1
|
Ren Y, Huang P, Huang X, Zhang L, Liu L, Xiang W, Liu L, He X. Alterations of DNA methylation profile in peripheral blood of children with simple obesity. Health Inf Sci Syst 2024; 12:26. [PMID: 38505098 PMCID: PMC10948706 DOI: 10.1007/s13755-024-00275-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024] Open
Abstract
Purpose To investigate the association between DNA methylation and childhood simple obesity. Methods Genome-wide analysis of DNA methylation was conducted on peripheral blood samples from 41 children with simple obesity and 31 normal controls to identify differentially methylated sites (DMS). Subsequently, gene functional analysis of differentially methylated genes (DMGs) was carried out. After screening the characteristic DMGs based on specific conditions, the methylated levels of these DMS were evaluated and verified by pyrosequencing. Receiver operating characteristic (ROC) curve analysis assessed the predictive efficacy of corresponding DMGs. Finally, Pearson correlation analysis revealed the correlation between specific DMS and clinical data. Results The overall DNA methylation level in the obesity group was significantly lower than in normal. A total of 241 DMS were identified. Functional pathway analysis revealed that DMGs were primarily involved in lipid metabolism, carbohydrate metabolism, amino acid metabolism, human diseases, among other pathways. The characteristic DMS within the genes Transcription factor A mitochondrial (TFAM) and Piezo type mechanosensitive ion channel component 1(PIEZO1) were recognized as CpG-cg05831083 and CpG-cg14926485, respectively. Furthermore, the methylation level of CpG-cg05831083 significantly correlated with body mass index (BMI) and vitamin D. Conclusions Abnormal DNA methylation is closely related to childhood simple obesity. The altered methylation of CpG-cg05831083 and CpG-cg14926485 could potentially serve as biomarkers for childhood simple obesity. Supplementary Information The online version contains supplementary material available at 10.1007/s13755-024-00275-w.
Collapse
Affiliation(s)
- Yi Ren
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
- Children’s Brain Development and Brain Injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
- Department of Pediatrics, Haikou Maternal and Child Health Hospital, Haikou, 570100 China
| | - Peng Huang
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
- Children’s Brain Development and Brain Injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
| | - Xiaoyan Huang
- Department of Genetics, Metabolism, and Endocrinology, Hainan Women and Children’s Medical Center, Haikou, 570100 China
| | - Lu Zhang
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
- Children’s Brain Development and Brain Injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
| | - Lingjuan Liu
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
- Children’s Brain Development and Brain Injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
| | - Wei Xiang
- Hainan Women and Children’s Medical Center, Haikou, 570100 China
- Children’s Hospital of Fudan University at Hainan, Haikou, 570100 China
- Children’s Hospital of Hainan Medical University, Haikou, 570100 China
| | - Liqun Liu
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
- Children’s Brain Development and Brain Injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
| | - Xiaojie He
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
- Laboratory of Pediatric Nephrology, Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, 410011 China
| |
Collapse
|
2
|
Braga EA, Fridman MV, Burdennyy AM, Loginov VI, Dmitriev AA, Pronina IV, Morozov SG. Various LncRNA Mechanisms in Gene Regulation Involving miRNAs or RNA-Binding Proteins in Non-Small-Cell Lung Cancer: Main Signaling Pathways and Networks. Int J Mol Sci 2023; 24:13617. [PMID: 37686426 PMCID: PMC10487663 DOI: 10.3390/ijms241713617] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial players in the pathogenesis of non-small-cell lung cancer (NSCLC). A competing binding of lncRNAs and mRNAs with microRNAs (miRNAs) is one of the most common mechanisms of gene regulation by lncRNAs in NSCLC, which has been extensively researched in the last two decades. However, alternative mechanisms that do not depend on miRNAs have also been reported. Among them, the most intriguing mechanism is mediated by RNA-binding proteins (RBPs) such as IGF2BP1/2/3, YTHDF1, HuR, and FBL, which increase the stability of target mRNAs. IGF2BP2 and YTHDF1 may also be involved in m6A modification of lncRNAs or target mRNAs. Some lncRNAs, such as DLGAP1-AS2, MALAT1, MNX1-AS1, and SNHG12, are involved in several mechanisms depending on the target: lncRNA/miRNA/mRNA interactome and through RBP. The target protein sets selected here were then analyzed using the DAVID database to identify the pathways overrepresented by KEGG, Wikipathways, and the Reactome pathway. Using the STRING website, we assessed interactions between the target proteins and built networks. Our analysis revealed that the JAK-STAT and Hippo signaling pathways, cytokine pathways, the VEGFA-VEGFR2 pathway, mechanisms of cell cycle regulation, and neovascularization are the most relevant to the effect of lncRNA on NSCLC.
