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Altinok Gunes B, Ozkan T, Karadag Gurel A, Dalkilic S, Belder N, Ozkeserli Z, Ozdag H, Beksac M, Sayinalp N, Yagci AM, Sunguroglu A. Transcriptome Analysis of Beta-Catenin-Related Genes in CD34+ Haematopoietic Stem and Progenitor Cells from Patients with AML. Mediterr J Hematol Infect Dis 2024; 16:e2024058. [PMID: 38984092 PMCID: PMC11232677 DOI: 10.4084/mjhid.2024.058] [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: 02/12/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024] Open
Abstract
Background Acute myeloid leukaemia (AML) is a disease of the haematopoietic stem cells(HSCs) that is characterised by the uncontrolled proliferation and impaired differentiation of normal haematopoietic stem/progenitor cells. Several pathways that control the proliferation and differentiation of HSCs are impaired in AML. Activation of the Wnt/beta-catenin signalling pathway has been shown in AML and beta-catenin, which is thought to be the key element of this pathway, has been frequently highlighted. The present study was designed to determine beta-catenin expression levels and beta-catenin-related genes in AML. Methods In this study, beta-catenin gene expression levels were determined in 19 AML patients and 3 controls by qRT-PCR. Transcriptome analysis was performed on AML grouped according to beta-catenin expression levels. Differentially expressed genes(DEGs) were investigated in detail using the Database for Annotation Visualisation and Integrated Discovery(DAVID), Gene Ontology(GO), Kyoto Encyclopedia of Genes and Genomes(KEGG), STRING online tools. Results The transcriptome profiles of our AML samples showed different molecular signature profiles according to their beta-catenin levels(high-low). A total of 20 genes have been identified as hub genes. Among these, TTK, HJURP, KIF14, BTF3, RPL17 and RSL1D1 were found to be associated with beta-catenin and poor survival in AML. Furthermore, for the first time in our study, the ELOV6 gene, which is the most highly up-regulated gene in human AML samples, was correlated with a poor prognosis via high beta-catenin levels. Conclusion It is suggested that the identification of beta-catenin-related gene profiles in AML may help to select new therapeutic targets for the treatment of AML.
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Affiliation(s)
- B Altinok Gunes
- Vocational School of Health Services, Ankara University, Ankara, Turkey
| | - T Ozkan
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - A Karadag Gurel
- Department of Medical Biology, Faculty of Medicine, Usak University, Usak, Turkey
| | - S Dalkilic
- Department of Molecular Biology, Faculty of Science, Firat University, Elazig, Turkey
| | - N Belder
- Ankara University Biotechnology Institute, Ankara, Turkey
| | - Z Ozkeserli
- Ankara University Biotechnology Institute, Ankara, Turkey
| | - H Ozdag
- Ankara University Biotechnology Institute, Ankara, Turkey
| | - M Beksac
- Department of Hematology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - N Sayinalp
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - A M Yagci
- Department of Internal Medicine, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - A Sunguroglu
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey
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Schaffrath R, Brinkmann U. Diphthamide - a conserved modification of eEF2 with clinical relevance. Trends Mol Med 2024; 30:164-177. [PMID: 38097404 DOI: 10.1016/j.molmed.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 02/17/2024]
Abstract
Diphthamide, a complex modification on eukaryotic translation elongation factor 2 (eEF2), assures reading-frame fidelity during translation. Diphthamide and enzymes for its synthesis are conserved in eukaryotes and archaea. Originally identified as target for diphtheria toxin (DT) in humans, its clinical relevance now proves to be broader than the link to pathogenic bacteria. Diphthamide synthesis enzymes (DPH1 and DPH3) are associated with cancer, and DPH gene mutations can cause diphthamide deficiency syndrome (DDS). Finally, new analyses provide evidence that diphthamide may restrict propagation of viruses including SARS-CoV-2 and HIV-1, and that DPH enzymes are targeted by viruses for degradation to overcome this restriction. This review describes how diphthamide is synthesized and functions in translation, and covers its clinical relevance in human development, cancer, and infectious diseases.
