific survival (DSS), overall survival (OS), and progression-free interval (PFI) (p < 0.05). Besides, arachidonate lipoxygenases 5 expression was negatively correlated with its methylation level and the arachidonate lipoxygenases 5 hypomethylation led to a worse prognosis (p < 0.05). The arachidonate lipoxygenases 5 expression also showed a positive connection with immune cells, while low-grade glioma patients with higher immune cell infiltration had poor survival probability (p < 0.05). Further, arachidonate lipoxygenases 5 might be involved in immune- and inflammation-related pathways. Importantly, arachidonate lipoxygenases 5 expression was negatively related to drug sensitivity. Conclusion: arachidonate lipoxygenases 5 might be a promising biomarker, and it probably occupies a vital role in immune cell infiltration in low-grade glioma.
Collapse
|
36
|
Yuan Z, Zhong Y, Hu H, Zhang W, Wang G. DEF6 has potential to be a biomarker for cancer prognosis: A pan-cancer analysis. Front Oncol 2023; 12:1064376. [PMID: 36686789 PMCID: PMC9848736 DOI: 10.3389/fonc.2022.1064376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/02/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction DEF6 is a gene associated with the immune system and is thought to play a crucial role in autoimmunity. There are few DEF6-related studies in cancer, and it is assumed that DEF6 is a proto-oncogene. There is currently no pan-cancer analysis of DEF6, and we performed a systematic and comprehensive pan-cancer analysis of DEF6 in an attempt to reveal its role and function in cancer. Methods The data were analyzed by mining databases available to the public and by using R software. Moreover, immunohistochemistry was used to validate the results. Results Our results revealed that DEF6 is commonly aberrantly expressed in cancer and its expression is strongly correlated with survival prognosis in a variety of cancer types. Through correlation analysis we found that DEF6 was associated with multiple immune genes and was closely related to immune infiltration. In the enrichment analysis, DEF6 may have cross-talk with multiple cancer pathways and exert oncogenic or pro-cancer functions. In addition, we collected pathological samples from colorectal cancer patients for immunohistochemical analysis and found that patients with higher immunohistochemical scores had more lymph node metastases, higher CA199, and bigger tumor size. Discussion Overall, DEF6 expression is closely related to cancers and has the potential to act as a cancer biomarker.
Collapse
|
37
|
Zhu P, Li X, Liu Y, Xiong J, Yuan D, Chen Y, Luo L, Huang J, Wang B, Nie Q, Wang S, Dang L, Li S, Shu Y, Zhang W, Zhou H, Fan L, Li Q. Methylation-mediated silencing of EDN3 promotes cervical cancer proliferation, migration and invasion. Front Oncol 2023; 13:1010132. [PMID: 36824133 PMCID: PMC9942821 DOI: 10.3389/fonc.2023.1010132] [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: 08/13/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Cervical cancer (CC) remains one of the leading causes of cancer-related deaths worldwide. However, cervical cancer is preceded by the pre-malignant cervical intraepithelial neoplasia (CIN) that can last for up to 20 years before becoming malignant. Therefore, early screening is the key to prevent the progression of cervical lesions into invasive cervical cancer and decrease the incidence. The genes, down-regulated and hypermethylated in cancers, may provide potential drug targets for cervical cancer. In our current study, using the datasets from Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases, we found that endothelin 3 (EDN3) was downregulated and hypermethylated in cervical squamous cell carcinoma (CSCC). The further analysis in GSE63514 (n=128) dataset and in our samples (n=221) found that the expression of EDN3 was decreased with the degree of cervical lesions. Pyrosequencing was performed to evaluate 4 CpG sites of the EDN3 promoter region in our samples (n=469). The data indicated that the methylation level of EDN3 was increased with the degree of cervical lesions. EDN3 silencing mediated by methylation can be blocked by 5-Azacytidine (5-Aza), a DNA methyltransferase 1 (DNMT1) inhibitor, treatment in cervical cancer cell lines. Ethynyldeoxyuridine (EdU) assay, would-healing assay, clone formation assay and transwell assay were conducted to investigate the biological function of EDN3 in cervical cancer cell lines. The results of these experiments confirmed that overexpression of EDN3 could inhibit the proliferation, clone formation, migration and invasion of cervical cancer cells. EDN3 may provide potential biomarker and therapeutic target for CSCC.