Collapse
Affiliation(s)
- Eleonora A. Braga
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Marina V. Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Alexey M. Burdennyy
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
| | - Vitaly I. Loginov
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
| | - Sergey G. Morozov
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
| |
Collapse
|
3
|
Zappe K, Kopic A, Scheichel A, Schier AK, Schmidt LE, Borutzki Y, Miedl H, Schreiber M, Mendrina T, Pirker C, Pfeiler G, Hacker S, Haslik W, Pils D, Bileck A, Gerner C, Meier-Menches S, Heffeter P, Cichna-Markl M. Aberrant DNA Methylation, Expression, and Occurrence of Transcript Variants of the ABC Transporter ABCA7 in Breast Cancer. Cells 2023; 12:1462. [PMID: 37296582 PMCID: PMC10252461 DOI: 10.3390/cells12111462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
The ABC transporter ABCA7 has been found to be aberrantly expressed in a variety of cancer types, including breast cancer. We searched for specific epigenetic and genetic alterations and alternative splicing variants of ABCA7 in breast cancer and investigated whether these alterations are associated with ABCA7 expression. By analyzing tumor tissues from breast cancer patients, we found CpGs at the exon 5-intron 5 boundary aberrantly methylated in a molecular subtype-specific manner. The detection of altered DNA methylation in tumor-adjacent tissues suggests epigenetic field cancerization. In breast cancer cell lines, DNA methylation levels of CpGs in promoter-exon 1, intron 1, and at the exon 5-intron 5 boundary were not correlated with ABCA7 mRNA levels. By qPCR involving intron-specific and intron-flanking primers, we identified intron-containing ABCA7 mRNA transcripts. The occurrence of intron-containing transcripts was neither molecular subtype-specific nor directly correlated with DNA methylation at the respective exon-intron boundaries. Treatment of breast cancer cell lines MCF-7, BT-474, SK-BR3, and MDA-MB-231 with doxorubicin or paclitaxel for 72 h resulted in altered ABCA7 intron levels. Shotgun proteomics revealed that an increase in intron-containing transcripts was associated with significant dysregulation of splicing factors linked to alternative splicing.
Collapse
Affiliation(s)
- Katja Zappe
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Antonio Kopic
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Alexandra Scheichel
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Ann-Katrin Schier
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Lukas Emanuel Schmidt
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Yasmin Borutzki
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Heidi Miedl
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Martin Schreiber
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Theresa Mendrina
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Pirker
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Georg Pfeiler
- Division of Gynecology and Gynecological Oncology, Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stefan Hacker
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Werner Haslik
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Dietmar Pils
- Division of Visceral Surgery, Department of General Surgery and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Samuel Meier-Menches
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Petra Heffeter
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| |
Collapse
|
4
|
da Silva Rodrigues G, Noronha NY, Almeida ML, Sobrinho ACDS, Watanabe LM, Pinhel MADS, de Lima JGR, Zhang R, Nonino CB, Alves CRR, Bueno Júnior CR. Exercise training modifies the whole blood DNA methylation profile in middle-aged and older women. J Appl Physiol (1985) 2023; 134:610-621. [PMID: 36701486 DOI: 10.1152/japplphysiol.00237.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This is a longitudinal single-arm clinical trial aimed to investigate whether exercise training would modify the whole blood methylation profile in healthy women. A total of 45 subjects were engaged in an exercise training protocol during a 14-wk follow up, consisting of aerobic cardiorespiratory and muscle strength exercises. Subjects were evaluated at baseline (PRE), after 7 wk of exercise training (POST 7), and after 14 wk of exercise training (POST 14). Functional primary outcomes included anthropometric, blood pressure, biochemical measurements, physical tests, and global health assessments. Blood samples were collected at each time point to determine the methylation profile using a DNA methylation array technique screening up to 850k different sites. Exercise training decreased blood pressure and triglyceride levels and enhanced physical performance, including upper- and lower-body maximum strength. Moreover, exercise training improved markers of quality of life. In the array analysis, 14 wk of exercise training changed the methylation of more than 800 sites. Across these differentially methylated sites, we found that differentially methylated sites in the promoter region were more hypermethylated after exercise training, suggesting that this hypermethylation process may affect the transcription process. When inputting the differentially methylated sites in pathway analysis, we found several metabolic pathways, including AMPK signaling, TGF-β signaling, and insulin signaling. This study demonstrates that exercise training promotes a robust change in the whole blood methylation profile and provides new insights into the key regulators of exercise-induced benefits.NEW & NOTEWORTHY We have shown that exercise training lowers blood pressure and triglyceride levels, improves physical performance, and improves quality of life in middle-aged and elderly women. Regarding epigenetic data, we noticed that more than 800 sites are differentially methylated in whole blood after physical training. We emphasize that the differentially methylated sites in the promoter region are more hypermethylated after physical training. In addition, this study shows that key members of metabolic pathways, including AMPK signaling, TGF-β signaling, and insulin signaling, are among the genes hypermethylated after physical exercise in older women.
