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Sajibu S, Sonder E, Tiwari A, Orjuela S, Parker HR, Frans OT, Gubler C, Marra G, Robinson MD. Validation of hypermethylated DNA regions found in colorectal cancers as potential aging-independent biomarkers of precancerous colorectal lesions. BMC Cancer 2023; 23:998. [PMID: 37853362 PMCID: PMC10585861 DOI: 10.1186/s12885-023-11487-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND We previously identified 16,772 colorectal cancer-associated hypermethylated DNA regions that were also detectable in precancerous colorectal lesions (preCRCs) and unrelated to normal mucosal aging. We have now conducted a study to validate 990 of these differentially methylated DNA regions (DMRs) in a new series of preCRCs. METHODS We used targeted bisulfite sequencing to validate these 990 potential biomarkers in 59 preCRC tissue samples (41 conventional adenomas, 18 sessile serrated lesions), each with a patient-matched normal mucosal sample. Based on differential DNA methylation tests, a panel of candidate DMRs was chosen on a subset of our cohort and then validated on the remaining part of our cohort and two publicly available datasets with respect to their stratifying potential between preCRCs and normal mucosa. RESULTS Strong statistical significance for the difference in methylation levels was observed across the full set of 990 investigated DMRs. From these, a selected candidate panel of 30 DMRs correctly identified 58/59 tumors (area under the receiver operating curve: 0.998). CONCLUSIONS These validated DNA hypermethylation markers can be exploited to develop more accurate noninvasive colorectal tumor screening assays.
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Affiliation(s)
- Sija Sajibu
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Emanuel Sonder
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Amit Tiwari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Stephany Orjuela
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Hannah R Parker
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | | | - Christoph Gubler
- Division of Gastroenterology, Triemli Hospital, Zurich, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.
- SIB Swiss Institute of Bioinformatics, Vaud, Switzerland.
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Ghatak S, Satapathy SR, Sjölander A. DNA Methylation and Gene Expression of the Cysteinyl Leukotriene Receptors as a Prognostic and Metastatic Factor for Colorectal Cancer Patients. Int J Mol Sci 2023; 24:ijms24043409. [PMID: 36834820 PMCID: PMC9963074 DOI: 10.3390/ijms24043409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Colorectal cancer (CRC), one of the leading causes of cancer-related deaths in the western world, is the third most common cancer for both men and women. As a heterogeneous disease, colon cancer (CC) is caused by both genetic and epigenetic changes. The prognosis for CRC is affected by a variety of features, including late diagnosis, lymph node and distant metastasis. The cysteinyl leukotrienes (CysLT), as leukotriene D4 and C4 (LTD4 and LTC4), are synthesized from arachidonic acid via the 5-lipoxygenase pathway, and play an important role in several types of diseases such as inflammation and cancer. Their effects are mediated via the two main G-protein-coupled receptors, CysLT1R and CysLT2R. Multiple studies from our group observed a significant increase in CysLT1R expression in the poor prognosis group, whereas CysLT2R expression was higher in the good prognosis group of CRC patients. Here, we systematically explored and established the role of the CysLTRs, cysteinyl leukotriene receptor 1(CYSLTR1) and cysteinyl leukotriene receptor 2 (CYSLTR2) gene expression and methylation in the progression and metastasis of CRC using three unique in silico cohorts and one clinical CRC cohort. Primary tumor tissues showed significant CYSLTR1 upregulation compared with matched normal tissues, whereas it was the opposite for the CYSLTR2. Univariate Cox proportional-hazards (CoxPH) analysis yielded a high expression of CYSLTR1 and accurately predicted high-risk patients in terms of overall survival (OS; hazard ratio (HR) = 1.87, p = 0.03) and disease-free survival [DFS] Hazard ratio [HR] = 1.54, p = 0.05). Hypomethylation of the CYSLTR1 gene and hypermethylation of the CYSLTR2 gene were found in CRC patients. The M values of the CpG probes for CYSLTR1 are significantly lower in primary tumor and metastasis samples than in matched normal samples, but those for CYSLTR2 are significantly higher. The differentially upregulated genes between tumor and metastatic samples were uniformly expressed in the high-CYSLTR1 group. Two epithelial-mesenchymal transition (EMT) markers, E-cadherin (CDH1) and vimentin (VIM) were significantly downregulated and upregulated in the high-CYSLTR1 group, respectively, but the result was opposite to that of CYSLTR2 expression in CRC. CDH1 expression was high in patients with less methylated CYSLTR1 but low in those with more methylated CYSLTR2. The EMT-associated observations were also validated in CC SW620 cell-derived colonospheres, which showed decreased E-cadherin expression in the LTD4 stimulated cells, but not in the CysLT1R knockdown SW620 cells. The methylation profiles of the CpG probes for CysLTRs significantly predicted lymph node (area under the curve [AUC] = 0.76, p < 0.0001) and distant (AUC = 0.83, p < 0.0001) metastasis. Intriguingly, the CpG probes cg26848126 (HR = 1.51, p = 0.03) for CYSLTR1, and cg16299590 (HR = 2.14, p = 0.03) for CYSLTR2 significantly predicted poor prognosis in terms of OS, whereas the CpG probe cg16886259 for CYSLTR2 significantly predicts a poor prognosis group in terms of DFS (HR = 2.88, p = 0.03). The CYSLTR1 and CYSLTR2 gene expression and methylation results were successfully validated in a CC patient cohort. In this study, we have demonstrated that CysLTRs' methylation and gene expression profile are associated with the progression, prognosis, and metastasis of CRC, which might be used for the assessment of high-risk CRC patients after validating the result in a larger CRC cohort.
