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Dwivedi Y, Roy B, Korla PK. Genome-wide methylome-based molecular pathologies associated with depression and suicide. Neuropsychopharmacology 2024:10.1038/s41386-024-02040-9. [PMID: 39645539 DOI: 10.1038/s41386-024-02040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 10/31/2024] [Accepted: 11/26/2024] [Indexed: 12/09/2024]
Abstract
Major depressive disorder (MDD) is a debilitating disorder. Suicide attempts are 5-times higher in MDD patients than in the general population. Interestingly, not all MDD patients develop suicidal thoughts or complete suicide. Thus, it is important to study the risk factors that can distinguish suicidality among MDD patients. The present study examined if DNA methylation changes can distinguish suicidal behavior among depressed subjects. Genome-wide DNA methylation was examined in the dorsolateral prefrontal cortex of depressed suicide (MDD+S; n = 15), depressed non-suicide (MDD-S; n = 17), and nonpsychiatric control (C; n = 16) subjects using 850 K Infinium Methylation EPIC BeadChip. The significantly differentially methylated genes were used to determine the functional enrichment of genes for ontological clustering and pathway analysis. Based on the number of CpG content and their relative distribution from specific landmark regions of genes, 32,958 methylation sites were identified across 12,574 genes in C vs. MDD+/-S subjects, 30,852 methylation sites across 12,019 genes in C vs. MDD-S, 41,648 methylation sites across 13,941 genes in C vs. MDD+S, and 49,848 methylation sites across 15,015 genes in MDD-S vs. MDD+S groups. A comparison of methylation sites showed 33,129 unique methylation sites and 5451 genes in the MDD-S group compared to the MDD+S group. Functional analysis suggested oxytocin, GABA, VGFA, TNFA, and mTOR pathways associated with suicide in the MDD group. Altogether, our data show a distinct pattern of DNA methylation, the genomic distribution of differentially methylated sites, gene enrichment, and pathways in MDD suicide compared to non-suicide MDD subjects.
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Affiliation(s)
- Yogesh Dwivedi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Bhaskar Roy
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Praveen Kumar Korla
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
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2
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Semik-Gurgul E, Pawlina-Tyszko K, Gurgul A, Szmatoła T, Rybińska J, Ząbek T. In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart. Mamm Genome 2024; 35:600-620. [PMID: 39143382 PMCID: PMC11522055 DOI: 10.1007/s00335-024-10057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024]
Abstract
DNA methylation and microRNA (miRNA) expression are epigenetic mechanisms essential for regulating tissue-specific gene expression and metabolic processes. However, high-resolution transcriptome, methylome, or miRNAome data is only available for a few model organisms and selected tissues. Up to date, only a few studies have reported on gene expression, DNA methylation, or miRNA expression in adult equine tissues at the genome-wide level. In the present study, we used RNA-Seq, miRNA-seq, and reduced representation bisulfite sequencing (RRBS) data from the heart, lung, and liver tissues of healthy cold-blooded horses to identify differentially expressed genes (DEGs), differentially expressed miRNA (DE miRNA) and differentially methylated sites (DMSs) between three types of horse tissues. Additionally, based on integrative omics analysis, we described the observed interactions of epigenetic mechanisms with tissue-specific gene expression alterations. The obtained data allowed identification from 4067 to 6143 DMSs, 9733 to 11,263 mRNAs, and 155 to 185 microRNAs, differentially expressed between various tissues. We pointed out specific genes whose expression level displayed a negative correlation with the level of CpG methylation and miRNA expression and revealed biological processes that they enrich. Furthermore, we confirmed and validated the accuracy of the Next-Generation Sequencing (NGS) results with bisulfite sequencing PCR (BSP) and quantitative PCR (qPCR). This comprehensive analysis forms a strong foundation for exploring the epigenetic mechanisms involved in tissue differentiation, especially the growth and development of the equine heart, lungs, and liver.
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Affiliation(s)
- Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland.
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland
| | - Justyna Rybińska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| | - Tomasz Ząbek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
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3
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Zang Z, Yin Y, Liu C, Zhu Q, Huang X, Li H, Yang R. IL21R hypomethylation as a biomarker for distinguishing benign and malignant breast tumours. Epigenetics 2024; 19:2352683. [PMID: 38723244 PMCID: PMC11086039 DOI: 10.1080/15592294.2024.2352683] [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: 10/27/2023] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
Some benign and malignant breast tumours are similar in pathological morphology, which are difficult to be distinguished in clinical diagnosis. In this study, we intended to explore novel biomarkers for differential diagnosis of benign and malignant breast tumours. Methylation EPIC 850K beadchip and RNA-sequencing were used to analyse 29 tissue samples from patients with early-stage breast cancer (BC) and benign breast tumours for differently methylated and expressed genes. The altered methylation of IL21R was semi-quantitatively validated in an independent study with 566 tissue samples (279 BC vs. 287 benign breast tumours) using mass spectrometry. Binary logistic regression analysis was performed to evaluate the association between IL21R methylation and BC. BC-associated IL21R hypomethylation and overexpression were identified in the discovery round. In the validation round, BC patients presented significant IL21R hypomethylation compared to women with benign breast tumours (ORs ≥1.29 per-10% methylation, p-values ≤ 5.69E-14), and this hypomethylation was even enhanced in BC patients with ER-negative and PR-negative tumours as well as with triple-negative tumours. The methylation of IL21R showed efficient discriminatory power to distinguish benign breast tumours from BC (area under curve (AUC) = 0.88), and especially from ER-negative BC (AUC = 0.95), PR-negative BC (AUC = 0.93) and triple-negative BC (AUC = 0.96). We disclosed significant IL21R hypomethylation in patients with BC compared to women with benign breast tumours, and revealed the somatic change of DNA methylation could be a potential biomarker for molecular pathology of BC.
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Affiliation(s)
- Zishan Zang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifei Yin
- Department of Thyroid and Breast Surgery, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiang Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuandong Huang
- Department of Thyroid and Breast Surgery, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Hong Li
- Department of Pathology, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
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O'Neill K, Pleasance E, Fan J, Akbari V, Chang G, Dixon K, Csizmok V, MacLennan S, Porter V, Galbraith A, Grisdale CJ, Culibrk L, Dupuis JH, Corbett R, Hopkins J, Bowlby R, Pandoh P, Smailus DE, Cheng D, Wong T, Frey C, Shen Y, Lewis E, Paulin LF, Sedlazeck FJ, Nelson JMT, Chuah E, Mungall KL, Moore RA, Coope R, Mungall AJ, McConechy MK, Williamson LM, Schrader KA, Yip S, Marra MA, Laskin J, Jones SJM. Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes. CELL GENOMICS 2024; 4:100674. [PMID: 39406235 PMCID: PMC11605692 DOI: 10.1016/j.xgen.2024.100674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/26/2024] [Accepted: 09/18/2024] [Indexed: 11/16/2024]
Abstract
The Long-Read Personalized OncoGenomics (POG) dataset comprises a cohort of 189 patient tumors and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the POG program and the Marathon of Hope Cancer Centres Network includes DNA and RNA short-read sequence data, analytics, and clinical information. We show the potential of long-read sequencing for resolving complex cancer-related structural variants, viral integrations, and extrachromosomal circular DNA. Long-range phasing facilitates the discovery of allelically differentially methylated regions (aDMRs) and allele-specific expression, including recurrent aDMRs in the cancer genes RET and CDKN2A. Germline promoter methylation in MLH1 can be directly observed in Lynch syndrome. Promoter methylation in BRCA1 and RAD51C is a likely driver behind homologous recombination deficiency where no coding driver mutation was found. This dataset demonstrates applications for long-read sequencing in precision medicine and is available as a resource for developing analytical approaches using this technology.
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Affiliation(s)
- Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Jeremy Fan
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Vahid Akbari
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Glenn Chang
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Katherine Dixon
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Signe MacLennan
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Vanessa Porter
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Andrew Galbraith
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - John H Dupuis
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard Corbett
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - James Hopkins
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Duane E Smailus
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Tina Wong
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Connor Frey
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Eleanor Lewis
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jessica M T Nelson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Robin Coope
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Melissa K McConechy
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Kasmintan A Schrader
- Hereditary Cancer Program, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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Ding H, Wang J, Zhao X, Xiu S, Cai H, Ma J, Fu L, Zhou J, Shen F, Zhang H, Chen Y, Li B, Yan J. Combination of circulating tumor cells, lncRNAs and DNA methylation for the diagnosis of endometrial carcinoma. Oncol Lett 2024; 28:545. [PMID: 39310026 PMCID: PMC11413727 DOI: 10.3892/ol.2024.14678] [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: 05/27/2024] [Accepted: 08/13/2024] [Indexed: 09/25/2024] Open
Abstract
Endometrial carcinoma (EC) is one of the most common gynecological malignant neoplasms, the prognosis of which is strongly related to the time of diagnosis, with an earlier diagnosis leading to a better prognosis. Therefore, effective diagnostic indicators and methods are needed to ensure early detection. The present study explored the following in EC: Circulating tumor cells (CTCs); the long noncoding RNAs (lncRNAs) RP4-616B8.5, RP11-389G6.3 and carboxy-terminal domain (CTD)-2377D24.6; and the methylation of cysteine dioxygenase type 1 (CDO1) and CUGBP Elav-like family member 4 (CELF4). In total, 85 patients, including 71 with EC, and 14 without EC (NO-EC) but with uterine fibroids or polyps, were included in the present study. In total, 46 patients with EC and 8 NO-EC patients underwent CTC detection. In the evaluation of the EC vs. NO-EC groups, the results showed that the CTC-positive rate of the EC group was 80.43% and that the area under the curve (AUC) value of CTCs was 0.8872 (P=0.0098). A total of 35 patients with EC and 14 NO-EC patients underwent detection of the RP4-616B8.5, RP11-389G6.3 and CTD-2377D24.6 lncRNAs. When the levels of the three lncRNAs RP4-616B8.5, RP11-389G6.3 and CTD-2377D24.6 were compared between the EC and NO-EC groups, they were higher in the EC group; the P-values were 0.0002, 0.0001 and <0.0001, respectively, and the AUC values were 0.8184, 0.8347 and 0.8265, respectively. In addition, a total of 35 patients with EC and 8 NO-EC patients underwent CDO1 and CELF4 DNA methylation analysis. The positive rates of the methylated genes CDO1 and CELF4 were 20% (7/35) and 5.71% (2/35), and the P-values of the comparisons between the EC and NO-EC groups were 0.1748 and 0.5004, respectively; the AUC values were 0.6000 and 0.5286. Furthermore, the combination of CTCs, and lncRNAs RP4-616B8.5, RP11-389G6.3 and CTD-2377D24.6 exhibited high performance in the detection of EC (AUC=0.9375).
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Affiliation(s)
- Hongmei Ding
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Xiaoyu Zhao
- Holosensor Medical Technology Ltd., Suzhou, Jiangsu 215000, P.R. China
| | - Shi Xiu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Honghong Cai
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Jingjing Ma
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Li Fu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Jinhua Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Fangrong Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Hong Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Bingyan Li
- Department of Nutrition and Food Hygiene, Medical College of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Jing Yan
- Holosensor Medical Technology Ltd., Suzhou, Jiangsu 215000, P.R. China
- Department of Veterinary Medicine, University of Cambridge, Cambridge 02138, UK
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Chen X, Su W, Chen J, Ouyang P, Gong J. ST3GAL4 promotes tumorigenesis in breast cancer by enhancing aerobic glycolysis. Hum Cell 2024; 38:1. [PMID: 39422756 DOI: 10.1007/s13577-024-01137-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 09/17/2024] [Indexed: 10/19/2024]
Abstract
Sialyltransferases are enzymes that play a crucial role in regulating cancer progression by modifying glycoproteins through sialylation. In particular, the ST3 beta-galactoside alpha-2,3-sialyltransferase 4 (ST3GAL4) enzyme is known to be upregulated in breast cancer, but its specific biological functions have not been fully understood. This study aimed to investigate the impact and mechanisms of ST3GAL4 on aerobic glycolysis in breast cancer. We examined ST3GAL4 expression in tumor tissue samples and breast cancer cell lines and also manipulated ST3GAL4 expression in breast cancer cells using lentivirus transduction. The study evaluated cellular processes such as cell viability, cell cycle progression, and aerobic glycolysis by measuring parameters like extracellular acidification rate, glucose uptake, lactate production, and lactate dehydrogenase A (LDHA) expression. We found that ST3GAL4 expression was consistently increased in tumor tissues and breast cancer cell lines. High ST3GAL4 expression was associated with a poor prognosis for patients with breast cancer. Inhibiting ST3GAL4 expression decreased cell viability, disrupted cell cycle progression, and reduced aerobic glycolysis and LDHA expression. Furthermore, suppressing ST3GAL4 expression in animal models reduced tumor growth and cell proliferation. Conversely, overexpressing ST3GAL4 promoted cell viability and cell cycle progression, but these effects were reversed when an inhibitor of aerobic glycolysis was used. The study provided evidence in cells and animal models that ST3GAL4 promotes tumorigenesis in breast cancer by enhancing aerobic glycolysis. These findings suggest that targeting ST3GAL4 may be a potential strategy for the treatment of breast cancer.