Collapse
Affiliation(s)
| | - Natália Y Noronha
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Mariana L Almeida
- College of Nursing of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Andressa C da S Sobrinho
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Lígia M Watanabe
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Marcela A de S Pinhel
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - João G R de Lima
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Ren Zhang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Carla B Nonino
- Health Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Christiano R R Alves
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Carlos R Bueno Júnior
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil.,College of Nursing of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.,School of Physical Education and Sport of Ribeirão Preto, University of Sao Paulo, Sao Paulo, Brazil
| |
Collapse
|
5
|
Herzog C, Vavourakis CD, Barrett JE, Karbon G, Villunger A, Wang J, Sundström K, Dillner J, Widschwendter M. HPV-induced host epigenetic reprogramming is lost upon progression to high-grade cervical intraepithelial neoplasia. Int J Cancer 2023; 152:2321-2330. [PMID: 36810770 DOI: 10.1002/ijc.34477] [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: 11/16/2022] [Revised: 01/11/2023] [Accepted: 02/07/2023] [Indexed: 02/23/2023]
Abstract
The impact of a pathogen on host disease can only be studied in samples covering the entire spectrum of pathogenesis. Persistent oncogenic human papilloma virus (HPV) infection is the most common cause for cervical cancer. Here, we investigate HPV-induced host epigenome-wide changes prior to development of cytological abnormalities. Using cervical sample methylation array data from disease-free women with or without an oncogenic HPV infection, we develop the WID (Women's cancer risk identification)-HPV, a signature reflective of changes in the healthy host epigenome related to high-risk HPV strains (AUC = 0.78, 95% CI: 0.72-0.85, in nondiseased women). Looking at HPV-associated changes across disease development, HPV-infected women with minor cytological alterations (cervical intraepithelial neoplasia grade 1/2, CIN1/2), but surprisingly not those with precancerous changes or invasive cervical cancer (CIN3+), show an increased WID-HPV index, indicating the WID-HPV may reflect a successful viral clearance response absent in progression to cancer. Further investigation revealed the WID-HPV is positively associated with apoptosis (ρ = 0.48; P < .001) and negatively associated with epigenetic replicative age (ρ = -0.43; P < .001). Taken together, our data suggest the WID-HPV captures a clearance response associated with apoptosis of HPV-infected cells. This response may be dampened or lost with increased underlying replicative age of infected cells, resulting in progression to cancer.
Collapse
Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Tirol, Austria.,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Tirol, Austria
| | - Charlotte D Vavourakis
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Tirol, Austria.,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Tirol, Austria
| | - James E Barrett
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Tirol, Austria.,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Tirol, Austria
| | - Gerlinde Karbon
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Jiangrong Wang
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Joakim Dillner
- Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Tirol, Austria.,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Tirol, Austria.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
| |
Collapse
|
6
|
Methylation Status of Gene Bodies of Selected microRNA Genes Associated with Neoplastic Transformation in Equine Sarcoids. Cells 2022; 11:cells11121917. [PMID: 35741046 PMCID: PMC9221590 DOI: 10.3390/cells11121917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 02/04/2023] Open
Abstract
Horses are of great importance in recreation, livestock production, as working animals in poorly developed countries, and for equine-assisted therapy. Equine sarcoids belong to the most commonly diagnosed tumors in this species. They may cause discomfort, pain, and can lead to the permanent impairment of motor function. The molecular bases of their formation are still under investigation. Our previous studies revealed altered microRNA (miRNA) expression and DNA methylation levels in sarcoid tumors. Abnormal patterns of methylation may be responsible for changes in gene expression levels, including microRNAs. Recently, the DNA methylation of gene bodies has also been shown to have an impact on gene expression. Thus, the aim of the study was to investigate the methylation pattern of gene bodies of chosen miRNAs identified in sarcoid tissue (miR-101, miR-10b, miR-200a, and miR-338-3p), which have also been established to play roles in neoplastic transformation. To this end, we applied qRT-PCR, Bisulfite Sequencing PCR (BSP), and Mquant methods. As a result, we identified the statistically significant downregulation of pri-mir-101-1, pri-mir-10b, and pri-mir-200a in the sarcoid samples in comparison to the control. The DNA methylation analysis revealed their hypermethylation. This suggests that DNA methylation may be one mechanism responsible for the downregulation of theses miRNAs. However, the identified differences in the methylation levels are not very high, which implies that other mechanisms may also underlie the downregulation of the expression of these miRNAs in equine sarcoids. For the first time, the results obtained shed light on microRNA expression regulation by gene body methylation in equine sarcoids and provide bases for further deeper studies on other mechanisms influencing the miRNA repertoire.