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Goldoost S, Zarredar H, Asadi M, Shirvaliloo M, Raeisi M. Expression and promoter methylation of mitogen-activated protein kinase 1 in tumor and marginal cells of breast cancer. Breast Dis 2023; 42:437-445. [PMID: 38143331 DOI: 10.3233/bd-230001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
AIM In the present study, we sought to explore potential differences in the expression and promoter methylation of mitogen-activated protein kinase 1 (MAPK1) between tumor and marginal cells of breast cancer lesions. METHODS A total of 50 randomly selected patients with breast cancer (BCa) undergoing needle biopsy were enrolled. Clinical specimens containing both tumor and marginal cells were collected and preserved. After DNA extraction using specific primers, MAPK1 mRNA and promoter methylation were measured with spectrophotometry at 260/280 nm absorption wavelengths. To deliver a comparative analysis, data from The Cancer Genome Atlas (TCGA) program regarding breast cancer (BRCA), were downloaded from Xena Functional Genomics Explorer and separately analyzed. The suitability of MAPK1 expression and promoter methylation as biomarkers for BCa was analyzed with receiver operating characteristic (ROC) curves. RESULTS We found a positive correlation between tumor stage and MAPK1 expression (P-value: 0.029) in BCa. Likewise, MAPK1 expression was significantly associated with lymph node metastasis (P-value: 0.018). There was a significant difference in the expression of MAPK1 mRNA between tumor and marginal cells of BCa and BRCA (P-value < 0.001). However, we did not find any statistically significant difference in MAPK1 promoter methylation between tumor and marginal cells of both BCa and BRCA. With an area under the curve (AUC) of 0.71, the diagnostic accuracy of MAPK1 expression in BCa and BRCA was validated. However, MAPK1 promoter methylation was not found to be a suitable biomarker. CONCLUSION Our findings suggest that while MAPK1 expression, might be a promising biomarker for evaluating oncogenic activity in patients suspected of BCa. We were not able to detect a prognostic/diagnostic role for MAPK1 promoter methylation.
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Affiliation(s)
- Solmaz Goldoost
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Habib Zarredar
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Asadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Shirvaliloo
- Future Science Group, London, UK
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mortaza Raeisi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Díez-Villanueva A, Sanz-Pamplona R, Solé X, Cordero D, Crous-Bou M, Guinó E, Lopez-Doriga A, Berenguer A, Aussó S, Paré-Brunet L, Obón-Santacana M, Moratalla-Navarro F, Salazar R, Sanjuan X, Santos C, Biondo S, Diez-Obrero V, Garcia-Serrano A, Alonso MH, Carreras-Torres R, Closa A, Moreno V. COLONOMICS - integrative omics data of one hundred paired normal-tumoral samples from colon cancer patients. Sci Data 2022; 9:595. [PMID: 36182938 PMCID: PMC9526730 DOI: 10.1038/s41597-022-01697-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Colonomics is a multi-omics dataset that includes 250 samples: 50 samples from healthy colon mucosa donors and 100 paired samples from colon cancer patients (tumor/adjacent). From these samples, Colonomics project includes data from genotyping, DNA methylation, gene expression, whole exome sequencing and micro-RNAs (miRNAs) expression. It also includes data from copy number variation (CNV) from tumoral samples. In addition, clinical data from all these samples is available. The aims of the project were to explore and integrate these datasets to describe colon cancer at molecular level and to compare normal and tumoral tissues. Also, to improve screening by finding biomarkers for the diagnosis and prognosis of colon cancer. This project has its own website including four browsers allowing users to explore Colonomics datasets. Since generated data could be reuse for the scientific community for exploratory or validation purposes, here we describe omics datasets included in the Colonomics project as well as results from multi-omics layers integration.