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Affiliation(s)
- Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
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Sun Y, Yao L, Man C, Gao Z, He R, Fan Y. Development and validation of cuproptosis-related lncRNAs associated with pancreatic cancer immune microenvironment based on single-cell. Front Immunol 2023; 14:1220760. [PMID: 37822927 PMCID: PMC10563513 DOI: 10.3389/fimmu.2023.1220760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
Background Cuproptosis, a novel mode of cell death associated with the tricarboxylic acid (TCA) cycle, is relevant to the development of cancer. However, the impact of single-cell-based Cuproptosis-associated lncRNAs on the Tumor immune microenvironment (TIME) of Pancreatic adenocarcinoma (PAAD) and its potential value for individualized immunotherapy has not been clarified. Methods 14 immune-related CRGs were screened by exploring the interaction between differentially expressed Immune-Related Genes (IRGs) and Cuproptosis-Related Genes (CRGs) in PAAD. Next, the expression amount and expression distribution of CRGs in single-cell samples were analyzed by focusing on 7-CRGs with significant expressions. On the one hand, MAP2K2, SOD1, and VEGFA, which were significantly differentially expressed between PAAD sites and normal tissues adjacent to them, were subjected to immunohistochemical validation and immune landscape analysis. On the other hand, from these 7-CRGs, prognostic signatures of lncRNAs were established by co-expression and LASSO-COX regression analysis, and their prognostic value and immune relevance were assessed. In addition, this study not only validated the hub CRGs and the lncRNAs constituting the signature in a PAAD animal model treated with immunotherapy-based combination therapy using immunohistochemistry and qRT-PCR but also explored the potential value of the combination of targeted, chemotherapy and immunotherapy. Results Based on the screening of 7-CRGs significantly expressed in a PAAD single-cell cohort and their co-expressed Cuproptosis-Related lncRNAs (CRIs), this study constructed a prognostic signature of 4-CRIs named CIR-score. A Nomogram integrating the CIR-score and clinical risk factors was constructed on this basis to predict the individualized survival of patients. Moreover, high and low-risk groups classified according to the median of signatures exhibited significant differences in clinical prognosis, immune landscape, bioenrichment, tumor burden, and drug sensitivity. And the immunohistochemical and qRT-PCR results of different mouse PAAD treatment strategies were consistent with the trend of inter-group variability in drug sensitivity of hub CRGs and CIR-score. The combination of immunotherapy, targeted therapy, and chemotherapy exhibited a better tumor suppression effect. Conclusion CIR-score, as a Cuproptosis-related TIME-specific prognostic signature based on PAAD single cells, not only predicts the prognosis and immune landscape of PAAD patients but also provides a new strategy for individualized immunotherapy-based combination therapy.
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Affiliation(s)
- Yimeng Sun
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Lin Yao
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Changfeng Man
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhenjun Gao
- Department of Gastroenterology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Rong He
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yu Fan
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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Bahado-Singh R, Vlachos KT, Aydas B, Gordevicius J, Radhakrishna U, Vishweswaraiah S. Precision Oncology: Artificial Intelligence and DNA Methylation Analysis of Circulating Cell-Free DNA for Lung Cancer Detection. Front Oncol 2022; 12:790645. [PMID: 35600397 PMCID: PMC9114890 DOI: 10.3389/fonc.2022.790645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/04/2022] [Indexed: 12/12/2022] Open
Abstract
Background Lung cancer (LC) is a leading cause of cancer-deaths globally. Its lethality is due in large part to the paucity of accurate screening markers. Precision Medicine includes the use of omics technology and novel analytic approaches for biomarker development. We combined Artificial Intelligence (AI) and DNA methylation analysis of circulating cell-free tumor DNA (ctDNA), to identify putative biomarkers for and to elucidate the pathogenesis of LC. Methods Illumina Infinium MethylationEPIC BeadChip array analysis was used to measure cytosine (CpG) methylation changes across the genome in LC. Six different AI platforms including support vector machine (SVM) and Deep Learning (DL) were used to identify CpG biomarkers and for LC detection. Training set and validation sets were generated, and 10-fold cross validation performed. Gene enrichment analysis using g:profiler and GREAT enrichment was used to elucidate the LC pathogenesis. Results Using a stringent GWAS significance threshold, p-value <5x10-8, we identified 4389 CpGs (cytosine methylation loci) in coding genes and 1812 CpGs in non-protein coding DNA regions that were differentially methylated in LC. SVM and three other AI platforms achieved an AUC=1.00; 95% CI (0.90-1.00) for LC detection. DL achieved an AUC=1.00; 95% CI (0.95-1.00) and 100% sensitivity and specificity. High diagnostic accuracies were achieved with only intragenic or only intergenic CpG loci. Gene enrichment analysis found dysregulation of molecular pathways involved in the development of small cell and non-small cell LC. Conclusion Using AI and DNA methylation analysis of ctDNA, high LC detection rates were achieved. Further, many of the genes that were epigenetically altered are known to be involved in the biology of neoplasms in general and lung cancer in particular.
