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Zhao B, Wang J, Sheng G, Wang Y, Yang T, Meng K. Identifying a Risk Signature of Methylation-Driven Genes as a Predictor of Survival Outcome for Colon Cancer Patients. Appl Biochem Biotechnol 2024; 196:4156-4165. [PMID: 37906409 DOI: 10.1007/s12010-023-04751-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2023] [Indexed: 11/02/2023]
Abstract
Aberrant expression of gene is driven by its promoter methylation and is the key molecular basis of carcinogenic processes. This study aimed at identifying a risk signature of methylation-driven (MD) genes and evaluating its prognostic value for colon cancer (CC) patients. The expression profiles of methylation and mRNA in CC samples were obtained from the TCGA database, and the MethylMix algorithm was used to identify MD genes. The relationships between their expression levels and overall survival (OS) of CC patients were analyzed, and a prognostic signature of MD genes was established. The risk score of gene signature was calculated, and the median was used to divide all patients into high (H) and low (L) risk groups. The prognostic value of gene signature was tested by the TCGA cohort and an independent validation cohort (GSE17538 dataset). In total, 69 MD genes were identified, and 7 were associated with OS of CC patients. Ultimately, 4 (TWIST1, LDOC1, EPHX3, and STC2) were screened out to establish a risk signature. The H-risk patients (>0.923) had a worse OS than L-risk patients (≤0.923) in both the TCGA (5-year cumulative survival: 52.9% vs 72.0%, P=0.005) and GSE17538 cohort (49.4% vs 69.3%, P=0.004). The AUC values of MD genes signature for the prediction of 3- and 5-year OS were 0.648 and 0.643 in the TCGA dataset and 0.634 and 0.624 in the GSE17538 dataset, respectively. The risk signature of four MD genes was identified as an independent predictor of OS for CC patients (HR for TCGA dataset: 2.071, 95% CI=1.196-3.586, P=0.009; HR for GSE17538 dataset: 2.021, 95% CI=1.290-3.166, P=0.002). The risk signature of four MD genes might be a useful prognostic tool and help doctors improve the clinical management of CC patients.
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Affiliation(s)
- Bochao Zhao
- Department of Gastrointestinal Surgery, Tianjin First Central Hospital, No.24 Fukang Road, Nankai District, Tianjin, 300190, People's Republic of China.
| | - Jingchao Wang
- Department of Gastrointestinal Surgery, Tianjin First Central Hospital, No.24 Fukang Road, Nankai District, Tianjin, 300190, People's Republic of China
| | - Guannan Sheng
- Department of Gastrointestinal Surgery, Tianjin First Central Hospital, No.24 Fukang Road, Nankai District, Tianjin, 300190, People's Republic of China
| | - Yiming Wang
- Department of Gastrointestinal Surgery, Tianjin First Central Hospital, No.24 Fukang Road, Nankai District, Tianjin, 300190, People's Republic of China
| | - Tao Yang
- Department of Gastrointestinal Surgery, Tianjin First Central Hospital, No.24 Fukang Road, Nankai District, Tianjin, 300190, People's Republic of China
| | - Kewei Meng
- Department of Gastrointestinal Surgery, Tianjin First Central Hospital, No.24 Fukang Road, Nankai District, Tianjin, 300190, People's Republic of China.
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Jevšinek Skok D, Hauptman N. In Silico Gene Prioritization Highlights the Significance of Bone Morphogenetic Protein 4 ( BMP4) Promoter Methylation across All Methylation Clusters in Colorectal Cancer. Int J Mol Sci 2023; 24:12692. [PMID: 37628872 PMCID: PMC10454928 DOI: 10.3390/ijms241612692] [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: 07/15/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The cytosine-phosphate-guanine (CpG) island methylator phenotype (CIMP) represents one of the pathways involved in the development of colorectal cancer, characterized by genome-wide hypermethylation. To identify samples exhibiting hypermethylation, we used unsupervised hierarchical clustering on genome-wide methylation data. This clustering analysis revealed the presence of four distinct subtypes within the tumor samples, namely, CIMP-H, CIMP-L, cluster 3, and cluster 4. These subtypes demonstrated varying levels of methylation, categorized as high, intermediate, and very low. To gain further insights, we mapped significant probes from all clusters to Ensembl Regulatory build 89, with a specific focus on those located within promoter regions or bound regions. By intersecting the methylated promoter and bound regions across all methylation subtypes, we identified a total of 253 genes exhibiting aberrant methylation patterns in the promoter regions across all four subtypes of colorectal cancer. Among these genes, our comprehensive genome-wide analysis highlights bone morphogenic protein 4 (BMP4) as the most prominent candidate. This significant finding was derived through the utilization of various bioinformatics tools, emphasizing the potential role of BMP4 in colorectal cancer development and progression.
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Affiliation(s)
- Daša Jevšinek Skok
- Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia;
| | - Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000 Ljubljana, Slovenia
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Li M, Zhu C, Xue Y, Miao C, He R, Li W, Zhang B, Yu W, Huang X, Lv M, Xu Y, Huang Q. A DNA methylation signature for the prediction of tumour recurrence in stage II colorectal cancer. Br J Cancer 2023; 128:1681-1689. [PMID: 36828869 PMCID: PMC10133253 DOI: 10.1038/s41416-023-02155-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND A major challenge in stage II colorectal carcinoma is to identify patients with increased risk of recurrence. Biomarkers that distinguish patients with poor prognosis from patients without recurrence are currently lacking. This study aims to develop a robust DNA methylation classifier that allows the prediction of recurrence and chemotherapy benefit in patients with stage II colorectal cancer. We performed a genome-wide DNA methylation capture sequencing in 243 stage II colorectal carcinoma samples and identified a relapse-specific DNA methylation signature consisting of eight CpG sites. METHODS Two hundred and forty-three patients with stage II CRC were enrolled in this study. In order to select differential methylation sites among recurrence and non-recurrence stage II CRC samples, DNA methylation profiles of 62 tumour samples including 31 recurrence and 31 nonrecurrence samples were analysed using the Agilent SureSelectXT Human Methyl-Seq, a comprehensive target enrichment system to analyse CpG methylation. Pyrosequencing was applied to quantify the methylation level of candidate DNA methylation sites in 243 patients. Least absolute shrinkage and selection operator (LASSO) method was employed to build the disease recurrence prediction classifier. RESULTS We identified a relapse-related DNA methylation signature consisting of eight CpG sites in stage II CRC by DNA methylation capture sequencing. The classifier showed significantly higher prognostic accuracy than any clinicopathological risk factors. The Kaplan-Meier survival curve showed an association of high-risk score with poor prognosis. In multivariate analysis, the signature was the most significant prognosis factor, with an HR of 2.80 (95% CI, 1.71-4.58, P < 0.001). The signature could identify patients who are suitable candidates for adjuvant chemotherapy. CONCLUSIONS An eight-CpG DNA methylation signature is a reliable prognostic and predictive tool for disease recurrence in patients with stage II CRC.
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Affiliation(s)
- Min Li
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Congcong Zhu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China
| | - Ying Xue
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Changhong Miao
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Ruiping He
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Baolong Zhang
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Minzhi Lv
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Department of Biostatistics, Clinical Research Unit, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China.
| | - Qihong Huang
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Shanghai Respiratory Research Institute, 180 Fenglin Road, 200032, Shanghai, P. R. China.
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Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Chong ZX, Ho WY, Yeap SK. Delineating the tumour-regulatory roles of EYA4. Biochem Pharmacol 2023; 210:115466. [PMID: 36849065 DOI: 10.1016/j.bcp.2023.115466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
Eyes absent homolog 4 (EYA4) is a protein that regulates many vital cellular processes and organogenesis pathways. It possesses phosphatase, hydrolase, and transcriptional activation functions. Mutations in the Eya4 gene can cause sensorineural hearing loss and heart disease. In most non-nervous system cancers such as those of the gastrointestinal tract (GIT), hematological and respiratory systems, EYA4 acts as a putative tumor suppressor. However, in nervous system tumors such as glioma, astrocytoma, and malignant peripheral nerve sheath tumor (MPNST), it plays a putative tumor-promoting role. EYA4 interacts with various signaling proteins of the PI3K/AKT, JNK/cJUN, Wnt/GSK-3β, and cell cycle pathways to exert its tumor-promoting or tumor-suppressing effect. The tissue expression level and methylation profiles of Eya4 can help predict the prognosis and anti-cancer treatment response among cancer patients. Targeting and altering Eya4 expression and activity could be a potential therapeutic strategy to suppress carcinogenesis. In conclusion, EYA4 may have both putative tumor-promoting and tumor-suppressing roles in different human cancers and has the potential to serve as a prognostic biomarker and therapeutic agent in various cancer types.
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Affiliation(s)
- Zhi Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Wan Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia.
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6
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Shen Y, Wang D, Yuan T, Fang H, Zhu C, Qin J, Xu X, Zhang C, Liu J, Zhang Y, Wen Z, Tang J, Wang Z. Novel DNA methylation biomarkers in stool and blood for early detection of colorectal cancer and precancerous lesions. Clin Epigenetics 2023; 15:26. [PMID: 36803423 PMCID: PMC9938553 DOI: 10.1186/s13148-023-01443-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Early detection and prevention of precancerous lesions can significantly reduce the morbidity and mortality of colorectal cancer (CRC). Here, we developed new candidate CpG site biomarkers for CRC and evaluated the diagnostic value of their expression in blood and stool samples of CRC and precancerous lesions. METHODS We analyzed 76 pairs of CRC and adjacent normal tissue samples, 348 stool samples, and 136 blood samples. Candidate biomarkers for CRC were screened using a bioinformatics database and identified using a quantitative methylation-specific PCR method. The methylation levels of the candidate biomarkers were validated using blood and stool samples. The divided stool samples were used to construct and validate a combined diagnostic model and to analyze the independent or combined diagnostic value of candidate biomarkers in stool samples of CRC and precancerous lesions. RESULTS Two candidate CpG site biomarkers for CRC, cg13096260 and cg12993163, were identified. Although both biomarkers demonstrated diagnostic performance to a certain extent when using blood samples, they showed better diagnostic value for different stages of CRC and AA with stool samples. CONCLUSIONS cg13096260 and cg12993163 detection in stool samples could be a promising approach for screening and early diagnosis of CRC and precancerous lesions.
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Affiliation(s)
- Yuguang Shen
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongyang Wang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianli Yuan
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongsheng Fang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Zhu
- Shanghai Biotechnology Corporation, Shanghai, China
| | - Juan Qin
- Shanghai Biotechnology Corporation, Shanghai, China
| | - Xiaojing Xu
- Shanghai Biotechnology Corporation, Shanghai, China
| | - Cheng Zhang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiahua Liu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanruohan Zhang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhoujin Wen
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Tang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Lin R, Qian Y, Zhang J, Xia D, Guo D, Hong L, Qing B, Xu M, Huang Y, Lin W, Chen G, Liu S. Genome-wide DNA methylation profiling of gastric cardia cancer. J Gastroenterol Hepatol 2023; 38:290-300. [PMID: 36342849 DOI: 10.1111/jgh.16054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND AND AIM Aberrant DNA methylation has been found in various cancer types including gastric cancer, yet the genome-wide DNA methylation profile of gastric cardia cancer (GCC) remains unclear. Therefore, we aimed to profile the DNA methylation pattern of GCC and identify promising diagnostic epigenetic biomarkers. METHODS We investigated the genome-wide DNA methylation pattern in eight pairs of GCC and adjacent normal tissues using Illumina 850K microarrays. Subsequently, bisulfite-pyrosequencing and quantitative real-time PCR were performed on eight pairs of GCC-adjacent normal tissues for validation. Finally, we performed immunohistochemistry to examine ADHFE1 expression on 126 pairs of GCC-adjacent normal samples. RESULTS DNA methylome analysis showed global hypomethylation and local hypermethylation of promoter cytosine-phosphate-guanine (CpG) islands (CGIs) in GCC tissues compared with gastric cardia normal mucosa (P < 2.2 × 10-16 ). Differential methylation analysis identified a total of 91 723 differentially-methylated probes (DMPs), and the candidate gene with the largest average DNA methylation difference mapped to ADHFE1 (mean Δβ = 0.53). Subsequently, three DMPs in the ADHFE1 promoter were validated by pyrosequencing. Notably, the mean methylation level of the three candidate DMPs (ADHFE1_cg08090772, ADHFE1_cg19283840, and ADHFE1_cg20295442) was negatively associated with ADHFE1 mRNA expression level (Spearman rho = -0.64, P = 0.01). Moreover, both mRNA (P = 0.0213) and protein (P < 0.0001) expression of ADHFE1 were significantly decreased in GCCs compared with the adjacent normal tissues. CONCLUSIONS Our results reveal DNA methylation aberrations in GCC and that ADHFE1 gene DNA methylation contributes to the risk of GCC, thus providing novel mechanistic insights into gastric cardia cancer carcinogenesis.
