1
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Meevassana J, Vongsuly CW, Nakbua T, Kamolratanakul S, Thitiwanichpiwong P, Bin-Alee F, Keelawat S, Kitkumthorn N. Selected Alu methylation levels in the gastric carcinogenesis cascade. PeerJ 2025; 13:e19485. [PMID: 40416611 PMCID: PMC12101442 DOI: 10.7717/peerj.19485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Accepted: 04/27/2025] [Indexed: 05/27/2025] Open
Abstract
Background Genome-wide hypomethylation, a common epigenetic change that occurs during cancer development, primarily affects repetitive elements, such as Alu repeats. Consequently, Alu repeats can be used as a surrogate marker of genomic hypomethylation. Methods In this study, we aimed to investigate the correlation between Alu methylation levels and the multistage course of gastric carcinogenesis. Results We found that the Alu methylation levels in gastric cancer tissue decreased compared with those in normal gastric tissue, with the change in methylation levels and pattern being most significant between chronic gastritis and intestinal metaplasia. Moreover, Alu methylation levels were not associated with Helicobacter pylori or Epstein-Barr virus infection. Conclusions Finally, our sensitivity and specificity analyses suggested that Alu methylation level can be used to distinguish gastric cancer tissue from normal tissue. Thus, Alu methylation level shows promise as biomarker for gastric cancer diagnosis.
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Affiliation(s)
- Jiraroch Meevassana
- Center of Excellence in Burn and Wound Care, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chawisa Wanda Vongsuly
- Center of Excellence in Burn and Wound Care, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tanchanok Nakbua
- Center of Excellence in Burn and Wound Care, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Supitcha Kamolratanakul
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Fardeela Bin-Alee
- Faculty of Medicine, Princess of Naradhiwas University, Narathiwat, Thailand
| | - Somboon Keelawat
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
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2
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Turvey GL, López de Alba E, Stewart E, Cook H, Alalti A, Gawne RT, Ainscough JFX, Mason AS, Coverley D. Epigenetic deprogramming by disruption of CIZ1-RNA nuclear assemblies in early-stage breast cancers. J Cell Biol 2025; 224:e202409123. [PMID: 40067149 PMCID: PMC11895699 DOI: 10.1083/jcb.202409123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 01/11/2025] [Accepted: 02/17/2025] [Indexed: 03/15/2025] Open
Abstract
CIZ1 is part of the RNA-dependent supramolecular assemblies that form around the inactive X-chromosome (Xi) in female cells and smaller assemblies throughout the nucleus in both sexes. Here, we show that CIZ1 C-terminal anchor domain (AD) is elevated in human breast tumor transcriptomes, even at stage I. Elevation correlates with deprotection of chromatin and upregulation of lncRNA-containing gene clusters in ∼10 Mb regions enriched in cancer-associated genes. We modeled the effect of AD on endogenous CIZ1-Xi assemblies and observed dominant-negative interference with their reformation after mitosis, leading to abnormal assemblies similar to those in breast cancer cells, and depletion of H2AK119ub1, H3K27me3, and Xist. Consistent alterations in gene expression were evident across the genome, showing that AD-mediated interference has a destabilizing effect, likely by unscheduled exposure of underlying chromatin to modifying enzymes. The data argue for a dominant, potent, and rapid effect of CIZ1 AD that can deprogram gene expression patterns and which may predispose incipient tumors to epigenetic instability.
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Affiliation(s)
- Gabrielle L. Turvey
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
| | - Ernesto López de Alba
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
| | - Emma Stewart
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
| | - Heather Cook
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
| | - Ahmad Alalti
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
| | - Richard T. Gawne
- York Biomedical Research Institute, University of York, York, UK
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York, UK
| | - Justin F.-X. Ainscough
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
| | - Andrew S. Mason
- York Biomedical Research Institute, University of York, York, UK
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York, UK
| | - Dawn Coverley
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
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3
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Yang S, Cheng M, Zhang S, Wang H, Wang J, Zhang X, Mi Y, Li S. DNMT3A facilitates breast cancer progression via regulating ADAMTS8 mediated EGFR-MEK-ERK activation. PLoS One 2025; 20:e0321889. [PMID: 40323963 PMCID: PMC12052109 DOI: 10.1371/journal.pone.0321889] [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: 11/10/2024] [Accepted: 03/12/2025] [Indexed: 05/07/2025] Open
Abstract
ADAMTS8 inactivation by epigenetic modifications has been reported in various tumors, and the dysregulation of ADAMTS8 expression is associated with poor clinical outcomes, cancer cell invasion, and metastasis. De novo methylation, involving DNMT3A, plays an important role in cancer development; however, it remains unclear whether DNMT3A regulates the progressive expression of breast cancer by regulating ADAMTS8. Through published cancer-related datasets and clinical validation, we found that ADAMTS8 and DNMT3A expression negatively correlated in breast cancer, and both associated with patient prognosis. Related cell experiments have shown that DNMT3A overexpression promotes breast cancer cell proliferation, migration, invasion, and apoptosis, whereas silencing DNMT3A has the opposite effect. Through Co-IP experiments, we confirmed that DNMT3A binds directly to ADAMTS8. Methylation-specific PCR (MSP) experiments confirmed that DNMT3A mediates ADAMTS8 promoter methylation in breast cancer. In addition, DNMT3A activated the EGFR-MEK-ERK signaling pathway by effectively downregulating ADAMTS8, whereas silencing ADAMTS8 effectively inhibited this signaling pathway. Taken together, our findings suggest that DNMT3A activates the EGFR-MEK-ERK signaling pathway by silencing ADAMTS8 transcription through methylation, thereby promoting breast cancer development. Therefore, DNMT3A may serve as an inhibitory target in breast cancer-targeted therapy.