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Affiliation(s)
- Xiaoqing Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jinan University, 613 West of Huangpu Avenue, Guangzhou, 510630, China
- Department of Breast Medicine, Foshan Women and Children Hospital, Foshan, 528000, China
| | - Weijie Su
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, China
| | - Jiewen Chen
- Department of Breast Medicine, Foshan Women and Children Hospital, Foshan, 528000, China
| | - Peng Ouyang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jinan University, 613 West of Huangpu Avenue, Guangzhou, 510630, China
| | - Jin Gong
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jinan University, 613 West of Huangpu Avenue, Guangzhou, 510630, China.
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Lavoro A, Falzone L, Gattuso G, Conti GN, Caltabiano R, Madonna G, Capone M, McCubrey JA, Ascierto PA, Libra M, Candido S. Identification of SLC22A17 DNA methylation hotspot as a potential biomarker in cutaneous melanoma. J Transl Med 2024; 22:887. [PMID: 39358721 PMCID: PMC11445995 DOI: 10.1186/s12967-024-05622-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 08/18/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Cancer onset and progression are driven by genetic and epigenetic alterations leading to oncogene activation and the silencing of tumor suppressor genes. Among epigenetic mechanisms, DNA methylation (methDNA) is gaining growing interest in cancer. Promoter hypomethylation is associated with oncogene activation while intragenic methDNA can be involved in transcriptional elongation, alternative spicing, and the activation of cryptic start sites. Several genes involved in the modulation of the tumor microenvironment are regulated by methDNA, including the Solute Carrier Family 22 Member 17 (SLC22A17), which is involved in iron trafficking and extracellular matrix remodeling cooperating with the Gelatinase-Associated Lipocalin (NGAL) ligand. However, the exact role of intragenic methDNA in cancer has not been fully investigated. Therefore, the aim of the present study is to explore the role of methDNA in the regulation of SLC22A17 in cutaneous melanoma (CM), used as a tumor model. METHODS Correlation and differential analyses between SLC22A17 expression and methDNA were performed using the data contained in The Cancer Genome Atlas and Gene Expression Omnibus databases. Functional studies on melanoma cell lines treated with 5-Azacytidine (5-Aza) were conducted to assess the correlation between methDNA and SLC22A17 expression. A validation study on the diagnostic potential of the in silico-identified SLC22A17 methDNA hotspot was finally performed by analyzing tissue samples obtained from CM patients and healthy controls. RESULTS The computational analyses revealed that SLC22A17 was significantly downregulated in CM, and its expression was related to promoter hypomethylation and intragenic hypermethylation. Moreover, SLC22A17 overexpression and hypermethylation of two intragenic methDNA hotspots were associated with a better clinical outcome in CM patients. The correlation between SLC22A17 methDNA and expression was confirmed in 5-Aza-treated cells. In agreement with in silico analyses, the SLC22A17 promoter methylation hotspot showed higher methDNA levels in CM samples compared to nevi. In addition, the methDNA levels of this hotspot were positively correlated with advanced CM. CONCLUSIONS The SLC22A17 methDNA hotspot could represent a promising biomarker for CM, highlighting the regulatory role of methDNA on SLC22A17 expression. These results pave the way for the identification of novel epigenetic biomarkers and therapeutic targets for the management of CM patients.
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Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy
| | - Luca Falzone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy.
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy
| | - Giuseppe N Conti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", University of Catania, Catania, I-95123, Italy
| | - Gabriele Madonna
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, I-80131, Italy
| | - Mariaelena Capone
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, I-80131, Italy
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, 27858, USA
| | - Paolo A Ascierto
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, I-80131, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, I- 95123, Italy.
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, I- 95123, Italy
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Silva-Hurtado TJ, Inocencio JF, Yong RL. Emerging applications of hypomethylating agents in the treatment of glioblastoma (Review). Mol Clin Oncol 2024; 21:59. [PMID: 39006906 PMCID: PMC11240870 DOI: 10.3892/mco.2024.2757] [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: 03/08/2024] [Accepted: 04/26/2024] [Indexed: 07/16/2024] Open
Abstract
DNA hypomethylating agents (HMAs) such as decitabine and 5-azacytidine have established roles in the treatment paradigms for myelodysplastic syndrome and acute myelogenous leukemia, where they are considered to exert their anticancer effects by restoring the expression of tumor suppressor genes. Due to their relatively favorable adverse effect profile and known ability to pass through the blood-brain barrier, applications in the treatment of glioblastoma (GBM) and other central nervous system malignancies are under active investigation. The present review examines the types of HMAs currently available, their known and less-understood antineoplastic mechanisms, and the evidence to date of their preclinical and clinical efficacy in glioblastoma and other solid malignancies. The present review discusses the potential synergies HMAs may have with established and emerging GBM treatments, including temozolomide, immune checkpoint inhibitors and cancer vaccines. Recent successes and setbacks in clinical trials for newly diagnosed and recurrent GBM are summarized in order to highlight opportunities for HMAs to improve therapeutic responses. Challenges for future clinical trials are also assessed.
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Affiliation(s)
- Thenzing J. Silva-Hurtado
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julio F. Inocencio
- Leo M. Davidoff Department of Neurosurgery, Montefiore Medical Center, Einstein College of Medicine, Bronx, NY 10461, USA
| | - Raymund L. Yong
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Fu H, Pickering H, Rubbi L, Ross TM, Zhou W, Reed EF, Pellegrini M. The response to influenza vaccination is associated with DNA methylation-driven regulation of T cell innate antiviral pathways. Clin Epigenetics 2024; 16:114. [PMID: 39169387 PMCID: PMC11340180 DOI: 10.1186/s13148-024-01730-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND The effect of vaccination on the epigenome remains poorly characterized. In previous research, we identified an association between seroprotection against influenza and DNA methylation at sites associated with the RIG-1 signaling pathway, which recognizes viral double-stranded RNA and leads to a type I interferon response. However, these studies did not fully account for confounding factors including age, gender, and BMI, along with changes in cell-type composition. RESULTS Here, we studied the influenza vaccine response in a longitudinal cohort vaccinated over two consecutive years (2019-2020 and 2020-2021), using peripheral blood mononuclear cells and a targeted DNA methylation approach. To address the effects of multiple factors on the epigenome, we designed a multivariate multiple regression model that included seroprotection levels as quantified by the hemagglutination-inhibition (HAI) assay test. CONCLUSIONS Our findings indicate that 179 methylation sites can be combined as potential signatures to predict seroprotection. These sites were not only enriched for genes involved in the regulation of the RIG-I signaling pathway, as found previously, but also enriched for other genes associated with innate immunity to viruses and the transcription factor binding sites of BRD4, which is known to impact T cell memory. We propose a model to suggest that the RIG-I pathway and BRD4 could potentially be modulated to improve immunization strategies.
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Affiliation(s)
- Hongxiang Fu
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Harry Pickering
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Liudmilla Rubbi
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Ted M Ross
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine F Reed
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
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Lin S, Hannon E, Reppell M, Waring JF, Smaoui N, Pivorunas V, Guay H, Chanchlani N, Bewshea C, Bai BYH, Kennedy NA, Goodhand JR, Mill J, Ahmad T. Whole Blood DNA Methylation Changes Are Associated with Anti-TNF Drug Concentration in Patients with Crohn's Disease. J Crohns Colitis 2024; 18:1190-1201. [PMID: 37551994 PMCID: PMC11324340 DOI: 10.1093/ecco-jcc/jjad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/23/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND AND AIMS Anti-tumour necrosis factor [TNF] treatment failure in patients with inflammatory bowel disease [IBD] is common and frequently related to low drug concentrations. In order to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy, we sought to define epigenetic biomarkers in whole blood at baseline associated with anti-TNF drug concentrations at week 14. METHODS DNA methylation from 1104 whole blood samples from 385 patients in the Personalised Anti-TNF Therapy in Crohn's disease [PANTS] study were assessed using the Illumina EPIC Beadchip [v1.0] at baseline and weeks 14, 30, and 54. We compared DNA methylation profiles in anti-TNF-treated patients who experienced primary non-response at week 14 if they were assessed at subsequent time points and were not in remission at week 30 or 54 [infliximab n = 99, adalimumab n = 94], with patients who responded at week 14 and when assessed at subsequent time points were in remission at week 30 or 54 [infliximab n = 99, adalimumab n = 93]. RESULTS Overall, between baseline and week 14, we observed 4999 differentially methylated positions [DMPs] annotated to 2376 genes following anti-TNF treatment. Pathway analysis identified 108 significant gene ontology terms enriched in biological processes related to immune system processes and responses. Epigenome-wide association [EWAS] analysis identified 323 DMPs annotated to 210 genes at baseline associated with higher anti-TNF drug concentrations at Week 14. Of these, 125 DMPs demonstrated shared associations with other common traits [proportion of shared CpGs compared with DMPs] including body mass index [23.2%], followed by C-reactive protein [CRP] [11.5%], smoking [7.4%], alcohol consumption per day [7.1%], and IBD type [6.8%]. EWAS of primary non-response to anti-TNF identified 20 DMPs that were associated with both anti-TNF drug concentration and primary non-response to anti-TNF with a strong correlation of the coefficients [Spearman's rho = -0.94, p <0.001]. CONCLUSION Baseline DNA methylation profiles may be used as a predictor for anti-TNF drug concentration at week 14 to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy.
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Affiliation(s)
- Simeng Lin
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Mark Reppell
- Precision Medicine Immunology, AbbVie Inc., Chicago, IL, USA
| | | | - Nizar Smaoui
- Precision Medicine Immunology, AbbVie Inc., Chicago, IL, USA
| | | | - Heath Guay
- Precision Medicine Immunology, AbbVie Inc., Chicago, IL, USA
| | - Neil Chanchlani
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Benjamin Y H Bai
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
- Postgraduate School of Life Sciences, University of Cambridge, Cambridge, UK
| | - Nicholas A Kennedy
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - James R Goodhand
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Tariq Ahmad
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
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Linscott JA, Miyagi H, Murthy PB, Yao S, Grass GD, Vosoughi A, Xu H, Wang X, Yu X, Yu A, Zemp L, Gilbert SM, Poch MA, Sexton WJ, Spiess PE, Li R. From Detection to Cure - Emerging Roles for Urinary Tumor DNA (utDNA) in Bladder Cancer. Curr Oncol Rep 2024; 26:945-958. [PMID: 38837106 DOI: 10.1007/s11912-024-01555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
PURPOSE OF REVIEW This review sought to define the emerging roles of urinary tumor DNA (utDNA) for diagnosis, monitoring, and treatment of bladder cancer. Building from early landmark studies the focus is on recent studies, highlighting how utDNA could aid personalized care. RECENT FINDINGS Recent research underscores the potential for utDNA to be the premiere biomarker in bladder cancer due to the constant interface between urine and tumor. Many studies find utDNA to be more informative than other biomarkers in bladder cancer, especially in early stages of disease. Points of emphasis include superior sensitivity over traditional urine cytology, broad genomic and epigenetic insights, and the potential for non-invasive, real-time analysis of tumor biology. utDNA shows promise for improving all phases of bladder cancer care, paving the way for personalized treatment strategies. Building from current research, future comprehensive clinical trials will validate utDNA's clinical utility, potentially revolutionizing bladder cancer management.