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Affiliation(s)
- Runhua Lin
- Department of Pathology, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Yanli Qian
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Jinhai Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Di Xia
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Dongming Guo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Liangli Hong
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Bojuan Qing
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Muming Xu
- Department of Abdominal Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Yiteng Huang
- Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Wenting Lin
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Guangcan Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Shuhui Liu
- Department of Pathology, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
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Zhou L, Pan LZ, Fan YJ. DNMT3b affects colorectal cancer development by regulating FLI1 through DNA hypermethylation. Kaohsiung J Med Sci 2023; 39:364-376. [PMID: 36655868 DOI: 10.1002/kjm2.12647] [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: 07/11/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 01/20/2023] Open
Abstract
Friend leukemia integration 1 (FLI1) is an ETS transcription factor family member. Here, we identified cg11017065 as the most hyper-methylated cytosine and guanine (CpG) in colorectal cancer (CRC), which belongs to the FLI1 gene. Moreover, integrated bioinformatics prediction and analysis of our cohort showed that FLI1 expression was downregulated and DNA methylation was elevated in CRC. Bioinformatics prediction also indicated that patients overexpressing FLI1 had higher survival rates than those with low FLI1 expression. CRC cells with ectopic expression of FLI1 had reduced invasion, migration, cloning ability and increased apoptosis. Furthermore, DNA-methyltransferase 3b (DNMT3b) was found to be significantly overexpressed in CRC, and low DNMT3b expression predicted a prolonged survival. DNMT3b bound to the FLI1 promoter. Inhibition of DNMT3b increased FLI1 expression and inhibited the malignant phenotype of CRC cells. Inhibition of FLI1 reversed the phenotypic modulation by DNMT3b depletion in vitro and in vivo. In conclusion, our data indicate that DNMT3b potentiates CRC cell proliferation, migration, and invasion through downregulating FLI1.
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Affiliation(s)
- Lei Zhou
- Department of Gastroenterology, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou, Jiangsu, People's Republic of China
| | - Li-Zhen Pan
- Department of Gastroenterology, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou, Jiangsu, People's Republic of China
| | - Yue-Juan Fan
- Department of Gastroenterology, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou, Jiangsu, People's Republic of China
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Huang H, Cao W, Long Z, Kuang L, Li X, Feng Y, Wu Y, Zhao Y, Chen Y, Sun P, Peng P, Zhang J, Yuan L, Li T, Hu H, Li G, Yang L, Zhang X, Hu F, Sun X, Hu D. DNA methylation-based patterns for early diagnostic prediction and prognostic evaluation in colorectal cancer patients with high tumor mutation burden. Front Oncol 2023; 12:1030335. [PMID: 36713578 PMCID: PMC9880489 DOI: 10.3389/fonc.2022.1030335] [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: 08/28/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Background Immune checkpoint inhibitor (ICI) therapy has proven to be a promising treatment for colorectal cancer (CRC). We aim to investigate the relationship between DNA methylation and tumor mutation burden (TMB) by integrating genomic and epigenetic profiles to precisely identify clinical benefit populations and to evaluate the effect of ICI therapy. Methods A total of 536 CRC tissues from the Cancer Genome Atlas (TCGA) with mutation data were collected and subjected to calculate TMB. 80 CRC patients with high TMB and paired normal tissues were selected as training sets and developed the diagnostic and prognostic methylation models, respectively. In the validation set, the diagnostic model was validated in our in-house 47 CRC tissues and 122 CRC tissues from the Gene Expression Omnibus (GEO) datasets, respectively. And a total of 38 CRC tissues with high TMB from the COLONOMICS dataset verified the prognostic model. Results A positive correlation between differential methylation positions and TMB level was observed in TCGA CRC cohort (r=0.45). The diagnostic score that consisted of methylation levels of four genes (ADHFE1, DOK6, GPR75, and MAP3K14-AS1) showed high diagnostic performance in the discovery (AUC=1.000) and two independent validation (AUC=0.946, AUC=0.857) datasets. Additionally, these four genes showed significant positive correlations with NK cells. The prognostic score containing three genes (POU3F3, SYN2, and TMEM178A) had significantly poorer survival in the high-risk TMB samples than those in the low-risk TMB samples (P=0.016). CRC patients with low-risk scores combined with TMB levels represent a favorable survival. Conclusions By integrating analyses of methylation and mutation data, it is suggested that DNA methylation patterns combined with TMB serve as a novel potential biomarker for early screening in more high-TMB populations and for evaluating the prognostic effect of CRC patients with ICI therapy.
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Affiliation(s)
- Hao Huang
- Department of General Practice, The Affiliated Luohu Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Weifan Cao
- Department of General Practice, The Affiliated Luohu Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Zhiping Long
- Department of Epidemiology, Public Health School of Harbin Medical University, Harbin, China
| | - Lei Kuang
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Xi Li
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yifei Feng
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yuying Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yang Zhao
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yinggang Chen
- Department of Gastrointestinal Surgery, Shenzhen Hospital, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Peng Sun
- Department of Gastrointestinal Surgery, Shenzhen Hospital, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Panxin Peng
- Department of Gastrointestinal Surgery, Shenzhen Hospital, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Jinli Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Lijun Yuan
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Tianze Li
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Huifang Hu
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Gairui Li
- Department of Chronic Disease Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Longkun Yang
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Xing Zhang
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Fulan Hu
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China,*Correspondence: Dongsheng Hu, ; Xizhuo Sun, ; Fulan Hu,
| | - Xizhuo Sun
- Department of General Practice, The Affiliated Luohu Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, China,*Correspondence: Dongsheng Hu, ; Xizhuo Sun, ; Fulan Hu,
| | - Dongsheng Hu
- Department of General Practice, The Affiliated Luohu Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, China,Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China,*Correspondence: Dongsheng Hu, ; Xizhuo Sun, ; Fulan Hu,
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10
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Jacksi M, Schad E, Buday L, Tantos A. Absence of Scaffold Protein Tks4 Disrupts Several Signaling Pathways in Colon Cancer Cells. Int J Mol Sci 2023; 24:ijms24021310. [PMID: 36674824 PMCID: PMC9861885 DOI: 10.3390/ijms24021310] [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: 12/03/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Tks4 is a large scaffold protein in the EGFR signal transduction pathway that is involved in several cellular processes, such as cellular motility, reactive oxygen species-dependent processes, and embryonic development. It is also implicated in a rare developmental disorder, Frank-ter Haar syndrome. Loss of Tks4 resulted in the induction of an EMT-like process, with increased motility and overexpression of EMT markers in colorectal carcinoma cells. In this work, we explored the broader effects of deletion of Tks4 on the gene expression pattern of HCT116 colorectal carcinoma cells by transcriptome sequencing of wild-type and Tks4 knockout (KO) cells. We identified several protein coding genes with altered mRNA levels in the Tks4 KO cell line, as well as a set of long non-coding RNAs, and confirmed these changes with quantitative PCR on a selected set of genes. Our results show a significant perturbation of gene expression upon the deletion of Tks4, suggesting the involvement of different signal transduction pathways over the well-known EGFR signaling.
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Affiliation(s)
- Mevan Jacksi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Department of Molecular Biology, Semmelweis University Medical School, 1094 Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence:
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11
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Li W, Ling L, Xiang L, Ding P, Yue W. Identification and validation of a risk model and molecular subtypes based on tryptophan metabolism-related genes to predict the clinical prognosis and tumor immune microenvironment in lower-grade glioma. Front Cell Neurosci 2023; 17:1146686. [PMID: 36925967 PMCID: PMC10011102 DOI: 10.3389/fncel.2023.1146686] [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: 01/17/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
Background Lower-grade glioma (LGG) is one of the most common malignant tumors in the central nervous system (CNS). Accumulating evidence have demonstrated that tryptophan metabolism is significant in tumor. Therefore, this study aims to comprehensively clarify the relationship between tryptophan metabolism-related genes (TRGs) and LGGs. Methods The expression level of TRGs in LGG and normal tissues was first analyzed. Next, the key TRGs with prognostic value and differential expression in LGGs were identified using the least absolute shrinkage and selection operator (LASSO) regression analysis. Subsequently, a risk model was constructed and Consensus clustering analysis was conducted based on the expression level of key TRGs. Then, the prognostic value, clinicopathological factors, and tumor immune microenvironment (TIME) characteristics between different risk groups and molecular subtypes were analyzed. Finally, the expression, prognosis, and TIME of each key TRGs were analyzed separately in LGG patients. Results A total of 510 patients with LGG from The Cancer Genome Atlas (TCGA) dataset and 1,152 normal tissues from the Genotype-Tissue Expression (GTEx) dataset were included to evaluate the expression level of TRGs. After LASSO regression analysis, we identified six key TRGs and constructed a TRGs risk model. The survival analysis revealed that the risk model was the independent predictor in LGG patients. And the nomogram containing risk scores and independent clinicopathological factors could accurately predict the prognosis of LGG patients. In addition, the results of the Consensus cluster analysis based on the expression of the six TRGs showed that it could classify the LGG patients into two distinct clusters, with significant differences in prognosis, clinicopathological factors and TIME between these two clusters. Finally, we validated the expression, prognosis and immune infiltration of six key TRGs in patients with LGG. Conclusion This study demonstrated that tryptophan metabolism plays an important role in the progression of LGG. In addition, the risk model and the molecular subtypes we constructed not only could be used as an indicator to predict the prognosis of LGG patients but also were closely related to the clinicopathological factors and TIME of LGG patients. Overall, our study provides theoretical support for the ultimate realization of precision treatment for patients with LGG.
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Affiliation(s)
- Wenxia Li
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China
| | - Ling Ling
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Lei Xiang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Peng Ding
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China
| | - Wei Yue
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China.,Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
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12
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Zhan L, Sun C, Zhang Y, Zhang Y, Jia Y, Wang X, Li F, Li D, Wang S, Yu T, Zhang J, Li D. Four methylation-driven genes detected by linear discriminant analysis model from early-stage colorectal cancer and their methylation levels in cell-free DNA. Front Oncol 2022; 12:949244. [PMID: 36158666 PMCID: PMC9491101 DOI: 10.3389/fonc.2022.949244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022] Open
Abstract
The process of colorectal cancer (CRC) formation is considered a typical model of multistage carcinogenesis in which aberrant DNA methylation plays an important role. In this study, 752 methylation-driven genes (MDGs) were identified by the MethylMix package based on methylation and gene expression data of CRC in The Cancer Genome Atlas (TCGA). Iterative recursive feature elimination (iRFE) based on linear discriminant analysis (LDA) was used to determine the minimum MDGs (iRFE MDGs), which could distinguish between cancer and cancer-adjacent tissues. Further analysis indicated that the changes in methylation levels of the four iRFE MDGs, ADHFE1-Cluster1, CNRIP1-Cluster1, MAFB, and TNS4, occurred in adenoma tissues, while changes did not occur until stage IV in cell-free DNA. Furthermore, the methylation levels of iRFE MDGs were correlated with the genes involved in the reprogramming process of somatic cells to pluripotent stem cells, which is considered the common signature of cancer cells and embryonic stem cells. The above results indicated that the four iRFE MDGs may play roles in the early stage of colorectal carcinogenesis and highlighted the complicated relationship between tissue DNA and cell-free DNA (cfDNA).
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Affiliation(s)
- Lei Zhan
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Changjian Sun
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Yu Zhang
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Yue Zhang
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Yuzhe Jia
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Xiaoyan Wang
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Feifei Li
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Donglin Li
- Orthopedics Department, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Shen Wang
- Department of Ultrasound and Special Diagnosis, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Tao Yu
- Nursing Department, Air Force Medical Center, PLA, Beijing, China
| | - Jingdong Zhang
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Deyang Li
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
- *Correspondence: Deyang Li,
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13
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Wang S, Xu D, Gao B, Yan S, Sun Y, Tang X, Jiao Y, Huang S, Zhang S. Heterogeneity Analysis of Bladder Cancer Based on DNA Methylation Molecular Profiling. Front Oncol 2022; 12:915542. [PMID: 35747826 PMCID: PMC9209659 DOI: 10.3389/fonc.2022.915542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Bladder cancer is a highly complex and heterogeneous malignancy. Tumor heterogeneity is a barrier to effective diagnosis and treatment of bladder cancer. Human carcinogenesis is closely related to abnormal gene expression, and DNA methylation is an important regulatory factor of gene expression. Therefore, it is of great significance for bladder cancer research to characterize tumor heterogeneity by integrating genetic and epigenetic characteristics. This study explored specific molecular subtypes based on DNA methylation status and identified subtype-specific characteristics using patient samples from the TCGA database with DNA methylation and gene expression were measured simultaneously. The results were validated using an independent cohort from GEO database. Four DNA methylation molecular subtypes of bladder cancer were obtained with different prognostic states. In addition, subtype-specific DNA methylation markers were identified using an information entropy-based algorithm to represent the unique molecular characteristics of the subtype and verified in the test set. The results of this study can provide an important reference for clinicians to make treatment decisions.
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Affiliation(s)
- Shuyu Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Dali Xu
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Bo Gao
- Department of Radiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuhan Yan
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yiwei Sun
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Xinxing Tang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yanjia Jiao
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Shan Huang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Shumei Zhang, ; Shan Huang,
| | - Shumei Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
- *Correspondence: Shumei Zhang, ; Shan Huang,
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14
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Yang M, Sun M, Zhang H. The Interaction Between Epigenetic Changes, EMT, and Exosomes in Predicting Metastasis of Colorectal Cancers (CRC). Front Oncol 2022; 12:879848. [PMID: 35712512 PMCID: PMC9197117 DOI: 10.3389/fonc.2022.879848] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/01/2022] [Indexed: 12/12/2022] Open
Abstract
Worldwide, colorectal cancer (CRC) ranks as the third most common malignancy, and the second most deadly with nearly one million attributable deaths in 2020. Metastatic disease is present in nearly 25% of newly diagnosed CRC, and despite advances in chemotherapy, less than 20% will remain alive at 5 years. Epigenetic change plays a key role in the epithelial-to-mesenchymal transition (EMT), which is a crucial phenotype for metastasis and mainly includes DNA methylation, non-coding RNAs (ncRNAs), and N6-methyladenosine (m6A) RNA, seemingly valuable biomarkers in CRCs. For ncRNAs, there exists a “molecular sponge effect” between long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs). The detection of exosomes is a novel method in CRC monitoring, especially for predicting metastasis. There is a close relationship between exosomes and EMT in CRCs. This review summarizes the close relationship between epigenetic changes and EMT in CRCs and emphasizes the crucial function of exosomes in regulating the EMT process.