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Affiliation(s)
- Anna Díez-Villanueva
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Rebeca Sanz-Pamplona
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Xavier Solé
- Molecular Biology CORE, Center for Biomedical Diagnostics, Hospital Clínic de Barcelona, 08036, Barcelona, Spain
- Translational Genomic and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036, Barcelona, Spain
| | - David Cordero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Marta Crous-Bou
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO) - Bellvitge Biomedical Research Institute (IDIBELL). L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Elisabet Guinó
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Adriana Lopez-Doriga
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Antoni Berenguer
- Rheumatology Department - Parc Taulí Research and Innovation Institute (I3PT), Barcelona, Spain
| | - Susanna Aussó
- TIC Salut Social Foundation. Ministry of Health of Generalitat de Catalunya, Barcelona, Spain
| | | | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ferran Moratalla-Navarro
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Ramon Salazar
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Medical Oncology Department. Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Xavier Sanjuan
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Pathology Service, Bellvitge University Hospital (HUB), Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Medical Oncology Department. Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Sebastiano Biondo
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Digestive Surgery Service, Bellvitge University Hospital (HUB). Hospitalet de Llobregat, Barcelona, Spain
| | - Virginia Diez-Obrero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
| | - Ainhoa Garcia-Serrano
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Maria Henar Alonso
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Robert Carreras-Torres
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Adria Closa
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
| | - Víctor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain.
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain.
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain.
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Knorr S, Skakkebæk A, Just J, Johannsen EB, Trolle C, Vang S, Lohse Z, Bytoft B, Damm P, Højlund K, Jensen DM, Gravholt CH. Epigenetic and transcriptomic alterations in offspring born to women with type 1 diabetes (the EPICOM study). BMC Med 2022; 20:338. [PMID: 36138412 PMCID: PMC9503228 DOI: 10.1186/s12916-022-02514-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Offspring born to women with pregestational type 1 diabetes (T1DM) are exposed to an intrauterine hyperglycemic milieu and has an increased risk of metabolic disease later in life. In this present study, we hypothesize that in utero exposure to T1DM alters offspring DNA methylation and gene expression, thereby altering their risk of future disease. METHODS Follow-up study using data from the Epigenetic, Genetic and Environmental Effects on Growth, Metabolism and Cognitive Functions in Offspring of Women with Type 1 Diabetes (EPICOM) collected between 2012 and 2013. SETTING Exploratory sub-study using data from the nationwide EPICOM study. PARTICIPANTS Adolescent offspring born to women with T1DM (n=20) and controls (n=20) matched on age, sex, and postal code. MAIN OUTCOME MEASURES This study investigates DNA methylation using the 450K-Illumina Infinium assay and RNA expression (RNA sequencing) of leucocytes from peripheral blood samples. RESULTS We identified 9 hypomethylated and 5 hypermethylated positions (p < 0.005, |ΔM-value| > 1) and 38 up- and 1 downregulated genes (p < 0.005, log2FC ≥ 0.3) in adolescent offspring born to women with T1DM compared to controls. None of these findings remained significant after correction for multiple testing. However, we identified differences in gene co-expression networks, which could be of biological significance, using weighted gene correlation network analysis. Interestingly, one of these modules was significantly associated with offspring born to women with T1DM. Functional enrichment analysis, using the identified changes in methylation and gene expression as input, revealed enrichment in disease ontologies related to diabetes, carbohydrate and glucose metabolism, pathways including MAPK1/MAPK3 and MAPK family signaling, and genes related to T1DM, obesity, atherosclerosis, and vascular pathologies. Lastly, by integrating the DNA methylation and RNA expression data, we identified six genes where relevant methylation changes corresponded with RNA expression (CIITA, TPM1, PXN, ST8SIA1, LIPA, DAXX). CONCLUSIONS These findings suggest the possibility for intrauterine exposure to maternal T1DM to impact later in life methylation and gene expression in the offspring, a profile that may be linked to the increased risk of vascular and metabolic disease later in life.