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Affiliation(s)
- Ray Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Kyriacos T Vlachos
- Department of Biomedical Sciences, Wayne State School of Medicine, Basic Medical Sciences, Detroit, MI, United States
| | - Buket Aydas
- Department of Healthcare Analytics, Meridian Health Plans, Detroit, MI, United States
| | | | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, United States
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Beaumont Research Institute, Royal Oak, MI, United States
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Zhang Q, Kuang M, An H, Zhang Y, Zhang K, Feng L, Zhang L, Cheng S. Peripheral blood transcriptome heterogeneity and prognostic potential in lung cancer revealed by RNA-Seq. J Cell Mol Med 2021; 25:8271-8284. [PMID: 34288383 PMCID: PMC8419186 DOI: 10.1111/jcmm.16773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 05/22/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
Understanding of the complex interaction between the peripheral immune system and lung cancer (LC) remains incomplete, limiting patient benefit. Here, we aimed to characterize the host peripheral immune response to LC and investigate its potential prognostic value. Bulk RNA-sequencing data of peripheral blood leucocytes (PBLs) from healthy volunteers and LC patients (n = 142) were analysed for characterization of host systemic immunity in LC. We observed broad blood transcriptome perturbations in LC patients that were heterogeneous, as two new subtypes were established independent of histology. Functionally, the heterogeneity between the two subtypes included dysregulation of diverse biological processes, such as the cell cycle, blood coagulation and inflammatory signalling pathways, together with the abundance and activity of blood cells, particularly lymphocytes and neutrophils, ultimately manifesting as differences in antitumour immune status. Based on these findings, a prognostic model composed of ten genes dysregulated in one LC subtype with relatively poor immune status was developed and validated in a Gene Expression Omnibus (GEO) data set (n = 108), helping to generate a prognostic nomogram. Collectively, our study provides novel and comprehensive insight into the heterogeneity of the host peripheral immune response to LC. The expression heterogeneity-based predictive model may help guide prognostic management for LC patients.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Manchao Kuang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haiyin An
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yajing Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Zhang
- Department of Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Zhang
- Department of Endoscopy ,National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Lucia RM, Huang WL, Alvarez A, Masunaka I, Ziogas A, Goodman D, Odegaard AO, Norden-Krichmar TM, Park HL. Association of mammographic density with blood DNA methylation. Epigenetics 2021; 17:531-546. [PMID: 34116608 PMCID: PMC9067527 DOI: 10.1080/15592294.2021.1928994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background: Altered DNA methylation may be an intermediate phenotype between breast cancer risk factors and disease. Mammographic density is a strong risk factor for breast cancer. However, no studies to date have identified an epigenetic signature of mammographic density. We performed an epigenome-wide association study of mammographic density. Methods: White blood cell DNA methylation was measured for 385 postmenopausal women using the Illumina Infinium MethylationEPIC BeadChip array. Differential methylation was assessed using genome-wide, probe-level, and regional analyses. We implemented a resampling-based approach to improve the stability of our findings. Results: On average, women with elevated mammographic density exhibited DNA hypermethylation within CpG islands and gene promoters compared to women with lower mammographic density. We identified 250 CpG sites for which DNA methylation was significantly associated with mammographic density. The top sites were located within genes associated with cancer, including HDLBP, TGFB2, CCT4, and PAX8, and were more likely to be located in regulatory regions of the genome. We also identified differential DNA methylation in 37 regions, including within the promoters of PAX8 and PF4, a gene involved in the regulation of angiogenesis. Overall, our results paint a picture of epigenetic dysregulation associated with mammographic density. Conclusion: Mammographic density is associated with differential DNA methylation throughout the genome, including within genes associated with cancer. Our results suggest the potential involvement of several genes in the biological mechanisms behind differences in breast density between women. Further studies are warranted to explore these potential mechanisms and potential links to breast cancer risk.