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15
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Liu W, Jiang H, Li Y. Silencing circular RNA-friend leukemia virus integration 1 restrained malignancy of CC cells and oxaliplatin resistance by disturbing dyskeratosis congenita 1. Open Life Sci 2022; 17:563-576. [PMID: 35647294 PMCID: PMC9123302 DOI: 10.1515/biol-2022-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 12/16/2021] [Accepted: 01/03/2022] [Indexed: 11/15/2022] Open
Abstract
Circular-RNA friend leukemia virus integration 1 (circ-FLI1; hsa_circ_0000370) is a noninvasive biomarker for the diagnosis of colon carcinoma (CC). Herein, we intended to investigate its functions and competing endogenous RNA (ceRNA) mechanisms in CC cells. In terms of expression status, circ-FLI1 was abnormally upregulated in CC patients’ tumors and cells, paralleled with DKC1 upregulation and miR-197-3p downregulation. Most strikingly, there was a direct target relationship between miR-197-3p and circ-FLI1 or DKC1 based on the starbase database, dual-luciferase reporter assay, and RNA immunoprecipitation. Functionally, the colony formation assay, MTS method, fluorescence-activated cell sorting method, cell cycle and apoptosis assays, and transwell assays were performed, and the results revealed that interfering circ-FLI1 and re-expressing miR-197-3p could restrict colony formation, cell viability, cell cycle progression, and migration/invasion of CC cells with apoptosis rate elevation; besides, they promoted oxaliplatin (L-OHP)-induced cell viability inhibition. Furthermore, there were counteractive effects between circ-FLI1 silencing and miR-197-3p depletion, miR-197-3p overexpression and DKC1 restoration on regulating CC cell functions and L-OHP resistance. With a xenograft tumor model, the anti-growth role of circ-FLI1 silencing was also found in vivo with or without L-OHP treatment. Collectively, we demonstrated that circ-FLI1 might confer L-OHP resistance and malignant progression of CC presumably through the circ-FLI1/miR-197-3p/DKC1 ceRNA axis.
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Affiliation(s)
- Weipeng Liu
- Department of Gastrointestinal Surgery, The First College of Clinical Medical Science, China Three Gorges University , Phase 3, Jiangshan Duojiao, Wujiagang District , Yichang City , Hubei, 443000 , China
| | - Hong Jiang
- Department of Gastrointestinal Surgery, The First College of Clinical Medical Science, China Three Gorges University , Phase 3, Jiangshan Duojiao, Wujiagang District , Yichang City , Hubei, 443000 , China
| | - Yuanqiang Li
- Department of Gastrointestinal Surgery, The First College of Clinical Medical Science, China Three Gorges University , Phase 3, Jiangshan Duojiao, Wujiagang District , Yichang City , Hubei, 443000 , China
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16
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Functional diversity in the RAS subfamily of small GTPases. Biochem Soc Trans 2022; 50:921-933. [PMID: 35356965 DOI: 10.1042/bst20211166] [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: 01/28/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022]
Abstract
RAS small GTPases regulate important signalling pathways and are notorious drivers of cancer development and progression. While most research to date has focused on understanding and addressing the oncogenic potential of three RAS oncogenes: HRAS, KRAS, and NRAS; the full RAS subfamily is composed of 35 related GTPases with diverse cellular functions. Most remain deeply understudied despite strong evolutionary conservation. Here, we highlight a group of 17 poorly characterized RAS GTPases that are frequently down-regulated in cancer and evidence suggests may function not as oncogenes, but as tumour suppressors. These GTPases remain largely enigmatic in terms of their cellular function, regulation, and interaction with effector proteins. They cluster within two families we designate as 'distal-RAS' (D-RAS; comprised of DIRAS, RASD, and RASL10) and 'CaaX-Less RAS' (CL-RAS; comprised of RGK, NKIRAS, RERG, and RASL11/12 GTPases). Evidence of a tumour suppressive role for many of these GTPases supports the premise that RAS subfamily proteins may collectively regulate cellular proliferation.
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17
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HOXD8 hypermethylation as a fully sensitive and specific biomarker for biliary tract cancer detectable in tissue and bile samples. Br J Cancer 2022; 126:1783-1794. [PMID: 35177798 PMCID: PMC9174245 DOI: 10.1038/s41416-022-01738-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/21/2022] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Background Biliary tract cancers (BTC) are rare but highly aggressive tumours with poor prognosis, usually detected at advanced stages. Herein, we aimed at identifying BTC-specific DNA methylation alterations. Methods Study design included statistical power and sample size estimation. A genome-wide methylation study of an explorative cohort (50 BTC and ten matched non-tumoral tissue samples) has been performed. BTC-specific altered CpG islands were validated in over 180 samples (174 BTCs and 13 non-tumoral controls). The final biomarkers, selected by a machine-learning approach, were validated in independent tissue (18 BTCs, 14 matched non-tumoral samples) and bile (24 BTCs, five non-tumoral samples) replication series, using droplet digital PCR. Results We identified and successfully validated BTC-specific DNA methylation alterations in over 200 BTC samples. The two-biomarker panel, selected by an in-house algorithm, showed an AUC > 0.97. The best-performing biomarker (chr2:176993479-176995557), associated with HOXD8, a pivotal gene in cancer-related pathways, achieved 100% sensitivity and specificity in a new series of tissue and bile samples. Conclusions We identified a novel fully efficient BTC biomarker, associated with HOXD8 gene, detectable both in tissue and bile by a standardised assay ready-to-use in clinical trials also including samples from non-invasive matrices.
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Zhang S, Zhang J, Zhang Q, Liang Y, Du Y, Wang G. Identification of Prognostic Biomarkers for Bladder Cancer Based on DNA Methylation Profile. Front Cell Dev Biol 2022; 9:817086. [PMID: 35174173 PMCID: PMC8841402 DOI: 10.3389/fcell.2021.817086] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022] Open
Abstract
Background: DNA methylation is an important epigenetic modification, which plays an important role in regulating gene expression at the transcriptional level. In tumor research, it has been found that the change of DNA methylation leads to the abnormality of gene structure and function, which can provide early warning for tumorigenesis. Our study aims to explore the relationship between the occurrence and development of tumor and the level of DNA methylation. Moreover, this study will provide a set of prognostic biomarkers, which can more accurately predict the survival and health of patients after treatment. Methods: Datasets of bladder cancer patients and control samples were collected from TCGA database, differential analysis was employed to obtain genes with differential DNA methylation levels between tumor samples and normal samples. Then the protein-protein interaction network was constructed, and the potential tumor markers were further obtained by extracting Hub genes from subnet. Cox proportional hazard regression model and survival analysis were used to construct the prognostic model and screen out the prognostic markers of bladder cancer, so as to provide reference for tumor prognosis monitoring and improvement of treatment plan. Results: In this study, we found that DNA methylation was indeed related with the occurrence of bladder cancer. Genes with differential DNA methylation could serve as potential biomarkers for bladder cancer. Through univariate and multivariate Cox proportional hazard regression analysis, we concluded that FASLG and PRKCZ can be used as prognostic biomarkers for bladder cancer. Patients can be classified into high or low risk group by using this two-gene prognostic model. By detecting the methylation status of these genes, we can evaluate the survival of patients. Conclusion: The analysis in our study indicates that the methylation status of tumor-related genes can be used as prognostic biomarkers of bladder cancer.
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Affiliation(s)
- Shumei Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Jingyu Zhang
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qichao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yingjian Liang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Youwen Du
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
- *Correspondence: Guohua Wang,
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Rimini M, Puzzoni M, Pedica F, Silvestris N, Fornaro L, Aprile G, Loi E, Brunetti O, Vivaldi C, Simionato F, Zavattari P, Scartozzi M, Burgio V, Ratti F, Aldrighetti L, Cascinu S, Casadei-Gardini A. Cholangiocarcinoma: new perspectives for new horizons. Expert Rev Gastroenterol Hepatol 2021; 15:1367-1383. [PMID: 34669536 DOI: 10.1080/17474124.2021.1991313] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Biliary tract cancer represents a heterogeneous group of malignancies characterized by dismal prognosis and scarce therapeutic options. AREA COVERED In the last years, a growing interest in BTC pathology has emerged, thus highlighting a significant heterogeneity of the pathways underlying the carcinogenesis process, from both a molecular and genomic point of view. A better understanding of these differences is mandatory to deepen the behavior of this complex disease, as well as to identify new targetable target mutations, with the aim to improve the survival outcomes. The authors decided to provide a comprehensive overview of the recent highlights on BTCs, with a special focus on the genetic, epigenetic and molecular alterations, which may have an interesting clinical application in the next future. EXPERT OPINION In the last years, the efforts resulted from international collaborations have led to the identification of new promising targets for precision medicine approaches in the BTC setting. Further investigations and prospective trials are needed, but the hope is that these new knowledge in cooperation with the new technologies and procedures, including bio-molecular and genomic analysis as well radiomic studies, will enrich the therapeutic armamentarium thus improving the survival outcomes in a such lethal and complex disease.
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Affiliation(s)
- Margherita Rimini
- Department of Oncology and Hematology, Division of Oncology, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Puzzoni
- Medical Oncology, University and University Hospital of Cagliari, Italy
| | - Federica Pedica
- Department of Pathology, San Raffaele Scientific Institute, Milan, Italy
| | - Nicola Silvestris
- Department of oncology, Instituto Di Ricovero E Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo Ii" of Bari, Bari, Italy.,Department of Biomedical Sciences and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - Lorenzo Fornaro
- Department of medical oncology, U.O. Oncologia Medica 2 Universitaria, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Giuseppe Aprile
- Department of Oncology, San Bortolo General Hospital, Azienda ULSS8 Berica, Vicenza, Italy
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Oronzo Brunetti
- Department of oncology, Instituto Di Ricovero E Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo Ii" of Bari, Bari, Italy
| | - Caterina Vivaldi
- Department of medical oncology, U.O. Oncologia Medica 2 Universitaria, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Francesca Simionato
- Department of Oncology, San Bortolo General Hospital, Azienda ULSS8 Berica, Vicenza, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Mario Scartozzi
- Medical Oncology, University and University Hospital of Cagliari, Italy
| | - Valentina Burgio
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Francesca Ratti
- Hepatobiliary Surgery Division, IRCCS San Raffaele and Vita-Salute University, Italy
| | - Luca Aldrighetti
- Hepatobiliary Surgery Division, IRCCS San Raffaele and Vita-Salute University, Italy
| | - Stefano Cascinu
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
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Interaction between Microsatellite Instability (MSI) and Tumor DNA Methylation in the Pathogenesis of Colorectal Carcinoma. Cancers (Basel) 2021; 13:cancers13194956. [PMID: 34638440 PMCID: PMC8508563 DOI: 10.3390/cancers13194956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary In colorectal cancer (CRC), mutations may occur in short, repeated DNA sequences, known as microsatellite instability (MSI). Tumor DNA methylation is another molecular change now recognized as an important biomarker in CRC. In a genome-wide scale, for the first time, we explored whether DNA methylation is associated with MSI status in CRC. We analyzed 250 paired samples (tumor and corresponding normal) from 125 CRC patients (m = 72, f = 53) at different stages. We found that many genes were methylated in tumor tissue compared to normal tissue. However, almost four times more genes showed such methylation changes in the tumor if the patient who also had MSI compared to patients without MSI. Our study shows an association of MSI and DNA methylation in CRC. The study also indicates an opportunity for potential use of certain immune checkpoint inhibitors (CTLA4 and HAVCR2 inhibitors) in CRC with MSI. Abstract In colorectal cancer (CRC), the role of microsatellite instability (MSI) is well known. In a genome-wide scale, for the first time, we explored whether differential methylation is associated with MSI. We analyzed 250 paired samples from 125 CRC patients (m = 72, f = 53) at different stages. Of them, 101 had left-sided CRC, 30 had MSI, 34 had somatic mutation in KRAS proto-oncogene (KRAS), and 6 had B-Raf proto-oncogene (BRAF) exon 15p.V600E mutation. MSI was more frequent in right-sided tumors (54% vs. 17%, p = 0.003). Among the microsatellite stable (MSS) CRC, a paired comparison revealed 1641 differentially methylated loci (DML) covering 686 genes at FDR 0.001 with delta beta ≥ 20%. Similar analysis in MSI revealed 6209 DML covering 2316 genes. ANOVA model including interaction (Tumor*MSI) revealed 23,322 loci, where the delta beta was different among MSI and MSS patients. Our study shows an association between MSI and tumor DNA methylation in the pathogenesis of CRC. Given the interaction seen in this study, it may be worth considering the MSI status while looking for methylation markers in CRC. The study also indicates an opportunity for potential use of certain immune checkpoint inhibitors (CTLA4 and HAVCR2 inhibitors) in CRC with MSI.