Collapse
|
7
|
Garcia-Prieto CA, Villanueva L, Bueno-Costa A, Davalos V, González-Navarro EA, Juan M, Urbano-Ispizua Á, Delgado J, Ortiz-Maldonado V, del Bufalo F, Locatelli F, Quintarelli C, Sinibaldi M, Soler M, Castro de Moura M, Ferrer G, Urdinguio RG, Fernandez AF, Fraga MF, Bar D, Meir A, Itzhaki O, Besser MJ, Avigdor A, Jacoby E, Esteller M. Epigenetic Profiling and Response to CD19 Chimeric Antigen Receptor T-Cell Therapy in B-Cell Malignancies. J Natl Cancer Inst 2022; 114:436-445. [PMID: 34581788 PMCID: PMC8902331 DOI: 10.1093/jnci/djab194] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/11/2021] [Accepted: 09/22/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR) T cells directed against CD19 (CART19) are effective in B-cell malignancies, but little is known about the molecular factors predicting clinical outcome of CART19 therapy. The increasingly recognized relevance of epigenetic changes in cancer immunology prompted us to determine the impact of the DNA methylation profiles of CART19 cells on the clinical course. METHODS We recruited 114 patients with B-cell malignancies, comprising 77 patients with acute lymphoblastic leukemia and 37 patients with non-Hodgkin lymphoma who were treated with CART19 cells. Using a comprehensive DNA methylation microarray, we determined the epigenomic changes that occur in the patient T cells upon transduction of the CAR vector. The effects of the identified DNA methylation sites on clinical response, cytokine release syndrome, immune effector cell-associated neurotoxicity syndrome, event-free survival, and overall survival were assessed. All statistical tests were 2-sided. RESULTS We identified 984 genomic sites with differential DNA methylation between CAR-untransduced and CAR-transduced T cells before infusion into the patient. Eighteen of these distinct epigenetic loci were associated with complete response (CR), adjusting by multiple testing. Using the sites linked to CR, an epigenetic signature, referred to hereafter as the EPICART signature, was established in the initial discovery cohort (n = 79), which was associated with CR (Fisher exact test, P < .001) and enhanced event-free survival (hazard ratio [HR] = 0.36; 95% confidence interval [CI] = 0.19 to 0.70; P = .002; log-rank P = .003) and overall survival (HR = 0.45; 95% CI = 0.20 to 0.99; P = .047; log-rank P = .04;). Most important, the EPICART profile maintained its clinical course predictive value in the validation cohort (n = 35), where it was associated with CR (Fisher exact test, P < .001) and enhanced overall survival (HR = 0.31; 95% CI = 0.11 to 0.84; P = .02; log-rank P = .02). CONCLUSIONS We show that the DNA methylation landscape of patient CART19 cells influences the efficacy of the cellular immunotherapy treatment in patients with B-cell malignancy.
Collapse
Affiliation(s)
- Carlos A Garcia-Prieto
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Lorea Villanueva
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Alberto Bueno-Costa
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Veronica Davalos
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | | | - Manel Juan
- Department of Immunology, Hospital Clinic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Álvaro Urbano-Ispizua
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Hematology, University of Barcelona (UB), Barcelona, Spain
| | - Julio Delgado
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
| | | | - Francesca del Bufalo
- Department of Paediatric Haematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Pediatrics, Sapienza University of Rome, Rome, Italy
| | - Concetta Quintarelli
- Department of Paediatric Haematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Matilde Sinibaldi
- Department of Paediatric Haematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marta Soler
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Manuel Castro de Moura
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Gerardo Ferrer
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Rocio G Urdinguio
- Nanomaterials and Nanotechnology Research Center (CINNCSIC), Health Research Institute of Asturias (ISPA), Institute of Oncology of Asturias (IUOPA), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
| | - Agustin F Fernandez
- Nanomaterials and Nanotechnology Research Center (CINNCSIC), Health Research Institute of Asturias (ISPA), Institute of Oncology of Asturias (IUOPA), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINNCSIC), Health Research Institute of Asturias (ISPA), Institute of Oncology of Asturias (IUOPA), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
| | - Diana Bar
- Division of Pediatric Hematology and Oncology, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Amilia Meir
- Division of Pediatric Hematology and Oncology, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Orit Itzhaki
- Ella Lemelbaum Institute for Immuno Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Avigdor
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Hematology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Elad Jacoby
- Division of Pediatric Hematology and Oncology, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manel Esteller
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Spain
| |
Collapse
|
8
|
Hanahan D. Hallmarks of Cancer: New Dimensions. Cancer Discov 2022; 12:31-46. [PMID: 35022204 DOI: 10.1158/2159-8290.cd-21-1059] [Citation(s) in RCA: 3506] [Impact Index Per Article: 1753.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/06/2023]
Abstract
The hallmarks of cancer conceptualization is a heuristic tool for distilling the vast complexity of cancer phenotypes and genotypes into a provisional set of underlying principles. As knowledge of cancer mechanisms has progressed, other facets of the disease have emerged as potential refinements. Herein, the prospect is raised that phenotypic plasticity and disrupted differentiation is a discrete hallmark capability, and that nonmutational epigenetic reprogramming and polymorphic microbiomes both constitute distinctive enabling characteristics that facilitate the acquisition of hallmark capabilities. Additionally, senescent cells, of varying origins, may be added to the roster of functionally important cell types in the tumor microenvironment. SIGNIFICANCE: Cancer is daunting in the breadth and scope of its diversity, spanning genetics, cell and tissue biology, pathology, and response to therapy. Ever more powerful experimental and computational tools and technologies are providing an avalanche of "big data" about the myriad manifestations of the diseases that cancer encompasses. The integrative concept embodied in the hallmarks of cancer is helping to distill this complexity into an increasingly logical science, and the provisional new dimensions presented in this perspective may add value to that endeavor, to more fully understand mechanisms of cancer development and malignant progression, and apply that knowledge to cancer medicine.