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Affiliation(s)
- Joshua A Linscott
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
| | - Hiroko Miyagi
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Prithvi B Murthy
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Sijie Yao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - G Daniel Grass
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Aram Vosoughi
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Hongzhi Xu
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alice Yu
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Logan Zemp
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Scott M Gilbert
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Michael A Poch
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Wade J Sexton
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Philippe E Spiess
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Roger Li
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Ahmed F, Mishra NK, Alghamdi OA, Khan MI, Ahmad A, Khan N, Rehan M. Deciphering KDM8 dysregulation and CpG methylation in hepatocellular carcinoma using multi-omics and machine learning. Epigenomics 2024; 16:961-983. [PMID: 39072393 PMCID: PMC11370911 DOI: 10.1080/17501911.2024.2374702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 06/25/2024] [Indexed: 07/30/2024] Open
Abstract
Aim: This study investigates the altered expression and CpG methylation patterns of histone demethylase KDM8 in hepatocellular carcinoma (HCC), aiming to uncover insights and promising diagnostics biomarkers.Materials & methods: Leveraging TCGA-LIHC multi-omics data, we employed R/Bioconductor libraries and Cytoscape to analyze and construct a gene correlation network, and LASSO regression to develop an HCC-predictive model.Results: In HCC, KDM8 downregulation is correlated with CpGs hypermethylation. Differential gene correlation analysis unveiled a liver carcinoma-associated network marked by increased cell division and compromised liver-specific functions. The LASSO regression identified a highly accurate HCC prediction signature, prominently featuring CpG methylation at cg02871891.Conclusion: Our study uncovers CpG hypermethylation at cg02871891, possibly influencing KDM8 downregulation in HCC, suggesting these as promising biomarkers and targets.
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Affiliation(s)
- Firoz Ahmed
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nitish Kumar Mishra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38015, USA
| | - Othman A Alghamdi
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammad Imran Khan
- Research Center, King Faisal Specialist Hospital & Research Centre, Jeddah, Saudi Arabia
- Department of Biochemistry & Molecular Medicine, College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
| | - Aamir Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Nargis Khan
- Snyder Institute of Chronic Diseases, Health Research & Innovation Center, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Mohammad Rehan
- Snyder Institute of Chronic Diseases, Health Research & Innovation Center, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
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Ciaccio AM, Tuttolomondo A. Epigenetics of cerebrovascular diseases: an update review of clinical studies. Epigenomics 2024; 16:1043-1055. [PMID: 39072474 PMCID: PMC11404611 DOI: 10.1080/17501911.2024.2377947] [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: 05/01/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024] Open
Abstract
Cerebrovascular diseases, especially stroke, are critical and heterogenous clinical conditions associated with high mortality and chronic disability. Genome-wide association studies reveal substantial stroke heritability, though specific genetic variants account for a minor fraction of stroke risk, suggesting an essential role for the epigenome. Epigenome-wide association studies and candidate gene approaches show that DNA methylation patterns significantly influence stroke susceptibility. Additionally, chromatin remodelers and non-coding RNA regulate gene expression in response to ischemic conditions. In this updated review, we summarized the progress of knowledge on epigenetics in the field of ischemic stroke underlying opportunities and challenges.
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Affiliation(s)
- Anna Maria Ciaccio
- Internal Medicine & Stroke Care Ward, PROMISE Department, University of Palermo, Piazza delle Cliniche n.2, 90127, Palermo, Italy
| | - Antonino Tuttolomondo
- Internal Medicine & Stroke Care Ward, PROMISE Department, University of Palermo, Piazza delle Cliniche n.2, 90127, Palermo, Italy
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Cristalli C, Scotlandi K. Targeting DNA Methylation Machinery in Pediatric Solid Tumors. Cells 2024; 13:1209. [PMID: 39056791 PMCID: PMC11275080 DOI: 10.3390/cells13141209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic regulatory mechanism that plays a critical role in a variety of cellular processes, including the regulation of cell fate during development, maintenance of cell identity, and genome stability. DNA methylation is tightly regulated by enzymatic reactions and its deregulation plays an important role in the development of cancer. Specific DNA methylation alterations have been found in pediatric solid tumors, providing new insights into the development of these tumors. In addition, DNA methylation profiles have greatly contributed to tune the diagnosis of pediatric solid tumors and to define subgroups of patients with different risks of progression, leading to the reduction in unwanted toxicity and the improvement of treatment efficacy. This review highlights the dysregulated DNA methylome in pediatric solid tumors and how this information provides promising targets for epigenetic therapies, particularly inhibitors of DNMT enzymes (DNMTis). Opportunities and limitations are considered, including the ability of DNMTis to induce viral mimicry and immune signaling by tumors. Besides intrinsic action against cancer cells, DNMTis have the potential to sensitize immune-cold tumors to immunotherapies and may represent a remarkable option to improve the treatment of challenging pediatric solid tumors.
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Affiliation(s)
- Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
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15
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Benedetti R, Di Crosta M, D’Orazi G, Cirone M. Post-Translational Modifications (PTMs) of mutp53 and Epigenetic Changes Induced by mutp53. BIOLOGY 2024; 13:508. [PMID: 39056701 PMCID: PMC11273943 DOI: 10.3390/biology13070508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
Wild-type (wt) p53 and mutant forms (mutp53) play a key but opposite role in carcinogenesis. wtP53 acts as an oncosuppressor, preventing oncogenic transformation, while mutp53, which loses this property, may instead favor this process. This suggests that a better understanding of the mechanisms activating wtp53 while inhibiting mutp53 may help to design more effective anti-cancer treatments. In this review, we examine possible PTMs with which both wt- and mutp53 can be decorated and discuss how their manipulation could represent a possible strategy to control the stability and function of these proteins, focusing in particular on mutp53. The impact of ubiquitination, phosphorylation, acetylation, and methylation of p53, in the context of several solid and hematologic cancers, will be discussed. Finally, we will describe some of the recent studies reporting that wt- and mutp53 may influence the expression and activity of enzymes responsible for epigenetic changes such as acetylation, methylation, and microRNA regulation and the possible consequences of such changes.
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Affiliation(s)
- Rossella Benedetti
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| | - Michele Di Crosta
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| | - Gabriella D’Orazi
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. D’Annunzio”, 66013 Chieti, Italy
| | - Mara Cirone
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
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Faldoni FLC, Bizinelli D, Souza CP, Santana IVV, Marques MMC, Rainho CA, Marchi FA, Rogatto SR. DNA methylation profile of inflammatory breast cancer and its impact on prognosis and outcome. Clin Epigenetics 2024; 16:89. [PMID: 38971778 PMCID: PMC11227707 DOI: 10.1186/s13148-024-01695-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 06/16/2024] [Indexed: 07/08/2024] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) is a rare disease characterized by rapid progression, early metastasis, and a high mortality rate. METHODS Genome-wide DNA methylation analysis (EPIC BeadChip platform, Illumina) and somatic gene variants (105 cancer-related genes) were performed in 24 IBCs selected from a cohort of 140 cases. RESULTS We identified 46,908 DMPs (differentially methylated positions) (66% hypomethylated); CpG islands were predominantly hypermethylated (39.9%). Unsupervised clustering analysis revealed three clusters of DMPs characterized by an enrichment of specific gene mutations and hormone receptor status. The comparison among DNA methylation findings and external datasets (TCGA-BRCA stages III-IV) resulted in 385 shared DMPs mapped in 333 genes (264 hypermethylated). 151 DMPs were associated with 110 genes previously detected as differentially expressed in IBC (GSE45581), and 68 DMPs were negatively correlated with gene expression. We also identified 4369 DMRs (differentially methylated regions) mapped on known genes (2392 hypomethylated). BCAT1, CXCL12, and TBX15 loci were selected and evaluated by bisulfite pyrosequencing in 31 IBC samples. BCAT1 and TBX15 had higher methylation levels in triple-negative compared to non-triple-negative, while CXCL12 had lower methylation levels in triple-negative than non-triple-negative IBC cases. TBX15 methylation level was associated with obesity. CONCLUSIONS Our findings revealed a heterogeneous DNA methylation profile with potentially functional DMPs and DMRs. The DNA methylation data provided valuable insights for prognostic stratification and therapy selection to improve patient outcomes.
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Affiliation(s)
- Flavia Lima Costa Faldoni
- Department of Clinical Genetics, University Hospital of Southern Denmark, Beriderbakken 4, 7100, Vejle, Denmark
- Department of Gynecology and Obstetrics, Medical School, São Paulo State University (UNESP), Botucatu, SP, 18618-687, Brazil
| | - Daniela Bizinelli
- Interunit Graduate Program in Bioinformatics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | | | | | | | - Claudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Fabio Albuquerque Marchi
- Department of Head and Neck Surgery, University of São Paulo Medical School, São Paulo, SP, 05402-000, Brazil
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo, SP, 01246-000, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Beriderbakken 4, 7100, Vejle, Denmark.
- Institute of Regional Health Research, University of Southern Denmark, 5000, Odense, Denmark.
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Kramer M, Goodwin S, Wappel R, Borio M, Offit K, Feldman DR, Stadler ZK, McCombie WR. Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601096. [PMID: 39005350 PMCID: PMC11244929 DOI: 10.1101/2024.06.27.601096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Despite significant advances in our understanding of genetic cancer susceptibility, known inherited cancer predisposition syndromes explain at most 20% of early-onset cancers. As early-onset cancer prevalence continues to increase, the need to assess previously inaccessible areas of the human genome, harnessing a trio or quad family-based architecture for variant filtration, may reveal further insights into cancer susceptibility. To assess a broader spectrum of variation than can be ascertained by multi-gene panel sequencing, or even whole genome sequencing with short reads, we employed long read whole genome sequencing using an Oxford Nanopore Technology (ONT) PromethION of 3 families containing an early-onset cancer proband using a trio or quad family architecture. Analysis included 2 early-onset colorectal cancer family trios and one quad consisting of two siblings with testicular cancer, all with unaffected parents. Structural variants (SVs), epigenetic profiles and single nucleotide variants (SNVs) were determined for each individual, and a filtering strategy was employed to refine and prioritize candidate variants based on the family architecture. The family architecture enabled us to focus on inapposite variants while filtering variants shared with the unaffected parents, significantly decreasing background variation that can hamper identification of potentially disease causing differences. Candidate d e novo and compound heterozygous variants were identified in this way. Gene expression, in matched neoplastic and pre-neoplastic lesions, was assessed for one trio. Our study demonstrates the feasibility of a streamlined analysis of genomic variants from long read ONT whole genome sequencing and a way to prioritize key variants for further evaluation of pathogenicity, while revealing what may be missing from panel based analyses.
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18
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Zhu Q, Xie J, Mei W, Zeng C. Methylated circulating tumor DNA in hepatocellular carcinoma: A comprehensive analysis of biomarker potential and clinical implications. Cancer Treat Rev 2024; 128:102763. [PMID: 38763055 DOI: 10.1016/j.ctrv.2024.102763] [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: 02/12/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
The intricate epigenetic landscape of hepatocellular carcinoma (HCC) is profoundly influenced by alterations in DNA methylation patterns. Understanding these alterations is crucial for unraveling the molecular mechanisms underlying HCC pathogenesis. Methylated circulating tumor DNA (ctDNA) presents itself as an encouraging avenue for biomarker discovery and holds substantial clinical implications in HCC management. This review comprehensively outlines the studies concerning DNA methylation in HCC and underscores the significance of methylated ctDNA within this context. Moreover, a variety of cfDNA methylation-based methodologies, such as 5hmC profiling, bisulfite-based, restriction enzyme-dependent, and enrichment-based methods, provide in-depth insights into the molecular pathology of HCC. Additionally, the integration of methylated ctDNA analysis into clinical practice represents a significant advancement in personalized HCC management. By facilitating cancer screening, prognosis assessment, and treatment response prediction, the utilization of methylated ctDNA signifies a pivotal stride toward enhancing patient care and outcomes in HCC.
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Affiliation(s)
- Qian Zhu
- Department of Gastroenterology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Jiaqi Xie
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Wuxuan Mei
- Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen 518110, China.
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Mukherjee N, Bolin EH, Qasim A, Orloff MS, Lupo PJ, Nembhard WN. DNA methylation of the Lamin A/C gene is associated with congenital heart disease. Birth Defects Res 2024; 116:e2381. [PMID: 39073036 DOI: 10.1002/bdr2.2381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/24/2024] [Accepted: 06/18/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Prior studies report associations of maternal serum Lamin A, encoded by the LMNA gene, with fetal congenital heart disease (CHD). It is unknown whether DNA methylation (DNAm) of cytosine-phosphate-guanine (CpG) sites in LMNA impacts the CHD susceptibility. METHODS We investigated the associations of LMNA DNAm with CHD using publicly available data of CHD cases (n = 197) and controls (n = 134) from the Gene Expression Omnibus repository. Peripheral blood DNAm was measured using Illumina 850 K BeadChip for cases and 450 K BeadChip for controls. We tested 31 LMNA CpGs to identify differences in DNAm between cases and controls using linear regression correcting for multiple testing with false discovery rate (FDR). In a case-only analysis, we tested the variations in LMNA DNAm between CHD subtypes. To identify the consistency of DNAm across tissue types we compared peripheral blood (n = 197) and heart tissue DNAm (n = 20) in CHD cases. RESULTS After adjusting for age, sex, and cell types there were significant differences in 17 of the 31 LMNA CpGs between CHD cases and controls (FDR p ≤ .05). We identified lower DNAm of cg09820673 at 3' UTR for hypoplastic left heart syndrome compared to other CHD subtypes. Three CpGs exhibited uniform DNAm in blood and heart tissues in cases. Eleven CpGs showed changes in the same direction in blood and heart tissues in cases compared to controls. CONCLUSION We identify statistically significant differences in LMNA DNAm between CHD cases and controls. Future studies should investigate the role of maternal LMNA DNAm in CHD development.