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Lezirovitz K, Vieira-Silva GA, Batissoco AC, Levy D, Kitajima JP, Trouillet A, Ouyang E, Zebarjadi N, Sampaio-Silva J, Pedroso-Campos V, Nascimento LR, Sonoda CY, Borges VM, Vasconcelos LG, Beck RMO, Grasel SS, Jagger DJ, Grillet N, Bento RF, Mingroni-Netto RC, Oiticica J. A rare genomic duplication in 2p14 underlies autosomal dominant hearing loss DFNA58. Hum Mol Genet 2021; 29:1520-1536. [PMID: 32337552 DOI: 10.1093/hmg/ddaa075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/02/2020] [Accepted: 04/20/2020] [Indexed: 02/07/2023] Open
Abstract
Here we define a ~200 Kb genomic duplication in 2p14 as the genetic signature that segregates with postlingual progressive sensorineural autosomal dominant hearing loss (HL) in 20 affected individuals from the DFNA58 family, first reported in 2009. The duplication includes two entire genes, PLEK and CNRIP1, and the first exon of PPP3R1 (protein coding), in addition to four uncharacterized long non-coding (lnc) RNA genes and part of a novel protein-coding gene. Quantitative analysis of mRNA expression in blood samples revealed selective overexpression of CNRIP1 and of two lncRNA genes (LOC107985892 and LOC102724389) in all affected members tested, but not in unaffected ones. Qualitative analysis of mRNA expression identified also fusion transcripts involving parts of PPP3R1, CNRIP1 and an intergenic region between PLEK and CNRIP1, in the blood of all carriers of the duplication, but were heterogeneous in nature. By in situ hybridization and immunofluorescence, we showed that Cnrip1, Plek and Ppp3r1 genes are all expressed in the adult mouse cochlea including the spiral ganglion neurons, suggesting changes in expression levels of these genes in the hearing organ could underlie the DFNA58 form of deafness. Our study highlights the value of studying rare genomic events leading to HL, such as copy number variations. Further studies will be required to determine which of these genes, either coding proteins or non-coding RNAs, is or are responsible for DFNA58 HL.
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Affiliation(s)
- Karina Lezirovitz
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Gleiciele A Vieira-Silva
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Ana C Batissoco
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Débora Levy
- Lipids, Oxidation, and Cell Biology Group, Head, Laboratory of Immunology (LIM19), Heart Institute (InCor), Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-900, Brazil
| | | | - Alix Trouillet
- Department of Otolaryngology - Head and Neck Surgery, Stanford University, Stanford, CA 94305, USA
| | - Ellen Ouyang
- Department of Otolaryngology - Head and Neck Surgery, Stanford University, Stanford, CA 94305, USA
| | - Navid Zebarjadi
- Department of Otolaryngology - Head and Neck Surgery, Stanford University, Stanford, CA 94305, USA
| | - Juliana Sampaio-Silva
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Vinicius Pedroso-Campos
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Larissa R Nascimento
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Cindy Y Sonoda
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Vinícius M Borges
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-900, Brazil
| | - Laura G Vasconcelos
- Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Roberto M O Beck
- Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Signe S Grasel
- Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Daniel J Jagger
- UCL Ear Institute, University College London, London WC1E 6BT, UK
| | - Nicolas Grillet
- Department of Otolaryngology - Head and Neck Surgery, Stanford University, Stanford, CA 94305, USA
| | - Ricardo F Bento
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Regina C Mingroni-Netto
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-900, Brazil
| | - Jeanne Oiticica
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
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22
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Bononi G, Tuccinardi T, Rizzolio F, Granchi C. α/β-Hydrolase Domain (ABHD) Inhibitors as New Potential Therapeutic Options against Lipid-Related Diseases. J Med Chem 2021; 64:9759-9785. [PMID: 34213320 PMCID: PMC8389839 DOI: 10.1021/acs.jmedchem.1c00624] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Much of the experimental evidence in the literature has linked altered lipid metabolism to severe diseases such as cancer, obesity, cardiovascular pathologies, diabetes, and neurodegenerative diseases. Therefore, targeting key effectors of the dysregulated lipid metabolism may represent an effective strategy to counteract these pathological conditions. In this context, α/β-hydrolase domain (ABHD) enzymes represent an important and diversified family of proteins, which are involved in the complex environment of lipid signaling, metabolism, and regulation. Moreover, some members of the ABHD family play an important role in the endocannabinoid system, being designated to terminate the signaling of the key endocannabinoid regulator 2-arachidonoylglycerol. This Perspective summarizes the research progress in the development of ABHD inhibitors and modulators: design strategies, structure-activity relationships, action mechanisms, and biological studies of the main ABHD ligands will be highlighted.
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Affiliation(s)
- Giulia Bononi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Flavio Rizzolio
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy.,Department of Molecular Sciences and Nanosystems, Ca' Foscari University, 30123 Venezia, Italy
| | - Carlotta Granchi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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23
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Chen Q, Wu Q, Peng Y. ADHFE1 is a correlative factor of patient survival in cancer. Open Life Sci 2021; 16:571-582. [PMID: 34179501 PMCID: PMC8216228 DOI: 10.1515/biol-2021-0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022] Open
Abstract
Alcohol dehydrogenase iron containing 1 (ADHFE1) encodes a hydroxyacid-oxoacid transhydrogenase participating in multiple biological processes. The role of ADHFE1 in cancer has not been fully uncovered. Herein, we performed data analysis to investigate the expression of ADHFE1 and the underlying regulatory mechanisms, its relationship with cancer patients’ survival, and the relevant pathways in cancer. A range of recognized, web-available databases and bioinformatics tools were used in this in silico study. We found that ADHFE1 was frequently downregulated and hypermethylated in various cancer cell lines and tissue samples. High expression of ADHFE1 was positively associated with favorable patient prognosis in breast, colon, and gastric cancers. Pathway analysis revealed its potential role in cancer-related biological processes, including energy metabolism, DNA replication, and cell cycle regulation. AHDFE1 mRNA expression and DNA methylation can potentially be used as diagnostic markers in cancer and might be of great value in predicting the survival of patients with cancer.
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Affiliation(s)
- Qi Chen
- Department of Traditional Chinese Medicine, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Qiyan Wu
- Cancer Center Key Lab, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Yaojun Peng
- Department of Emergency, The First Medical Centre, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
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24
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Nicotinamide N-Methyltransferase in Acquisition of Stem Cell Properties and Therapy Resistance in Cancer. Int J Mol Sci 2021; 22:ijms22115681. [PMID: 34073600 PMCID: PMC8197977 DOI: 10.3390/ijms22115681] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
The activity of nicotinamide N-methyltransferase (NNMT) is tightly linked to the maintenance of the nicotinamide adenine dinucleotide (NAD+) level. This enzyme catalyzes methylation of nicotinamide (NAM) into methyl nicotinamide (MNAM), which is either excreted or further metabolized to N1-methyl-2-pyridone-5-carboxamide (2-PY) and H2O2. Enzymatic activity of NNMT is important for the prevention of NAM-mediated inhibition of NAD+-consuming enzymes poly-adenosine -diphosphate (ADP), ribose polymerases (PARPs), and sirtuins (SIRTs). Inappropriately high expression and activity of NNMT, commonly present in various types of cancer, has the potential to disrupt NAD+ homeostasis and cellular methylation potential. Largely overlooked, in the context of cancer, is the inhibitory effect of 2-PY on PARP-1 activity, which abrogates NNMT's positive effect on cellular NAD+ flux by stalling liberation of NAM and reducing NAD+ synthesis in the salvage pathway. This review describes, and discusses, the mechanisms by which NNMT promotes NAD+ depletion and epigenetic reprogramming, leading to the development of metabolic plasticity, evasion of a major tumor suppressive process of cellular senescence, and acquisition of stem cell properties. All these phenomena are related to therapy resistance and worse clinical outcomes.
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25
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Jensen SØ, Øgaard N, Nielsen HJ, Bramsen JB, Andersen CL. Enhanced Performance of DNA Methylation Markers by Simultaneous Measurement of Sense and Antisense DNA Strands after Cytosine Conversion. Clin Chem 2021; 66:925-933. [PMID: 32460325 DOI: 10.1093/clinchem/hvaa100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/03/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Most existing DNA methylation-based methods for detection of circulating tumor DNA (ctDNA) are based on conversion of unmethylated cytosines to uracil. After conversion, the 2 DNA strands are no longer complementary; therefore, targeting only 1 DNA strand merely utilizes half of the available input DNA. We investigated whether the sensitivity of methylation-based ctDNA detection strategies could be increased by targeting both DNA strands after bisulfite conversion. METHODS Dual-strand digital PCR assays were designed for the 3 colorectal cancer (CRC)-specific methylation markers KCNQ5, C9orf50, and CLIP4 and compared with previously reported single-strand assays. Performance was tested in tumor and leukocyte DNA, and the ability to detect ctDNA was investigated in plasma from 43 patients with CRC stages I to IV and 42 colonoscopy-confirmed healthy controls. RESULTS Dual-strand assays quantified close to 100% of methylated control DNA input, whereas single-strand assays quantified approximately 50%. Furthermore, dual-strand assays showed a 2-fold increase in the number of methylated DNA copies detected when applied to DNA purified from tumor tissue and plasma from CRC patients. When the results of the 3 DNA methylation markers were combined into a ctDNA detection test and applied to plasma, the dual-strand assay format detected 86% of the cancers compared with 74% for the single-strand assay format. The specificity was 100% for both the dual- and single-strand test formats. CONCLUSION Dual-strand assays enabled more sensitive detection of methylated ctDNA than single-strand assays.
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Affiliation(s)
- Sarah Ø Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology, Center for Surgical Research, Hvidovre Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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26
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Howarth KD, Mirza T, Cooke SL, Chin SF, Pole JC, Turro E, Eldridge MD, Garcia RM, Rueda OM, Boursnell C, Abraham JE, Caldas C, Edwards PAW. NRG1 fusions in breast cancer. Breast Cancer Res 2021; 23:3. [PMID: 33413557 PMCID: PMC7788813 DOI: 10.1186/s13058-020-01377-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/30/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND NRG1 gene fusions may be clinically actionable, since cancers carrying the fusion transcripts can be sensitive to tyrosine kinase inhibitors. The NRG1 gene encodes ligands for the HER2(ERBB2)-ERBB3 heterodimeric receptor tyrosine kinase, and the gene fusions are thought to lead to autocrine stimulation of the receptor. The NRG1 fusion expressed in the breast cancer cell line MDA-MB-175 serves as a model example of such fusions, showing the proposed autocrine loop and exceptional drug sensitivity. However, its structure has not been properly characterised, its oncogenic activity has not been fully explained, and there is limited data on such fusions in breast cancer. METHODS We analysed genomic rearrangements and transcripts of NRG1 in MDA-MB-175 and a panel of 571 breast cancers. RESULTS We found that the MDA-MB-175 fusion-originally reported as a DOC4(TENM4)-NRG1 fusion, lacking the cytoplasmic tail of NRG1-is in reality a double fusion, PPP6R3-TENM4-NRG1, producing multiple transcripts, some of which include the cytoplasmic tail. We hypothesise that many NRG1 fusions may be oncogenic not for lacking the cytoplasmic domain but because they do not encode NRG1's nuclear-localised form. The fusion in MDA-MB-175 is the result of a very complex genomic rearrangement, which we partially characterised, that creates additional expressed gene fusions, RSF1-TENM4, TPCN2-RSF1, and MRPL48-GAB2. We searched for NRG1 rearrangements in 571 breast cancers subjected to genome sequencing and transcriptome sequencing and found four cases (0.7%) with fusions, WRN-NRG1, FAM91A1-NRG1, ARHGEF39-NRG1, and ZNF704-NRG1, all splicing into NRG1 at the same exon as in MDA-MB-175. However, the WRN-NRG1 and ARHGEF39-NRG1 fusions were out of frame. We identified rearrangements of NRG1 in many more (8% of) cases that seemed more likely to inactivate than to create activating fusions, or whose outcome could not be predicted because they were complex, or both. This is not surprising because NRG1 can be pro-apoptotic and is inactivated in some breast cancers. CONCLUSIONS Our results highlight the complexity of rearrangements of NRG1 in breast cancers and confirm that some do not activate but inactivate. Careful interpretation of NRG1 rearrangements will therefore be necessary for appropriate patient management.
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Affiliation(s)
- Karen D. Howarth
- Hutchison-MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Present addresses: Inivata Ltd, Babraham Research Park, Cambridge, CB22 3FH UK
| | - Tashfina Mirza
- Hutchison-MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Present addresses: Francis Crick Institute, Midland Road, London, NW1 1AT UK
| | - Susanna L. Cooke
- Hutchison-MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Present addresses: Wolfson Wohl Cancer Research Centre, Garscube Estate, Bearsden, G61 1QH UK
| | - Suet-Feung Chin
- Department of Oncology, Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Jessica C. Pole
- Hutchison-MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Present addresses: Illumina Cambridge, Granta Park, Great Abington, Cambridge, CB21 6GP UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0PT UK
- Present addresses: Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Matthew D. Eldridge
- Department of Oncology, Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Raquel Manzano Garcia
- Department of Oncology, Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Oscar M. Rueda
- Department of Oncology, Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
- Present addresses: MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0SR UK
| | - Chris Boursnell
- Department of Oncology, Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Jean E. Abraham
- Department of Oncology, Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
- Cambridge Breast Cancer Research Unit, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre at Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Carlos Caldas
- Department of Oncology, Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
- Cambridge Breast Cancer Research Unit, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre at Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Paul A. W. Edwards
- Hutchison-MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Oncology, Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
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27
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Oliver EE, Hughes EK, Puckett MK, Chen R, Lowther WT, Howlett AC. Cannabinoid Receptor Interacting Protein 1a (CRIP1a) in Health and Disease. Biomolecules 2020; 10:biom10121609. [PMID: 33261012 PMCID: PMC7761089 DOI: 10.3390/biom10121609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022] Open
Abstract
Endocannabinoid signaling depends upon the CB1 and CB2 cannabinoid receptors, their endogenous ligands anandamide and 2-arachidonoylglycerol, and intracellular proteins that mediate responses via the C-terminal and other intracellular receptor domains. The CB1 receptor regulates and is regulated by associated G proteins predominantly of the Gi/o subtypes, β-arrestins 1 and 2, and the cannabinoid receptor-interacting protein 1a (CRIP1a). Evidence for a physiological role for CRIP1a is emerging as data regarding the cellular localization and function of CRIP1a are generated. Here we summarize the neuronal distribution and role of CRIP1a in endocannabinoid signaling, as well as discuss investigations linking CRIP1a to development, vision and hearing sensory systems, hippocampus and seizure regulation, and psychiatric disorders including schizophrenia. We also examine the genetic and epigenetic association of CRIP1a within a variety of cancer subtypes. This review provides evidence upon which to base future investigations on the function of CRIP1a in health and disease.