Collapse
Affiliation(s)
- Douglas Hanahan
- Ludwig Institute for Cancer Research - Lausanne Branch, Lausanne, Switzerland. The Swiss Institute for Experimental Cancer Research (ISREC) within the School of Life Sciences at the Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland. The Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
| |
Collapse
|
9
|
Vietri MT, D'Elia G, Benincasa G, Ferraro G, Caliendo G, Nicoletti GF, Napoli C. DNA methylation and breast cancer: A way forward (Review). Int J Oncol 2021; 59:98. [PMID: 34726251 DOI: 10.3892/ijo.2021.5278] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
The current management of breast cancer (BC) lacks specific non‑invasive biomarkers able to provide an early diagnosis of the disease. Epigenetic‑sensitive signatures are influenced by environmental exposures and are mediated by direct molecular mechanisms, mainly guided by DNA methylation, which regulate the interplay between genetic and non‑genetic risk factors during cancerogenesis. The inactivation of tumor suppressor genes due to promoter hypermethylation is an early event in carcinogenesis. Of note, targeted tumor suppressor genes are frequently hypermethylated in patient‑derived BC tissues and peripheral blood biospecimens. In addition, epigenetic alterations in triple‑negative BC, as the most aggressive subtype, have been identified. Thus, detecting both targeted and genome‑wide DNA methylation changes through liquid‑based assays appears to be a useful clinical strategy for early detection, more accurate risk stratification and a personalized prediction of therapeutic response in patients with BC. Of note, the DNA methylation profile may be mapped by isolating the circulating tumor DNA from the plasma as a more accessible biospecimen. Furthermore, the sensitivity to treatment with chemotherapy, hormones and immunotherapy may be altered by gene‑specific DNA methylation, suggesting novel potential drug targets. Recently, the use of epigenetic drugs administered alone and/or with anticancer therapies has led to remarkable results, particularly in patients with BC resistant to anticancer treatment. The aim of the present review was to provide an update on DNA methylation changes that are potentially involved in BC development and their putative clinical utility in the fields of diagnosis, prognosis and therapy.
Collapse
Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanna D'Elia
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuseppe Ferraro
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Gemma Caliendo
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanni Francesco Nicoletti
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| |
Collapse
|
10
|
van den Berg I, Smid M, Coebergh van den Braak RRJ, van de Wiel MA, van Deurzen CHM, de Weerd V, Martens JWM, IJzermans JNM, Wilting SM. A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer. Mol Oncol 2021; 15:3348-3362. [PMID: 34510716 PMCID: PMC8637568 DOI: 10.1002/1878-0261.13098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/04/2021] [Accepted: 09/09/2021] [Indexed: 12/25/2022] Open
Abstract
Consensus molecular subtypes (CMSs) can guide precision treatment of colorectal cancer (CRC). We aim to identify methylation markers to distinguish between CMS2 and CMS3 in patients with CRC, for which an easy test is currently lacking. To this aim, fresh‐frozen tumor tissue of 239 patients with stage I‐III CRC was analyzed. Methylation profiles were obtained using the Infinium HumanMethylation450 BeadChip. We performed adaptive group‐regularized logistic ridge regression with post hoc group‐weighted elastic net marker selection to build prediction models for classification of CMS2 and CMS3. The Cancer Genome Atlas (TCGA) data were used for validation. Group regularization of the probes was done based on their location either relative to a CpG island or relative to a gene present in the CMS classifier, resulting in two different prediction models and subsequently different marker panels. For both panels, even when using only five markers, accuracies were > 90% in our cohort and in the TCGA validation set. Our methylation marker panel accurately distinguishes between CMS2 and CMS3. This enables development of a targeted assay to provide a robust and clinically relevant classification tool for CRC patients.
Collapse
Affiliation(s)
- Inge van den Berg
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | | | - Mark A van de Wiel
- Department of Epidemiology & Data Science, Amsterdam University Medical Center, Amsterdam Public Health research institute, The Netherlands
| | | | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Jan N M IJzermans
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| |
Collapse
|
11
|
Esteller M. DNA methylation in cancer: From mouse to human and back again. EBioMedicine 2021; 68:103393. [PMID: 34044220 PMCID: PMC8167211 DOI: 10.1016/j.ebiom.2021.103393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 11/06/2022] Open
Affiliation(s)
- Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid 28029, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
| |
Collapse
|
12
|
Höglund A, Henriksen R, Fogelholm J, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The methylation landscape and its role in domestication and gene regulation in the chicken. Nat Ecol Evol 2020; 4:1713-1724. [PMID: 32958860 DOI: 10.1038/s41559-020-01310-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 08/26/2020] [Indexed: 01/06/2023]
Abstract
Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.