Collapse
Affiliation(s)
- Peng Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
| | - Xiang Li
- Department of Gynaecology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yujie Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
| | - Jing Xiong
- Department of Gynaecology and Obstetrics, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Qing Li, ; Jing Xiong,
| | - Ding Yuan
- Health Management Center, Xiangya Hospital, Central South University, Changsha, China
| | - Yan Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- Xiangya Medical Laboratory, Central South University, Changsha, China
| | - Lili Luo
- Department of Gynaecology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Ju Huang
- Department of Gynaecology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Binbin Wang
- Department of Obstetrics and Gynecology, Loudi Central Hospital, Loudi, China
| | - Quanfang Nie
- Department of Obstetrics and Gynecology, Loudi Central Hospital, Loudi, China
| | - Shuli Wang
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Liying Dang
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Shu Li
- Xiangya Medical Laboratory, Central South University, Changsha, China
| | - Yan Shu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
| | - Lan Fan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- *Correspondence: Qing Li, ; Jing Xiong,
| |
Collapse
|
38
|
Wei L, Li H, Xiao M, Zhou C, Liu J, Weng S, Wei R. CCNF is a potential pancancer biomarker and immunotherapy target. Front Oncol 2023; 13:1109378. [PMID: 37168372 PMCID: PMC10164972 DOI: 10.3389/fonc.2023.1109378] [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: 11/27/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Background CCNF catalyzes the transfer of ubiquitin molecules from E2 ubiquitin-conjugating enzymes to target proteins, thereby regulating the G1/S or G2/M transition of tumor cells. Thus far, CCNF expression and its potential as a pancancer biomarker and immunotherapy target have not been reported. Methods TCGA datasets and the R language were used to analyze the pancancer gene expression, protein expression, and methylation levels of CCNF; the relationship of CCNF expression with overall survival (OS), recurrence-free survival (RFS), immune matrix scores, sex and race; and the mechanisms for posttranscriptional regulation of CCNF. Results CCNF expression analysis showed that CCNF mRNA expression was higher in cancer tissues than in normal tissues in the BRCA, CHOL, COAD, ESCA, HNSC, LUAD, LUSC, READ, STAD, and UCEC; CCNF protein expression was also high in many cancer tissues, indicating that it could be an important predictive factor for OS and RFS. CCNF overexpression may be caused by CCNF hypomethylation. CCNF expression was also found to be significantly different between patients grouped based on sex and race. Overexpression of CCNF reduces immune and stromal cell infiltration in many cancers. Posttranscriptional regulation analysis showed that miR-98-5p negatively regulates the expression of the CCNF gene. Conclusion CCNF is overexpressed across cancers and is an adverse prognostic factor in terms of OS and RFS in many cancers; this phenomenon may be related to hypomethylation of the CCNF gene, which could lead to cancer progression and worsen prognosis. In addition, CCNF expression patterns were significantly different among patients grouped by sex and race. Its overexpression reduces immune and stromal cell infiltration. miR-98-5p negatively regulates CCNF gene expression. Hence, CCNF is a potential pancancer biomarker and immunotherapy target.