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Affiliation(s)
- Rachel M Lucia
- Department of Epidemiology, University of California, Irvine, USA
| | - Wei-Lin Huang
- Department of Epidemiology, University of California, Irvine, USA
| | - Andrea Alvarez
- Department of Medicine, University of California, Irvine, USA
| | - Irene Masunaka
- Department of Medicine, University of California, Irvine, USA
| | - Argyrios Ziogas
- Department of Medicine, University of California, Irvine, USA
| | - Deborah Goodman
- Department of Epidemiology, University of California, Irvine, USA
| | | | | | - Hannah Lui Park
- Department of Epidemiology, University of California, Irvine, USA.,Department of Pathology and Laboratory Medicine, University of California, Irvine, USA
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Ge X, Yuan L, Cheng B, Dai K. Identification of seven tumor-educated platelets RNAs for cancer diagnosis. J Clin Lab Anal 2021; 35:e23791. [PMID: 33955587 PMCID: PMC8183939 DOI: 10.1002/jcla.23791] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Tumor-educated platelets (TEPs) may enable blood-based cancer diagnosis. This study aimed to identify diagnostic TEPs genes involved in carcinogenesis. MATERIALS AND METHODS The TEPs differentially expressed genes (DEGs) between healthy samples and early/advanced cancer samples were obtained using bioinformatics. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis were used to identify the pathways and functional annotation of TEPs DEGs. Protein-protein interaction of these TEPs DEGs was analyzed based on the STRING database and visualized by Cytoscape software. The correlation analysis and diagnostic analysis were performed to evaluate the diagnostic value of TEPs mRNAs expression for early/advanced cancers. Quantitative real-time PCR (qRT-PCR) was applied to validate the role of DEGs in cancers. RESULTS TEPs mRNAs were mostly involved in protein binding, extracellular matrix, and cellular protein metabolic process. RSL24D1 was negatively correlated to early-stage cancers compared to healthy controls and may be potentially used for early cancer diagnosis. In addition, HPSE, IFI27, LGALS3BP, CRYM, HBD, COL6A3, LAMB2, and IFITM3 showed an upward trend in the expression from early to advanced cancer stages. Moreover, ARL2, FCGR2A, and KLHDC8B were positively associated with advanced, metastatic cancers compared to healthy controls. Among the 12 selected DEGs, the expression of 7 DEGs, including RSL24D1, IFI27, CRYM, HBD, IFITM3, FCGR2A, and KLHDC8B, were verified by the qRT-PCR method. CONCLUSION This study suggests that the 7-gene TEPs liquid-biopsy biomarkers may be used for cancer diagnosis and monitoring.
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Affiliation(s)
- Xinxin Ge
- The First Affiliated Hospital and Collaborative Innovation Center of HematologyJiangsu Institute of HematologyCyrus Tang Medical InstituteState Key Laboratory of Radiation Medicine and ProtectionKey Laboratory of Thrombosis and HemostasisMinistry of HealthNational Clinical Research Center for Hematological DiseasesSoochow UniversitySuzhouChina
| | - Liuxia Yuan
- The First Affiliated Hospital and Collaborative Innovation Center of HematologyJiangsu Institute of HematologyCyrus Tang Medical InstituteState Key Laboratory of Radiation Medicine and ProtectionKey Laboratory of Thrombosis and HemostasisMinistry of HealthNational Clinical Research Center for Hematological DiseasesSoochow UniversitySuzhouChina
| | - Bin Cheng
- The First Affiliated Hospital and Collaborative Innovation Center of HematologyJiangsu Institute of HematologyCyrus Tang Medical InstituteState Key Laboratory of Radiation Medicine and ProtectionKey Laboratory of Thrombosis and HemostasisMinistry of HealthNational Clinical Research Center for Hematological DiseasesSoochow UniversitySuzhouChina
| | - Kesheng Dai
- The First Affiliated Hospital and Collaborative Innovation Center of HematologyJiangsu Institute of HematologyCyrus Tang Medical InstituteState Key Laboratory of Radiation Medicine and ProtectionKey Laboratory of Thrombosis and HemostasisMinistry of HealthNational Clinical Research Center for Hematological DiseasesSoochow UniversitySuzhouChina