Collapse
Affiliation(s)
- Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M Guerrero-Bosagna
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.,Evolutionary Biology Centrum, Dept of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.
| |
Collapse
|
13
|
Li Z, Xia J, Fang M, Xu Y. Epigenetic regulation of lung cancer cell proliferation and migration by the chromatin remodeling protein BRG1. Oncogenesis 2019; 8:66. [PMID: 31695026 PMCID: PMC6834663 DOI: 10.1038/s41389-019-0174-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 01/10/2023] Open
Abstract
Malignant lung cancer cells are characterized by uncontrolled proliferation and migration. Aberrant lung cancer cell proliferation and migration are programmed by altered cancer transcriptome. The underlying epigenetic mechanism is unclear. Here we report that expression levels of BRG1, a chromatin remodeling protein, were significantly up-regulated in human lung cancer biopsy specimens of higher malignancy grades compared to those of lower grades. Small interfering RNA mediated depletion or pharmaceutical inhibition of BRG1 suppressed proliferation and migration of lung cancer cells. BRG1 depletion or inhibition was paralleled by down-regulation of cyclin B1 (CCNB1) and latent TGF-β binding protein 2 (LTBP2) in lung cancer cells. Further analysis revealed that BRG1 directly bound to the CCNB1 promoter to activate transcription in response to hypoxia stimulation by interacting with E2F1. On the other hand, BRG1 interacted with Sp1 to activate LTBP2 transcription. Mechanistically, BRG1 regulated CCNB1 and LTBP2 transcription by altering histone modifications on target promoters. Specifically, BRG1 recruited KDM3A, a histone H3K9 demethylase, to remove dimethyl H3K9 from target gene promoters thereby activating transcription. KDM3A knockdown achieved equivalent effects as BRG1 silencing by diminishing lung cancer proliferation and migration. Of interest, BRG1 directly activated KDM3A transcription by forming a complex with HIF-1α. In conclusion, our data unveil a novel epigenetic mechanism whereby malignant lung cancer cells acquired heightened ability to proliferate and migrate. Targeting BRG1 may yield effective interventional strategies against malignant lung cancers.
Collapse
Affiliation(s)
- Zilong Li
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Jun Xia
- Department of Respiratory Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China.
| | - Mingming Fang
- Department of Clinical Medicine and Laboratory Center for Experimental Medicine, Jiangsu Health Vocational College, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China. .,Institute of Biomedical Research, Liaocheng University, Liaocheng, China.
| |
Collapse
|
14
|
Cardial Tobias G, Lucas Penteado Gomes J, Paula Renó Soci U, Fernandes T, Menezes de Oliveira E. A Landscape of Epigenetic Regulation by MicroRNAs to the Hallmarks of Cancer and Cachexia: Implications of Physical Activity to Tumor Regression. Epigenetics 2019. [DOI: 10.5772/intechopen.84847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
|
15
|
Hwang SH, Yeom H, Eom SY, Lee YM, Lee M. Genome-wide DNA methylation changes in transformed foci induced by nongenotoxic carcinogens. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:576-587. [PMID: 30848857 DOI: 10.1002/em.22285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/15/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
In vitro cell transformation assays (CTA) have been proposed as a method to identify possible nongenotoxic carcinogens. However, the current protocols do not provide information on the mechanism of action of the test articles. In this study, we combined an in vitro Bhas 42 CTA and sequencing-based DNA methylation profiling analysis to elucidate the carcinogenic mechanism associated with nongenotoxic carcinogens. Three nongenotoxic carcinogens were evaluated: cadmium chloride, methyl carbamate, and lithocholic acid. Methylation profiles were generated for the two nongenotoxic carcinogens (cadmium chloride and lithocholic acid) that were positive in Bhas 42 CTA. Methyl carbamate did not exhibit any promoter activity. Approximately 9.8% of all differentially methylated regions (DMRs) identified in cadmium chloride-induced transformed foci overlapped with DMRs in lithocholic acid-induced transformed foci. Interestingly, overlapping DMRs showed more hypermethylation than individual DMRs. In addition, the DMRs in CpG island elements common to both nongenotoxic carcinogens showed considerably more bias toward hypermethylated DMRs than those unique to either cadmium chloride or lithocholic acid. Pathway enrichment analysis revealed that genes harboring hypermethylated DMRs were significantly enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including pathways in cancer, basal cell carcinoma, and Wnt signaling. The genes harboring hypomethylated DMRs were significantly related to mRNA surveillance pathway, RNA transport, and autophagy. Taken together, our preliminary results on genome-wide methylation analysis of cell clones from nongenotoxic carcinogen-induced foci could be exploited for CTAs improvement, but further research will be required to standardize and assess the specificity and sensitivity of this combined approach. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Sung-Hee Hwang
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Hojin Yeom
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Seong Yun Eom
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Yong-Moon Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheoungju-si, Chungcheongbuk-do 28160, Republic of Korea
| | - Michael Lee
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
- INU Human Genome Center, Incheon National University, Incheon 22012, Republic of Korea
| |
Collapse
|
16
|
Martínez-Cano J, Campos-Sánchez E, Cobaleda C. Epigenetic Priming in Immunodeficiencies. Front Cell Dev Biol 2019; 7:125. [PMID: 31355198 PMCID: PMC6635466 DOI: 10.3389/fcell.2019.00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022] Open
Abstract
Immunodeficiencies (IDs) are disorders of the immune system that increase susceptibility to infections and cancer, and are therefore associated with elevated morbidity and mortality. IDs can be primary (not caused by other condition or exposure) or secondary due to the exposure to different agents (infections, chemicals, aging, etc.). Most primary immunodeficiencies (PIDs) are of genetic origin, caused by mutations affecting genes with key roles in the development or function of the cells of the immune system. A large percentage of PIDs are associated with a defective development and/or function of lymphocytes and, especially, B cells, the ones in charge of generating the different types of antibodies. B-cell development is a tightly regulated process in which many different factors participate. Among the regulators of B-cell differentiation, a correct epigenetic control of cellular identity is essential for normal cell function. With the advent of next-generation sequencing (NGS) techniques, more and more alterations in different types of epigenetic regulators are being described at the root of PIDs, both in humans and in animal models. At the same time, it is becoming increasingly clear that epigenetic alterations triggered by the exposure to environmental agents have a key role in the development of secondary immunodeficiencies (SIDs). Due to their largely reversible nature, epigenetic modifications are quickly becoming key therapeutic targets in other diseases where their contribution has been known for more time, like cancer. Here, we establish a parallelism between IDs and the nowadays accepted role of epigenetics in cancer initiation and progression, and propose that epigenetics forms a "third axis" (together with genetics and external agents) to be considered in the etiology of IDs, and linking PIDs and SIDs at the molecular level. We therefore postulate that IDs arise due to a variable contribution of (i) genetic, (ii) environmental, and (iii) epigenetic causes, which in fact form a continuum landscape of all possible combinations of these factors. Additionally, this implies the possibility of a fully epigenetically triggered mechanism for some IDs. This concept would have important prophylactic and translational implications, and would also imply a more blurred frontier between primary and secondary immunodeficiencies.