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Affiliation(s)
- Sine Knorr
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Hedeager 3, 2. fl, 8200, Aarhus, DK, Denmark. .,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark. .,Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark.
| | - Anne Skakkebæk
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Jesper Just
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Emma B Johannsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christian Trolle
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Zuzana Lohse
- Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark
| | - Birgitte Bytoft
- Center for Pregnant Women with Diabetes, Department of Obstetrics, Rigshospitalet, Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peter Damm
- Center for Pregnant Women with Diabetes, Department of Obstetrics, Rigshospitalet, Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kurt Højlund
- Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark
| | - Dorte M Jensen
- Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark
| | - Claus H Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhang L, Li D, Gao L, Fu J, Sun S, Huang H, Zhang D, Jia C, Zheng T, Cui B, Liu Y, Zhao Y. Promoter Methylation of QKI as a Potential Specific Biomarker for Early Detection of Colorectal Cancer. Front Genet 2022; 13:928150. [PMID: 36017498 PMCID: PMC9395658 DOI: 10.3389/fgene.2022.928150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Early and specific detection of cancer provides an opportunity for appropriate treatment. Although studies have suggested that QKI is a tumor suppressor gene, no studies have evaluated the diagnostic utility of QKI methylation in colorectal cancer (CRC). Here, we evaluated the methylation status of QKI by integrating the methylation data of tissues and cell lines of multiple cancer types. The diagnostic performance of QKI was analyzed in the discovery dataset from the TCGA CRC 450K array (n = 440) and tested in the test sets (n = 845) from the GEO. The methylation level of QKI was further validated in our independent dataset (n = 388) using targeted bisulfite sequencing. All detected CpG sites in the QKI promoter showed CRC-specific hypermethylation in 31 types of tumor tissues. In the discovery dataset, six consecutive CpG sites achieved high diagnostic performances, with AUCs ranging from 0.821 to 0.930. In the test set, a region (chr6: 163,834,452–163,834,924) including four consecutive CpG sites had robust diagnostic ability in distinguishing CRC and adenoma from normal samples. In the validation dataset, similar robust results were observed in both early- and advanced-stage CRC patients. In addition, QKI exhibited hypermethylation in the cfDNA of patients with CRC (n = 14). Collectively, the QKI promoter is a CRC-specific methylation biomarker and holds great promise for improving the diagnosis using minimally invasive biopsy.
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Affiliation(s)
- Lei Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Dapeng Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Lijing Gao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Jinming Fu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Simin Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Hao Huang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Ding Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Chenyang Jia
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Ting Zheng
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
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8
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Wang H, Zhang R, Li E, Yan R, Ma B, Ma Q. Pan-Cancer Transcriptome and Immune Infiltration Analyses Reveal the Oncogenic Role of Far Upstream Element-Binding Protein 1 (FUBP1). Front Mol Biosci 2022; 9:794715. [PMID: 35274005 PMCID: PMC8902172 DOI: 10.3389/fmolb.2022.794715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Despite increasing evidence to support the relationship between FUBP1 and tumorigenesis in some types of cancers, there have been no analyses from a pan-cancer perspective. Here, we are the first to investigate the putative oncogenic role of FUBP1 in 33 cancer types based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Dysregulated FUBP1 expression was observed in most cancer types, and high FUBP1 expression suggests poor prognosis in cancers such as ACC, KICH, LIHC, LUAD, LUSC, SARC, CESC, and SKCM. Missense mutation is the most common type of FUBP1 mutation, and R430 in KH_4 is a predominant mutation site. Enhanced phosphorylation of FUBP1 at the S120 site has been observed in clear cell RCC, lung adenocarcinoma, and pediatric brain cancer specimens from African-American and Asian individuals. The expression of FUBP1 was found to be negatively correlated with the infiltration of CD8+ T lymphocytes in GBM, HNSC-HPV- and UCEC but positively correlated with that of tumor-associated fibroblasts in CESC, ESCA, HNSC, LIHC, LUAD, PAAD, and THYM. Furthermore, RNA splicing and spliceosome signaling were predominantly enriched in both GO and KEGG analyses of the functional mechanism of FUBP1. Briefly, this pan-cancer analysis comprehensively revealed the multifaceted characteristics and oncogenic role of FUBP1 in different human cancers.