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Arranz MJ, Gallego-Fabrega C, Martín-Blanco A, Soler J, Elices M, Dominguez-Clavé E, Salazar J, Vega D, Briones-Buixassa L, Pascual JC. A genome-wide methylation study reveals X chromosome and childhood trauma methylation alterations associated with borderline personality disorder. Transl Psychiatry 2021; 11:5. [PMID: 33414392 PMCID: PMC7791113 DOI: 10.1038/s41398-020-01139-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Borderline personality disorder (BPD) is a severe and highly prevalent psychiatric disorder, more common in females than in males and with notable differences in presentation between genders. Recent studies have shown that epigenetic modifications such as DNA methylation may modulate gene × environment interactions and impact on neurodevelopment. We conducted an epigenome wide study (Illumina Infinium HumanMethylation450k beadchip) in a group of BPD patients with (N = 49) and without (N = 47) childhood traumas and in a control group (N = 44). Results were confirmed in a replication cohort (N = 293 BPD patients and N = 114 controls) using EpiTYPER assays. Differentially methylated CpG sites were observed in several genes and intragenic regions in the X chromosome (PQBP1, ZNF41, RPL10, cg07810091 and cg24395855) and in chromosome 6 (TAP2). BPD patients showed significantly lower methylation levels in these CpG sites than healthy controls. These differences seemed to be increased by the existence of childhood trauma. Comparisons between BPD patients with childhood trauma and patients and controls without revealed significant differences in four genes (POU5F1, GGT6, TNFRSF13C and FAM113B), none of them in the X chromosome. Gene set enrichment analyses revealed that epigenetic alterations were more frequently found in genes controlling oestrogen regulation, neurogenesis and cell differentiation. These results suggest that epigenetic alterations in the X chromosome and oestrogen-regulation genes may contribute to the development of BPD and explain the differences in presentation between genders. Furthermore, childhood trauma events may modulate the magnitude of the epigenetic alterations contributing to BPD.
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Affiliation(s)
- María J. Arranz
- grid.414875.b0000 0004 1794 4956Fundació Docència i Recerca Mutua Terrassa, Terrassa, Spain ,grid.7722.00000 0001 1811 6966Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Institut de Recerca Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Cristina Gallego-Fabrega
- grid.414875.b0000 0004 1794 4956Fundació Docència i Recerca Mutua Terrassa, Terrassa, Spain ,grid.7722.00000 0001 1811 6966Stroke Pharmacogenomics and Genetics Group, Institut de Recerca Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Ana Martín-Blanco
- grid.7722.00000 0001 1811 6966Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Institut de Recerca Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain ,grid.413396.a0000 0004 1768 8905Department of Psychiatry, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain ,grid.7080.fDepartment of Psychiatry and Forensic Medicine & Institute of Neurosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joaquim Soler
- grid.7722.00000 0001 1811 6966Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Institut de Recerca Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain ,grid.413396.a0000 0004 1768 8905Department of Psychiatry, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain ,grid.7080.fDepartment of Psychiatry and Forensic Medicine & Institute of Neurosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Matilde Elices
- grid.7722.00000 0001 1811 6966Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Institut de Recerca Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain ,grid.413396.a0000 0004 1768 8905Department of Psychiatry, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain ,grid.7080.fDepartment of Psychiatry and Forensic Medicine & Institute of Neurosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elisabet Dominguez-Clavé
- grid.413396.a0000 0004 1768 8905Department of Psychiatry, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Juliana Salazar
- grid.7722.00000 0001 1811 6966Translational Medical Oncology Laboratory, Institut de Recerca Biomèdica Sant Pau (IIB-Sant Pau), Bellaterra, Spain
| | - Daniel Vega
- grid.7080.fDepartment of Psychiatry and Forensic Medicine & Institute of Neurosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain ,Psychiatry and Mental Health Department, Hospital of Igualada, Consorci Sanitari de l’Anoia & Fundació Sanitària d’Igualada, Igualada, Spain
| | - Laia Briones-Buixassa