Collapse
Affiliation(s)
| | | | - César Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas –Universidad Autónoma de Madrid), Madrid, Spain
| |
Collapse
|
17
|
Kok DE, Steegenga WT, Smid EJ, Zoetendal EG, Ulrich CM, Kampman E. Bacterial folate biosynthesis and colorectal cancer risk: more than just a gut feeling. Crit Rev Food Sci Nutr 2018; 60:244-256. [DOI: 10.1080/10408398.2018.1522499] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dieuwertje E. Kok
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Wilma T. Steegenga
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Eddy J. Smid
- Laboratory of Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Cornelia M. Ulrich
- Department of Population Health Sciences and Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
18
|
Campos-Sanchez E, Martínez-Cano J, Del Pino Molina L, López-Granados E, Cobaleda C. Epigenetic Deregulation in Human Primary Immunodeficiencies. Trends Immunol 2018; 40:49-65. [PMID: 30509895 DOI: 10.1016/j.it.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are immune disorders resulting from defects in genes involved in immune regulation, and manifesting as an increased susceptibility to infections, autoimmunity, and cancer. However, the molecular basis of some prevalent entities remains poorly understood. Epigenetic control is essential for immune functions, and epigenetic alterations have been identified in different PIDs, including syndromes such as immunodeficiency-centromeric-instability-facial-anomalies, Kabuki, or Wolf-Hirschhorn, among others. Although the epigenetic changes may differ among these PIDs, the reversibility of epigenetic modifications suggests that they might become potential therapeutic targets. Here, we review recent mechanistic advances in our understanding of epigenetic alterations associated with certain PIDs, propose that a fully epigenetically driven mechanism might underlie some PIDs, and discuss the possible prophylactic and therapeutic implications.
Collapse
Affiliation(s)
- Elena Campos-Sanchez
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Jorge Martínez-Cano
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Lucía Del Pino Molina
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain.
| | - Cesar Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain.
| |
Collapse
|
19
|
Arechederra M, Daian F, Yim A, Bazai SK, Richelme S, Dono R, Saurin AJ, Habermann BH, Maina F. Hypermethylation of gene body CpG islands predicts high dosage of functional oncogenes in liver cancer. Nat Commun 2018; 9:3164. [PMID: 30089774 PMCID: PMC6082886 DOI: 10.1038/s41467-018-05550-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications such as aberrant DNA methylation reshape the gene expression repertoire in cancer. Here, we used a clinically relevant hepatocellular carcinoma (HCC) mouse model (Alb-R26Met) to explore the impact of DNA methylation on transcriptional switches associated with tumorigenesis. We identified a striking enrichment in genes simultaneously hypermethylated in CpG islands (CGIs) and overexpressed. These hypermethylated CGIs are located either in the 5′-UTR or in the gene body region. Remarkably, such CGI hypermethylation accompanied by gene upregulation also occurs in 56% of HCC patients, which belong to the “HCC proliferative-progenitor” subclass. Most of the genes upregulated and with hypermethylated CGIs in the Alb-R26Met HCC model undergo the same change in a large proportion of HCC patients. Among reprogrammed genes, several are well-known oncogenes. For others not previously linked to cancer, we demonstrate here their action together as an “oncogene module”. Thus, hypermethylation of gene body CGIs is predictive of elevated oncogene levels in cancer, offering a novel stratification strategy and perspectives to normalise cancer gene dosages. Changes in the DNA methylation status are commonly observed in cancer but their impact on cancer development is unclear. Here, combining DNA methylation and expression profiles from a murine model of hepatocellular carcinoma with those from human samples, the authors report an epigenetic reprogramming process ensuring increased dosage of an “oncogene module”.