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Affiliation(s)
| | | | | | | | - Baoan Ma
- *Correspondence: Qiong Ma, ; Baoan Ma,
| | - Qiong Ma
- *Correspondence: Qiong Ma, ; Baoan Ma,
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9
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Díez-Villanueva A, Jordà M, Carreras-Torres R, Alonso H, Cordero D, Guinó E, Sanjuan X, Santos C, Salazar R, Sanz-Pamplona R, Moreno V. Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue. Clin Epigenetics 2021; 13:162. [PMID: 34419169 PMCID: PMC8380335 DOI: 10.1186/s13148-021-01148-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/07/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA methylation is involved in the regulation of gene expression and phenotypic variation, but the inter-relationship between genetic variation, DNA methylation and gene expression remains poorly understood. Here we combine the analysis of genetic variants related to methylation markers (methylation quantitative trait loci: mQTLs) and gene expression (expression quantitative trait loci: eQTLs) with methylation markers related to gene expression (expression quantitative trait methylation: eQTMs), to provide novel insights into the genetic/epigenetic architecture of colocalizing molecular markers. RESULTS Normal mucosa from 100 patients with colon cancer and 50 healthy donors included in the Colonomics project have been analyzed. Linear models have been used to find mQTLs and eQTMs within 1 Mb of the target gene. From 32,446 eQTLs previously detected, we found a total of 6850 SNPs, 114 CpGs and 52 genes interrelated, generating 13,987 significant combinations of co-occurring associations (meQTLs) after Bonferromi correction. Non-redundant meQTLs were 54, enriched in genes involved in metabolism of glucose and xenobiotics and immune system. SNPs in meQTLs were enriched in regulatory elements (enhancers and promoters) compared to random SNPs within 1 Mb of genes. Three colorectal cancer GWAS SNPs were related to methylation changes, and four SNPs were related to chemerin levels. Bayesian networks have been used to identify putative causal relationships among associated SNPs, CpG and gene expression triads. We identified that most of these combinations showed the canonical pathway of methylation markers causes gene expression variation (60.1%) or non-causal relationship between methylation and gene expression (33.9%); however, in up to 6% of these combinations, gene expression was causing variation in methylation markers. CONCLUSIONS In this study we provided a characterization of the regulation between genetic variants and inter-dependent methylation markers and gene expression in a set of 150 healthy colon tissue samples. This is an important finding for the understanding of molecular susceptibility on colon-related complex diseases.
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Affiliation(s)
- Anna Díez-Villanueva
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Spain
| | - Robert Carreras-Torres
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Henar Alonso
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - David Cordero
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Xavier Sanjuan
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Pathology Department, University Hospital Bellvitge (HUB), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Medical Oncology Service, Catalan Institute of Oncology (ICO), Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Ramón Salazar
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Medical Oncology Service, Catalan Institute of Oncology (ICO), Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain.
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain.
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain.
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain.
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10
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Orjuela S, Parker HR, Sajibu S, Cereatti F, Sauter M, Buffoli F, Robinson MD, Marra G. Disentangling tumorigenesis-associated DNA methylation changes in colorectal tissues from those associated with ageing. Epigenetics 2021; 17:677-694. [PMID: 34369258 DOI: 10.1080/15592294.2021.1952375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Physiological ageing and tumorigenesis are both associated with epigenomic alterations in human tissue cells, the most extensively investigated of which entails de novo cytosine methylation (i.e., hypermethylation) within the CpG dinucleotides of CpG islands. Genomic regions that become hypermethylated during tumorigenesis are generally believed to overlap regions that acquire methylation in normal tissues as an effect of ageing. To define the extension of this overlap, we analysed the DNA methylomes of 48 large-bowel tissue samples taken from women of different ages during screening colonoscopy: 18 paired samples of normal and lesional tissues from donors harbouring a precancerous lesion and 12 samples of normal mucosa from tumour-free donors. Each sample was subjected to targeted, genome-wide bisulphite sequencing of ~2.5% of the genome, including all CpG islands. In terms of both its magnitude and extension along the chromatin, tumour-associated DNA hypermethylation in these regions was much more conspicuous than that observed in the normal mucosal samples from older (vs. younger) tumour-free donors. 83% of the ageing-associated hypermethylated regions (n = 2501) coincided with hypermethylated regions observed in tumour samples. However, 86% of the regions displaying hypermethylation in precancerous lesions (n = 16,772) showed no methylation changes in the ageing normal mucosa. The tumour-specificity of this latter hypermethylation was validated using published sets of data on DNA methylation in normal and neoplastic colon tissues. This extensive set of genomic regions displaying tumour-specific hypermethylation represents a rich vein of putative biomarkers for the early, non-invasive detection of colorectal tumours in women of all ages.