- Psychiatry and Mental Health Department, Hospital of Igualada, Consorci Sanitari de l’Anoia & Fundació Sanitària d’Igualada, Igualada, Spain
| | - Juan Carlos Pascual
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Institut de Recerca Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain. .,Department of Psychiatry, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain. .,Department of Psychiatry and Forensic Medicine & Institute of Neurosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Heo Y, Heo J, Han SS, Kim WJ, Cheong HS, Hong Y. Difference of copy number variation in blood of patients with lung cancer. Int J Biol Markers 2020; 36:3-9. [PMID: 33307925 DOI: 10.1177/1724600820980739] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related deaths worldwide. Copy number variation (CNV) in several genetic regions correlate with cancer susceptibility. Hence, this study evaluated the association between CNV and non-small cell lung cancer (NSCLC) in the peripheral blood. METHODS Blood samples of 150 patients with NSCLC and 150 normal controls were obtained from a bioresource center (Seoul, Korea). Through an epigenome-wide analysis using the MethylationEPIC BeadChip method, we extracted CNVs by using an SVS8 software-supplied multivariate method. We compared CNV frequencies between the NSCLC and controls, and then performed stratification analyses according to smoking status. RESULTS We acquired 979 CNVs, with 582 and 967 copy-number gains and losses, respectively. We identified five nominally significant associations (ACOT1, NAA60, GSDMD, HLA-DPA1, and SLC35B3 genes). Among the current smokers, the NSCLC group had more CNV losses and gains at the GSDMD gene in chromosome 8 (P=0.02) and at the ACOT1 gene in chromosome 14 (P=0.03) than the control group. It also had more CNV losses at the NAA60 gene in chromosome 16 (P=0.03) among non-smokers. In the NSCLC group, current smokers had more CNV gains and losses at the ACOT1 gene in chromosome 14 (P=0.003) and at HLA-DPA1 gene in chromosome 6 (P=0.02), respectively, than non-smokers. CONCLUSION Five nominally significant associations were found between the NSCLC and CNVs. CNVs are associated with the mechanism of lung cancer development. However, the role of CNVs in lung cancer development needs further investigation.
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Affiliation(s)
- Yeonjeong Heo
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Jeongwon Heo
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Seon-Sook Han
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Yoonki Hong
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
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Cai Q, He B, Xie H, Zhang P, Peng X, Zhang Y, Zhao Z, Wang X. Identification of a novel prognostic DNA methylation signature for lung adenocarcinoma based on consensus clustering method. Cancer Med 2020; 9:7488-7502. [PMID: 32860318 PMCID: PMC7571836 DOI: 10.1002/cam4.3343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/06/2020] [Accepted: 07/12/2020] [Indexed: 12/22/2022] Open
Abstract
Abnormal DNA methylation persists throughout carcinogenesis and cancer development. Hence, gene promoter methylation may act as a prognostic tool and provide new potential therapeutic targets for patients with lung adenocarcinoma (LUAD). In this study, to explore prognostic methylation signature, data regarding DNA methylation and RNA-seq, and clinical data of patients with LUAD from the Cancer Genome Atlas database (TCGA) were downloaded. After data preprocessing, the methylation data were divided into training (N = 405) and test sets (N = 62). Then, patients in the training set were assigned to five subgroups based on their different methylation levels using the consensus clustering method. We comprehensively analyzed the survival information, methylation levels, and clinical variables, including American Joint Committee on Cancer (AJCC) stage, tumor-node-metastasis (TNM) staging, age, smoking history, and gender of these five groups. Subsequently, we identified a 16-CpG prognostic signature and constructed a prognostic model, which was verified in the test set. Further analyses showed stable prognostic performance in the stratified cohorts. In conclusion, the new predictive DNA methylation signature proposed in this study may be used as an independent biomarker to assess the overall survival of LUAD patients and provide bioinformatics information for development of targeted therapy.