Collapse
Affiliation(s)
- Lifang Wei
- Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Huiming Li
- Department of Preventive Medicine, Medical School of Yichun University, Yichun, China
| | - Mengjun Xiao
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
| | - Cuiling Zhou
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
| | - Jiliang Liu
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
| | - Shilian Weng
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
- *Correspondence: Ruda Wei, ; Shilian Weng,
| | - Ruda Wei
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
- *Correspondence: Ruda Wei, ; Shilian Weng,
| |
Collapse
|
39
|
Blood-based DNA methylation signatures in cancer: A systematic review. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166583. [PMID: 36270476 DOI: 10.1016/j.bbadis.2022.166583] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
DNA methylation profiles are in dynamic equilibrium via the initiation of methylation, maintenance of methylation and demethylation, which control gene expression and chromosome stability. Changes in DNA methylation patterns play important roles in carcinogenesis and primarily manifests as hypomethylation of the entire genome and the hypermethylation of individual loci. These changes may be reflected in blood-based DNA, which provides a non-invasive means for cancer monitoring. Previous blood-based DNA detection objects primarily included circulating tumor DNA/cell-free DNA (ctDNA/cfDNA), circulating tumor cells (CTCs) and exosomes. Researchers gradually found that methylation changes in peripheral blood mononuclear cells (PBMCs) also reflected the presence of tumors. Blood-based DNA methylation is widely used in early diagnosis, prognosis prediction, dynamic monitoring after treatment and other fields of clinical research on cancer. The reversible methylation of genes also makes them important therapeutic targets. The present paper summarizes the changes in DNA methylation in cancer based on existing research and focuses on the characteristics of the detection objects of blood-based DNA, including ctDNA/cfDNA, CTCs, exosomes and PBMCs, and their application in clinical research.
Collapse
|
40
|
Abstract
There is no evidence showing that the expression of procollagen C-endopeptidase enhancer (PCOLCE) is associated with human tumors, and pan-cancer analysis is not available. Based on public databases such as the cancer genome atlas, we investigated the potential role of PCOLCE expression in 33 different human tumors. PCOLCE expression in 11 tumors was significantly correlated with tumor prognosis and was a prognostic predictor for pancreatic adenocarcinoma, thymoma and CES. We also found that PCOLCE expression correlated with the immune microenvironment of tumors and the level of cancer-associated fibroblast infiltration. PCOLCE is a potential predictor of small molecule targeted drugs and immune checkpoint inhibitors. Finally, we found by enrichment analysis that PCOLCE localizes to extracellular structures and the extracellular matrix and exerts substantial effects on tumors through the PI3K-Akt and AGE-RAGE signaling pathways. We have a preliminary and relatively comprehensive understanding of the role of PCOLCE in various tumors.
Collapse
Affiliation(s)
- Hui Gao
- Department of Breast Surgery, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, PR China
| | - Qiuyun Li
- Department of Breast Surgery, The Affiliated Cancer Hospital of Guangxi Medical University, Nanning, PR China
- * Correspondence: Qiuyun Li, Department of Breast Surgery, The Affiliated Cancer Hospital of Guangxi Medical University, Nanning 530000, PR China (e-mail: )
| |
Collapse
|
41
|
Zheng M, Wang W, Bu Y, Liu J, Ma J, Wang R, Ren X, Lu Z, Li J, Cai J. Pan-Cancer Analysis of the Roles and Driving Forces of RAB42. Biomolecules 2022; 13:biom13010043. [PMID: 36671428 PMCID: PMC9855782 DOI: 10.3390/biom13010043] [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: 10/28/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
RAB42 is a member of the RAS family. However, the roles and driving forces for RAB42 in tumors remain elusive. In this study, we performed a comprehensive pan-cancer analysis of the roles and regulatory mechanisms of RAB42 using bioinformatics and experiments. Online databases such as Sanger Box, ACLBI and TIDE were used to search for the expression levels, prognostic value and immune features of RAB42. We observed that RAB42 expression was upregulated in most tumors and was closely associated with poor prognosis. Enrichment analysis indicated that RAB42 was related to multiple biological functions, especially the immune process. RAB42 expression had a positive correlation with immune cell infiltration and immune checkpoint gene expression. RAB42 had a high predictive value for immunotherapy efficiency. Our study screened out susceptible drugs for the RAB42 protein by sensitivity analysis and virtual screening. Many key driver genes such as TP53 contributed to RAB42 expression. DNA methylation, super-enhancer and non-coding RNAs were the epigenetic factors responsible for RAB42 expression. In brief, RAB42 could serve as a diagnostic and prognostic biomarker in many tumor types. RAB42 might be a predictive biomarker and a new target for immunotherapy. Genetic and epigenetic factors were essential for RAB42 overexpression in tumors.