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Affiliation(s)
- Emily E. Oliver
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Medical Center Blvd, Winston-Salem, NC 20157, USA; (E.E.O.); (E.K.H.); (M.K.P.); (R.C.)
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 20157, USA;
| | - Erin K. Hughes
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Medical Center Blvd, Winston-Salem, NC 20157, USA; (E.E.O.); (E.K.H.); (M.K.P.); (R.C.)
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 20157, USA;
| | - Meaghan K. Puckett
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Medical Center Blvd, Winston-Salem, NC 20157, USA; (E.E.O.); (E.K.H.); (M.K.P.); (R.C.)
| | - Rong Chen
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Medical Center Blvd, Winston-Salem, NC 20157, USA; (E.E.O.); (E.K.H.); (M.K.P.); (R.C.)
| | - W. Todd Lowther
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 20157, USA;
| | - Allyn C. Howlett
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Medical Center Blvd, Winston-Salem, NC 20157, USA; (E.E.O.); (E.K.H.); (M.K.P.); (R.C.)
- Correspondence: ; Tel.: +1-336-716-8545
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28
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Sarparast M, Dattmore D, Alan J, Lee KSS. Cytochrome P450 Metabolism of Polyunsaturated Fatty Acids and Neurodegeneration. Nutrients 2020; 12:E3523. [PMID: 33207662 PMCID: PMC7696575 DOI: 10.3390/nu12113523] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022] Open
Abstract
Due to the aging population in the world, neurodegenerative diseases have become a serious public health issue that greatly impacts patients' quality of life and adds a huge economic burden. Even after decades of research, there is no effective curative treatment for neurodegenerative diseases. Polyunsaturated fatty acids (PUFAs) have become an emerging dietary medical intervention for health maintenance and treatment of diseases, including neurodegenerative diseases. Recent research demonstrated that the oxidized metabolites, particularly the cytochrome P450 (CYP) metabolites, of PUFAs are beneficial to several neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease; however, their mechanism(s) remains unclear. The endogenous levels of CYP metabolites are greatly affected by our diet, endogenous synthesis, and the downstream metabolism. While the activity of omega-3 (ω-3) CYP PUFA metabolites and omega-6 (ω-6) CYP PUFA metabolites largely overlap, the ω-3 CYP PUFA metabolites are more active in general. In this review, we will briefly summarize recent findings regarding the biosynthesis and metabolism of CYP PUFA metabolites. We will also discuss the potential mechanism(s) of CYP PUFA metabolites in neurodegeneration, which will ultimately improve our understanding of how PUFAs affect neurodegeneration and may identify potential drug targets for neurodegenerative diseases.
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Affiliation(s)
- Morteza Sarparast
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA;
| | - Devon Dattmore
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA;
| | - Jamie Alan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA;
| | - Kin Sing Stephen Lee
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA;
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA;
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29
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Liu Y, Huang H, Fu J, Zhang Y, Xu J, Zhang L, Sun S, Zhao L, Zhang D, Onwuka JU, Sun H, Cui B, Zhao Y. Colorectal cancer patients with CASK promotor heterogeneous and homogeneous methylation display different prognosis. Aging (Albany NY) 2020; 12:20561-20586. [PMID: 33113509 PMCID: PMC7655177 DOI: 10.18632/aging.103928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Homogenous DNA methylation clearly affects clinical outcomes. However, less is known about the effects of heterogeneous methylation. We aimed to investigate the different effects between CASK promoter methylation heterogeneity and homogeneity on colorectal cancer (CRC) patients' prognosis. The methylation status of CASK in 296 tumor tissues and 255 adjacent normal tissues were evaluated using Methylation-sensitive high-resolution melting (MS-HRM). Digital MS-HRM (dMS-HRM) visualized heterogeneous methylation and subsequent sequencing provided exact patterns. Log-rank test and Cox regression model were adopted to assess the association between CASK methylation status and CRC prognosis with propensity score (PS) method to control confounding biases. Heterogeneous methylation was detected in both tumor (52.2%) and non-neoplastic tissue surrounding the tumor (62.4%). It occurred more frequently in lower levels of tumor invasion (P = 0.002) and male patients (P < 0.001). Compared with heterogeneous methylation, patients with CASK homogeneous methylation presented poorer overall survival (OS) (HR: 1.919, 95% CI: 1.146-3.212, P = 0.013) and disease-free survival (DFS) (HR: 1.913, 95% CI: 1.146-3.194, P = 0.013). This unfavorable effect still existed among older (≥ 50), Dukes staging C/D, and rectal cancer patients. MS-HRM and dMS-HRM when combined can assess the degree and complexity of heterogeneous methylation with a visible pattern.
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Affiliation(s)
- Ying Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Hao Huang
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Jinming Fu
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Yuanyuan Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Jing Xu
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Lei Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Simin Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Liyuan Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Ding Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Justina Ucheojor Onwuka
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Hongru Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Binbin Cui
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
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Renzi A, Morandi L, Lenzi J, Rigillo A, Bettini G, Bellei E, Giacomini A, Tinto D, Sabattini S. Analysis of DNA methylation and TP53 mutational status for differentiating feline oral squamous cell carcinoma from non-neoplastic mucosa: A preliminary study. Vet Comp Oncol 2020; 18:825-837. [PMID: 32506786 DOI: 10.1111/vco.12624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/13/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022]
Abstract
Feline oral squamous cell carcinoma (FOSCC) is characterized by high local invasiveness and early bone lysis. The late diagnosis largely limits the efficacy of therapy and increases treatment-related morbidity. The aim of this exploratory study was to assess the methylation pattern of 10 candidate genes and TP53 mutational status in histologic samples of FOSCC. Results were compared with normal oral mucosa and oral inflammatory lesions, in order to establish a gene panel for FOSCC detection. For 10 cats, the above analyses were also performed on oral brushing samples, in order to explore the utility of these methods for screening purposes. Thirty-one FOSCC, 25 chronic inflammatory lesions and 12 controls were included. TP53 mutations were significantly more frequent in the FOSCC (68%) than in the non-neoplastic oral mucosa (3%; P <.001). Based on lasso regression analysis, a step-wise algorithm including TP53, FLI1, MiR124-1, KIF1A and MAGEC2 was proposed. The algorithm allowed to differentiate FOSCC with 94% sensitivity and 100% specificity (accuracy, 97%). When applying the proposed algorithm on 10 brushing samples, accuracy decreased to 80%. These results indicate that the altered DNA methylation of specific genes is present in FOSCC, together with a significant proportion of TP53 mutations. Such alterations are infrequent in normal oral mucosa and chronic stomatitis in cats, suggesting their involvement in feline oral carcinogenesis and their utility as diagnostic biomarkers. Further studies on a high number of brushing samples will be needed to assess the utility of a screening test for the early detection of FOSCC.
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Affiliation(s)
- Andrea Renzi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Luca Morandi
- Department of Biomedical and Neuromotor Sciences, Functional MR Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Jacopo Lenzi
- Department of Biomedical and Neuromotor Sciences, Section of Hygiene, Public Health and Medical Statistics, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Antonella Rigillo
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Giuliano Bettini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Emma Bellei
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Alessandra Giacomini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Debora Tinto
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Silvia Sabattini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
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31
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Xu Y, Zhao W, Mo Y, Ma N, Midorikawa K, Kobayashi H, Hiraku Y, Oikawa S, Zhang Z, Huang G, Takeuchi K, Murata M. Combination of RERG and ZNF671 methylation rates in circulating cell-free DNA: A novel biomarker for screening of nasopharyngeal carcinoma. Cancer Sci 2020; 111:2536-2545. [PMID: 32324312 PMCID: PMC7385361 DOI: 10.1111/cas.14431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/02/2020] [Accepted: 04/19/2020] [Indexed: 12/12/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a prevalent malignancy in Southeast Asia, hence, identifying easily detectable biomarkers for NPC screening is essential for better diagnosis and prognosis. Using genome-wide and targeted analyses based on next-generation sequencing approaches, we previously showed that gene promoters are hypermethylated in NPC tissues. To confirm whether DNA methylation rates of genes could be used as biomarkers for NPC screening, 79 histologically diagnosed NPC patients and 29 noncancer patients were recruited. A convenient quantitative analysis of DNA methylation using real-time PCR (qAMP) was carried out, involving pretreatment of tissue DNA, and circulating cell-free DNA (ccfDNA) from nonhemolytic plasma, with methylation-sensitive and/or methylation-dependent restriction enzymes. The qAMP analyses revealed that methylation rates of RERG, ZNF671, ITGA4, and SHISA3 were significantly higher in NPC primary tumor tissues compared to noncancerous tissues, with sufficient diagnostic accuracy of the area under receiver operating characteristic curves (AUC). Interestingly, higher methylation rates of RERG in ccfDNA were statistically significant and yielded a very good AUC; however, those of ZNF671, ITGA4, and SHISA3 were not significant. Furthermore, the combination of methylation rates of RERG and ZNF671 in ccfDNA showed higher diagnostic accuracy than either of them individually. In conclusion, the methylation rates of specific genes in ccfDNA can serve as novel biomarkers for early detection and screening of NPC.
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Affiliation(s)
- Yifei Xu
- Department of Environmental and Molecular MedicineMie University Graduate School of MedicineTsuJapan
- Department of Otorhinolaryngology – Head and Neck SurgeryMie University Graduate School of MedicineTsuJapan
- Department of Otorhinolaryngology – Head and Neck SurgeryFirst Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Weilin Zhao
- Department of Otorhinolaryngology – Head and Neck SurgeryFirst Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Yingxi Mo
- Department of ResearchAffiliated Tumor Hospital of Guangxi Medical UniversityNanningChina
| | - Ning Ma
- Graduate School of Health ScienceSuzuka University of Medical ScienceSuzukaJapan
| | - Kaoru Midorikawa
- Department of Environmental and Molecular MedicineMie University Graduate School of MedicineTsuJapan
| | - Hatasu Kobayashi
- Department of Environmental and Molecular MedicineMie University Graduate School of MedicineTsuJapan
| | - Yusuke Hiraku
- Department of Environmental and Molecular MedicineMie University Graduate School of MedicineTsuJapan
- Department of Environmental HealthUniversity of Fukui School of Medical ScienceEiheijiJapan
| | - Shinji Oikawa
- Department of Environmental and Molecular MedicineMie University Graduate School of MedicineTsuJapan
| | - Zhe Zhang
- Department of Otorhinolaryngology – Head and Neck SurgeryFirst Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Guangwu Huang
- Department of Otorhinolaryngology – Head and Neck SurgeryFirst Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Kazuhiko Takeuchi
- Department of Otorhinolaryngology – Head and Neck SurgeryMie University Graduate School of MedicineTsuJapan
| | - Mariko Murata
- Department of Environmental and Molecular MedicineMie University Graduate School of MedicineTsuJapan
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Sun X, Chen D, Jin Z, Chen T, Lin A, Jin H, Zhu Y, Lai M. Genome-wide methylation and expression profiling identify methylation-associated genes in colorectal cancer. Epigenomics 2019; 12:19-36. [PMID: 31833403 DOI: 10.2217/epi-2019-0133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: To identify methylation-associated genes in the carcinogenesis of colorectal cancer (CRC). Materials & methods: Genome-wide patterns of DNA methylation and gene expression in CRC tissues and adjacent normal tissues were determined and further validated in The Cancer Genome Atlas data and Chinese CRC patients, respectively. Gene overexpression and knockdown cells were constructed to investigate their biological roles in CRC. Results: After validations, hypermethylation of eight genes were found to be correlated with their reduced transcription, and hypomethyaltion of three genes were associated with their upregulation. CADM3, CNRIP1, GRHL2, GRIA4, GSTM2 and NRXN1 were associated with the overall survival of CRC patients. CNRIP1 and GSTM2 were mainly responsible for the proliferation in CRC cells. Conclusion: A total of 11 genes may be promising biomarkers for CRC.