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Affiliation(s)
- Qidong Cai
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Boxue He
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Hui Xie
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Pengfei Zhang
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xiong Peng
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yuqian Zhang
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zhenyu Zhao
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xiang Wang
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
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Yang L, Zhang J, Yang G, Xu H, Lin J, Shao L, Li J, Guo C, Du Y, Guo L, Li X, Han-Zhang H, Wang C, Chuai S, Ye J, Kang Q, Liu H, Ying J, Wang Y. The prognostic value of a Methylome-based Malignancy Density Scoring System to predict recurrence risk in early-stage Lung Adenocarcinoma. Theranostics 2020; 10:7635-7644. [PMID: 32685009 PMCID: PMC7359091 DOI: 10.7150/thno.44229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
Current NCCN guidelines do not recommend the use of adjuvant chemotherapy for stage IA lung adenocarcinoma patients with R0 surgery. However, 25% to 40% of patients with stage IA disease experience recurrence. Stratifying patients according to the recurrence risk may tailor adjuvant therapy and surveillance imaging for those with a higher risk. However, prognostic markers are often identified by comparing high-risk and low-risk cases which might introduce bias due to the widespread interpatient heterogeneity. Here, we developed a scoring system quantifying the degree of field cancerization in adjacent normal tissues and revealed its association with disease-free survival (DFS). Methods: We recruited a cohort of 44 patients with resected stage IA lung adenocarcinoma who did not receive adjuvant therapy. Both tumor and adjacent normal tissues were obtained from each patient and subjected to capture-based targeted genomic and epigenomic profiling. A novel methylome-based scoring system namely malignancy density ratio (MD ratio) was developed based on 39 patients by comparing tumor and corresponding adjacent normal tissues of each patient. A MD score was then obtained by Wald statistics. The correlations of MD ratio, MD score, and genomic features with clinical outcome were investigated. Results: Patients with a high-risk MD ratio showed a significantly shorter postsurgical DFS compared with those with a low-risk MD ratio (HR=4.47, P=0.01). The MD ratio was not associated with T stage (P=1), tumor cell fraction (P=0.748) nor inflammatory status (p=0.548). Patients with a high-risk MD score also demonstrated an inferior DFS (HR=4.69, P=0.039). In addition, multivariate analysis revealed EGFR 19 del (HR=5.39, P=0.012) and MD score (HR= 7.90, P=0.01) were independent prognostic markers. Conclusion: The novel methylome-based scoring system, developed by comparing the signatures between tumor and corresponding adjacent normal tissues of individual patients, largely minimizes the bias of interpatient heterogeneity and reveals a robust prognostic value in patients with resected lung adenocarcinoma.
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Yu H, Raut JR, Schöttker B, Holleczek B, Zhang Y, Brenner H. Individual and joint contributions of genetic and methylation risk scores for enhancing lung cancer risk stratification: data from a population-based cohort in Germany. Clin Epigenetics 2020; 12:89. [PMID: 32552915 PMCID: PMC7301507 DOI: 10.1186/s13148-020-00872-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Risk stratification for lung cancer (LC) screening is so far mostly based on smoking history. This study aimed to assess if and to what extent such risk stratification could be enhanced by additional consideration of genetic risk scores (GRSs) and epigenetic risk scores defined by DNA methylation. METHODS We conducted a nested case-control study of 143 incident LC cases and 1460 LC-free controls within a prospective cohort of 9949 participants aged 50-75 years with 14-year follow-up. Lifetime smoking history was obtained in detail at recruitment. We built a GRS based on 31 previously identified LC-associated single-nucleotide polymorphisms (SNPs) and a DNA methylation score (MRS) based on methylation of 151 previously identified smoking-associated cytosine-phosphate-guanine (CpG) loci. We evaluated associations of GRS and MRS with LC incidence by logistic regression models, controlling for age, sex, smoking status, and pack-years. We compared the predictive performance of models based on pack-years alone with models additionally including GRS and/or MRS using the area under the receiver operating characteristic curve (AUC), net reclassification improvement (NRI), and integrated discrimination improvement (IDI). RESULTS GRS and MRS showed moderate and strong associations with LC risk even after comprehensive adjustment for smoking history (adjusted odds ratio [95% CI] comparing highest with lowest quartile 1.93 [1.05-3.71] and 5.64 [2.13-17.03], respectively). Similar associations were also observed within the risk groups of ever and heavy smokers. Addition of GRS and MRS furthermore strongly enhanced LC prediction beyond prediction by pack-years (increase of optimism-corrected AUC among heavy smokers from 0.605 to 0.654, NRI 26.7%, p = 0.0106, IDI 3.35%, p = 0.0036), the increase being mostly attributable to the inclusion of MRS. CONCLUSIONS Consideration of MRS, by itself or in combination with GRS, may strongly enhance LC risk stratification.
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Affiliation(s)
- Haixin Yu
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,Medical Faculty Heidelberg, University of Heidelberg, Im Neuenheimer Feld 672, 69120, Heidelberg, Germany
| | - Janhavi R Raut
- Medical Faculty Heidelberg, University of Heidelberg, Im Neuenheimer Feld 672, 69120, Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,Network Aging Research, University of Heidelberg, Bergheimer Straße 20, 69115, Heidelberg, Germany
| | - Bernd Holleczek
- Saarland Cancer Registry, Krebsregister Saarland, Präsident-Baltz-Straße 5, 66119, Saarbrücken, Germany
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany. .,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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