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Affiliation(s)
- Nandini Mukherjee
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Elijah H Bolin
- Department of Pediatrics, Section of Cardiology, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Amna Qasim
- Department of Pediatrics, Section of Cardiology, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Mohammed S Orloff
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Philip J Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Wendy N Nembhard
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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Tanaka Y, Nakanishi Y, Furuhata E, Nakada KI, Maruyama R, Suzuki H, Suzuki T. FLI1 is associated with regulation of DNA methylation and megakaryocytic differentiation in FPDMM caused by a RUNX1 transactivation domain mutation. Sci Rep 2024; 14:14080. [PMID: 38890442 PMCID: PMC11189521 DOI: 10.1038/s41598-024-64829-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Familial platelet disorder with associated myeloid malignancies (FPDMM) is an autosomal dominant disease caused by heterozygous germline mutations in RUNX1. It is characterized by thrombocytopenia, platelet dysfunction, and a predisposition to hematological malignancies. Although FPDMM is a precursor for diseases involving abnormal DNA methylation, the DNA methylation status in FPDMM remains unknown, largely due to a lack of animal models and challenges in obtaining patient-derived samples. Here, using genome editing techniques, we established two lines of human induced pluripotent stem cells (iPSCs) with different FPDMM-mimicking heterozygous RUNX1 mutations. These iPSCs showed defective differentiation of hematopoietic progenitor cells (HPCs) and megakaryocytes (Mks), consistent with FPDMM. The FPDMM-mimicking HPCs showed DNA methylation patterns distinct from those of wild-type HPCs, with hypermethylated regions showing the enrichment of ETS transcription factor (TF) motifs. We found that the expression of FLI1, an ETS family member, was significantly downregulated in FPDMM-mimicking HPCs with a RUNX1 transactivation domain (TAD) mutation. We demonstrated that FLI1 promoted binding-site-directed DNA demethylation, and that overexpression of FLI1 restored their megakaryocytic differentiation efficiency and hypermethylation status. These findings suggest that FLI1 plays a crucial role in regulating DNA methylation and correcting defective megakaryocytic differentiation in FPDMM-mimicking HPCs with a RUNX1 TAD mutation.
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Affiliation(s)
- Yuki Tanaka
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yuri Nakanishi
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Erina Furuhata
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Ken-Ichi Nakada
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Rino Maruyama
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Takahiro Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan.
- Department of Obstetrics & Gynecology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
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21
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Nair VD, Pincas H, Smith GR, Zaslavsky E, Ge Y, Amper MAS, Vasoya M, Chikina M, Sun Y, Raja AN, Mao W, Gay NR, Esser KA, Smith KS, Zhao B, Wiel L, Singh A, Lindholm ME, Amar D, Montgomery S, Snyder MP, Walsh MJ, Sealfon SC. Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures. CELL GENOMICS 2024; 4:100421. [PMID: 38697122 PMCID: PMC11228891 DOI: 10.1016/j.xgen.2023.100421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/07/2023] [Accepted: 09/12/2023] [Indexed: 05/04/2024]
Abstract
Regular exercise has many physical and brain health benefits, yet the molecular mechanisms mediating exercise effects across tissues remain poorly understood. Here we analyzed 400 high-quality DNA methylation, ATAC-seq, and RNA-seq datasets from eight tissues from control and endurance exercise-trained (EET) rats. Integration of baseline datasets mapped the gene location dependence of epigenetic control features and identified differing regulatory landscapes in each tissue. The transcriptional responses to 8 weeks of EET showed little overlap across tissues and predominantly comprised tissue-type enriched genes. We identified sex differences in the transcriptomic and epigenomic changes induced by EET. However, the sex-biased gene responses were linked to shared signaling pathways. We found that many G protein-coupled receptor-encoding genes are regulated by EET, suggesting a role for these receptors in mediating the molecular adaptations to training across tissues. Our findings provide new insights into the mechanisms underlying EET-induced health benefits across organs.
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Affiliation(s)
- Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hanna Pincas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gregory R Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mary Anne S Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mital Vasoya
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Weiguang Mao
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nicole R Gay
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Karyn A Esser
- Department of Physiology and Aging, University of Florida, Gainesville, FL 32610, USA
| | - Kevin S Smith
- Departments of Pathology and Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Bingqing Zhao
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Laurens Wiel
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Aditya Singh
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Malene E Lindholm
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - David Amar
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Stephen Montgomery
- Departments of Pathology and Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Martin J Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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22
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Klokkaris A, Migdalska-Richards A. An Overview of Epigenetic Changes in the Parkinson's Disease Brain. Int J Mol Sci 2024; 25:6168. [PMID: 38892355 PMCID: PMC11172855 DOI: 10.3390/ijms25116168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Parkinson's disease is a progressive neurodegenerative disorder, predominantly of the motor system. Although some genetic components and cellular mechanisms of Parkinson's have been identified, much is still unknown. In recent years, emerging evidence has indicated that non-DNA-sequence variation (in particular epigenetic mechanisms) is likely to play a crucial role in the development and progression of the disease. Here, we present an up-to-date overview of epigenetic processes including DNA methylation, DNA hydroxymethylation, histone modifications and non-coding RNAs implicated in the brain of those with Parkinson's disease. We will also discuss the limitations of current epigenetic research in Parkinson's disease, the advantages of simultaneously studying genetics and epigenetics, and putative novel epigenetic therapies.
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Affiliation(s)
| | - Anna Migdalska-Richards
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK;
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23
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Ma T, Zhang Q, Zhang S, Yue D, Wang F, Ren Y, Zhang H, Wang Y, Wu Y, Liu LE, Yu F. Research progress of human key DNA and RNA methylation-related enzymes assay. Talanta 2024; 273:125872. [PMID: 38471421 DOI: 10.1016/j.talanta.2024.125872] [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: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Gene methylation-related enzymes (GMREs) are disfunction and aberrantly expressed in a variety of cancers, such as lung, gastric, and pancreatic cancers and have important implications for human health. Therefore,it is critical for early diagnosis and therapy of tumor to develop strategies that allow rapid and sensitive quantitative and qualitative detection of GMREs. With the development of modern analytical techniques and the application of various biosensors, there are numerous methods have been developed for analysis of GMREs. Therefore, this paper provides a systematic review of the strategies for level and activity assay of various GMREs including methyltransferases and demethylase. The detection methods mainly involve immunohistochemistry, colorimetry, fluorescence, chemiluminescence, electrochemistry, etc. Then, this review also addresses the coordinated role of various detection probes, novel nanomaterials, and signal amplification methods. The aim is to highlight potential challenges in the present field, to expand the analytical application of GMREs detection strategies, and to meet the urgent need for future disease diagnosis and intervention.
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Affiliation(s)
- Tiantian Ma
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Qiongwen Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuying Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Dan Yue
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fanting Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yujie Ren
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Hengmiao Zhang
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Yinuo Wang
- Zhengzhou Foreign Language School, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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24
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Liu H, Yue W, Shao S, Sun J, Yang Y, Dai X. Global analysis of DNA methylation changes during experimented lingual carcinogenesis. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2024; 42:319-328. [PMID: 39049651 PMCID: PMC11190864 DOI: 10.7518/hxkq.2024.2023416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/05/2024] [Indexed: 07/27/2024]
Abstract
OBJECTIVES This study aims to assess the role of DNA methylation changes in tongue cancer through a comprehensive analysis of global DNA methylation alterations during experimental lingual carcinogenesis. METHODS C57BL/6J mice were subjected to 16-week oral administration of 4-nitroquinoline-1-oxide (4NQO, 50 mg/L). Lingual mucosa samples, being representative of normal tissue (week 0) and early (week 12) and advanced (week 28) tumorigenesis, were harvested for microarray and methylated DNA immunoprecipitation sequencing (MeDIP-Seq). The mRNA and promoter methylation of transforming growth factor-beta-signaling protein 1 (SMAD1) were evaluated with real-time quantitative reverse transcription polymerase chain reaction and Massarray in human lingual mucosa and tongue cancer cell lines. RESULTS The cytosine guanine island (CGI) methylation level observed at 28 weeks surpassed that of both 12 weeks and 0 weeks. The promoter methylation level at 12 weeks exceeded that at 0 weeks. Notably, 208 differentially expressed genes were negatively correlated to differential methylation in promoters among 0, 12, and 28 weeks. The mRNA of SMAD1 was upregulated, concurrent with a decrease in promoter methylation levels in cell lines compared to normal mucosa. CONCLUSIONS DNA methylation changed during lingual carcinogenesis. Overexpression of SMAD1 was correlated to promoter hypomethylation in tongue cancer cell lines.
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Affiliation(s)
- Hua Liu
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China
| | - Wanyuan Yue
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China
| | - Shuai Shao
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China
| | - Jiaping Sun
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China
| | - Ying Yang
- Dept. of Pathology, First Affiliated Hospital of Kunming Medical University, Kunming 650031, China
| | - Xiaoming Dai
- Maxillofacial Service of Department of Plastic Surgery, First Affiliated Hospital of Kunming Medical University, Kunming 650031, China
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25
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Xiang S, Wang M, Li Q, Yang Z. Unveiling the role of HACE1 in cervical cancer: implications for human papillomavirus infection and prognosis. Transl Cancer Res 2024; 13:2175-2186. [PMID: 38881936 PMCID: PMC11170517 DOI: 10.21037/tcr-23-2120] [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: 11/16/2023] [Accepted: 04/17/2024] [Indexed: 06/18/2024]
Abstract
Background Cervical cancer, one of the prevalent malignancies among females, is closely associated with human papillomavirus (HPV) infection. Homologous to the E6-AP carboxyl terminus (HECT) domain and ankyrin repeat containing E3 ubiquitin-protein ligase 1 (HACE1) plays pivotal roles in various cancers. This study aimed to elucidate the expression of HACE1 in cervical cancer and its correlation with clinical features. Methods From The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA-CESC) and Gene Expression Omnibus (GEO, GSE6791) datasets, we obtained RNA-Seq profiles and associated clinical information. Differential gene analysis was conducted using the R "limma" package. Implications for HPV infection and the overall survival (OS) of cervical cancer were determined by performing differential expression analysis and the Cox proportional hazards regression model. Immunohistochemical analyses were used to validate the expression in cervical cancer and normal cervical tissue. Further, nomogram was constructed to predict OS in cervical cancer. Whether the model was credible was evaluated according to receiver operating characteristic (ROC) curves and concordance curves. To further evaluate the potential functions of HACE1, we conducted functional enrichment analysis. Finally, we assessed methylation levels in HPV+ and HPV- patients in the TCGA-CESC dataset. Results Utilizing TCGA and GSE6791 datasets, we observed significant upregulation of HACE1 in cervical cancer patients, particularly linked to HPV infection. Immunohistochemical staining revealed enhanced HACE1 expression in tumor tissues. Further analysis demonstrated a significant positive correlation between elevated HACE1 and HPV-associated proteins (E1, E6, and E7). Moreover, high HACE1 expression was associated with adverse prognosis in cervical cancer patients. Multivariate Cox analysis indicated that HACE1 could serve as an independent prognostic factor. We developed a prognostic model integrating HPV subtypes, the International Federation of Gynecology and Obstetrics (FIGO) staging, and HACE1, exhibiting strong predictive efficacy for cervical cancer prognosis. Gene enrichment analysis indicated HACE1's potential involvement in multiple signaling pathways during cervical cancer progression, while the demethylation of cg03002526 in HPV-positive patients might contribute to HACE1 upregulation. Conclusions Our study reveals that HACE1 upregulation is associated with cervical cancer, particularly in HPV-positive patients. HACE1 emerges as an independent prognostic factor, linked to unfavorable outcomes.