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Affiliation(s)
- Xiaohui Sun
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Diyu Chen
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, PR China
| | - Ziqi Jin
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Tianhui Chen
- Group of Molecular Epidemiology & Cancer Precision Prevention, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Aifen Lin
- Human Tissue Bank/Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, PR China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou 310020, PR China
| | - Yimin Zhu
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China.,Department of Respiratory Diseases, Sir Run Run Shaw Hospital Affiliated to School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310020, PR China
| | - Maode Lai
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, PR China
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Jensen SØ, Øgaard N, Ørntoft MBW, Rasmussen MH, Bramsen JB, Kristensen H, Mouritzen P, Madsen MR, Madsen AH, Sunesen KG, Iversen LH, Laurberg S, Christensen IJ, Nielsen HJ, Andersen CL. Novel DNA methylation biomarkers show high sensitivity and specificity for blood-based detection of colorectal cancer-a clinical biomarker discovery and validation study. Clin Epigenetics 2019; 11:158. [PMID: 31727158 PMCID: PMC6854894 DOI: 10.1186/s13148-019-0757-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023] Open
Abstract
Background Early detection plays an essential role to reduce colorectal cancer (CRC) mortality. While current screening methods suffer from poor compliance, liquid biopsy-based strategies for cancer detection is rapidly gaining promise. Here, we describe the development of TriMeth, a minimal-invasive blood-based test for detection of early-stage colorectal cancer. The test is based on assessment of three tumour-specific DNA methylation markers in circulating cell-free DNA. Results A thorough multi-step biomarker discovery study based on DNA methylation profiles of more than 5000 tumours and blood cell populations identified CRC-specific DNA methylation markers. The DNA methylation patterns of biomarker candidates were validated by bisulfite sequencing and methylation-specific droplet digital PCR in CRC tumour tissue and peripheral blood leucocytes. The three best performing markers were first applied to plasma from 113 primarily early-stage CRC patients and 87 age- and gender-matched colonoscopy-verified controls. Based on this, the test scoring algorithm was locked, and then TriMeth was validated in an independent cohort comprising 143 CRC patients and 91 controls. Three DNA methylation markers, C9orf50, KCNQ5, and CLIP4, were identified, each capable of discriminating plasma from colorectal cancer patients and healthy individuals (areas under the curve 0.86, 0.91, and 0.88). When combined in the TriMeth test, an average sensitivity of 85% (218/256) was observed (stage I: 80% (33/41), stage II: 85% (121/143), stage III: 89% (49/55), and stage IV: 88% (15/17)) at 99% (176/178) specificity in two independent plasma cohorts. Conclusion TriMeth enables detection of early-stage colorectal cancer with high sensitivity and specificity. The reported results underline the potential utility of DNA methylation-based detection of circulating tumour DNA in the clinical management of colorectal cancer.
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Affiliation(s)
- Sarah Østrup Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Mai-Britt Worm Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Jesper Bertram Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | | | | | | | | | | | | | - Søren Laurberg
- Department of Surgery, Aarhus University Hospital, Aarhus, Denmark
| | - Ib Jarle Christensen
- Center for Surgical Research, Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark
| | - Hans Jørgen Nielsen
- Center for Surgical Research, Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
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Fang WL, Chen MH, Huang KH, Chang SC, Lin CH, Chao Y, Lo SS, Li AFY, Wu CW, Shyr YM. Analysis of the clinical significance of DNA methylation in gastric cancer based on a genome-wide high-resolution array. Clin Epigenetics 2019; 11:154. [PMID: 31675985 PMCID: PMC6824057 DOI: 10.1186/s13148-019-0747-5] [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: 05/01/2019] [Accepted: 09/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation is involved in gastric carcinogenesis and may serve as a useful biomarker in the diagnosis and detection of gastric cancer (GC) recurrence. RESULTS A total of 157 patients who received surgery for GC were enrolled in the present study. A genome-wide methylation analysis was performed in tumor and adjacent normal tissues for the discovery set of 16 GC patients; the top three hypermethylated CpG sites of DNA promoters were selected for validation in tissue and plasma samples for the validation set of 141 GC patients. The frequencies of the top three hypermethylated genes in available patient tissues (n = 141) and plasma samples (n = 106) were 41.8% and 38.7%, respectively, for ADAM19; 40.4% and 42.5%, respectively, for FLI1; and 56.7% and 50.9%, respectively, for MSC. In both tissue and plasma samples, FLI1 hypermethylation was associated with more advanced GC and liver and distant lymphatic metastasis, and ADAM19 hypermethylation was associated with more stage IV GC. In plasma samples, MSC hypermethylation was more common in non-superficial type GC than samples without MSC hypermethylation. In both tissue and plasma samples, patients with methylation of all the three genes had significantly more liver metastases, distant lymphatic metastases, and paraaortic lymph node metastases than patients with two or fewer hypermethylated genes. The survival analysis showed that only for stage III GC, patients with hypermethylation of two or three genes had a worse 5-year disease-free survival rate than those with hypermethylation of one or none of the three genes. Subgroup analysis showed that FLI1 hypermethylation in both tissue and plasma samples was associated with liver metastasis in MSI-/EBV- GC, and MSC hypermethylation in tissue samples was correlated with liver metastasis in MSI+ or EBV+ GC. Patients with FLI1 hypermethylation in plasma samples had a significantly worse 5-year disease-free survival rate than those without FLI1 hypermethylation in MSI-/EBV- GC. FLI1 hypermethylation was an independent prognostic factor affecting the overall survival and disease-free survival in both tissue and plasma samples. CONCLUSIONS DNA methylation is a useful biomarker for predicting tumor recurrence patterns and GC patient survival.
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Affiliation(s)
- Wen-Liang Fang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd, Beitou District, Taipei City, Taiwan, 11217. .,School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.
| | - Ming-Huang Chen
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,Department of Oncology, Taipei Veterans General Hospital, Taipei City, Taiwan, 11217
| | - Kuo-Hung Huang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd, Beitou District, Taipei City, Taiwan, 11217.,School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217
| | - Shih-Ching Chang
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, 11217
| | - Chien-Hsing Lin
- Genome Research Center, National Yang-Ming University, Taipei City, Taiwan, 11217
| | - Yee Chao
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,Department of Oncology, Taipei Veterans General Hospital, Taipei City, Taiwan, 11217
| | - Su-Shun Lo
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,National Yang-Ming University Hospital, Yilan County, Taiwan, 26058
| | - Anna Fen-Yau Li
- School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217.,Department of Pathology, Taipei Veterans General Hospital, Taipei City, 11217, Taiwan
| | - Chew-Wun Wu
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd, Beitou District, Taipei City, Taiwan, 11217.,School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217
| | - Yi-Ming Shyr
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd, Beitou District, Taipei City, Taiwan, 11217.,School of Medicine, National Yang-Ming University, Taipei City, Taiwan, 11217
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Hu YH, Ma S, Zhang XN, Zhang ZY, Zhu HF, Ji YH, Li J, Qian XL, Wang YX. Hypermethylation Of ADHFE1 Promotes The Proliferation Of Colorectal Cancer Cell Via Modulating Cell Cycle Progression. Onco Targets Ther 2019; 12:8105-8115. [PMID: 31632063 PMCID: PMC6782030 DOI: 10.2147/ott.s223423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignancies worldwide. Studies have demonstrated that epigenetic modifications play essential roles in the development of CRC. ADHFE1 is a differentially expressed gene that has been reported to be hypermethylated in CRC. However, the role and mechanism of ADHFE1 in the proliferation of CRC remain unclear. Materials and methods ADHFE1 expression was analyzed in CRC tissues by IHC and qRT-PCR, and the relationship between ADHFE1 expression and the clinicopathological parameters was analyzed. Cell proliferation were assessed by the in vitro and in vivo experimental models. GSEA assay was performed to explore the mechanism of ADHFE1 in the proliferation of CRC. Flow cytometry and Western blot were used to detect the activation of the cell cycle signaling. Bisulfite genomic sequence (BSP) assay was used to test the methylation degree of ADHFE1 gene promoter in CRC tissues. Results Here, we verified that ADHFE1 was down-regulated and hypermethylated in CRC tissues. The down-regulation of ADHFE1 was correlated with poor differentiation and advanced TNM stage of CRC patients. And ADHFE1 expression restored when the CRC cell line SW620 was treated with the demethylating agent 5-Aza-CdR. Overexpression of ADHFE1 inhibited the proliferation of CRC, while ADHFE1 knockdown promoted the proliferation of CRC cells in vitro and in vivo. Moreover, ADHFE1 overexpression could induce a significant G1-S cell cycle arrest in CRC cells and vice versa. Conclusion Hypermethylation of ADHFE1 might promote cell proliferation by modulating cell cycle progression in CRC, potentially providing a new therapeutic target for CRC patients.
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Affiliation(s)
- Yu-Han Hu
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Shuai Ma
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Xiang-Nan Zhang
- Department of Pathology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Zhe-Ying Zhang
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Hui-Fang Zhu
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China.,Department of Pathology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Ying-Hua Ji
- Department of Oncology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Jian Li
- Department of Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Xin-Lai Qian
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China.,Department of Pathology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Yong-Xia Wang
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China.,Department of Pathology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
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Epigenetic loss of AOX1 expression via EZH2 leads to metabolic deregulations and promotes bladder cancer progression. Oncogene 2019; 39:6265-6285. [PMID: 31383940 DOI: 10.1038/s41388-019-0902-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/24/2022]
Abstract
Advanced Bladder Cancer (BLCA) remains a clinical challenge that lacks effective therapeutic measures. Here, we show that distinct, stage-wise metabolic alterations in BLCA are associated with the loss of function of aldehyde oxidase (AOX1). AOX1 associated metabolites have a high predictive value for advanced BLCA and our findings demonstrate that AOX1 is epigenetically silenced during BLCA progression by the methyltransferase activity of EZH2. Knockdown (KD) of AOX1 in normal bladder epithelial cells re-wires the tryptophan-kynurenine pathway resulting in elevated NADP levels which may increase metabolic flux through the pentose phosphate (PPP) pathway, enabling increased nucleotide synthesis, and promoting cell invasion. Inhibition of NADP synthesis rescues the metabolic effects of AOX1 KD. Ectopic AOX1 expression decreases NADP production, PPP flux and nucleotide synthesis, while decreasing invasion in cell line models and suppressing growth in tumor xenografts. Further gain and loss of AOX1 confirm the EZH2-dependent activation, metabolic deregulation, and tumor growth in BLCA. Our findings highlight the therapeutic potential of AOX1 and provide a basis for the development of prognostic markers for advanced BLCA.
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Liang Y, Zhang C, Dai DQ. Identification of differentially expressed genes regulated by methylation in colon cancer based on bioinformatics analysis. World J Gastroenterol 2019; 25:3392-3407. [PMID: 31341364 PMCID: PMC6639549 DOI: 10.3748/wjg.v25.i26.3392] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/09/2019] [Accepted: 06/01/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND DNA methylation, acknowledged as a key modification in the field of epigenetics, regulates gene expression at the transcriptional level. Aberrant methylation in DNA regulatory regions could upregulate oncogenes and downregulate tumor suppressor genes without changing the sequences. However, studies of methylation in the control of gene expression are still inadequate. In the present research, we performed bioinformatics analysis to clarify the function of methylation and supply candidate methylation-related biomarkers and drivers for colon cancer.
AIM To identify and analyze methylation-regulated differentially expressed genes (MeDEGs) in colon cancer by bioinformatics analysis.
METHODS We downloaded RNA expression profiles, Illumina Human Methylation 450K BeadChip data, and clinical data of colon cancer from The Cancer Genome Atlas project. MeDEGs were identified by analyzing the gene expression and methylation levels using the edgeR and limma package in R software. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed in the DAVID database and KEGG Orthology-Based Annotation System 3.0, respectively. We then conducted Kaplan–Meier survival analysis to explore the relationship between methylation and expression and prognosis. Gene set enrichment analysis (GSEA) and investigation of protein-protein interactions (PPI) were performed to clarify the function of prognosis-related genes.
RESULTS A total of 5 up-regulated and 81 down-regulated genes were identified as MeDEGs. GO and KEGG pathway analyses indicated that MeDEGs were enriched in multiple cancer-related terms. Furthermore, Kaplan–Meier survival analysis showed that the prognosis was negatively associated with the methylation status of glial cell-derived neurotrophic factor (GDNF) and reelin (RELN). In PPI networks, GDNF and RELN interact with neural cell adhesion molecule 1. Besides, GDNF can interact with GDNF family receptor alpha (GFRA1), GFRA2, GFRA3, and RET. RELN can interact with RAFAH1B1, disabled homolog 1, very low-density lipoprotein receptor, lipoprotein receptor-related protein 8, and NMDA 2B. Based on GSEA, hypermethylation of GDNF and RELN were both significantly associated with pathways including “RNA degradation,” “ribosome,” “mismatch repair,” “cell cycle” and “base excision repair.”
CONCLUSION Aberrant DNA methylation plays an important role in colon cancer progression. MeDEGs that are associated with the overall survival of patients may be potential targets in tumor diagnosis and treatment.