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Affiliation(s)
- Stephany Orjuela
- Institute of Molecular Cancer Research, University of Zurich, Switzerland.,Department of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Switzerland
| | - Hannah R Parker
- Institute of Molecular Cancer Research, University of Zurich, Switzerland.,Department of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Switzerland
| | - Sija Sajibu
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
| | | | - Matthias Sauter
- Division of Gastroenterology, Triemli Hospital Zurich, Switzerland
| | | | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
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11
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Hao L, Yang Z. Dynamical Mechanisms for Gene Regulation Mediated by Two Noncoding RNAs in Long-Term Memory Formation. Neural Plast 2021; 2021:6668389. [PMID: 33833791 DOI: 10.1155/2021/6668389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/26/2021] [Accepted: 03/08/2021] [Indexed: 02/03/2023] Open
Abstract
Noncoding RNAs such as miRNAs and piRNAs have long-lasting effects on the regulation of gene expression involved in long-term synaptic changes. To characterize gene regulation mediated by small noncoding RNAs associated with long-term memory in Aplysia, we consider two noncoding RNAs stimulated by 5-HT into a gene regulatory network motif model, including miR-124 that binds to and inhibits the mRNA of CREB1 and piR-F that facilitates serotonin-dependent DNA methylation to lead to repression of CREB2. Codimension-1 and -2 bifurcation analyses of 5-HT regulating both miR-124 and piR-F and a negative feedback strength for oscillation reveal rich dynamical properties of bistability and oscillations robust to variations in all other parameters. More importantly, we verify three stimulus protocols of 5-HT in experiments by our model and find that application of five pulses of 5-HT leads to a transient decrease of miR-124 but increase of piR-F concentrations, which matters sustained high level of CREB1 concentration associated with long-term memory. Furthermore, we perform bifurcation analyses for the concentrations of miR-124 and piR-F as two parameters to explore dynamical mechanisms underlying the epigenetic regulation in long-term memory formation. This study provides insights into revealing regulatory roles of epigenetic changes in gene expression involving noncoding RNAs associated with synaptic plasticity.
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12
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Devall M, Sun X, Yuan F, Cooper GS, Willis J, Weisenberger DJ, Casey G, Li L. Racial Disparities in Epigenetic Aging of the Right vs Left Colon. J Natl Cancer Inst 2020; 113:1779-1782. [PMID: 33377907 PMCID: PMC8634501 DOI: 10.1093/jnci/djaa206] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/27/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
There are well-documented racial differences in age-of-onset and laterality of colorectal cancer. Epigenetic age acceleration is postulated to be an underlying factor. However, comparative studies of side-specific colonic tissue epigenetic aging are lacking. Here, we performed DNA methylation analysis of matched right and left biopsies of normal colon from 128 individuals. Among African Americans (n = 88), the right colon showed accelerated epigenetic aging as compared with individual-matched left colon (1.51 years; 95% confidence interval [CI] = 0.62 to 2.40 years; 2-sided P = .001). In contrast, among European Americans (n = 40), the right colon shows remarkable age deceleration (1.93 years; 95% CI = 0.65 to 3.21 years; 2-sided P = .004). Further, epigenome-wide analysis of DNA methylation identifies a unique pattern of hypermethylation in African American right colon. Our study is the first to report such race and side-specific differences in epigenetic aging of normal colon, providing novel insight into the observed younger age-of-onset and relative preponderance of right-side colon neoplasia in African Americans.
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Affiliation(s)
- Matthew Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Xiangqing Sun
- Department of Family Medicine, University of Virginia, Charlottesville, VA, USA
| | - Fangcheng Yuan
- Department of Family Medicine, University of Virginia, Charlottesville, VA, USA
| | - Gregory S Cooper
- Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Joseph Willis
- Department of Pathology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA, USA,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA,Correspondence to: Li Li, MD, PhD, Department of Family Medicine, University of Virginia School of Medicine, McKim Hall, Room 3156, 1415 Jefferson Park Avenue, PO Box 800729, Charlottesville, VA 22908 ()
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