Collapse
Affiliation(s)
- Mingzhu Zheng
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Wenhao Wang
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Yulan Bu
- Department of Radiotherapy, Affiliated Hospital of Weifang Medical University, Weifang 261031, China
| | - Jing Liu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Jingang Ma
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Rui Wang
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Xiaomin Ren
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Zhong Lu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Jiaqiu Li
- Jinming Yu Academician Workstation of Oncology, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261031, China
- Correspondence: (J.L.); (J.C.)
| | - Jinwei Cai
- Department of Oncology, People’s Hospital of Kecheng District, Quzhou 324000, China
- Correspondence: (J.L.); (J.C.)
| |
Collapse
|
42
|
Wei S, Wang W, Liu S, Sun B, Zeng Q, Wang G, Luo P, Zhang A. Genome-wide DNA methylation pattern in whole blood of patients with coal-burning arsenic poisoning. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 248:114323. [PMID: 36436256 DOI: 10.1016/j.ecoenv.2022.114323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/31/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Exposure to coal-burning arsenic leads to an increased risk of cancer, multi-systems damage and chronic diseases, with DNA methylation one potential mechanism of arsenic toxicity. There are few studies on genome-wide methylation in the coal-burning arsenic poisoning population. Illumina 850 K methylation beadchip is the most suitable technology for DNA methylation of epigenome-wide association analysis. This study used 850 K to detect changes in Genome-wide DNA methylation in whole blood samples of 12 patients with coal-burning arsenic poisoning ( Arsenic poisoning group) and four healthy control participants (Healthy control group). There is clearly abnormal genome-wide DNA methylation in coal-burning arsenic poisoning, with 647 significantly different methylation positions, 524 different methylation regions and 335 significantly different methylation genes in arsenic poisoning patients compared with healthy controls. Further functional analysis of Gene ontology (GO) and Kyoto encyclopedia of genes (KEGG) found 592 GO items and 131 KEGG pathways between patients of coal-burning arsenic poisoning and healthy control. Then, analysis of gene degree and combined-score identified NAPRT1, NT5C3B, NEDD4L, SLC22A3 and RAB11B as target genes. Further validation by qRT-PCR indicates that mRNA expression of five genes changes significantly in the arsenic poisoning group (n = 72) compared to the healthy control group (n = 72). These results showed the genome-wide methylation pattern and highlighted five critical genes within the coal-burning arsenic poisoning population that involve Nicotinate and nicotinamide metabolism, Choline metabolism in cancer, and Ubiquitin mediated proteolysis. Next, the methylation profile of coal burning arsenic poisoning will be further excavation and the mechanism of coal burning arsenic poisoning will be further explored from five genes related pathways and functions.
Collapse
Affiliation(s)
- Shaofeng Wei
- Department of Nutrition and Food Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China; The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China.
| | - Wenjing Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China; The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China
| | - Shiwen Liu
- Department of Nutrition and Food Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China; The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China
| | - Baofei Sun
- Department of Nutrition and Food Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China; The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China
| | - Qibing Zeng
- Department of Nutrition and Food Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China; The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China
| | - Guoze Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China; The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China
| | - Peng Luo
- Department of Nutrition and Food Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China; The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China
| | - Aihua Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China; The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, People's Republic of China.