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Affiliation(s)
- Yu Liang
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Cheng Zhang
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Dong-Qiu Dai
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
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38
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Affiliation(s)
- Christine Beedham
- Honorary Senior Lecturer, Faculty of Life Sciences, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
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39
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Del Portillo A, Komissarova EV, Bokhari A, Hills C, de Gonzalez AK, Kongkarnka S, Remotti HE, Sepulveda JL, Sepulveda AR. Downregulation of Friend Leukemia Integration 1 ( FLI1) follows the stepwise progression to gastric adenocarcinoma. Oncotarget 2019; 10:3852-3864. [PMID: 31231464 PMCID: PMC6570468 DOI: 10.18632/oncotarget.26974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/04/2019] [Indexed: 12/14/2022] Open
Abstract
Gastric adenocarcinoma (GC) is a leading cause of cancer-related deaths worldwide. The transcription factor gene Friend Leukemia Integration 1 (FLI1) is methylated and downregulated in human GC tissues. Using human GC samples, we determined which cells downregulate FLI1, when FLI1 downregulation occurs, if FLI1 downregulation correlates with clinical-pathologic characteristics, and whether FLI1 plays a role in invasion and/or proliferation of cultured cells. We analyzed stomach tissues from 98 patients [8 normal mucosa, 8 intestinal metaplasia (IM), 7 dysplasia, 91 GC] by immunohistochemistry for FLI1. Epithelial cells from normal, IM, and low-grade dysplasia (LGD) showed strong nuclear FLI1 staining. GC epithelial cells showed significantly less nuclear FLI1 staining as compared to normal epithelium, IM and LGD (P=1.2×10-5, P=1.4×10-6 and P=0.006, respectively). FLI1 expression did not correlate with tumor stage or differentiation, but was associated with patient survival, depending on tumor differentiation. We tested the functional role of FLI1 by assaying proliferation and invasion in cultured GC cells. Lentiviral-transduced FLI1 overexpression in GC AGS cells inhibited invasion by 73.5% (P = 0.001) and proliferation by 31.5% (P = 0.002), as compared to controls. Our results support a combined role for FLI1 as a suppressor of invasiveness and proliferation in gastric adenocarcinoma, specifically in the transition from pre-cancer lesions and dysplasia to invasive adenocarcinoma, and suggest that FLI1 may be a prognostic biomarker of survival in gastric cancers.
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Affiliation(s)
- Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Elena V Komissarova
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aqiba Bokhari
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Caitlin Hills
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne Koehne de Gonzalez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarawut Kongkarnka
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Helen E Remotti
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jorge L Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Antonia R Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
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LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer. PLoS One 2018; 13:e0204371. [PMID: 30388122 PMCID: PMC6214495 DOI: 10.1371/journal.pone.0204371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/06/2018] [Indexed: 12/23/2022] Open
Abstract
Although modern methods of whole genome DNA methylation analysis have a wide range of applications, they are not suitable for clinical diagnostics due to their high cost and complexity and due to the large amount of sample DNA required for the analysis. Therefore, it is crucial to be able to identify a relatively small number of methylation sites that provide high precision and sensitivity for the diagnosis of pathological states. We propose an algorithm for constructing limited subsamples from high-dimensional data to form diagnostic panels. We have developed a tool that utilizes different methods of selection to find an optimal, minimum necessary combination of factors using cross-entropy loss metrics (LogLoss) to identify a subset of methylation sites. We show that the algorithm can work effectively with different genome methylation patterns using ensemble-based machine learning methods. Algorithm efficiency, precision and robustness were evaluated using five genome-wide DNA methylation datasets (totaling 626 samples), and each dataset was classified into tumor and non-tumor samples. The algorithm produced an AUC of 0.97 (95% CI: 0.94-0.99, 9 sites) for prostate adenocarcinoma and an AUC of 1.0 (from 2 to 6 sites) for urothelial bladder carcinoma, two types of kidney carcinoma and colorectal carcinoma. For prostate adenocarcinoma we showed that identified differential variability methylation patterns distinguish cluster of samples with higher recurrence rate (hazard ratio for recurrence = 0.48, 95% CI: 0.05-0.92; log-rank test, p-value < 0.03). We also identified several clusters of correlated interchangeable methylation sites that can be used for the elaboration of biological interpretation of the resulting models and for further selection of the sites most suitable for designing diagnostic panels. LogLoss-BERAF is implemented as a standalone python code and open-source code is freely available from https://github.com/bioinformatics-IBCH/logloss-beraf along with the models described in this article.
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Sun X, Tian Y, Zheng Q, Zheng R, Lin A, Chen T, Zhu Y, Lai M. A novel discriminating colorectal cancer model for differentiating normal and tumor tissues. Epigenomics 2018; 10:1463-1475. [DOI: 10.2217/epi-2018-0063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xiaohui Sun
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Yiping Tian
- Key Laboratory of Disease Proteomics of Zhejiang Province & Department of Pathology, School of Medicine, Zhejiang University, Hangzhou 310058, PR China
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou 310022, PR China
| | - Qianqian Zheng
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Ruizhi Zheng
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Aifen Lin
- Human Tissue Bank/Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, PR China
| | - Tianhui Chen
- Group of Molecular Epidemiology & Cancer Precision Prevention, Zhejiang Academy of Medical Sciences, Hangzhou, PR China
| | - Yimin Zhu
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Maode Lai
- Key Laboratory of Disease Proteomics of Zhejiang Province & Department of Pathology, School of Medicine, Zhejiang University, Hangzhou 310058, PR China
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HPV16-Related Cervical Cancers and Precancers Have Increased Levels of Host Cell DNA Methylation in Women Living with HIV. Int J Mol Sci 2018; 19:ijms19113297. [PMID: 30360578 PMCID: PMC6274896 DOI: 10.3390/ijms19113297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 02/07/2023] Open
Abstract
Data on human papillomavirus (HPV) type-specific cervical cancer risk in women living with human immunodeficiency virus (WLHIV) are needed to understand HPV–HIV interaction and to inform prevention programs for this population. We assessed high-risk HPV type-specific prevalence in cervical samples from 463 WLHIV from South Africa with different underlying, histologically confirmed stages of cervical disease. Secondly, we investigated DNA hypermethylation of host cell genes ASCL1, LHX8, and ST6GALNAC5, as markers of advanced cervical disease, in relation to type-specific HPV infection. Overall, HPV prevalence was 56% and positivity increased with severity of cervical disease: from 28.0% in cervical intraepithelial neoplasia (CIN) grade 1 or less (≤CIN1) to 100% in invasive cervical cancer (ICC). HPV16 was the most prevalent type, accounting for 9.9% of HPV-positive ≤CIN1, 14.3% of CIN2, 31.7% of CIN3, and 45.5% of ICC. HPV16 was significantly more associated with ICC and CIN3 than with ≤CIN1 (adjusted for age, ORMH 7.36 (95% CI 2.33–23.21) and 4.37 (95% CI 1.81–10.58), respectively), as opposed to non-16 high-risk HPV types. Methylation levels of ASCL1, LHX8, and ST6GALNAC5 in cervical scrapes of women with CIN3 or worse (CIN3+) associated with HPV16 were significantly higher compared with methylation levels in cervical scrapes of women with CIN3+ associated with non-16 high-risk HPV types (p-values 0.017, 0.019, and 0.026, respectively). When CIN3 and ICC were analysed separately, the same trend was observed, but the differences were not significant. Our results confirm the key role that HPV16 plays in uterine cervix carcinogenesis, and suggest that the evaluation of host cell gene methylation levels may monitor the progression of cervical neoplasms also in WLHIV.
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Novel epigenetic markers for gastric cancer risk stratification in individuals after Helicobacter pylori eradication. Gastric Cancer 2018; 21:745-755. [PMID: 29427040 DOI: 10.1007/s10120-018-0803-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/27/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND The risk stratification of healthy individuals after Helicobacter pylori eradication is an urgent issue. The assessment of aberrant DNA methylation accumulated in gastric tissues with normal appearance, which can reflect overall epigenomic damage, is a promising strategy. We aimed to establish novel epigenetic cancer risk markers for H. pylori-eradicated individuals. METHODS Gastric mucosa was collected from eight healthy volunteers without H. pylori infection (G1), 75 healthy individuals with gastric atrophy (G2), and 94 gastric cancer patients (G3) after H. pylori eradication. Genome-wide analysis was conducted using Infinium 450 K and differentially methylated probes were screened using large difference and iEVORA-based methods. Bisulfite pyrosequencing was used for validation. RESULTS Screening, using 8 G1, 12 G2, and 12 G3 samples, isolated 57 candidates unmethylated in G1 and differentially methylated in G3 compared with G2. Validation for nine candidate markers (FLT3, LINC00643, RPRM, JAM2, ELMO1, BHLHE22, RIMS1, GUSBP5, and ZNF3) in 63 G2 and 82 G3 samples showed that all of them had significantly higher methylation levels in G3 than in G2 (P < 0.0001). Their methylation levels were highly correlated, which indicated that they reflect overall epigenomic damage. The candidates had sufficient performance (AUC: 0.70-0. 80) and high odds ratios (5.43-23.41), some of which were superior to a previous marker, miR-124a-3. The methylation levels of our novel markers were not associated with gastric atrophy, gender, or age. CONCLUSIONS Novel epigenetic markers for gastric cancer risk optimized for H. pylori-eradicated individuals were established.
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Molnár B, Galamb O, Péterfia B, Wichmann B, Csabai I, Bodor A, Kalmár A, Szigeti KA, Barták BK, Nagy ZB, Valcz G, Patai ÁV, Igaz P, Tulassay Z. Gene promoter and exon DNA methylation changes in colon cancer development - mRNA expression and tumor mutation alterations. BMC Cancer 2018; 18:695. [PMID: 29945573 PMCID: PMC6020382 DOI: 10.1186/s12885-018-4609-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/18/2018] [Indexed: 12/28/2022] Open
Abstract
Background DNA mutations occur randomly and sporadically in growth-related genes, mostly on cytosines. Demethylation of cytosines may lead to genetic instability through spontaneous deamination. Aims were whole genome methylation and targeted mutation analysis of colorectal cancer (CRC)-related genes and mRNA expression analysis of TP53 pathway genes. Methods Long interspersed nuclear element-1 (LINE-1) BS-PCR followed by pyrosequencing was performed for the estimation of global DNA metlyation levels along the colorectal normal-adenoma-carcinoma sequence. Methyl capture sequencing was done on 6 normal adjacent (NAT), 15 adenomatous (AD) and 9 CRC tissues. Overall quantitative methylation analysis, selection of top hyper/hypomethylated genes, methylation analysis on mutation regions and TP53 pathway gene promoters were performed. Mutations of 12 CRC-related genes (APC, BRAF, CTNNB1, EGFR, FBXW7, KRAS, NRAS, MSH6, PIK3CA, SMAD2, SMAD4, TP53) were evaluated. mRNA expression of TP53 pathway genes was also analyzed. Results According to the LINE-1 methylation results, overall hypomethylation was observed along the normal-adenoma-carcinoma sequence. Within top50 differential methylated regions (DMRs), in AD-N comparison TP73, NGFR, PDGFRA genes were hypermethylated, FMN1, SLC16A7 genes were hypomethylated. In CRC-N comparison DKK2, SDC2, SOX1 genes showed hypermethylation, while ERBB4, CREB5, CNTN1 genes were hypomethylated. In certain mutation hot spot regions significant DNA methylation alterations were detected. The TP53 gene body was addressed by hypermethylation in adenomas. APC, TP53 and KRAS mutations were found in 30, 15, 21% of adenomas, and in 29, 53, 29% of CRCs, respectively. mRNA expression changes were observed in several TP53 pathway genes showing promoter methylation alterations. Conclusions DNA methylation with consecutive phenotypic effect can be observed in a high number of promoter and gene body regions through CRC development. Electronic supplementary material The online version of this article (10.1186/s12885-018-4609-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary. .,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary.
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Bodor
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.,Institute of Mathematics and Informatics, Faculty of Sciences, University of Pécs, Ifjúság útja 6, Pécs, H-7624, Hungary
| | - Alexandra Kalmár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Krisztina Andrea Szigeti
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barbara Kinga Barták
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsófia Brigitta Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Péter Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
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Shiao SPK, Xiao H, Dong L, Wang X, Liu K, She J, Shi H. Genome wide DNA differential methylation regions in colorectal cancer patients in relation to blood related family members, obese and non-obese controls - a preliminary report. Oncotarget 2018; 9:25557-25571. [PMID: 29876008 PMCID: PMC5986643 DOI: 10.18632/oncotarget.25374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/25/2018] [Indexed: 01/20/2023] Open
Abstract
Despite evidences linking methylation changes in the cancer tissues, little is known about the methylation modification in the peripheral blood. With the current study, we identified differential methylation regions (DMRs) across human genome by collecting the blood samples of colorectal cancer (CRC) patients compared to that of their blood-related family who shared genetic inheritance and environmental influences, and unrelated obese and non-obese controls by accessing publicly available Gene Expression Omnibus data. We performed genome-wide analyses using the reduced representation bisulfite sequencing (RRBS) method covering about 25% of CpGs for whole human genome of the four groups (n = 5 each). In comparison to the non-obese controls, we observed significant DMRs in CRC for genes involved in tumorigenesis including MLH3, MSH2, MSH6, SEPT9, GNAS; and glucose transporter genes associated with obesity and diabetes including SLC2A1/GLUT1, and SLC2A3/GLUT3 that were reported on methylation being modified in cancer tissues. In addition, we observed significant DMRs in CRC for genes involved in the methylation pathways including PEMT, ALDH1L1, and DNMT3A. CRC and family members shared significant DMRs for genes of tumorigenesis including MSH2, SEPT9, GNAS, SLC2A1/GLUT1 and SLC2A3/GLUT3); and CAMK1, GLUT1/SLC2A1 and GLUT3/SLC2A3 genes involved in glucose and insulin metabolism that played vital role in development of obesity and diabetes. Our study provided evidences that these differentially methylated genes in the blood could potentially serve as candidate biomarkers for CRC diagnostic and may provide further understanding on CRC progression. Further studies are warranted to validate these methylation changes for diagnostic and prevention of CRC.