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Affiliation(s)
- Siyang Xiang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mingqiong Wang
- Department of Nuclear Medicine, The People's Hospital of Chongqing Liangjiang New Area, Chongqing, China
| | - Qinke Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhu Yang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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26
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Fu H, Pickering H, Rubbi L, Ross TM, Zhou W, Reed EF, Pellegrini M. The response to influenza vaccination is associated with DNA methylation-driven regulation of T cell innate antiviral pathways. RESEARCH SQUARE 2024:rs.3.rs-4324518. [PMID: 38826189 PMCID: PMC11142309 DOI: 10.21203/rs.3.rs-4324518/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background The effect of vaccination on the epigenome remains poorly characterized. In previous research, we identified an association between seroprotection against influenza and DNA methylation at sites associated with the RIG-1 signaling pathway, which recognizes viral double-stranded RNA and leads to a type I interferon response. However, these studies did not fully account for confounding factors including age, gender, and BMI, along with changes in cell type composition. Results Here, we studied the influenza vaccine response in a longitudinal cohort vaccinated over two consecutive years (2019-2020 and 2020-2021), using peripheral blood mononuclear cells and a targeted DNA methylation approach. To address the effects of multiple factors on the epigenome, we designed a multivariate multiple regression model that included seroprotection levels as quantified by the hemagglutination-inhibition (HAI) assay test. Conclusions Our findings indicate that 179 methylation sites can be combined as potential signatures to predict seroprotection. These sites were not only enriched for genes involved in the regulation of the RIG-I signaling pathway, as found previously, but also enriched for other genes associated with innate immunity to viruses and the transcription factor binding sites of BRD4, which is known to impact T cell memory. We propose a model to suggest that the RIG-I pathway and BRD4 could potentially be modulated to improve immunization strategies.
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27
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Shen HT, Hung CS, Davis C, Su CM, Liao LM, Shih HM, Lee KD, Ansar M, Lin RK. Hypermethylation of the Gene Body in SRCIN1 Is Involved in Breast Cancer Cell Proliferation and Is a Potential Blood-Based Biomarker for Early Detection and a Poor Prognosis. Biomolecules 2024; 14:571. [PMID: 38785978 PMCID: PMC11118508 DOI: 10.3390/biom14050571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Breast cancer is a leading cause of cancer mortality in women worldwide. Using the Infinium MethylationEPIC BeadChip, we analyzed plasma sample methylation to identify the SRCIN1 gene in breast cancer patients. We assessed SRCIN1-related roles and pathways for their biomarker potential. To verify the methylation status, quantitative methylation-specific PCR (qMSP) was performed on genomic DNA and circulating cell-free DNA samples, and mRNA expression analysis was performed using RT‒qPCR. The results were validated in a Western population; for this analysis, the samples included plasma samples from breast cancer patients from the USA and from The Cancer Genome Atlas (TCGA) cohort. To study the SRCIN1 pathway, we conducted cell viability assays, gene manipulation and RNA sequencing. SRCIN1 hypermethylation was identified in 61.8% of breast cancer tissues from Taiwanese patients, exhibiting specificity to this malignancy. Furthermore, its presence correlated significantly with unfavorable 5-year overall survival outcomes. The levels of methylated SRCIN1 in the blood of patients from Taiwan and the USA correlated with the stage of breast cancer. The proportion of patients with high methylation levels increased from 0% in healthy individuals to 63.6% in Stage 0, 80% in Stage I and 82.6% in Stage II, with a sensitivity of 78.5%, an accuracy of 90.3% and a specificity of 100%. SRCIN1 hypermethylation was significantly correlated with increased SRCIN1 mRNA expression (p < 0.001). Knockdown of SRCIN1 decreased the viability of breast cancer cells. SRCIN1 silencing resulted in the downregulation of ESR1, BCL2 and various cyclin protein expressions. SRCIN1 hypermethylation in the blood may serve as a noninvasive biomarker, facilitating early detection and prognosis evaluation, and SRCIN1-targeted therapies could be used in combination regimens for breast cancer patients.
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Affiliation(s)
- Hsieh-Tsung Shen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- EG BioMed US Inc., Covina, CA 91722, USA;
| | - Chin-Sheng Hung
- EG BioMed US Inc., Covina, CA 91722, USA;
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
- Division of Breast Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei 110301, Taiwan
| | - Clilia Davis
- International Master Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
| | - Chih-Ming Su
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
| | - Li-Min Liao
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
| | - Hsiu-Ming Shih
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
| | - Kuan-Der Lee
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- Comprehensive Cancer Center, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Muhamad Ansar
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Ruo-Kai Lin
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- EG BioMed US Inc., Covina, CA 91722, USA;
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 110301, Taiwan
- Graduate Institute of Pharmacognosy, Ph.D. Program in Drug Discovery and Development Industry, Masters Program for Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan
- Clinical Trial Center, Taipei Medical University Hospital, Taipei 110301, Taiwan
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28
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Mahmood M, Taufiq I, Mazhar S, Hafeez F, Malik K, Afzal S. Revolutionizing personalized cancer treatment: the synergy of next-generation sequencing and CRISPR/Cas9. Per Med 2024; 21:175-190. [PMID: 38708901 DOI: 10.1080/17410541.2024.2341610] [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: 10/26/2023] [Accepted: 04/08/2024] [Indexed: 05/07/2024]
Abstract
In the context of cancer heterogeneity, the synergistic action of next-generation sequencing (NGS) and CRISPR/Cas9 plays a promising role in the personalized treatment of cancer. NGS enables high-throughput genomic profiling of tumors and pinpoints specific mutations that primarily lead to cancer. Oncologists use this information obtained from NGS in the form of DNA profiling or RNA analysis to tailor precision strategies based on an individual's unique molecular signature. Furthermore, the CRISPR technique enables precise editing of cancer-specific mutations, allowing targeted gene modifications. Harnessing the potential insights of NGS and CRISPR/Cas9 heralds a remarkable frontier in cancer therapeutics with unprecedented precision, effectiveness and minimal off-target effects.
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Affiliation(s)
- Muniba Mahmood
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Izza Taufiq
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Sana Mazhar
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Faiqa Hafeez
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Kausar Malik
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Samia Afzal
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
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29
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Tian H, Luan P, Liu Y, Li G. Tet-mediated DNA methylation dynamics affect chromosome organization. Nucleic Acids Res 2024; 52:3654-3666. [PMID: 38300758 DOI: 10.1093/nar/gkae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
DNA Methylation is a significant epigenetic modification that can modulate chromosome states, but its role in orchestrating chromosome organization has not been well elucidated. Here we systematically assessed the effects of DNA Methylation on chromosome organization with a multi-omics strategy to capture DNA Methylation and high-order chromosome interaction simultaneously on mouse embryonic stem cells with DNA methylation dioxygenase Tet triple knock-out (Tet-TKO). Globally, upon Tet-TKO, we observed weakened compartmentalization, corresponding to decreased methylation differences between CpG island (CGI) rich and poor domains. Tet-TKO could also induce hypermethylation for the CTCF binding peaks in TAD boundaries and chromatin loop anchors. Accordingly, CTCF peak generally weakened upon Tet-TKO, which results in weakened TAD structure and depletion of long-range chromatin loops. Genes that lost enhancer-promoter looping upon Tet-TKO showed DNA hypermethylation in their gene bodies, which may compensate for the disruption of gene expression. We also observed distinct effects of Tet1 and Tet2 on chromatin organization and increased DNA methylation correlation on spatially interacted fragments upon Tet inactivation. Our work showed the broad effects of Tet inactivation and DNA methylation dynamics on chromosome organization.
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Affiliation(s)
- Hao Tian
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Pengfei Luan
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yaping Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Guoqiang Li
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
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Song B, Yu J, Li X, Li J, Fan J, Liu H, Wei W, Zhang L, Gu K, Liu D, Zhao K, Wu J. Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement. Genome Biol 2024; 25:87. [PMID: 38581061 PMCID: PMC10996114 DOI: 10.1186/s13059-024-03220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown. RESULTS Here, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening. CONCLUSIONS Our study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.
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Affiliation(s)
- Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jinshan Yu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jing Fan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Hainan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Weilin Wei
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Lingchao Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Dongliang Liu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China.
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Shi Z, Guo X, Hu X, Li R, Li X, Lu J, Jin M, Jiang X. DNA methylation profiling identifies epigenetic signatures of early gastric cancer. Virchows Arch 2024; 484:687-695. [PMID: 38507065 DOI: 10.1007/s00428-024-03765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Research on the DNA methylation status of gastric cancer (GC) has primarily focused on identifying invasive GC to develop biomarkers for diagnostic. However, DNA methylation in noninvasive GC remains unclear. We conducted a comprehensive DNA methylation profiling study of differentiated-type intramucosal GCs (IMCs). Illumina 850K microarrays were utilized to assess the DNA methylation profiles of formalin-fixed paraffin-embedded tissues from eight patients who were Epstein-Barr virus-negative and DNA mismatch repair proficient, including IMCs and paired adjacent nontumor mucosa. Gene expression profiling microarray data from the GEO database were analyzed via bioinformatics to identify candidate methylation genes. The final validation was conducted using quantitative real-time PCR, the TCGA methylation database, and single-sample gene set enrichment analysis (GSEA). Genome-wide DNA methylation profiling revealed a global decrease in methylation in IMCs compared with nontumor tissues. Differential methylation analysis between IMCs and nontumor tissues identified 449 differentially methylated probes, with a majority of sites showing hypomethylation in IMCs compared with nontumor tissues (66.1% vs 33.9%). Integrating two RNA-seq microarray datasets, we found one hypomethylation-upregulated gene: eEF1A2, overlapped with our DNA methylation data. The mRNA expression of eEF1A2 was higher in twenty-four IMC tissues than in their paired adjacent nontumor tissues. GSEA indicated that the functions of eEF1A2 were associated with the development of IMCs. Furthermore, TCGA data indicated that eEF1A2 is hypomethylated in advanced GC. Our study illustrates the implications of DNA methylation alterations in IMCs and suggests that aberrant hypomethylation and high mRNA expression of eEF1A2 might play a role in IMCs development.
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Affiliation(s)
- Zhongyue Shi
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xinmeng Guo
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xiumei Hu
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ruiqi Li
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xue Li
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jun Lu
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Mulan Jin
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
| | - Xingran Jiang
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
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Shi Z, Liu X, Li D, Fan X, He L, Zhou D, Lin H. Construction of a prognostic model based on genome-wide methylation analysis of miRNAs for hepatocellular carcinoma. Epigenomics 2024; 16:513-527. [PMID: 38477016 PMCID: PMC11160443 DOI: 10.2217/epi-2023-0365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Aim: Using the methylation level of miRNA genes to develop a prognostic model for patients with hepatocellular carcinoma (HCC). Materials & methods: least absolute shrinkage and selection operator and multivariate Cox regression analyses were performed to develop a prognostic model. One miRNA in the model was selected for verification. Results: A prognostic model was developed using eight miRNAs. The areas under the curve for predicting overall survival at 1, 3 and 5 years were 0.75, 0.81 and 0.81. miR-223 was found to be hypomethylated in 160 HCC tissues, and its methylation level was associated with Barcelona Clinic Liver Cancer stages and the prognosis of patients with HCC. Conclusion: The prognostic model based on miRNA methylation levels has the capability to partially forecast the prognosis of patients with HCC.
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Affiliation(s)
- Zhaoqi Shi
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Xiaolong Liu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Duguang Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Lifeng He
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Daizhan Zhou
- Life Science Research Center, The First Affiliated Hospital of Xinxiang Medical University, Weihui, 453100, Henan, China
| | - Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
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Sorroche BP, Miranda KC, Beltrami CM, Arantes LMRB, Kowalski LP, Marchi FA, Rogatto SR, Almeida JD. HOXA1 3'UTR Methylation Is a Potential Prognostic Biomarker in Oral Squamous cell Carcinoma. Cancers (Basel) 2024; 16:874. [PMID: 38473236 DOI: 10.3390/cancers16050874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND HOXA1 is a prognostic marker and a potential predictive biomarker for radioresistance in head and neck tumors. Its overexpression has been associated with promoter methylation and a worse prognosis in oral squamous cell carcinoma (OSCC) patients. However, opposite outcomes are also described. The effect of the methylation of this gene on different gene regions, other than the promoter, remains uncertain. We investigated the methylation profile at different genomic regions of HOXA1 in OSCC and correlated differentially methylated CpG sites with clinicopathological data. METHODS The HOXA1 DNA methylation status was evaluated by analyzing data from The Cancer Genome Atlas and three Gene Expression Omnibus datasets. Significant differentially methylated CpG sites were considered with a |∆β| ≥ 0.10 and a Bonferroni-corrected p-value < 0.01. Differentially methylated CpGs were validated by pyrosequencing using two independent cohorts of 15 and 47 OSCC patients, respectively. RESULTS Compared to normal tissues, we found significantly higher DNA methylation levels in the 3'UTR region of HOXA1 in OSCC. Higher methylation levels in tumor samples were positively correlated with smoking habits and patients' overall survival. CONCLUSIONS Our findings suggest that HOXA1 gene body methylation is a promising prognostic biomarker for OSCC with potential clinical applications in patient monitoring.