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Affiliation(s)
- Shan Yang
- Department of Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Breast Cancer Molecular Medicine, Shijiazhuang, Hebei, China
| | - Meng Cheng
- Department of Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shaonan Zhang
- Department of Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Haoqi Wang
- Department of Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Breast Cancer Molecular Medicine, Shijiazhuang, Hebei, China
| | - Jiaxing Wang
- Department of Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xi Zhang
- Department of Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yunzhe Mi
- Department of Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Sainan Li
- Department of Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Breast Cancer Molecular Medicine, Shijiazhuang, Hebei, China
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4
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Nocito MC, Hantel C, Lerario AM, Mastrorocco F, De Martino L, Musicco C, Perrotta ID, Scalise M, Indiveri C, Giannattasio S, Val P, Lanzino M, Pezzi V, Casaburi I, Sirianni R. A targetable antioxidant defense mechanism to EZH2 inhibitors enhances tumor cell vulnerability to ferroptosis. Cell Death Dis 2025; 16:291. [PMID: 40229247 PMCID: PMC11997205 DOI: 10.1038/s41419-025-07607-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: 07/05/2024] [Accepted: 03/31/2025] [Indexed: 04/16/2025]
Abstract
Epigenetic changes are present in all human cancers and are responsible for switching on or off genes, thus controlling tumor cell transcriptome. These changes occur through DNA methylation, histone modifiers and readers, chromatin remodelers, and microRNAs. The histone H3 methyl-transferase EZH2 gene is overexpressed in several cancer types, including adrenocortical carcinoma (ACC), a rare cancer still lacking a targeted therapy. EZH2 inhibitors (EZH2i) have been tested in several clinical trials, but their effectiveness was limited by the toxic effects of the therapeutic doses. We tested several EZH2i on ACC cells, and observed a significant reduction in cell growth only with doses much higher than those required to prevent H3 methylation. We found that all tested EZH2i doses affected lipid metabolism genes, ROS, and glutathione production. Transcript changes correlated with metabolic data, which suggested the effects of EZH2i on ferroptosis. We found that EZH2i dose-dependently increased SLC7A11/glutathione axis and glutathione peroxidase-4 (GPX4), required to counteract lipid peroxidation and ferroptosis. A GPX4 inhibitor synergized with EZH2i, making low doses - which otherwise do not affect cell viability - able to significantly reduce ACC cell growth in vitro and in vivo. Importantly, we found that the anti-ferroptosis defense mechanism induced by EZH2i is a common response for several aggressive tumor phenotypes, uncovering a general co-targetable mechanism that could limit EZH2i effectiveness. Correcting this antioxidant response by ferroptosis inducers may be a new combination therapy that will easily find clinical applications.
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Affiliation(s)
- Marta C Nocito
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Constanze Hantel
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), 8091, Zürich, Switzerland
- Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, 01307, Dresden, Germany
| | - Antonio M Lerario
- Departments of Molecular and Integrative Physiology and Internal Medicine, University of Michigan, Medical School, 48104, Ann Arbor, MI, USA
| | - Fabrizio Mastrorocco
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), 70126, Bari, Italy
| | - Luca De Martino
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), 70126, Bari, Italy
| | - Clara Musicco
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), 70126, Bari, Italy
| | - Ida D Perrotta
- Centre for Microscopy and Microanalysis (CM2), Department of Biology, Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036, Rende, Italy
| | - Mariafrancesca Scalise
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036, Rende, Italy
| | - Cesare Indiveri
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), 70126, Bari, Italy
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036, Rende, Italy
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy (CNR), 70126, Bari, Italy
| | - Pierre Val
- France iGReD (Institute of Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000, Clermont-Ferrand, France
| | - Marilena Lanzino
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy.
- Centro Sanitario, University of Calabria, Ponte P. Bucci, 87036, Rende, Italy.
| | - Vincenzo Pezzi
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy.
| | - Ivan Casaburi
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy
| | - Rosa Sirianni
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036, Rende, Italy.