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Affiliation(s)
- S Pamela K Shiao
- College of Nursing, Augusta University, Augusta, GA, USA.,Medical College of Georgia, Augusta University, Augusta, GA, USA.,Center for Biotechnology and Genomic Medicine, Augusta, GA, USA
| | - Haiyan Xiao
- College of Nursing, Augusta University, Augusta, GA, USA
| | - Lixin Dong
- College of Nursing, Augusta University, Augusta, GA, USA
| | - Xiaoling Wang
- Medical College of Georgia, Augusta University, Augusta, GA, USA.,Georgia Prevention Institute, Augusta, GA, USA
| | - Kebin Liu
- Medical College of Georgia, Augusta University, Augusta, GA, USA.,Georgia Cancer Center, Augusta, GA, USA
| | - Jinxiong She
- Medical College of Georgia, Augusta University, Augusta, GA, USA.,Center for Biotechnology and Genomic Medicine, Augusta, GA, USA
| | - Huidong Shi
- Medical College of Georgia, Augusta University, Augusta, GA, USA.,Georgia Cancer Center, Augusta, GA, USA
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Symonds EL, Pedersen SK, Murray DH, Jedi M, Byrne SE, Rabbitt P, Baker RT, Bastin D, Young GP. Circulating tumour DNA for monitoring colorectal cancer-a prospective cohort study to assess relationship to tissue methylation, cancer characteristics and surgical resection. Clin Epigenetics 2018; 10:63. [PMID: 29796114 PMCID: PMC5956533 DOI: 10.1186/s13148-018-0500-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/10/2018] [Indexed: 12/19/2022] Open
Abstract
Background Cell-free circulating tumour-derived DNA (ctDNA) can be detected by testing for methylated BCAT1 and IKZF1 DNA, which has proven sensitivity for colorectal cancer (CRC). A prospective correlative biomarker study between presence of methylated BCAT1 and IKZF1 in tissue and blood was conducted in cases with CRC to explore how detection of such ctDNA biomarkers relates to cancer characteristics, methylation in tissue and surgical resection of the primary cancer. Methods Enrolled patients with invasive CRC had blood collected at diagnosis, prior to any treatment or surgery (peri-diagnostic sample). A subgroup of patients also had cancer and adjacent non-neoplastic tissue collected at surgical resection, as well as a second blood sample collected within 12 months of surgery (post-surgery sample). DNA was extracted from all samples and assayed for methylated BCAT1 and IKZF1 to determine the degree of methylation in tissue and the presence of ctDNA in blood. Results Of 187 cases providing peri-diagnostic blood samples, tissue was available in 91, and 93 provided at least one post-surgery blood sample for marker analysis. Significant methylation of either BCAT1 or IKZF1 was seen in 86/91 (94.5%) cancer tissues, with levels independent of stage and higher than that observed in adjacent non-neoplastic specimens (P < 0.001). ctDNA methylated in BCAT1 or IKZF1 was detected in 116 (62.0%) cases at diagnosis and was significantly more likely to be detected with later stage (P < 0.001) and distal tumour location (P = 0.004). Of the 91 patients who provided pre-and post-surgery blood samples, 47 patients were ctDNA-positive at diagnosis and 35 (74.5%) became negative after tumour resection. Conclusion This study has shown that BCAT1 and IKZF1 methylation are common events in CRC with almost all cancer tissues showing significant levels of methylation in the two genes. The presence of ctDNA in blood is stage-related and show rapid reversion to negative following surgical resection. Monitoring methylated BCAT1 and IKZF1 levels could therefore inform adequacy of surgical resection. Trial registration Australian New Zealand Clinical Trial Registry number 12611000318987. Registered 25 March 2011. Electronic supplementary material The online version of this article (10.1186/s13148-018-0500-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erin L Symonds
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia.,2Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia Australia
| | | | - David H Murray
- Clinical Genomics Pty Ltd, North Ryde, New South Wales Australia
| | - Maher Jedi
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Susan E Byrne
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Philippa Rabbitt
- 4Colorectal Surgery, Division of Surgery and Perioperative Medicine, Flinders Medical Centre, Bedford Park, South Australia Australia
| | - Rohan T Baker
- Clinical Genomics Pty Ltd, North Ryde, New South Wales Australia
| | - Dawn Bastin
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
| | - Graeme P Young
- 1Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University of South Australia, Bedford Park, South Australia 5042 Australia
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Gallardo-Gómez M, Moran S, Páez de la Cadena M, Martínez-Zorzano VS, Rodríguez-Berrocal FJ, Rodríguez-Girondo M, Esteller M, Cubiella J, Bujanda L, Castells A, Balaguer F, Jover R, De Chiara L. A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples. Clin Epigenetics 2018; 10:53. [PMID: 29686738 PMCID: PMC5902929 DOI: 10.1186/s13148-018-0487-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/02/2018] [Indexed: 12/16/2022] Open
Abstract
Background Colorectal cancer is the fourth cause of cancer-related deaths worldwide, though detection at early stages associates with good prognosis. Thus, there is a clear demand for novel non-invasive tests for the early detection of colorectal cancer and premalignant advanced adenomas, to be used in population-wide screening programs. Aberrant DNA methylation detected in liquid biopsies, such as serum circulating cell-free DNA (cfDNA), is a promising source of non-invasive biomarkers. This study aimed to assess the feasibility of using cfDNA pooled samples to identify potential serum methylation biomarkers for the detection of advanced colorectal neoplasia (colorectal cancer or advanced adenomas) using microarray-based technology. Results cfDNA was extracted from serum samples from 20 individuals with no colorectal findings, 20 patients with advanced adenomas, and 20 patients with colorectal cancer (stages I and II). Two pooled samples were prepared for each pathological group using equal amounts of cfDNA from 10 individuals, sex-, age-, and recruitment hospital-matched. We measured the methylation levels of 866,836 CpG positions across the genome using the MethylationEPIC array. Pooled serum cfDNA methylation data meets the quality requirements. The proportion of detected CpG in all pools (> 99% with detection p value < 0.01) exceeded Illumina Infinium methylation data quality metrics of the number of sites detected. The differential methylation analysis revealed 1384 CpG sites (5% false discovery rate) with at least 10% difference in the methylation level between no colorectal findings controls and advanced neoplasia, the majority of which were hypomethylated. Unsupervised clustering showed that cfDNA methylation patterns can distinguish advanced neoplasia from healthy controls, as well as separate tumor tissue from healthy mucosa in an independent dataset. We also observed that advanced adenomas and stage I/II colorectal cancer methylation profiles, grouped as advanced neoplasia, are largely homogenous and clustered close together. Conclusions This preliminary study shows the viability of microarray-based methylation biomarker discovery using pooled serum cfDNA samples as an alternative approach to tissue specimens. Our strategy sets an open door for deciphering new non-invasive biomarkers not only for colorectal cancer detection, but also for other types of cancers.
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Affiliation(s)
- María Gallardo-Gómez
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Sebastian Moran
- 2Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - María Páez de la Cadena
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Vicenta Soledad Martínez-Zorzano
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Francisco Javier Rodríguez-Berrocal
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Mar Rodríguez-Girondo
- 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, The Netherlands.,4SiDOR Research Group and Centro de Investigaciones Biomédicas (CINBIO), Faculty of Economics and Business Administration, University of Vigo, Vigo, Spain
| | - Manel Esteller
- 2Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Joaquín Cubiella
- 5Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Biomédica Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - Luis Bujanda
- 6Department of Gastroenterology, Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Antoni Castells
- 7Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Francesc Balaguer
- 7Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Rodrigo Jover
- 8Department of Gastroenterology, Hospital General Universitario de Alicante, Alicante, Spain
| | - Loretta De Chiara
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
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Verlaat W, Snoek BC, Heideman DAM, Wilting SM, Snijders PJF, Novianti PW, van Splunter AP, Peeters CFW, van Trommel NE, Massuger LFAG, Bekkers RLM, Melchers WJG, van Kemenade FJ, Berkhof J, van de Wiel MA, Meijer CJLM, Steenbergen RDM. Identification and Validation of a 3-Gene Methylation Classifier for HPV-Based Cervical Screening on Self-Samples. Clin Cancer Res 2018; 24:3456-3464. [PMID: 29632006 DOI: 10.1158/1078-0432.ccr-17-3615] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/22/2018] [Accepted: 04/02/2018] [Indexed: 01/09/2023]
Abstract
Purpose: Offering self-sampling of cervico-vaginal material for high-risk human papillomavirus (hrHPV) testing is an effective method to increase the coverage in cervical screening programs. Molecular triage directly on hrHPV-positive self-samples for colposcopy referral opens the way to full molecular cervical screening. Here, we set out to identify a DNA methylation classifier for detection of cervical precancer (CIN3) and cancer, applicable to lavage and brush self-samples.Experimental Design: We determined genome-wide DNA methylation profiles of 72 hrHPV-positive self-samples, using the Infinium Methylation 450K Array. The selected DNA methylation markers were evaluated by multiplex quantitative methylation-specific PCR (qMSP) in both hrHPV-positive lavage (n = 245) and brush (n = 246) self-samples from screening cohorts. Subsequently, logistic regression analysis was performed to build a DNA methylation classifier for CIN3 detection applicable to self-samples of both devices. For validation, an independent set of hrHPV-positive lavage (n = 199) and brush (n = 287) self-samples was analyzed.Results: Genome-wide DNA methylation profiling revealed 12 DNA methylation markers for CIN3 detection. Multiplex qMSP analysis of these markers in large series of lavage and brush self-samples yielded a 3-gene methylation classifier (ASCL1, LHX8, and ST6GALNAC5). This classifier showed a very good clinical performance for CIN3 detection in both lavage (AUC = 0.88; sensitivity = 74%; specificity = 79%) and brush (AUC = 0.90; sensitivity = 88%; specificity = 81%) self-samples in the validation set. Importantly, all self-samples from women with cervical cancer scored DNA methylation-positive.Conclusions: By genome-wide DNA methylation profiling on self-samples, we identified a highly effective 3-gene methylation classifier for direct triage on hrHPV-positive self-samples, which is superior to currently available methods. Clin Cancer Res; 24(14); 3456-64. ©2018 AACR.
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Affiliation(s)
- Wina Verlaat
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Barbara C Snoek
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Daniëlle A M Heideman
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Saskia M Wilting
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Peter J F Snijders
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Putri W Novianti
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands
| | - Annina P van Splunter
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Carel F W Peeters
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands
| | - Nienke E van Trommel
- Department of Gynecology, Antoni van Leeuwenhoek Hospital/Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Leon F A G Massuger
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ruud L M Bekkers
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Johannes Berkhof
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, the Netherlands
| | - Chris J L M Meijer
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Renske D M Steenbergen
- Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.
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Wei J, Li G, Zhang J, Zhou Y, Dang S, Chen H, Wu Q, Liu M. Integrated analysis of genome-wide DNA methylation and gene expression profiles identifies potential novel biomarkers of rectal cancer. Oncotarget 2018; 7:62547-62558. [PMID: 27566576 PMCID: PMC5308745 DOI: 10.18632/oncotarget.11534] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
DNA methylation was regarded as the promising biomarker for rectal cancer diagnosis. However, the optimal methylation biomarkers with ideal diagnostic performance for rectal cancer are still limited. To identify new molecular markers for rectal cancer, we mapped DNA methylation and transcriptomic profiles in the six rectal cancer and paired normal samples. Further analysis revealed the hypermethylated probes in cancer prone to be located in gene promoter. Meanwhile, transcriptome analysis presented 773 low-expressed and 1,161 over-expressed genes in rectal cancer. Correction analysis identified a panel of 36 genes with an inverse correlation between methylation and gene expression levels, including 10 known colorectal cancer related genes. From the other 26 novel marker genes, GFRA1 and GSTM2 were selected for further analysis on the basis of their biological functions. Further experiment analysis confirmed their methylation and expression status in a larger number (44) of rectal cancer samples, and ROC curves showed higher AUC than SEPT9, which has been used as a biomarker in rectal cancer. Our data suggests that aberrant DNA methylation of contiguous CpG sites in methylation array may be potential diagnostic markers of rectal cancer.
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Affiliation(s)
- Jiufeng Wei
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Jinning Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Yuhui Zhou
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Shuwei Dang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Hongsheng Chen
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, P.R. China
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
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50
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Porcellini E, Laprovitera N, Riefolo M, Ravaioli M, Garajova I, Ferracin M. Epigenetic and epitranscriptomic changes in colorectal cancer: Diagnostic, prognostic, and treatment implications. Cancer Lett 2018; 419:84-95. [PMID: 29360561 DOI: 10.1016/j.canlet.2018.01.049] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/07/2018] [Accepted: 01/12/2018] [Indexed: 12/12/2022]
Abstract
A cancer cell is the final product of a complex mixture of genetic, epigenetic and epitranscriptomic alterations, whose final interplay contribute to cancer onset and progression. This is specifically true for colorectal cancer, a tumor with a strong epigenetic component, which acts earlier than any other genetic alteration in promoting cancer cell malignant transformation. The pattern of progressive, and usually subtype-specific, DNA and histone modifications that occur in colorectal cancer has been extensively studied in the last decade, providing plenty of data to explore. For this tumor, it became recently evident that also RNA modifications play a relevant role in the activation of oncogenes or repression of tumor suppressor genes. In this review we provide a brief overview of all epigenetic and epitranscriptomic changes that have been found associated to colorectal cancer till now. We explore the impact of these alterations in cancer prognosis and response to treatment and discuss their potential use as cancer biomarkers.
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Affiliation(s)
- Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Noemi Laprovitera
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Ingrid Garajova
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.
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