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Affiliation(s)
- Bruna Pereira Sorroche
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil
| | - Keila Cristina Miranda
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos 12224-300, Brazil
| | | | | | - Luiz Paulo Kowalski
- Head and Neck Surgery and Otorhinolaryngology Department, AC Camargo Cancer Center, Latin American Cooperative Oncology Group, São Paulo 01509-010, Brazil
- Head and Neck Surgery Department and LIM 28, University of São Paulo Medical School, São Paulo 01246-903, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo 01246-000, Brazil
- Clinical Hospital of the University of Sao Paulo Medical School (HCFMUSP), São Paulo 05403-010, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos 12224-300, Brazil
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Wang S, Li G, Du H, Feng J. Low-dose radiation from CT examination induces DNA double-strand breaks and detectable changes of DNA methylation in peripheral blood cells. Int J Radiat Biol 2024; 100:197-208. [PMID: 37812067 DOI: 10.1080/09553002.2023.2267667] [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: 07/07/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Radiation burden from CT examinations increases rapidly with the increased clinical use frequency. Previous studies have disclosed the association between radiation exposure and increased double-strand breaks (DSBs) and changes in DNA methylation. However, whether the induced DSBs by CT examination recover within 24h and whether a CT examination induces detectable gene-specific methylation changes are still unclear. The aim of the present study was to analyze γ-H2AX in the peripheral blood lymphocyte (PBL) of healthy adults before and after CT examination and to discover the differentially methylated positions (DMPs) along with an analysis of DNA methylation changes caused by CT examination. MATERIALS AND METHODS Peripheral blood samples of 4 ml were drawn from 20 healthy volunteers at three time points: before CT examination, after CT examination 1h, and after CT examination 24h. γ-H2AX immunofluorescence and Illumina Infinium Human Methylation EPIC BeadChip (850k BeadChip) were used respectively for the test of DSBs and the epigenome-wide DNA methylation analysis. Linear mixed-effect (LME) models were used to evaluate the impacts of doses represented by different parameters and foci on genome-wide DNA methylation. RESULTS The number of γ-H2AX foci per cell at 1h showed linear dose-responses for the radiation doses represented by CT index volume (CTDIvol), dose length product (DLP), and blood absorbed dose, respectively. Residual γ-H2AX foci was observed after CT examination at 24h (p < .001). DMPs and γ-H2AX foci changes could be found within 1h. One CpG site related to PAX5 was significantly changed by using most of the parameters in LME models and did not recover till 24h. CONCLUSIONS Residual γ-H2AX foci exist after CT examination at 24h. The DNA methylation changes induced by CT examination may not recover within 24h. The DNA methylation had been changed as early as at 1h. The PAX5-related CpG site may be a potential biomarker of low-dose radiation. CLINICAL RELEVANCE The biological effects and the cancer risks of CT examination are still unclear. The present study is an effort to document the CT scan-induced events in 24h in vivo. The CT scanning area should be strictly limited, and non-essential repeated operations shouldn't be performed within 24h.
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Affiliation(s)
- Shuo Wang
- Department of Oral and Maxillofacial Radiology, Peking University School and Hospital of Stomatology and National Engineering Laboratory for Digital and Material Technology of Stomatology and Beijing Key Laboratory of Digital Stomatology, Beijing, China
| | - Gang Li
- Department of Oral and Maxillofacial Radiology, Peking University School and Hospital of Stomatology and National Engineering Laboratory for Digital and Material Technology of Stomatology and Beijing Key Laboratory of Digital Stomatology, Beijing, China
| | - Han Du
- Department of Oral and Maxillofacial Radiology, Peking University School and Hospital of Stomatology and National Engineering Laboratory for Digital and Material Technology of Stomatology and Beijing Key Laboratory of Digital Stomatology, Beijing, China
| | - Jiling Feng
- Department of Oral and Maxillofacial Radiology, Peking University School and Hospital of Stomatology and National Engineering Laboratory for Digital and Material Technology of Stomatology and Beijing Key Laboratory of Digital Stomatology, Beijing, China
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Ehrlich M, Ehrlich KC, Lacey M, Baribault C, Sen S, Estève PO, Pradhan S. Epigenetics of Genes Preferentially Expressed in Dissimilar Cell Populations: Myoblasts and Cerebellum. EPIGENOMES 2024; 8:4. [PMID: 38390894 PMCID: PMC10885033 DOI: 10.3390/epigenomes8010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
While studying myoblast methylomes and transcriptomes, we found that CDH15 had a remarkable preference for expression in both myoblasts and cerebellum. To understand how widespread such a relationship was and its epigenetic and biological correlates, we systematically looked for genes with similar transcription profiles and analyzed their DNA methylation and chromatin state and accessibility profiles in many different cell populations. Twenty genes were expressed preferentially in myoblasts and cerebellum (Myob/Cbl genes). Some shared DNA hypo- or hypermethylated regions in myoblasts and cerebellum. Particularly striking was ZNF556, whose promoter is hypomethylated in expressing cells but highly methylated in the many cell populations that do not express the gene. In reporter gene assays, we demonstrated that its promoter's activity is methylation sensitive. The atypical epigenetics of ZNF556 may have originated from its promoter's hypomethylation and selective activation in sperm progenitors and oocytes. Five of the Myob/Cbl genes (KCNJ12, ST8SIA5, ZIC1, VAX2, and EN2) have much higher RNA levels in cerebellum than in myoblasts and displayed myoblast-specific hypermethylation upstream and/or downstream of their promoters that may downmodulate expression. Differential DNA methylation was associated with alternative promoter usage for Myob/Cbl genes MCF2L, DOK7, CNPY1, and ANK1. Myob/Cbl genes PAX3, LBX1, ZNF556, ZIC1, EN2, and VAX2 encode sequence-specific transcription factors, which likely help drive the myoblast and cerebellum specificity of other Myob/Cbl genes. This study extends our understanding of epigenetic/transcription associations related to differentiation and may help elucidate relationships between epigenetic signatures and muscular dystrophies or cerebellar-linked neuropathologies.
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Hayward Human Genetics Center, Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Kenneth C Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
| | - Carl Baribault
- Information Technology, Tulane University, New Orleans, LA 70118, USA
| | - Sagnik Sen
- Genome Biology Division, New England Biolabs, Ipswich, MA 01938, USA
| | | | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Ipswich, MA 01938, USA
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Dairo O, DePaula Oliveira L, Schaffer E, Vidotto T, Mendes AA, Lu J, Huynh SV, Hicks J, Sowalsky AG, De Marzo AM, Joshu CE, Hanratty B, Sfanos KS, Isaacs WB, Haffner MC, Lotan TL. FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:152-163. [PMID: 38112617 PMCID: PMC10795515 DOI: 10.1158/2767-9764.crc-23-0248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Fatty acid synthase (FASN) catalyzes the synthesis of long-chain saturated fatty acids and is overexpressed during prostatic tumorigenesis, where it is the therapeutic target in several ongoing trials. However, the mechanism of FASN upregulation in prostate cancer remains unclear. Here, we examine FASN gene CpG methylation pattern by InfiniumEPIC profiling and whole-genome bisulfite sequencing across multiple racially diverse primary and metastatic prostate cancer cohorts, comparing with FASN protein expression as measured by digitally quantified IHC assay and reverse phase protein array analysis or FASN gene expression. We demonstrate that the FASN gene body is hypomethylated and overexpressed in primary prostate tumors compared with benign tissue, and FASN gene methylation is significantly inversely correlated with FASN protein or gene expression in both primary and metastatic prostate cancer. Primary prostate tumors with ERG gene rearrangement have increased FASN expression and we find evidence of FASN hypomethylation in this context. FASN expression is also significantly increased in prostate tumors from carriers of the germline HOXB13 G84E mutation compared with matched controls, consistent with a report that HOXB13 may contribute to epigenetic regulation of FASN in vitro. However, in contrast to previous studies, we find no significant association of FASN expression or methylation with self-identified race in models that include ERG status across two independent primary tumor cohorts. Taken together, these data support a potential epigenetic mechanism for FASN regulation in the prostate which may be relevant for selecting patients responsive to FASN inhibitors. SIGNIFICANCE Here, we leverage multiple independent primary and metastatic prostate cancer cohorts to demonstrate that FASN gene body methylation is highly inversely correlated with FASN gene and protein expression. This finding may shed light on epigenetic mechanisms of FASN regulation in prostate cancer and provides a potentially useful biomarker for selecting patients in future trials of FASN inhibitors.
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Affiliation(s)
- Oluwademilade Dairo
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Ethan Schaffer
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Thiago Vidotto
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Adrianna A. Mendes
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jiayun Lu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sophie Vo Huynh
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jessica Hicks
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Adam G. Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, NCI, Bethesda, Maryland
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Corrine E. Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Brian Hanratty
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Karen S. Sfanos
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - William B. Isaacs
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland
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Liang Y, Zhou Y, Xie D, Yin F, Luo X. Hypermethylation and low expression of FANCC involved in multi-walled carbon nanotube-induced toxicity on ARPE-19 cells. ENVIRONMENTAL RESEARCH 2024; 241:117619. [PMID: 37952855 DOI: 10.1016/j.envres.2023.117619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Multi-walled carbon nanotube (MWCNT) exposure was observed to cause damages on the viability of ocular cells, however, the underlying mechanisms remain not well understood. Epigenetic alterations that regulate gene expression have been identified as a major responsiveness to environmental challenge. Thus, the aim of this study was to screen methylation-regulated genes involved in MWCNT exposure. The Illumina Human Methylation 850 K array was employed to determine the genome-wide DNA methylation profile of human retinal pigment epithelial cell line (ARPE-19) exposed to 50% inhibition concentration of MWCNTs (100 μg/ml) for 24 h or without (n = 3 for each group). Then, the transcriptome data obtained by high-throughput RNA sequencing previously were integrated with DNA methylome to identify the overlapped genes. As a result, the integrative bioinformatics analysis identified that compared with controls, FA complementation group C (FANCC) was hypermethylated and downregulated in MWCNT-exposed ARPE-19 cells. Quantitative real-time polymerase chain reaction analysis confirmed the mRNA expression level of FANCC was significantly decreased following MWCNT treatment and the addition of DNA methylation inhibitor 5-Aza-deoxycytidine (10 μM) reversed this decrease. Pyrosequencing analysis further validated the hypermethylation status at the 5'-untranslated promoter region of FANCC (cg14583550) in MWCNT-exposed ARPE-19 cells. Protein-protein interaction network and function analyses predicted that FANCC may contribute to MWCNT-induced cytotoxicity by interacting with heat shock protein 90 beta family member 1 and then upregulating cytokine interleukin-6 and apoptosis biomarker caspase 3. In conclusion, the present study links the epigenetic modification of FANCC with the pathogenesis of MWCNT-induced retinal toxicity.
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Affiliation(s)
- Yunxia Liang
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China
| | - Yang Zhou
- School of Textile Science and Engineering/State Key Laboratory of New Textile Materials and Advanced Processing Technology, Wuhan Textile University, Wuhan, 430200, China.
| | - Dongli Xie
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China
| | - Fei Yin
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China
| | - Xiaogang Luo
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China.
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Sacdalan DB, Ul Haq S, Lok BH. Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications. Curr Oncol 2024; 31:482-500. [PMID: 38248118 PMCID: PMC10814449 DOI: 10.3390/curroncol31010033] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.
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Affiliation(s)
- Danielle Benedict Sacdalan
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
| | - Sami Ul Haq
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Schulich School of Medicine & Dentistry, Western University, 1151 Richmond St, London, ON N6A 5C1, Canada
| | - Benjamin H. Lok
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, 101 College Street, Room 15-701, Toronto, ON M5G 1L7, Canada
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Reynolds SR, Zhang Z, Salas LA, Christensen BC. Tumor microenvironment deconvolution identifies cell-type-independent aberrant DNA methylation and gene expression in prostate cancer. Clin Epigenetics 2024; 16:5. [PMID: 38173042 PMCID: PMC10765773 DOI: 10.1186/s13148-023-01609-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/25/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Among men, prostate cancer (PCa) is the second most common cancer and the second leading cause of cancer death. Etiologic factors associated with both prostate carcinogenesis and somatic alterations in tumors are incompletely understood. While genetic variants associated with PCa have been identified, epigenetic alterations in PCa are relatively understudied. To date, DNA methylation (DNAm) and gene expression (GE) in PCa have been investigated; however, these studies did not correct for cell-type proportions of the tumor microenvironment (TME), which could confound results. METHODS The data (GSE183040) consisted of DNAm and GE data from both tumor and adjacent non-tumor prostate tissue of 56 patients who underwent radical prostatectomies prior to any treatment. This study builds upon previous studies that examined methylation patterns and GE in PCa patients by using a novel tumor deconvolution approach to identify and correct for cell-type proportions of the TME in its epigenome-wide association study (EWAS) and differential expression analysis (DEA). RESULTS The inclusion of cell-type proportions in EWASs and DEAs reduced the scope of significant alterations associated with PCa. We identified 2,093 significantly differentially methylated CpGs (DMC), and 51 genes associated with PCa, including PCA3, SPINK1, and AMACR. CONCLUSIONS This work illustrates the importance of correcting for cell types of the TME when performing EWASs and DEAs on PCa samples, and establishes a more confounding-adverse methodology. We identified a more tumor-cell-specific set of altered genes and epigenetic marks that can be further investigated as potential biomarkers of disease or potential therapeutic targets.
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Affiliation(s)
- Samuel R Reynolds
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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Akhouri V, Majumder S, Gaikwad AB. Targeting DNA methylation in diabetic kidney disease: A new perspective. Life Sci 2023; 335:122256. [PMID: 37949210 DOI: 10.1016/j.lfs.2023.122256] [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: 09/20/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Diabetic kidney disease (DKD) is a leading diabetic complication causing significant mortality among people around the globe. People with poor glycemic control accompanied by hyperinsulinemia, dyslipidemia, hypertension, and obesity develop diabetic complications. These diabetic patients develop epigenetic changes and suffer from diabetic kidney complications even after subsequent glucose control, the phenomenon that is recognized as metabolic memory. DNA methylation is an essential epigenetic modification that contributes to the development and progression of several diabetic complications, including DKD. The aberrant DNA methylation pattern at CpGs sites within several genes, such as mTOR, RPTOR, IRS2, GRK5, SLC27A3, LCAT, and SLC1A5, associated with the accompanying risk factors exacerbate the DKD progression. Although drugs such as azacytidine and decitabine have been approved to target DNA methylation for diseases such as hematological malignancies, none have been approved for the treatment of DKD. More importantly, no DNA hypomethylation-targeting drugs have been approved for any disease conditions. Understanding the alteration in DNA methylation and its association with the disease risk factors is essential to target DKD effectively. This review has discussed the abnormal DNA methylation pattern and the kidney tissue-specific expression of critical genes involved in DKD onset and progression. Moreover, we also discuss the new possible therapeutic approach that can be exploited for treating DNA methylation aberrancy in a site-specific manner against DKD.
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Affiliation(s)
- Vivek Akhouri
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Syamantak Majumder
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Anil Bhanudas Gaikwad
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India.
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Zhang F, Zhang X, Zhang H, Lin D, Fan H, Guo S, An F, Zhao Y, Li J, Schrodi SJ, Zhang D. Pan-precancer and cancer DNA methylation profiles revealed significant tissue specificity of interrupted biological processes in tumorigenesis. Epigenetics 2023; 18:2231222. [PMID: 37393582 DOI: 10.1080/15592294.2023.2231222] [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: 03/03/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
DNA methylation (DNAme) alterations are known to initiate from the precancerous stage of tumorigenesis. Herein, we investigated the global and local patterns of DNAme perturbations in tumorigenesis by analysing the genome-wide DNAme profiles of the cervix, colorectum, stomach, prostate, and liver at precancerous and cancer stages. We observed global hypomethylation in tissues of both two stages, except for the cervix, whose global DNAme level in normal tissue was lower than that of the other four tumour types. For alterations shared by both stages, there were common hyper-methylation (sHyperMethyl) and hypo-methylation (sHypoMethyl) changes, of which the latter type was more frequently identified in all tissues. Biological pathways interrupted by sHyperMethyl and sHypoMethyl alterations demonstrated significant tissue specificity. DNAme bidirectional chaos indicated by the enrichment of both sHyperMethyl and sHypoMethyl changes in the same pathway was observed in most tissues and was a common phenomenon, particularly in liver lesions. Moreover, for the same enriched pathways, different tissues may be affected by distinct DNAme types. For the PI3K-Akt signalling pathway, sHyperMethyl enrichment was observed in the prostate dataset, but sHypoMethyl enrichment was observed in the colorectum and liver datasets. Nevertheless, they did not show an increased possibility in survival prediction of patients in comparison with other DNAme types. Additionally, our study demonstrated that gene-body DNAme changes of tumour suppressor genes and oncogenes may persist from precancerous lesions to the tumour. Overall, we demonstrate the tissue specificity and commonality of cross-stage alterations in DNA methylation profiles in multi-tissue tumorigenesis.
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Affiliation(s)
- Feifan Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Xin Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Haikun Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Dongdong Lin
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Hailang Fan
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Fang An
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Yaqian Zhao
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Jun Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
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Jenkins BD, Rossi E, Pichardo C, Wooten W, Pichardo M, Tang W, Dorsey TH, Ajao A, Hutchison R, Moubadder L, McCullough LE, Bailey-Whyte M, Ambs S. Neighborhood Deprivation and DNA Methylation and Expression of Cancer Genes in Breast Tumors. JAMA Netw Open 2023; 6:e2341651. [PMID: 37930698 PMCID: PMC10628736 DOI: 10.1001/jamanetworkopen.2023.41651] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/23/2023] [Indexed: 11/07/2023] Open
Abstract
Importance The biological processes that underlie the association of neighborhood environment with chronic diseases, such as cancer, remain poorly understood. Objective To determine whether differences in breast tissue DNA methylation are associated with neighborhood deprivation among Black and White women with breast cancer. Design, Setting, and Participants This cross-sectional study collected breast tissue from women undergoing surgery for breast cancer between January 1, 1993, and December 31, 2003. Participants were recruited through the University of Maryland Medical Center, with additional collection sites at Baltimore-area hospitals. Data analysis was performed from March 1 through December 1, 2022. Exposure Year 2000 census tract-level socioeconomic deprivation measured via neighborhood deprivation index (NDI) as a standardized score, with Black and White race being ascertained through self-report. Main Outcome and Measures The primary outcome was tissue DNA methylation using genome-wide measurements. The secondary outcome was tissue gene expression. Results Participants included 185 women with breast cancer (110 Black [59.5%], 75 White [40.5%]). Mean (SD) age at surgery was 56.0 (14.1) years. Neighborhood deprivation was higher for Black women than for White women (Mean [SD] NDI, 2.96 [3.03] for Black women and -0.54 [1.91] for White women; difference, -3.50; 95% CI, -4.22 to -2.79; P < .001). In unstratified analysis, 8 hypomethylated CpG sites were identified as associated with the NDI, including sites in 2 tumor suppressor genes, LRIG1 and WWOX. Moreover, expression of the 2 genes inversely correlated with neighborhood deprivation. In the race-stratified analysis, the negative correlation between the LRIG1 gene body CpG site cg26131019 and the NDI remained significant in Black women. A neighborhood deprivation-associated decrease in gene expression was also observed for LRIG1 and WWOX in tumors from Black women. Conclusions and Relevance In this study, high neighborhood deprivation was associated with differences in tissue DNA methylation and gene expression among Black women. These findings suggest that continued investment in public health interventions and policy changes at the neighborhood level may help to remedy biological alterations that could make minoritized populations more susceptible to chronic diseases.
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Affiliation(s)
- Brittany D. Jenkins
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Emily Rossi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Catherine Pichardo
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, Maryland
| | - William Wooten
- Department of Biostatistics, University of Maryland School of Medicine, Baltimore, Maryland
| | - Margaret Pichardo
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, Maryland
| | - Tiffany H. Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Anuoluwapo Ajao
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Ruby Hutchison
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Leah Moubadder
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Lauren E. McCullough
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Maeve Bailey-Whyte
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- School of Medicine, University of Limerick, Limerick, Ireland
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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Vera-Chang MN, Danforth JM, Stuart M, Goodarzi AA, Brand M, Richardson RB. Profound DNA methylomic differences between single- and multi-fraction alpha irradiations of lung fibroblasts. Clin Epigenetics 2023; 15:174. [PMID: 37891670 PMCID: PMC10612361 DOI: 10.1186/s13148-023-01564-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/05/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Alpha (α)-radiation is a ubiquitous environmental agent with epigenotoxic effects. Human exposure to α-radiation at potentially harmful levels can occur repetitively over the long term via inhalation of naturally occurring radon gas that accumulates in enclosed spaces, or as a result of a single exposure from a nuclear accident. Alterations in epigenetic DNA methylation (DNAm) have been implicated in normal aging and cancer pathogenesis. Nevertheless, the effects of aberrations in the methylome of human lung cells following exposure to single or multiple α-irradiation events on these processes remain unexplored. RESULTS We performed genome-wide DNAm profiling of human embryonic lung fibroblasts from control and irradiated cells using americium-241 α-sources. Cells were α-irradiated in quadruplicates to seven doses using two exposure regimens, a single-fraction (SF) where the total dose was given at once, and a multi-fraction (MF) method, where the total dose was equally distributed over 14 consecutive days. Our results revealed that SF irradiations were prone to a decrease in DNAm levels, while MF irradiations mostly increased DNAm. The analysis also showed that the gene body (i.e., exons and introns) was the region most altered by both the SF hypomethylation and the MF hypermethylation. Additionally, the MF irradiations induced the highest number of differentially methylated regions in genes associated with DNAm biomarkers of aging, carcinogenesis, and cardiovascular disease. The DNAm profile of the oncogenes and tumor suppressor genes suggests that the fibroblasts manifested a defensive response to the MF α-irradiation. Key DNAm events of ionizing radiation exposure, including changes in methylation levels in mitochondria dysfunction-related genes, were mainly identified in the MF groups. However, these alterations were under-represented, indicating that the mitochondria undergo adaptive mechanisms, aside from DNAm, in response to radiation-induced oxidative stress. CONCLUSIONS We identified a contrasting methylomic profile in the lung fibroblasts α-irradiated to SF compared with MF exposures. These findings demonstrate that the methylome response of the lung cells to α-radiation is highly dependent on both the total dose and the exposure regimen. They also provide novel insights into potential biomarkers of α-radiation, which may contribute to the development of innovative approaches to detect, prevent, and treat α-particle-related diseases.
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Affiliation(s)
- Marilyn N Vera-Chang
- Radiobiology and Health Branch, Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, K0J 1J0, Canada
| | - John M Danforth
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Marilyne Stuart
- Environment and Waste Technologies Branch, Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, K0J 1J0, Canada
| | - Aaron A Goodarzi
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Marjorie Brand
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8L6, Canada
| | - Richard B Richardson
- Radiobiology and Health Branch, Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, K0J 1J0, Canada.
- McGill Medical Physics Unit, Cedars Cancer Centre-Glen Site, Montreal, QC, H4A 3J1, Canada.
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Zhu A, Zong Y, Wei S, Li Y, Fan Y, Liu S, Gao X. Pan-cancer Analysis of the Disulfidptosis-related Gene NCKAP1 and Its Prognostic Value for Lung Adenocarcinoma. J Cancer 2023; 14:3351-3367. [PMID: 37928421 PMCID: PMC10622996 DOI: 10.7150/jca.88650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND The nck-associated protein 1 (NCKAP1) of the disulfidptosis-related gene is essential in programmed cell death. However, a comprehensive analysis of the biological significance of NCKAP1 in pan-cancer is lacking. METHODS Gene expression matrices and clinical expression information of cancers were obtained from The Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEX) databases. A comprehensive analysis of NCKAP1 expression, biological function, gene mutation, immune cell infiltration, DNA methylation, and drug sensitivity profiles in pan-cancer was performed using the Timer2.0, HPA, GEPIA, STRING, cBioPortal, UALCAN and CellMiner databases. The prognostic value of NCKAP1 was investigated based on COX regression analysis and the Kaplan-Meier(K-M) curves. A nomogram was established to verify the clinical value of NCKAP1 for LUAD. The correlation between NCKAP1 and immune cells and signaling pathways were investigated by single-sample gene set enrichment analysis(ssGSEA). Validation was performed using PCR, Western Blot (WB), and Transwell assays. RESULT Significant differences in expression levels, mutation levels, and methylation levels of NCKAP1 between tumor and normal samples. NCKAP1 affects the prognosis of various cancers. NCKAP1 is strongly associated with microsatellite instability (MSI) and tumor mutational burden (TMB). The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicate that NCKAP1 is strongly associated with cell death and tumor immunity. The expression of NCKAP1 affects the sensitivity to various drugs. Moreover, NCKAP1 is an independent predictor of prognosis in LUAD patients. The results of ssGSEA showed that elevated NCKAP1 expression was positively correlated with multiple immune-related signaling pathways. PCR analysis showed that the expression of NCKAP1 was increased in LUAD cells. Transwell invasion assay showed that overexpression of NCKAP1 resulted in enhanced invasion of LUAD cells. CONCLUSIONS We comprehensively analyzed the relationship between NCKAP1 and pan-cancer and its potential clinical value. NCKAP1 could be a potential immune marker for various cancers (especially LUAD), providing new insights and insights for cancer therapy.