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Lauzon-Young C, Silva A, Sadikovic B. Epigenomic insights and computational advances in hematologic malignancies. Mol Cytogenet 2025; 18:9. [PMID: 40221777 PMCID: PMC11993968 DOI: 10.1186/s13039-025-00712-9] [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: 01/02/2025] [Accepted: 04/04/2025] [Indexed: 04/14/2025] Open
Abstract
Hematologic malignancies (HMs) encompass a diverse spectrum of cancers originating from the blood, bone marrow, and lymphatic systems, with myeloid malignancies representing a significant and complex subset. This review provides a focused analysis of their classification, prevalence, and incidence, highlighting the persistent challenges posed by their intricate genetic and epigenetic landscapes in clinical diagnostics and therapeutics. The genetic basis of myeloid malignancies, including chromosomal translocations, somatic mutations, and copy number variations, is examined in detail, alongside epigenetic modifications with a specific emphasis on DNA methylation. We explore the dynamic interplay between genetic and epigenetic factors, demonstrating how these mechanisms collectively shape disease progression, therapeutic resistance, and clinical outcomes. Advances in diagnostic modalities, particularly those integrating epigenomic insights, are revolutionizing the precision diagnosis of HMs. Key approaches such as nano-based contrast agents, optical imaging, flow cytometry, circulating tumor DNA analysis, and somatic mutation testing are discussed, with particular attention to the transformative role of machine learning in epigenetic data analysis. DNA methylation episignatures have emerged as a pivotal tool, enabling the development of highly sensitive and specific diagnostic and prognostic assays that are now being adopted in clinical practice. We also review the impact of computational advancements and data integration in refining diagnostic and therapeutic strategies. By combining genomic and epigenomic profiling techniques, these innovations are accelerating biomarker discovery and clinical translation, with applications in precision oncology becoming increasingly evident. Comprehensive genomic datasets, coupled with artificial intelligence, are driving actionable insights into the biology of myeloid malignancies and facilitating the optimization of patient management strategies. Finally, this review emphasizes the translational potential of these advancements, focusing on their tangible benefits for patient care and outcomes. By synthesizing current knowledge and recent innovations, we underscore the critical role of precision medicine and epigenomic research in transforming the diagnosis and treatment of myeloid malignancies, setting the stage for ongoing advancements and broader clinical implementation.
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Affiliation(s)
- Carolyn Lauzon-Young
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Ananilia Silva
- Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada.
- Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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6
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Zheng X, Liu X, Guo Y, Lv Y, Lin C, Wang D, Wang S, Liu Y, Hu X. Physical exercise and epigenetic modifications in skeletal muscle, brain, and heart. Epigenetics Chromatin 2025; 18:12. [PMID: 40114219 PMCID: PMC11927307 DOI: 10.1186/s13072-025-00576-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 02/21/2025] [Indexed: 03/22/2025] Open
Abstract
The origins of many diseases can be traced to the dynamic interplay of genetic predispositions and environmental exposures post-birth. Epigenetic modifications have recently gained prominence as a significant mediator between genetic information and environmental factors, influencing the occurrence and progression of disease. There is a burgeoning body of evidence supports that physical exercise, acting as an external environmental stimulus, exerts a discernible impact on major epigenetic modifications, including histone modifications, DNA methylation, RNA methylation, and non-coding RNA. This effect assumes a pivotal role in the pathogenesis of various human diseases. Exploring the epigenetic molecular mechanisms through which physical exercise enhances human health holds the promise of deepening our understanding of how it improves physiological functions, mitigates disease risks, and establishes a theoretical foundation for employing physical exercise as a non-pharmacological intervention in disease prevention and treatment.
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Affiliation(s)
- Xi Zheng
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, PR China
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, PR China
| | - Xueli Liu
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, PR China
| | - Yuqian Guo
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, PR China
| | - Yi Lv
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, PR China
| | - Chensheng Lin
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, PR China
| | - Dan Wang
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, PR China
| | - Shaobing Wang
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, PR China
| | - Yiping Liu
- Provincial University Key Laboratory of Sport and Health Science, School of Physical Education and Sport Sciences, Fujian Normal University, Fuzhou, PR China.
| | - Xuefeng Hu
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, PR China.
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7
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Galicia-Moreno M, Monroy-Ramirez HC, Caloca-Camarena F, Arceo-Orozco S, Muriel P, Sandoval-Rodriguez A, García-Bañuelos J, García-González A, Navarro-Partida J, Armendariz-Borunda J. A new opportunity for N-acetylcysteine. An outline of its classic antioxidant effects and its pharmacological potential as an epigenetic modulator in liver diseases treatment. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025; 398:2365-2386. [PMID: 39436429 DOI: 10.1007/s00210-024-03539-0] [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: 07/11/2024] [Accepted: 10/10/2024] [Indexed: 10/23/2024]
Abstract
Liver diseases represent a worldwide health problem accountable for two million deaths per year. Oxidative stress is critical for the development of these diseases. N-acetyl cysteine (NAC) is effective in preventing liver damage, both in experimental and clinical studies, and evidence has shown that the pharmacodynamic mechanisms of NAC are related to its antioxidant nature and ability to modulate key signaling pathways. Here, we provide a comprehensive description of the beneficial effects of NAC in the treatment of liver diseases, addressing the first evidence of its role as a scavenger and precursor of reduced glutathione, along with studies showing its immunomodulatory action, as well as the ability of NAC to modulate epigenetic hallmarks. We searched the PubMed database using the following keywords: oxidative stress, liver disease, epigenetics, antioxidants, NAC, and antioxidant therapies. There was no time limit to gather all available information on the subject. NAC has shown efficacy in treating liver damage, exerting mechanisms of action different from those of free radical scavengers. Like different antioxidant therapies, its effectiveness and safety are related to the administered dose; therefore, designing new pharmacological formulations for this drug is imperative to achieve an adequate response. Finally, there is still much to explore regarding its effect on epigenetic marker characteristics of liver damage, turning it into a drug with broad therapeutic potential. According to the literature reviewed, NAC could be an appropriate option in clinical studies related to hepatic injury and, in the future, a repurposing alternative for treating liver diseases.
