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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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2
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Epigenetic insights in the diagnosis, prognosis, and treatment selection in CRC, an updated review. Mol Biol Rep 2022; 49:10013-10022. [PMID: 35727475 DOI: 10.1007/s11033-022-07569-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 05/05/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND/AIM The gradual accumulation of genetic and epigenetic alterations can lead to the development of colorectal cancer. In the last decade much research has been done to discover how methylation as an epigenetic alteration leads to carcinogenesis. While Methylation is a biological process, it can influence gene expression by affecting the promoter activity. This article reviews the role of methylation in critical pathways in CRC. METHODS In this study using appropriate keywords, all research and review articles related to the role of methylation on different cancers were collected and analyzed. Also, existing information on methylation detection methods and therapeutic sensitivity or resistance due to DNA methylation were reviewed. RESULTS The results of this survey revealed that while Methylation is a biological process, it can influence gene expression by affecting the promoter activity. Promoter methylation is associated with up or downregulation of genes involved in critical pathways, including cell cycle, DNA repair, and cell adherence. Hence promoter methylation can be used as a molecular tool for early diagnosis, improving treatment, and predicting treatment resistance. CONCLUSION Current knowledge on potential methylation biomarkers for diagnosis and prognoses of CRC has also been discussed. Our survey proposes that a multi-biomarker panel is more efficient than a single biomarker in the early diagnosis of CRC.
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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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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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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: 10] [Impact Index Per Article: 2.0] [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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Roles of Methylated DNA Biomarkers in Patients with Colorectal Cancer. DISEASE MARKERS 2019; 2019:2673543. [PMID: 30944663 PMCID: PMC6421784 DOI: 10.1155/2019/2673543] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/22/2018] [Indexed: 12/25/2022]
Abstract
Colorectal cancer (CRC) is a leading cancer globally; therefore, early diagnosis and surveillance of this cancer are of paramount importance. Current methods of CRC diagnosis rely heavily on endoscopy or radiological imaging. Noninvasive tests including serum detection of the carcinoembryonic antigen (CEA) and faecal occult blood testing (FOBT) are associated with low sensitivity and specificity, especially at early stages. DNA methylation biomarkers have recently been found to have higher accuracy in CRC detection and enhanced prediction of prognosis and chemotherapy response. The most widely studied biomarker in CRC is methylated septin 9 (SEPT9), which is the only FDA-approved methylation-based biomarker for CRC. Apart from SEPT9, other methylated biomarkers including tachykinin-1 (TAC1), somatostatin (SST), and runt-related transcription factor 3 (RUNX3) have been shown to effectively detect CRC in a multitude of sample types. This review will discuss the performances of various methylated biomarkers used for CRC diagnosis and monitoring, when used alone or in combination.
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Ye X, Mo M, Xu S, Yang Q, Wu M, Zhang J, Chen B, Li J, Zhong Y, Huang Q, Cai C. The hypermethylation of p16 gene exon 1 and exon 2: potential biomarkers for colorectal cancer and are associated with cancer pathological staging. BMC Cancer 2018; 18:1023. [PMID: 30348132 PMCID: PMC6198490 DOI: 10.1186/s12885-018-4921-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023] Open
Abstract
Background Tumor suppressor gene p16 promoter hypermethylation has been widely studied in colorectal cancer (CRC), yet its clinicopathological significance remains controversial. The methylation alterations of other regions within p16 gene are still rarely researched. The present study aimed to explore the methylation changes of p16 gene body in CRC and to find whether they were associated with clinicopathological staging of CRC. Methods Paired colorectal cancer tissues and corresponding adjacent normal tissues from 30 CRC patients were collected. The methylation levels of two CpG islands within p16 gene body, exon 1 and exon 2, were accurately assessed simultaneously by a LC-MS/MS method. The p16 protein expressions were assessed by immunohistochemistry assay. Statistical analyses were carried out using SPSS 17.0 software. Heat-map analysis was carried out by HemI 1.0 software. Results In the present study, CRC tissues showed more highly methylated than adjacent normal tissues at both CpG islands of p16 gene. And exon 2 hypermethylation was higher and more frequent than exon 1. The ROC curve analysis showed that the simultaneous use of both indicators had excellent sensitivity and specificity for distinguishing CRC tissues and adjacent normal tissues. Following, the methylation level of p16 exon 1/2 was negatively related to p16 protein expression. Further correlation analysis revealed that p16 exon 1 hypermethylation was associated with N/Dukes staging (p = 0.033), and p16 exon 2 hypermethylaiton was associated with T staging (p = 0.035). Conclusions The p16 gene body was remarkably hyper-methylated in CRC tissues and associated with p16 protein expression and cancer clinicopathological staging. The combination of p16 exon 1 and exon 2 could better reflect the overall methylation status of p16 gene body and provide potential biomarkers of CRC.
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Affiliation(s)
- Xiaoxia Ye
- Department of Histology and Embryology, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Mingming Mo
- Analysis Center, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Simin Xu
- Institute of Neurology, Affiliated Hospital, Guangdong Medical University, No. 2 Wenming Dong Road, Zhanjiang, Guangdong, 524023, People's Republic of China
| | - Qingjin Yang
- Analysis Center, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Minhua Wu
- Department of Histology and Embryology, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Junjie Zhang
- Analysis Center, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Bin Chen
- Analysis Center, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Jian Li
- Analysis Center, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Yu Zhong
- Analysis Center, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Qionglin Huang
- Analysis Center, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China
| | - Chun Cai
- Analysis Center, Guangdong Medical University, Zhanjiang, 524023, People's Republic of China.
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