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Affiliation(s)
- Ankang Zhu
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Department of Cardiothoracic Surgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yan Zong
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Shuai Wei
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Department of Cardiothoracic Surgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yinuo Li
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yan Fan
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Department of Cardiothoracic Surgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Shaodong Liu
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Department of Cardiothoracic Surgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xingcai Gao
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Department of Cardiothoracic Surgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
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Gao X, Bu H, Ge J, Gao X, Wang Y, Zhang Z, Wang L. A Comprehensive Analysis of the Prognostic, Immunological and Diagnostic Role of CCNF in Pan-cancer. J Cancer 2023; 14:2431-2442. [PMID: 37670965 PMCID: PMC10475360 DOI: 10.7150/jca.86597] [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: 05/29/2023] [Accepted: 07/17/2023] [Indexed: 09/07/2023] Open
Abstract
Background: Cyclin F (CCNF) represents a pivotal constituent within the family of cell cycle proteins, which also belongs to the F-box protein family and acts as a critical regulatory factor in cell cycle transition. Its heightened expression has been consistently identified across various cancer types, including breast, pancreatic, and colorectal cancer. Nonetheless, a comprehensive exploration of CCNF's involvement in pan-cancer remains lacking. Methods: This study collected transcriptomic data and clinical information from several databases, including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and BioGPS detabase. Employing bioinformatics methods, we investigated the potential oncogenic role of CCNF, utilizing various databases such as cBioPortal, Human Protein Atlas (HPA), TIMER2, UALCAN, GEPIA, GSCALite, and CTD detabase. These analyses focused on exploring CCNF expression, prognosis, gene mutations, immune cell infiltration, DNA methylation levels, and targeted chemical drugs across different tumor types. Additionally, we obtained CCNF-related genes from GeneMANIA and GEPIA databases and conducted GO and KEGG enrichment analyses to gain deeper insights into the biological processes associated with CCNF. Furthermore, we validated the differential expression of CCNF in normal human breast cancer and breast cancer cell lines using experimental verification. Results: CCNF exhibited upregulation in the majority of cancer types, demonstrating early diagnostic potential in 15 cancers and prognostic implications for adverse outcomes across numerous malignancies. Furthermore, CCNF was found to be linked with markers of the tumor immune microenvironment in various cancers. Additionally, CCNF expression influenced genetic alterations in pan-cancer. Enrichment analysis revealed that CCNF primarily participates in crucial biological pathways such as the cell cycle, p53 signaling pathway, and cellular senescence pathways. RT-qpcr and WB assays further confirmed that CCNF expression was higher in human cancer cell lines than in normal cell lines. Conclusion: The underlying role and mechanism of CCNF in pan-cancer were elucidated through comprehensive bioinformatics analysis and experimental validation. CCNF holds promise as an invaluable early detection indicator and tumor biomarker, offering potential targets for tumor treatment and prevention.
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Affiliation(s)
- Xiaofeng Gao
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
- Medicine Research Institute /Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
| | - Huitong Bu
- College of Biology, Hunan University, Hunan, Changsha, 410012, PR China
| | - Juanjuan Ge
- Medicine Research Institute /Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
| | - Xuzheng Gao
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
| | - Ying Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
| | - Zhenwang Zhang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
- Medicine Research Institute /Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
- Medicine Research Institute /Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, PR China
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Wang SS, Lewis MJ, Pitzalis C. DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis. Biomedicines 2023; 11:1987. [PMID: 37509625 PMCID: PMC10377185 DOI: 10.3390/biomedicines11071987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Rheumatoid arthritis (RA) is a complex condition that displays heterogeneity in disease severity and response to standard treatments between patients. Failure rates for conventional, target synthetic, and biologic disease-modifying rheumatic drugs (DMARDs) are significant. Although there are models for predicting patient response, they have limited accuracy, require replication/validation, or for samples to be obtained through a synovial biopsy. Thus, currently, there are no prediction methods approved for routine clinical use. Previous research has shown that genetics and environmental factors alone cannot explain the differences in response between patients. Recent studies have demonstrated that deoxyribonucleic acid (DNA) methylation plays an important role in the pathogenesis and disease progression of RA. Importantly, specific DNA methylation profiles associated with response to conventional, target synthetic, and biologic DMARDs have been found in the blood of RA patients and could potentially function as predictive biomarkers. This review will summarize and evaluate the evidence for DNA methylation signatures in treatment response mainly in blood but also learn from the progress made in the diseased tissue in cancer in comparison to RA and autoimmune diseases. We will discuss the benefits and challenges of using DNA methylation signatures as predictive markers and the potential for future progress in this area.
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Affiliation(s)
- Susan Siyu Wang
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
| | - Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
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Fischer J, Schulz MH. Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data. Bioinformatics 2023; 39:btad386. [PMID: 37326968 PMCID: PMC10310462 DOI: 10.1093/bioinformatics/btad386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/17/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023] Open
Abstract
MOTIVATION DNA CpG methylation (CpGm) has proven to be a crucial epigenetic factor in the mammalian gene regulatory system. Assessment of DNA CpG methylation values via whole-genome bisulfite sequencing (WGBS) is, however, computationally extremely demanding. RESULTS We present FAst MEthylation calling (FAME), the first approach to quantify CpGm values directly from bulk or single-cell WGBS reads without intermediate output files. FAME is very fast but as accurate as standard methods, which first produce BS alignment files before computing CpGm values. We present experiments on bulk and single-cell bisulfite datasets in which we show that data analysis can be significantly sped-up and help addressing the current WGBS analysis bottleneck for large-scale datasets without compromising accuracy. AVAILABILITY AND IMPLEMENTATION An implementation of FAME is open source and licensed under GPL-3.0 at https://github.com/FischerJo/FAME.
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Affiliation(s)
- Jonas Fischer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken 66123, Germany
| | - Marcel H Schulz
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken 66123, Germany
- Institute of Cardiovascular Regeneration, Department of Medicine, Goethe University, Frankfurt am Main 60590, Germany
- Cardio-Pulmonary Institute, Goethe University, Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhein-Main, Frankfurt am Main 60590, Germany
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Dalle Nogare M, D'Annunzio S, Vazza G, Regazzo D, Picello L, Denaro L, Voltan G, Scaroni C, Ceccato F, Occhi G. The Methylation Analysis of the Glucose-Dependent Insulinotropic Polypeptide Receptor (GIPR) Locus in GH-Secreting Pituitary Adenomas. Int J Mol Sci 2023; 24:ijms24119264. [PMID: 37298217 DOI: 10.3390/ijms24119264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The glucose-dependent insulinotropic polypeptide receptor (GIPR) is aberrantly expressed in about one-third of GH-secreting pituitary adenomas (GH-PAs) and has been associated with a paradoxical increase of GH after a glucose load. The reason for such an overexpression has not yet been clarified. In this work, we aimed to evaluate whether locus-specific changes in DNA methylation patterns could contribute to this phenomenon. By cloning bisulfite-sequencing PCR, we compared the methylation pattern of the GIPR locus in GIPR-positive (GIPR+) and GIPR-negative (GIPR-) GH-PAs. Then, to assess the correlation between Gipr expression and locus methylation, we induced global DNA methylation changes by treating the lactosomatotroph GH3 cells with 5-aza-2'-deoxycytidine. Differences in methylation levels were observed between GIPR+ and GIPR- GH-PAs, both within the promoter (31.9% vs. 68.2%, p < 0.05) and at two gene body regions (GB_1 20.7% vs. 9.1%; GB_2 51.2% vs. 65.8%, p < 0.05). GH3 cells treated with 5-aza-2'-deoxycytidine showed a ~75% reduction in Gipr steady-state level, possibly associated with the observed decrease in CpGs methylation. These results indicate that epigenetic regulation affects GIPR expression in GH-PAs, even though this possibly represents only a part of a much more complex regulatory mechanism.
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Affiliation(s)
| | - Sarah D'Annunzio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Giovanni Vazza
- Department of Biology, University of Padova, 35128 Padova, Italy
| | - Daniela Regazzo
- Endocrinology Unit, Department of Medicine, Padova University Hospital, 35121 Padova, Italy
| | - Luna Picello
- Department of Biology, University of Padova, 35128 Padova, Italy
| | - Luca Denaro
- Academic Neurosurgery, Department of Neurosciences, Padova University Hospital, 35121 Padova, Italy
| | - Giacomo Voltan
- Endocrinology Unit, Department of Medicine, Padova University Hospital, 35121 Padova, Italy
| | - Carla Scaroni
- Endocrinology Unit, Department of Medicine, Padova University Hospital, 35121 Padova, Italy
| | - Filippo Ceccato
- Endocrinology Unit, Department of Medicine, Padova University Hospital, 35121 Padova, Italy
| | - Gianluca Occhi
- Department of Biology, University of Padova, 35128 Padova, Italy
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Lau BT, Almeda A, Schauer M, McNamara M, Bai X, Meng Q, Partha M, Grimes SM, Lee H, Heestand GM, Ji HP. Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing. Genome Med 2023; 15:33. [PMID: 37138315 PMCID: PMC10155347 DOI: 10.1186/s13073-023-01178-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/04/2023] [Indexed: 05/05/2023] Open
Abstract
Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This approach generated up to 200 million reads for a single cfDNA sample from cancer patients, an order of magnitude improvement over existing nanopore sequencing methods. We developed a single-molecule classifier to determine whether individual reads originated from a tumor or immune cells. Leveraging methylomes of matched tumors and immune cells, we characterized cfDNA methylomes of cancer patients for longitudinal monitoring during treatment.
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Affiliation(s)
- Billy T Lau
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Alison Almeda
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Marie Schauer
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Madeline McNamara
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Xiangqi Bai
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Qingxi Meng
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Mira Partha
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Susan M Grimes
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Gregory M Heestand
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
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50
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Bertoni APS, Valandro C, Brasil RÁ, Zeiser FA, Wink MR, Furlanetto TW, da Costa CA. NT5E DNA methylation in papillary thyroid cancer: Novel opportunities for precision oncology. Mol Cell Endocrinol 2023; 570:111915. [PMID: 37059175 DOI: 10.1016/j.mce.2023.111915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/01/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023]
Abstract
The ectoenzyme CD73, encoded by the NT5E gene, has emerged as a potential prognostic and therapeutic marker for papillary thyroid carcinoma (PTC), which has increased in incidence in recent decades. Here, from The Cancer Genome Atlas Thyroid Cancer (TCGA-THCA) database, we extracted and combined clinical features, levels of NT5E mRNA, and DNA methylation of PTC samples and performed multivariate and random forest analyses to evaluate the prognostic relevance and the potential of discriminating between adjacent non-malignant and thyroid tumor samples. As a result, we revealed that lower levels of methylation at the cg23172664 site were independently associated with BRAF-like phenotype (p = 0.002), age over 55 years (p = 0.012), presence of capsule invasion (p = 0.007) and presence of positive lymph node metastasis (LNM) (p = 0.04). The methylation levels of cg27297263 and cg23172664 sites showed significant and inversely correlations with levels of NT5E mRNA expression (r = -0.528 and r = -0.660, respectively), and their combination was able to discriminate between adjacent non-malignant and tumor samples with a precision of 96%-97% and 84%-85%, respectively. These data suggest that combining cg23172664 and cg27297263 sites may bring new insights to reveal new subsets of patients with papillary thyroid carcinoma.
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Affiliation(s)
- Ana Paula Santin Bertoni
- Software Innovation Laboratory - SOFTWARELAB, Applied Computing Graduate Program, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil; Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, RS, Brazil
| | - Cleiton Valandro
- Software Innovation Laboratory - SOFTWARELAB, Applied Computing Graduate Program, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Rafael Ávila Brasil
- Software Innovation Laboratory - SOFTWARELAB, Applied Computing Graduate Program, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Felipe André Zeiser
- Software Innovation Laboratory - SOFTWARELAB, Applied Computing Graduate Program, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Márcia Rosângela Wink
- Software Innovation Laboratory - SOFTWARELAB, Applied Computing Graduate Program, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Tania Weber Furlanetto
- Programa de Pós-Graduação em Medicina: Ciências Médicas, UFRGS, Porto Alegre, RS, Brazil
| | - Cristiano André da Costa
- Software Innovation Laboratory - SOFTWARELAB, Applied Computing Graduate Program, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil.
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