| |
Collapse
|
43
|
Zhu LR, Zheng W, Gao Q, Chen T, Pan ZB, Cui W, Cai M, Fang H. Epigenetics and genetics of hepatoblastoma: Linkage and treatment. Front Genet 2022; 13:1070971. [DOI: 10.3389/fgene.2022.1070971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022] Open
Abstract
Hepatoblastoma is a malignant embryonal tumor with multiple differentiation modes and is the clearest liver malignancy in children. However, little is known about genetic and epigenetic events in Hepatoblastoma. Increased research has recently demonstrated, unique genetic and epigenetic events in Hepatoblastoma, providing insights into its origin and precise treatment. Some genetic disorders and congenital factors are associated with the risk of Hepatoblastoma development, such as the Beckwith-Wiedemann syndrome, Familial Adenomatous polyposis, and Hemihypertrophy. Epigenetic modifications such as DNA modifications, histone modifications, and non-coding RNA regulation are also essential in the development of Hepatoblastoma. Herein, we reviewed genetic and epigenetic events in Hepatoblastoma, focusing on the relationship between these events and cancer susceptibility, tumor growth, and prognosis. By deciphering the genetic and epigenetic associations in Hepatoblastoma, tumor pathogenesis can be clarified, and guide the development of new anti-cancer drugs and prevention strategies.
Collapse
|
44
|
Mapping Genetics and Epigenetics to Explore the Pathways beyond the Correlated Ageing Phenotype. Genes (Basel) 2022; 13:genes13112169. [DOI: 10.3390/genes13112169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/11/2022] [Accepted: 11/19/2022] [Indexed: 11/22/2022] Open
Abstract
Ageing is defined by the decline in the biological and physiological functions over time, which leads to health problems and increases risks of diseases. The modern societies are characterised by an ageing population, which represents challenges for the healthcare system. Within this context, there is a need to better understand the biological mechanisms beyond ageing in order to optimise geriatric therapies and medical approaches. Herein, we suggest exploring the genetic and epigenetic patterns related to ageing and correlate them with the ageing-related phenotype of the biological entities in order to establish mechanistic links and map the molecular pathways. Such links would have diverse implications in basic research, in clinics, as well as for therapeutic studies.
Collapse
|
45
|
Integrative and Comprehensive Pan-Cancer Analysis of Lymphocyte-Specific Protein Tyrosine Kinase in Human Tumors. Int J Mol Sci 2022; 23:ijms232213998. [PMID: 36430477 PMCID: PMC9697346 DOI: 10.3390/ijms232213998] [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: 09/06/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Lymphocyte-specific protein tyrosine kinase (LCK) is common in a variety of hematologic malignancies but comparatively less common in solid tumors. This study aimed to explore the potential diagnostic and prognostic value of LCK across tumors through integrative and comprehensive pan-cancer analysis, as well as experimental validation. Multiple databases were used to explore the expression, alteration, prognostic value, association with immune infiltration, and potential functional pathways of LCK in pan-cancers. The results were further validated by western blotting and qPCR of patient samples as well as tumor cell lines. High LCK expression typically represents a better prognosis. Notably, drug sensitivity prediction of LCK identified P-529 as a candidate for drug development. Gene Annotations (GO) and KEGG analyses showed significant enrichment of PD-L1 and the T-cell receptor pathway. The results from patient samples and tumor cell lines confirmed these conclusions in LIHC. In conclusion, LCK is differentially expressed in multiple tumors and normal tissues. Further analysis highlighted its association with prognostic implications, pan-cancer genetic alterations, and immune signatures. Our data provide evidence for a diagnostic marker of LCK and the possible use of LCK as a target for the treatment of tumors.
Collapse
|
46
|
Frasca D. Several areas of overlap between obesity and aging indicate obesity as a biomarker of accelerated aging of human B cell function and antibody responses. Immun Ageing 2022; 19:48. [PMID: 36289515 PMCID: PMC9598013 DOI: 10.1186/s12979-022-00301-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/19/2022] [Indexed: 11/10/2022]
Abstract
Aging and obesity are high risk factors for several conditions and diseases. They are both associated with systemic inflammation and they are both ameliorated by a healthy life style, suggesting that they may share cellular and molecular pathways and underlying mechanisms. A close relationship between aging and obesity is also supported by the observation that the aging overweight/obese population is increasing worldwide, and mechanisms involved will be presented here. A focus of our work is to evaluate if obesity may be considered a good biomarker of accelerated aging of human antibody responses. We will summarize our published results showing the effects of obesity in accelerating age defects in the peripheral B cell pool and how these lead to dysfunctional humoral immunity.
Collapse
Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, RMSB 3153, 1600 NW 10th Ave, Miami, FL, 33136, USA.
| |
Collapse
|
47
|
Gu Z, Yang J, Yang M, Deng Y, Jiao Y. Immunomodulatory effects of decitabine in pearl oyster Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2022; 129:191-198. [PMID: 36029945 DOI: 10.1016/j.fsi.2022.08.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Decitabine (DAC), an inhibitor of DNA methyltransferase, is typically used to reverse DNA methylation and is considered an epigenetic modifying drug. DNA methylation is crucial to the regulation of gene expression without altering genetic information. Our previous research showed that the DNA methylation levels of many immune-related genes changed after the pre-grafting condition in pearl production. In the present study, we evaluated the DNA methylation level and analyzed transcriptome, enzyme, and antimicrobial activities after DAC treatment to evaluate the effect of DAC on DNA methylation and immune system of pearl oyster Pinctada fucata martensii. Results showed that DAC significantly decreased the level of global DNA methylation in the hemocytes of the pearl oysters. Transcriptome analysis obtained 577 differentially expressed genes (DEGs) between the control and DAC treatment group. The DEGs were mainly enriched in the following pathways: "Relaxin signaling pathway," "Cytosolic DNA-sensing pathway," "Platelet activation," and "Peroxisome," and related genes were overexpressed after DAC treatment. DAC treatment resulted in a substantial increase in the levels of serum superoxide dismutase, interleukin-17, phenol oxidase, tumor necrosis factor, and antimicrobial activity, compared with the control. These results suggested that DAC can alter DNA methylation level, activate immune-related genes, and improve the level of humoral immunity in pearl oysters, thereby increasing our understanding of the mechanism underlying DNA methylation in immune regulation.
Collapse
Affiliation(s)
- Zefeng Gu
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Jingmiao Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Min Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
| |
Collapse
|
48
|
A Methylation Diagnostic Model Based on Random Forests and Neural Networks for Asthma Identification. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2679050. [PMID: 36213574 PMCID: PMC9534672 DOI: 10.1155/2022/2679050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022]
Abstract
Background Asthma significantly impacts human life and health as a chronic disease. Traditional treatments for asthma have several limitations. Artificial intelligence aids in cancer treatment and may also accelerate our understanding of asthma mechanisms. We aimed to develop a new clinical diagnosis model for asthma using artificial neural networks (ANN). Methods Datasets (GSE85566, GSE40576, and GSE13716) were downloaded from Gene Expression Omnibus (GEO) and identified differentially expressed CpGs (DECs) enriched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Random forest (RF) and ANN algorithms further identified gene characteristics and built clinical models. In addition, two external validation datasets (GSE40576 and GSE137716) were used to validate the diagnostic ability of the model. Results The methylation analysis tool (ChAMP) considered DECs that were up-regulated (n =121) and down-regulated (n =20). GO results showed enrichment of actin cytoskeleton organization and cell-substrate adhesion, shigellosis, and serotonergic synapses. RF (random forest) analysis identified 10 crucial DECs (cg05075579, cg20434422, cg03907390, cg00712106, cg05696969, cg22862094, cg11733958, cg00328720, and cg13570822). ANN constructed the clinical model according to 10 DECs. In two external validation datasets (GSE40576 and GSE137716), the Area Under Curve (AUC) for GSE137716 was 1.000, and AUC for GSE40576 was 0.950, confirming the reliability of the model. Conclusion Our findings provide new methylation markers and clinical diagnostic models for asthma diagnosis and treatment.
Collapse
|
49
|
Basha NJ, Basavarajaiah SM. An insight into therapeutic efficacy of heterocycles as histone modifying enzyme inhibitors that targets cancer epigenetic pathways. Chem Biol Drug Des 2022; 100:682-698. [PMID: 36059065 DOI: 10.1111/cbdd.14135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 01/10/2023]
Abstract
Histone modifying enzymes are the key regulators involved in the post-translational modification of histone and non-histone. These enzymes are responsible for the epigenetic control of cellular functions. However, deregulation of the activity of these enzymes results in uncontrolled disorders such as cancer and inflammatory and neurological diseases. The study includes histone acetyltransferases, deacetylases, methyl transferases, demethylases, DNA methyl transferases, and their potent inhibitors which are in a clinical trial and used as medicinal drugs. The present review covers the heterocycles as target-specific inhibitors of histone-modifying enzyme, more specifically histone acetyltransferases. This review also confers more recent reports on heterocycles as potential HAT inhibitors covered from 2016-2022 and future perspectives of these heterocycles in epigenetic therapy.
Collapse
Affiliation(s)
- N Jeelan Basha
- Department of Chemistry, Indian Academy Degree College-Autonomous, Bengaluru, Karnataka, India
| | - S M Basavarajaiah
- P.G. Department of Chemistry, Vijaya College, Bengaluru, Karnataka, India
| |
Collapse
|
50
|
Lin XH, Zhang DY, Liu ZY, Tang WQ, Chen RX, Li DP, Weng S, Dong L. lncRNA-AC079061.1/VIPR1 axis may suppress the development of hepatocellular carcinoma: a bioinformatics analysis and experimental validation. Lab Invest 2022; 20:379. [PMID: 36038907 PMCID: PMC9422102 DOI: 10.1186/s12967-022-03573-7] [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: 03/15/2022] [Accepted: 08/04/2022] [Indexed: 11/12/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most malignant tumors to threaten human life, and the survival rate remains low due to delayed diagnosis. Meanwhile, lncRNAs have great potential for application in tumor prognosis, therefore relevant research in hepatocellular carcinoma is indispensable. Methods Based on the EZH2 expression, the differentially expressed lncRNAs DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) were identified in hepatocellular carcinoma by using the TCGA database. Bioinformatics technology was utilized to determine the effect of key genes in HCC progression. The methylation and immune infiltration analyses were performed to explore the underlying function of hub genes. Finally, cellular function experiments were performed to investigate the association between identified genes and biological phenotypes in HCC. Results lncRNA-AC079061.1, hsa-miR-765, and VIPR1 were identified as independent factors that affect the prognosis of hepatocellular carcinoma. The immune infiltration analyses revealed that lncRNA-AC079061.1 can alter the immune microenvironment and thus inhibit the development of HCC by regulating the expression of an immune-related gene (VIPR1). Methylation analyses demonstrated that VIPR1 expression is negatively related to the methylation level in HCC. Experimental results suggested that lncRNA-AC079061.1 and VIPR1 were frequently downregulated in HCC cells, while hsa-miR-765 was significantly upregulated. Moreover, the lncRNA-AC079061.1/VIPR1 axis suppressed the proliferation and invasion of HCC cells. Conclusion The present study identified the lncRNA-AC079061.1/VIPR1 axis as a novel biomarker that inhibited the proliferation and invasion of hepatocellular carcinoma, affecting the ultimate disease outcome. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03573-7.
Collapse
Affiliation(s)
- Xia-Hui Lin
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Shanghai Institute of Liver Disease, Shanghai, 200032, China
| | - Dan-Ying Zhang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Shanghai Institute of Liver Disease, Shanghai, 200032, China
| | - Zhi-Yong Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Shanghai Institute of Liver Disease, Shanghai, 200032, China
| | - Wen-Qing Tang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Shanghai Institute of Liver Disease, Shanghai, 200032, China
| | - Rong-Xin Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Dong-Ping Li
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Shanghai Institute of Liver Disease, Shanghai, 200032, China
| | - Shuqiang Weng
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Shanghai Institute of Liver Disease, Shanghai, 200032, China.
| | - Ling Dong
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Shanghai Institute of Liver Disease, Shanghai, 200032, China.
| |
Collapse
|