Collapse
Affiliation(s)
- Maria Arechederra
- Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Aix Marseille Univ, 13009, Marseille, France
| | - Fabrice Daian
- Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Aix Marseille Univ, 13009, Marseille, France
| | - Annie Yim
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Sehrish K Bazai
- Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Aix Marseille Univ, 13009, Marseille, France
| | - Sylvie Richelme
- Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Aix Marseille Univ, 13009, Marseille, France
| | - Rosanna Dono
- Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Aix Marseille Univ, 13009, Marseille, France
| | - Andrew J Saurin
- Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Aix Marseille Univ, 13009, Marseille, France
| | - Bianca H Habermann
- Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Aix Marseille Univ, 13009, Marseille, France
| | - Flavio Maina
- Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Parc Scientifique de Luminy, Aix Marseille Univ, 13009, Marseille, France.
| |
Collapse
|
20
|
Mahabir S, Willett WC, Friedenreich CM, Lai GY, Boushey CJ, Matthews CE, Sinha R, Colditz GA, Rothwell JA, Reedy J, Patel AV, Leitzmann MF, Fraser GE, Ross S, Hursting SD, Abnet CC, Kushi LH, Taylor PR, Prentice RL. Research Strategies for Nutritional and Physical Activity Epidemiology and Cancer Prevention. Cancer Epidemiol Biomarkers Prev 2018; 27:233-244. [PMID: 29254934 PMCID: PMC7992195 DOI: 10.1158/1055-9965.epi-17-0509] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/02/2017] [Accepted: 12/04/2017] [Indexed: 12/24/2022] Open
Abstract
Very large international and ethnic differences in cancer rates exist, are minimally explained by genetic factors, and show the huge potential for cancer prevention. A substantial portion of the differences in cancer rates can be explained by modifiable factors, and many important relationships have been documented between diet, physical activity, and obesity, and incidence of important cancers. Other related factors, such as the microbiome and the metabolome, are emerging as important intermediary components in cancer prevention. It is possible with the incorporation of newer technologies and studies including long follow-up and evaluation of effects across the life cycle, additional convincing results will be produced. However, several challenges exist for cancer researchers; for example, measurement of diet and physical activity, and lack of standardization of samples for microbiome collection, and validation of metabolomic studies. The United States National Cancer Institute convened the Research Strategies for Nutritional and Physical Activity Epidemiology and Cancer Prevention Workshop on June 28-29, 2016, in Rockville, Maryland, during which the experts addressed the state of the science and areas of emphasis. This current paper reflects the state of the science and priorities for future research. Cancer Epidemiol Biomarkers Prev; 27(3); 233-44. ©2017 AACR.
Collapse
Affiliation(s)
- Somdat Mahabir
- Environmental Epidemiology Branch, Epidemiology and Genomics Research Program (EGRP), Division of Cancer Control and Population Sciences (DCCPS), National Cancer Institute (NCI), Bethesda, Maryland.
| | - Walter C Willett
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
| | - Christine M Friedenreich
- Department of Cancer Epidemiology and Prevention Research, Cancer Control Alberta, Alberta Health Services, Edmonton, Alberta, Canada
| | - Gabriel Y Lai
- Environmental Epidemiology Branch, Epidemiology and Genomics Research Program (EGRP), Division of Cancer Control and Population Sciences (DCCPS), National Cancer Institute (NCI), Bethesda, Maryland
| | - Carol J Boushey
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Charles E Matthews
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), NCI, Bethesda, Maryland
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), NCI, Bethesda, Maryland
| | - Graham A Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University and Alvin J. Siteman Cancer Center, St. Louis, Missouri
| | - Joseph A Rothwell
- Nutrition and Metabolism Section, Biomarkers Group, International Agency for Cancer Research (IARC), Lyon, France
| | - Jill Reedy
- Risk Factor Assessment Branch, EGRP, DCCPS, NCI, Bethesda, Maryland
| | - Alpa V Patel
- Cancer Prevention Study-3, American Cancer Society, Atlanta, Georgia
| | - Michael F Leitzmann
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Gary E Fraser
- School of Public Health, School of Medicine, Loma Linda University, Loma Linda, California
| | - Sharon Ross
- Nutritional Science Research Group, Division of Cancer Prevention, NCI, Bethesda, Maryland
| | - Stephen D Hursting
- Nutrition Research Institute, Lineberger Comprehensive Cancer Center and University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Christian C Abnet
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), NCI, Bethesda, Maryland
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Philip R Taylor
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), NCI, Bethesda, Maryland
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| |
Collapse
|
21
|
Epigenetics and MicroRNAs in Cancer. Int J Mol Sci 2018; 19:ijms19020459. [PMID: 29401683 PMCID: PMC5855681 DOI: 10.3390/ijms19020459] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
The ability to reprogram the transcriptional circuitry by remodeling the three-dimensional structure of the genome is exploited by cancer cells to promote tumorigenesis. This reprogramming occurs because of hereditable chromatin chemical modifications and the consequent formation of RNA-protein-DNA complexes that represent the principal actors of the epigenetic phenomena. In this regard, the deregulation of a transcribed non-coding RNA may be both cause and consequence of a cancer-related epigenetic alteration. This review summarizes recent findings that implicate microRNAs in the aberrant epigenetic regulation of cancer cells.
Collapse
|