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Affiliation(s)
- Marina Galicia-Moreno
- Instituto de Biologia Molecular en Medicina y Terapia Génica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, 44340, Guadalajara, Jalisco, Mexico
| | - Hugo Christian Monroy-Ramirez
- Instituto de Biologia Molecular en Medicina y Terapia Génica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, 44340, Guadalajara, Jalisco, Mexico
| | - Fernando Caloca-Camarena
- Instituto de Biologia Molecular en Medicina y Terapia Génica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, 44340, Guadalajara, Jalisco, Mexico
- Programa de Doctorado en Farmacología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, 44340, Guadalajara, Jalisco, Mexico
| | - Scarlet Arceo-Orozco
- Instituto de Biologia Molecular en Medicina y Terapia Génica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, 44340, Guadalajara, Jalisco, Mexico
| | - Pablo Muriel
- Laboratorio de Hepatologia Experimental, Departamento de Farmacologia, Cinvestav-IPN, 07000, Mexico City, Mexico
| | - Ana Sandoval-Rodriguez
- Instituto de Biologia Molecular en Medicina y Terapia Génica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, 44340, Guadalajara, Jalisco, Mexico
| | - Jesús García-Bañuelos
- Instituto de Biologia Molecular en Medicina y Terapia Génica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, 44340, Guadalajara, Jalisco, Mexico
| | | | | | - Juan Armendariz-Borunda
- Instituto de Biologia Molecular en Medicina y Terapia Génica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, 44340, Guadalajara, Jalisco, Mexico.
- Tecnológico de Monterrey, EMCS, 45201, Zapopan, Jalisco, Mexico.
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Das T, Bhar S, Ghosh D, Kabi B, Kar K, Chandra A. A promising future for breast cancer therapy with hydroxamic acid-based histone deacetylase inhibitors. Bioorg Chem 2025; 156:108169. [PMID: 39862739 DOI: 10.1016/j.bioorg.2025.108169] [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: 11/27/2024] [Revised: 01/10/2025] [Accepted: 01/13/2025] [Indexed: 01/27/2025]
Abstract
Histone deacetylases (HDACs) play a critical role in chromatin remodelling and modulating the activity of various histone proteins. Aberrant HDAC functions has been related to the progression of breast cancer (BC), making HDAC inhibitors (HDACi) promising small-molecule therapeutics for its treatment. Hydroxamic acid (HA) is a significant pharmacophore due to its strong metal-chelating ability, HDAC inhibition properties, MMP inhibition abilities, and more. They were found to increase the efficacy of the approved drugs when used in combination. In this review we presented bioinformatic analysis using available data from the Cancer Genome Atlas and Genotype-Tissue Expression databases, outlined the recent advancements in the application of HA-based HDACi for BC during preclinical investigation and clinical trials, tried to offer the rationale for targeting HDAC in BC with HA-based HDACi, summarised the challenges faced in the successful clinical application of HDACi, and proposed potential strategies to address these challenges, aiming to enhance treatment outcomes in BC. Abbreviations: ABCG2, ATP-binding cassette super-family G member 2; ABC, ATP-binding cassette; ADP, Adenosine diphosphate; APC, Antigen presenting cell; AML, Acute myeloid leukemia; ARH1, Aplysia ras homolog 1; BCRP, Breast cancer resistance protein; BRCA, Breast invasive carcinoma; Bax, B-cell lymphoma associated X; CK5, Cytokeratin 5; CK14, Cytokeratin 14; CK17, Cytokeratin 17; CoRESTMiDAC, Co-repressor for element-1-silencing transcription factor; CRM1, Chromosomal maintenance 1; CTCL, Cutaneous T-cell lymphoma; DNMT, DNA methyltransferase; DFS, Disease-free survival; ER, Oestrogen receptor; EMT, Epithelial-mesenchymal transition; FGFR1, Fibroblast growth factor receptor 1; GEPIA, Gene Expression Profiling Interactive Analysis; GTEx, Genotype tissue expression; HAT, Histone acetylase; HDAC, Histone deacetylase; HDF, Human dermal fibroblast; HER2, Human epidermal growth factor receptor 2; HDLP, Histone deacetylase-like protein; Hsp90, Heat shock protein 90; HSF1, Heat shock factor 1; HeLa, Henrietta Lacks; HER1, Human epidermal growth factor receptor 1; IARC, International Agency for Research on Cancer; IL-10, Interleukin-10; KAP1, KRAB associated protein 1; MDM2, Mouse double minute 2 homolog; MDR, Multidrug resistance; MCF-7, Michigan cancer foundation-7; MEF-2, Myocyte enhancer factor-2MMP- Matrix metalloproteinase; NAD, Nicotinamide adenine dinucleotide; NuRD, Nucleosome remodelling and deacetylation; NF- κ B, Nuclear factor kappa light chain enhancer of activated B cell; NES, Nuclear export signal; NLS, Nuclear localization signal; NCoR, Nuclear receptor corepressor; NCT, National clinical trial; OS, Overall survival; PR, Progesterone receptor; PI3K, Phosphoinositide 3-kinase; PAX3, Paired box gene 3; P-gp, P-glycoprotein; ROS, Reactive oxygen species; SIRT, Sirtuin; SMRT, Silencing mediator for retinoid and thyroid receptor; STAT3, Signal transducer and activator of transcription-3; SAR, Structure-activity relationship; SHP1, Src homology region 2 domain-containing phosphatase 1; SAHA, Suberoylanilide hydroxamic acid; SMEDDS, Self micro emulsifying drug delivery system; TNBC, Triple-negative breast cancer; TSA, Trichostatin A; ZBG, Zinc binding group.
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Affiliation(s)
- Tanima Das
- Department of In Vitro Carcinogenesis and Cellular Chemotherapy, Chittaranjan National Cancer Institute, 37, S. P. Mukherjee Road, Kolkata 700026, India
| | - Sunandita Bhar
- Department of In Vitro Carcinogenesis and Cellular Chemotherapy, Chittaranjan National Cancer Institute, 37, S. P. Mukherjee Road, Kolkata 700026, India
| | - Diya Ghosh
- Department of In Vitro Carcinogenesis and Cellular Chemotherapy, Chittaranjan National Cancer Institute, 37, S. P. Mukherjee Road, Kolkata 700026, India
| | - Bikash Kabi
- Department of In Vitro Carcinogenesis and Cellular Chemotherapy, Chittaranjan National Cancer Institute, 37, S. P. Mukherjee Road, Kolkata 700026, India
| | - Kanisha Kar
- Department of In Vitro Carcinogenesis and Cellular Chemotherapy, Chittaranjan National Cancer Institute, 37, S. P. Mukherjee Road, Kolkata 700026, India
| | - Arpita Chandra
- Department of In Vitro Carcinogenesis and Cellular Chemotherapy, Chittaranjan National Cancer Institute, 37, S. P. Mukherjee Road, Kolkata 700026, India.
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9
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Colemon A, Prioleau T, Rouse C, Pendergast AM. ABL Kinases Modulate EZH2 Phosphorylation and Signaling in Metastatic Triple Negative Breast Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.18.638898. [PMID: 40027835 PMCID: PMC11870601 DOI: 10.1101/2025.02.18.638898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Triple-negative breast cancer (TNBC) remains a leading cause of cancer associated deaths in women owing to its highly metastatic potential and limited treatment options. Recent studies have shown that expression of proteins associated with epigenetic regulation of gene expression are associated with metastatic relapse, however targeting epigenetic regulatory proteins has not resulted in effective therapies for TNBC in the clinic. The ABL tyrosine kinases promote metastasis of breast cancer cells in mouse models. However, a role of ABL kinases in the regulation of epigenetic processes in solid tumor metastasis remains unexplored. Here we show that inactivation of ABL kinases in bone metastatic TNBC cells led to a significant enrichment in gene signatures associated with the PRC2 protein complex, revealing a functional link between ABL kinases and the PRC2 complex. ABL inactivation promotes EZH2-T487 phosphorylation through the regulation of a FAK-CDK1 signaling axis. We find that phosphorylated EZH2 T487 or a phosphomimic EZH2 T487D mutant exhibit increased binding to non-canonical binding partners of EZH2 including c-MYC and ZMYND8. Notably, we identify a therapeutic vulnerability in TNBC cells whereby combination treatment with ABL allosteric inhibitors and EZH2 inhibitors elicits a synergistic decrease in TNBC cell survival in vitro, and impairs TNBC metastasis, prolonging survival of tumor-bearing mice treated with the combination therapy. One Sentence Summary ABL Kinases indirectly impact EZH2 catalytic activity by blocking a signaling cascade that leads to changes in the phosphorylation, protein interactions, and function of the PRC2 catalytic component EZH2 in TNBC.
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Najia MA, Jha DK, Zhang C, Laurent B, Kubaczka C, Markel A, Li C, Morris V, Tompkins A, Hensch L, Qin Y, Chapuy B, Huang YC, Morse M, Marunde MR, Vaidya A, Gillespie ZB, Howard SA, North TE, Dominguez D, Keogh MC, Schlaeger TM, Shi Y, Li H, Shipp MM, Blainey PC, Daley GQ. Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.31.635709. [PMID: 39975048 PMCID: PMC11838449 DOI: 10.1101/2025.01.31.635709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Genes involved in the regulation of chromatin structure are frequently disrupted in cancer, contributing to an aberrant transcriptome and phenotypic plasticity. Yet, therapeutics targeting mutant forms of chromatin-modifying enzymes have yielded only modest clinical utility, underscoring the difficulty of targeting the epigenomic underpinnings of aberrant gene regulatory networks. Here, we sought to identify novel epigenetic vulnerabilities in diffuse large B-cell lymphoma (DLBCL). Through phenotypic screens and biochemical analysis, we demonstrated that inhibition of the H3K9 demethylases KDM4A and KDM4C elicits potent, subtype-agnostic cytotoxicity by antagonizing transcriptional networks associated with B-cell identity and epigenetically rewiring heterochromatin. KDM4 demethylases associated with the KRAB zinc finger ZNF587, and their enzymatic inhibition led to DNA replication stress and DNA damage-einduced cGAS-STING activation. Broad surveys of transcriptional data from patients also revealed KDM4 family dysregulation in several other cancer types. To explore this potential therapeutic avenue, we performed high-throughput small molecule screens with H3K9me3 nucleosome substrates and identified novel KDM4 demethylase inhibitors. AI-guided protein-ligand binding predictions suggested diverse modes of action for various small molecule hits. Our findings underscore the relevance of targeting fundamental transcriptional and epigenetic mechanisms for anti-cancer therapy.
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Affiliation(s)
- Mohamad Ali Najia
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Deepak K. Jha
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Cheng Zhang
- Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, 55902, USA
| | - Benoit Laurent
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Caroline Kubaczka
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Arianna Markel
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Christopher Li
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Vivian Morris
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Allison Tompkins
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Luca Hensch
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Yue Qin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bjoern Chapuy
- Division of Hematologic Neoplasia, Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Charité, University Medical Center Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Yu-Chung Huang
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Michael Morse
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | | | | | | | | | - Trista E. North
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Thorsten M. Schlaeger
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115, USA
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hu Li
- Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, 55902, USA
| | - Margaret M. Shipp
- Division of Hematologic Neoplasia, Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, 02115, USA
| | - Paul C. Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - George Q. Daley
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115 USA
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
- Lead contact
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Li Z, Chen X, Li Y, Xu Y, Zhou Y. Aberrant DNA Methylation in Esophageal Squamous Cell Carcinoma and its Clinical Implications in Systemic Chemotherapy. Int J Med Sci 2025; 22:1002-1014. [PMID: 39991775 PMCID: PMC11843145 DOI: 10.7150/ijms.109161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Accepted: 01/25/2025] [Indexed: 02/25/2025] Open
Abstract
Esophageal cancer is a significant global health concern, with esophageal squamous cell carcinoma being the predominant subtype in high-incidence regions like China. Despite advances in multidisciplinary treatments, the prognosis for ESCC remains poor, with systemic chemotherapy facing the challenge of drug resistance. Epigenetic alterations, particularly DNA methylation, play a crucial role in ESCC carcinogenesis and therapeutic response. Aberrant DNA methylations, including global hypomethylation and promoter-specific hyper-methylation, disrupt critical pathways such as cell cycle regulation, apoptosis, and DNA repair, contributing to chemoresistance. Several studies have identified methylation markers that predict treatment response, particularly for chemotherapy, targeted therapy and immunotherapy, such as p16 and GPX3 for cisplatin, MTHFR for 5-FU, CHFR for paclitaxel. DNA methyltransferase inhibitors and other epigenetic therapies are being explored to reverse these methylation changes and enhance therapeutic efficacy. However, the clinical utility of these markers remains limited due to the lack of large-scale validation and concerns over off-target effects. This review aims to summarize all aberrant methylation alterations in ESCC and the clinical implications of aberrantly methylated candidate genes identified in ESCC systemic chemotherapy, with the goal of further understanding the underlying molecular mechanisms, refining methylation-targeting therapies, and integrating them with conventional treatments to improve patient outcomes.
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Affiliation(s)
- Zhao Li
- Department of Health Prevention and Care, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 Dahua Road, Beijing 100730, China
| | - Xi Chen
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 Dahua Road, Beijing, 100730, China
| | - Yongkang Li
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, No. 5 Dong Dan San Tiao, Beijing, 100005, China
| | - Yan Xu
- Department of Health Prevention and Care, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 Dahua Road, Beijing 100730, China
| | - Yang Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuan Nanli No.17, Beijing 100021, China
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12
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Andrysik Z, Espinosa JM. Harnessing p53 for targeted cancer therapy: new advances and future directions. Transcription 2025; 16:3-46. [PMID: 40031988 PMCID: PMC11970777 DOI: 10.1080/21541264.2025.2452711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Revised: 01/07/2025] [Accepted: 01/08/2025] [Indexed: 03/05/2025] Open
Abstract
The transcription factor p53 is the most frequently impaired tumor suppressor in human cancers. In response to various stress stimuli, p53 activates transcription of genes that mediate its tumor-suppressive functions. Distinctive characteristics of p53 outlined here enable a well-defined program of genes involved in cell cycle arrest, apoptosis, senescence, differentiation, metabolism, autophagy, DNA repair, anti-viral response, and anti-metastatic functions, as well as facilitating autoregulation within the p53 network. This versatile, anti-cancer network governed chiefly by a single protein represents an immense opportunity for targeted cancer treatment, since about half of human tumors retain unmutated p53. During the last two decades, numerous compounds have been developed to block the interaction of p53 with the main negative regulator MDM2. However, small molecule inhibitors of MDM2 only induce a therapeutically desirable apoptotic response in a limited number of cancer types. Moreover, clinical trials of the MDM2 inhibitors as monotherapies have not met expectations and have revealed hematological toxicity as a characteristic adverse effect across this drug class. Currently, combination treatments are the leading strategy for enhancing efficacy and reducing adverse effects of MDM2 inhibitors. This review summarizes efforts to identify and test therapeutics that work synergistically with MDM2 inhibitors. Two main types of drugs have emerged among compounds used in the following combination treatments: first, modulators of the p53-regulated transcriptome (including chromatin modifiers), translatome, and proteome, and second, drugs targeting the downstream pathways such as apoptosis, cell cycle arrest, DNA repair, metabolic stress response, immune response, ferroptosis, and growth factor signaling. Here, we review the current literature in this field, while also highlighting overarching principles that could guide target selection in future combination treatments.
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Affiliation(s)
- Zdenek Andrysik
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joaquin M. Espinosa
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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13
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Rajendran P, Prasad M, Ali EM, Sekar R, AlZahrani AM, Karobari MI, Genena MAM, Abdallah BM. Molecular insight into histone methylation as a novel target for oral squamous cell carcinoma: future hope in personalised medicine. J Cancer 2025; 16:1575-1590. [PMID: 39991574 PMCID: PMC11843246 DOI: 10.7150/jca.103243] [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: 09/04/2024] [Accepted: 01/17/2025] [Indexed: 02/25/2025] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most prevalent type of malignant epithelial neoplasm that affects the oral cavity. It has been a significant health concern in many countries for a long time since it was usually treated with surgery, radiation, and/or chemotherapy. Drug resistance is the primary issue in patient populations and scientific research, which promotes OSCC tumour cell invasion and migration. Thus, identifying highly specific therapeutic targets could be the potential approach for more successful treatment of OSCC. It is still challenging to understand the genetic causes of oral carcinogenesis due to its highly varied clinic-pathological parameters. It is important to remember that signaling channels and complexes that affect chromatin accessibility control gene expression, which in turn affects cell development and differentiation. Histones undergo post-translational alteration to give this platform. Understanding the processes of gene regulation through histone methylation and its modifications could enhance the early detection, prognostic prediction, and therapy of OSCC. To be properly used as a therapeutic target, histone methylation in OSCC requires more investigation. This review details the dysregulated histone methylation and the modifying enzymes linked to the development and aetiology of OSCC. Furthermore, the part that lysine methylation plays in cell migration, chemo-resistance, and OSCC invasion is also investigated.
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Affiliation(s)
- Peramaiyan Rajendran
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Monisha Prasad
- Centre for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 602105, TN, India
| | - Enas M Ali
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Ramya Sekar
- Department of Oral & Maxillofacial Pathology and Oral Microbiology, Meenakshi Ammal Dental College and Hospital, Meenakshi Academy of Higher Education and Research (Deemed to be University), Chennai, Tamil Nadu, India
| | - Abdullah M AlZahrani
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Mohmed Isaqali Karobari
- Department of Conservative Dentistry and Endodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Marwa Azmy M. Genena
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Basem M Abdallah
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
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14
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Seres M, Spacayova K, Sulova Z, Spaldova J, Breier A, Pavlikova L. Dynamic Multilevel Regulation of EGFR, KRAS, and MYC Oncogenes: Driving Cancer Cell Proliferation Through (Epi)Genetic and Post-Transcriptional/Translational Pathways. Cancers (Basel) 2025; 17:248. [PMID: 39858030 PMCID: PMC11763799 DOI: 10.3390/cancers17020248] [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: 12/03/2024] [Revised: 01/09/2025] [Accepted: 01/10/2025] [Indexed: 01/27/2025] Open
Abstract
The epidermal growth factor receptor (EGFR) regulates gene expression through two primary mechanisms: as a growth factor in the nucleus, where it translocates upon binding its ligand, or via its intrinsic tyrosine kinase activity in the cytosol, where it modulates key signaling pathways such as RAS/MYC, PI3K, PLCγ, and STAT3. During tumorigenesis, these pathways become deregulated, leading to uncontrolled proliferation, enhanced migratory and metastatic capabilities, evasion of programmed cell death, and resistance to chemotherapy or radiotherapy. The RAS and MYC oncogenes are pivotal in tumorigenesis, driving processes such as resistance to apoptosis, replicative immortality, cellular invasion and metastasis, and metabolic reprogramming. These oncogenes are subject to regulation by a range of epigenetic and post-transcriptional modifications. This review focuses on the deregulation of EGFR, RAS, and MYC expression caused by (epi)genetic alterations and post-translational modifications. It also explores the therapeutic potential of targeting these regulatory proteins, emphasizing the importance of phenotyping neoplastic tissues to inform the treatment of cancer.
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Affiliation(s)
- Mario Seres
- Institute of Molecular Physiology and Genetics, Centre of Bioscience, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.S.); (K.S.); (Z.S.)
| | - Katarina Spacayova
- Institute of Molecular Physiology and Genetics, Centre of Bioscience, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.S.); (K.S.); (Z.S.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Zdena Sulova
- Institute of Molecular Physiology and Genetics, Centre of Bioscience, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.S.); (K.S.); (Z.S.)
| | - Jana Spaldova
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia;
| | - Albert Breier
- Institute of Molecular Physiology and Genetics, Centre of Bioscience, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.S.); (K.S.); (Z.S.)
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia;
| | - Lucia Pavlikova
- Institute of Molecular Physiology and Genetics, Centre of Bioscience, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.S.); (K.S.); (Z.S.)
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15
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Zhong Y, Wang R, Huang Z, Hu Z, Peng B, Chen B, Sun L. Identification of SETD4 as an Onco-Immunological Biomarker Encompassing the Tumor Microenvironment, Prognoses, and Therapeutic Responses in Various Human Cancers. Immun Inflamm Dis 2025; 13:e70126. [PMID: 39817582 PMCID: PMC11736640 DOI: 10.1002/iid3.70126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 11/24/2024] [Accepted: 01/03/2025] [Indexed: 01/18/2025] Open
Abstract
BACKGROUND SET domain-containing protein 4 (SETD4) is a histone methyltransferase that has been shown to modulate cell proliferation, differentiation, and inflammatory responses by regulating histone H4 trimethylation (H4K20me3). Previous reports have demonstrated its function in the quiescence of cancer stem cells as well as drug resistance in several cancers. A limited number of systematic studies have examined SETD4's role in the tumor microenvironment, pathogenesis, prognosis, and therapeutic response. METHODS Utilizing The Cancer Genome Atlas database, and other publicly accessible platforms, we comprehensively analyzed SETD4 gene expression, methylation patterns, and prognostic significance. Furthermore, we investigated its association with cancer-related pathways, the immune microenvironment, immunotherapy markers, and drug resistance signatures of chemotherapy. Additionally, qRT-PCR was performed to validate SETD4 expression in clinical specimens. RESULTS The expression of SETD4 was abnormal across a variety of cancer types and the expression of SETD4 in colorectal cancer tissues was verified in clinical specimens. The upregulation of SETD4 may be a prognostic risk factor predicting poor overall survival and progression-free survival. The analysis revealed that the mRNA level of SETD4 was modulated by promoter methylation, and patients with lower methylation levels showed shorter survival times. Pathway analysis showed that SETD4 influenced several key cell cycle pathways, including the G2M checkpoint, and mitotic spindle pathways. In addition, SETD4 negatively affects immune cell infiltration in most cancers, including B cells, CD8 T cells, and macrophages. The correlation between SETD4 and cancer stemness as well as homologous recombination deficiency varied across tumor types, suggesting that SETD4 may play a multifaceted role in tumor resistance. Notably, we identified several potential agents targeting SETD4. CONCLUSIONS This study demonstrates that SETD4 is an immune-oncogenic molecule in multiple cancers, with the potential to be a diagnosis, prognosis, and targeted therapy marker.
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Affiliation(s)
- Yuyun Zhong
- Department of Health Management CenterThe Third Affiliated Hospital of Southern Medical UniversityGuangzhouChina
- The Guangzhou Bay Area Institute of BiomedicineGuangzhouChina
| | - Ruiqi Wang
- Department of Pharmacy, Zhuhai People's HospitalZhuhai Hospital Affiliated With Jinan UniversityZhuhaiChina
| | - Zijie Huang
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan UniversityJinan UniversityGuangzhouGuangdongChina
| | - Zhaoting Hu
- Department of Health Management CenterThe Third Affiliated Hospital of Southern Medical UniversityGuangzhouChina
| | - Bin Peng
- Department of Thoracic SurgeryThe First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's HospitalShenzhenChina
| | - Bin Chen
- Department of Health Management CenterThe Third Affiliated Hospital of Southern Medical UniversityGuangzhouChina
- The Guangzhou Bay Area Institute of BiomedicineGuangzhouChina
| | - Liyue Sun
- Second Department of OncologyGuangdong Second Provincial General HospitalGuangzhouChina
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Verma R, Kumar K, Bhatt S, Yadav M, Kumar M, Tagde P, Rajinikanth PS, Tiwari A, Tiwari V, Nagpal D, Mittal V, Kaushik D. Untangling Breast Cancer: Trailing Towards Nanoformulations-based Drug Development. RECENT PATENTS ON NANOTECHNOLOGY 2025; 19:76-98. [PMID: 37519201 DOI: 10.2174/1872210517666230731091046] [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: 01/02/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
All over the world, cancer death and prevalence are increasing. Breast cancer (BC) is the major cause of cancer mortality (15%) which makes it the most common cancer in women. BC is defined as the furious progression and quick division of breast cells. Novel nanotechnology-based approaches helped in improving survival rate, metastatic BC is still facing obstacles to treat with an expected overall 23% survival rate. This paper represents epidemiology, classification (non-invasive, invasive and metastatic), risk factors (genetic and non-genetic) and treatment challenges of breast cancer in brief. This review paper focus on the importance of nanotechnology-based nanoformulations for treatment of BC. This review aims to deliver elementary insight and understanding of the novel nanoformulations in BC treatment and to explain to the readers for enduring designing novel nanomedicine. Later, we elaborate on several types of nanoformulations used in tumor therapeutics such as liposomes, dendrimers, polymeric nanomaterials and many others. Potential research opportunities for clinical application and current challenges related to nanoformulations utility for the treatment of BC are also highlighted in this review. The role of artificial intelligence is elaborated in detail. We also confer the existing challenges and perspectives of nanoformulations in effective tumor management, with emphasis on the various patented nanoformulations approved or progression of clinical trials retrieved from various search engines.
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Affiliation(s)
- Ravinder Verma
- Department of Pharmaceutical Sciences, Chaudhary Bansi Lal University, Bhiwani, Haryana, 127021, India
| | - Kuldeep Kumar
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Shailendra Bhatt
- Shrinathji Institute of Pharmacy, Shrinathji Society for Higher Education, Upali Oden, Nathdwara, Rajasmand, Rajasthan, India
| | - