1
|
Epigenetic mechanisms underlying subtype heterogeneity and tumor recurrence in prostate cancer. Nat Commun 2023; 14:567. [PMID: 36732329 PMCID: PMC9895058 DOI: 10.1038/s41467-023-36253-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
|
2
|
Epigenetic reprogramming during prostate cancer progression: A perspective from development. Semin Cancer Biol 2021; 83:136-151. [PMID: 33545340 DOI: 10.1016/j.semcancer.2021.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022]
Abstract
Conrad Waddington's theory of epigenetic landscape epitomize the process of cell fate and cellular decision-making during development. Wherein the epigenetic code maintains patterns of gene expression in pluripotent and differentiated cellular states during embryonic development and differentiation. Over the years disruption or reprogramming of the epigenetic landscape has been extensively studied in the course of cancer progression. Cellular dedifferentiation being a key hallmark of cancer allow us to take cues from the biological processes involved during development. Here, we discuss the role of epigenetic landscape and its modifiers in cell-fate determination, differentiation and prostate cancer progression. Lately, the emergence of RNA-modifications has also furthered our understanding of epigenetics in cancer. The overview of the epigenetic code regulating androgen signalling, and progression to aggressive neuroendocrine stage of PCa reinforces its gene regulatory functions during the development of prostate gland as well as cancer progression. Additionally, we also highlight the clinical implications of cancer cell epigenome, and discuss the recent advancements in the therapeutic strategies targeting the advanced stage disease.
Collapse
|
3
|
Hudlikar R, Wang L, Wu R, Li S, Peter R, Shannar A, Chou PJ, Liu X, Liu Z, Kuo HCD, Kong AN. Epigenetics/Epigenomics and Prevention of Early Stages of Cancer by Isothiocyanates. Cancer Prev Res (Phila) 2020; 14:151-164. [PMID: 33055265 DOI: 10.1158/1940-6207.capr-20-0217] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/26/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022]
Abstract
Cancer is a complex disease and cancer development takes 10-50 years involving epigenetics. Evidence suggests that approximately 80% of human cancers are linked to environmental factors impinging upon genetics/epigenetics. Because advanced metastasized cancers are resistant to radiotherapy/chemotherapeutic drugs, cancer prevention by relatively nontoxic chemopreventive "epigenetic modifiers" involving epigenetics/epigenomics is logical. Isothiocyanates are relatively nontoxic at low nutritional and even higher pharmacologic doses, with good oral bioavailability, potent antioxidative stress/antiinflammatory activities, possess epigenetic-modifying properties, great anticancer efficacy in many in vitro cell culture and in vivo animal models. This review summarizes the latest advances on the role of epigenetics/epigenomics by isothiocyanates in prevention of skin, colon, lung, breast, and prostate cancers. The exact molecular mechanism how isothiocyanates modify the epigenetic/epigenomic machinery is unclear. We postulate "redox" processes would play important roles. In addition, isothiocyanates sulforaphane and phenethyl isothiocyanate, possess multifaceted molecular mechanisms would be considered as "general" cancer preventive agents not unlike chemotherapeutic agents like platinum-based or taxane-based drugs. Analogous to chemotherapeutic agents, the isothiocyanates would need to be used in combination with other nontoxic chemopreventive phytochemicals or drugs such as NSAIDs, 5-α-reductase/aromatase inhibitors targeting different signaling pathways would be logical for the prevention of progression of tumors to late advanced metastatic states.
Collapse
Affiliation(s)
- Rasika Hudlikar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Lujing Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Shanyi Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Rebecca Peter
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Ahmad Shannar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Pochung Jordan Chou
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Xia Liu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Department of Pharmacology, School of Basic Medical Science, Lanzhou University, Lanzhou, China
| | - Zhigang Liu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Department of Food and Pharmaceutical Engineering, Guiyang University, Guiyang, China
| | - Hsiao-Chen Dina Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Graduate Program in Pharmaceutical Science, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
| |
Collapse
|
4
|
Screening and Identification of Key Biomarkers for Bladder Cancer: A Study Based on TCGA and GEO Data. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8283401. [PMID: 32047816 PMCID: PMC7003274 DOI: 10.1155/2020/8283401] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/18/2019] [Accepted: 12/26/2019] [Indexed: 12/22/2022]
Abstract
Bladder cancer (BLCA) is a common malignant cancer, and it is the most common genitourinary cancer in the world. The recurrence rate is the highest of all cancers, and the treatment of BLCA has only slightly improved over the past 30 years. Genetic and environmental factors play an important role in the development and progression of BLCA. However, the mechanism of cancer development remains to be proven. Therefore, the identification of potential oncogenes is urgent for developing new therapeutic directions and designing novel biomarkers for the diagnosis and prognosis of BLCA. Based on this need, we screened overlapping differentially expressed genes (DEG) from the GSE7476, GSE13507, and TCGA BLCA datasets. To identify the central genes from these DEGs, we performed a protein-protein interaction network analysis. To investigate the role of DEGs and the underlying mechanisms in BLCA, we performed Gene Ontology (GO) and Kyoto Gene and Genomic Encyclopedia (KEGG) analysis; we identified the hub genes via different evaluation methods in cytoHubba and then selected the target genes by performing survival analysis. Finally, the relationship between these target genes and tumour immunity was analysed to explore the roles of these genes. In summary, our current studies indicate that both cell division cycle 20 (CDC20) and abnormal spindle microtubule assembly (ASPM) genes are potential prognostic biomarkers for BLCA. It may also be a potential immunotherapeutic target with future clinical significance.
Collapse
|
5
|
Gao X, Zheng W, Ye L, Wen X, Wang S, Cao H, Liu X, Huang D, Wang F, Zhang S. Exploration of bladder cancer-associated methylated miRNAs by methylated DNA immunoprecipitation sequencing. Onco Targets Ther 2019; 12:6165-6174. [PMID: 31534349 PMCID: PMC6682176 DOI: 10.2147/ott.s192248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/20/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The current study aimed to explore the association between two epigenomic components, miRNA and DNA methylation, in bladder cancer (BC). METHODS Eight paired samples of tumor tissue and matched adjacent normal tissues from BC patients were subjected to methylated DNA immunoprecipitation sequencing and sRNA-Seq for differentially methylated miRNA genes and differential miRNA analysis. The miRNAs regulated by DNA methylation were screened and their functions involved in BC were analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) as well as a miRNA-mRNA interaction network. RESULTS The methylation levels of 212 genes were different between tumors and normal tissues with specific enrichment at transcription initiation and termination sites. Among these genes, 154 were hypermethylated and 58 were hypomethylated. GO and KEGG pathway enrichment analysis indicated that differentially methylated miRNA genes were mainly enriched in tumor-associated GO terms and signaling pathways. Pairwise statistical analysis of MeDIP-Seq and sRNA-Seq data showed that there are 154 and 165 candidate methylation-regulated genes in tumors and normal tissues, respectively. Notably, an interaction network indicated that the miRNAs regulated by methylation regulated a broad range of mRNAs associated with cancer development and progression. In particular, the most differentially expressed miRNAs were validated by qRT-PCR, such that miR-145-5p was downregulated and miR-182-5p was upregulated in patients with bladder cancer. CONCLUSION A large number of miRNA genes were modified by methylation in BC. Identification of changes in the expression of these miRNAs provides a great deal of important information for BC diagnosis.
Collapse
Affiliation(s)
- Xin Gao
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Wenwen Zheng
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou510655, Guangdong, People’s Republic of China
| | - Lili Ye
- Department of Clinical Laboratory, Jilin Provincial Tumor Hospital, Changchun130012, People’s Republic of China
| | - Xiaohong Wen
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Shunlan Wang
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Hui Cao
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Xi Liu
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Denggao Huang
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Fei Wang
- Department of Urology, People’s Hospital of Hainan Province, Haikou570311, Hainan, People’s Republic of China
| | - Shufang Zhang
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| |
Collapse
|
6
|
Zhang S, Cao H, Ye L, Wen X, Wang S, Zheng W, Zhang Y, Huang D, Gao Y, Liu H, He H, Gao X, Chen Y, Chen M, Xiang Y, Wang F. Cancer-associated methylated lncRNAs in patients with bladder cancer. Am J Transl Res 2019; 11:3790-3800. [PMID: 31312389 PMCID: PMC6614623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/11/2019] [Indexed: 06/10/2023]
Abstract
Epigenetic modifications via DNA methylation and long non-coding RNAs (lncRNAs) have been identified in bladder cancer (BC). However, DNA methylation of lncRNAs involved in BC has not been elucidated. Here, DNA immunoprecipitation-sequencing (MeDIP-seq) and RNA-sequencing (RNA-seq) were carried out using eight paired tumor and adjacent normal tissue samples from patients with BC. Differences in methylation patterns between tumors and controls were compared and the percentage of differentially methylated genes, including lncRNA genes, was calculated. RNA-seq data were subjected to gene ontology (GO), Kyoto encyclopedia of genes, and genomes (KEGG) analysis. The association between DNA methylation modification and lncRNA expression was determined by pairwise analysis of MeDIP-seq and RNA-seq data. The most enriched motifs in the promoter region, as well as the methylated density in the 3 kb region surrounding super-enhancers of lncRNA genes, were analyzed. A peak of 5mC methylation in the region 2 kb upstream of the transcription start site (TSS), with the lowest point in the TSS region, was observed. In total, 436 and 239 genes were identified to be hyper and hypomethylated, respectively, in BC tissue around the TSS region. RNA-seq revealed differentially expressed lncRNAs between tumor and normal tissues, many of which were cancer-associated lncRNAs based on GO and KEGG pathway analysis. Combined MeDIP-seq and RNA-seq analysis revealed that expression of 26 lncRNAs were candidates of 5mC controlled genes. The possible link between 5mC modification and differential lncRNAs may relate to enrichment of 5mC reads in the region surrounding super-enhancers of lncRNA. Survival analysis indicated that the methylated lncRNA, LINC00574, was associated with shorter overall survival time in patients with BC (HR = 1.7, p-value = 0.035). Taken together, these findings indicate that lncRNAs genes are under control of DNA methylation. Methylated lncRNA genes, which are transcripted to LINC00574, may serve as biomarkers for BC prognosis.
Collapse
Affiliation(s)
- Shufang Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Hui Cao
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Lili Ye
- Clincal Laboratory, Jilin Cancer HospitalChangchun 130021, Jilin, China
| | - Xiaohong Wen
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Shunlan Wang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Wenwen Zheng
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-Sen UniversityGuangzhou 510655, Guangdong, China
| | - Yingai Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Denggao Huang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Yuanhui Gao
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Haifang Liu
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Haowei He
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Xin Gao
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Yinyi Chen
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Mei Chen
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Yang Xiang
- Department of Urology, Affiliated Haikou Hospital of Xiangya Medical College, Central South UniversityHaikou 570208, Hainan, China
| | - Fei Wang
- Department of Urology, People’s Hospital of Hainan ProvinceHaikou 570311, Hainan, China
| |
Collapse
|
7
|
Verma S, Shukla S, Pandey M, MacLennan GT, Gupta S. Differentially Expressed Genes and Molecular Pathways in an Autochthonous Mouse Prostate Cancer Model. Front Genet 2019; 10:235. [PMID: 30972102 PMCID: PMC6445055 DOI: 10.3389/fgene.2019.00235] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/04/2019] [Indexed: 12/17/2022] Open
Abstract
Prostate cancer remains a major public health problem and the second leading cause of cancer-related deaths in men in the United States. The present study aims to understand the molecular pathway(s) of prostate cancer which is essential for early detection and treatment. Dorsolateral prostate from 20 week transgenic adenocarcinoma of the mouse prostate (TRAMP) mice, which spontaneously develops prostate cancer and recapitulates human disease and age-matched non-transgenic littermates were utilized for microarray analysis. Mouse genome network and pathway analyses were mapped to the human genome using the Ingenuity Pathway Analysis (IPA) database for annotation, visualization, and integrated discovery. In total, 136 differentially expressed genes, including 32 downregulated genes and 104 upregulated genes were identified in the dorsolateral prostate of TRAMP, compared to non-transgenic mice. A subset of differentially expressed genes were validated by qRT-PCR. Alignment with human genome database identified 18 different classes of proteins, among these, 36% were connected to the nucleic acid binding, including ribosomal proteins, which play important role in protein synthesis—the most enriched pathway in the development of prostate cancer. Furthermore, the results suggest deregulation of signaling molecules (9%) and enzyme modulators (8%) affect various pathways. An imbalance in other protein classes, including transporter proteins (7%), hydrolases (6%), oxidoreductases, and cytoskeleton proteins (5%), contribute to cancer progression. Our study evaluated the underlying pathways and its connection to human prostate cancer, which may further help assess the risk of disease development and progression and identify potential targets for therapeutic intervention.
Collapse
Affiliation(s)
- Shiv Verma
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Sanjeev Shukla
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Mitali Pandey
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Vancouver Prostate Center, Vancouver, BC, Canada
| | - Gregory T MacLennan
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Sanjay Gupta
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Department of Nutrition, Case Western Reserve University, Cleveland, OH, United States.,Department of Urology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, United States.,Division of General Medical Sciences, Case Comprehensive Cancer Center, Cleveland, OH, United States
| |
Collapse
|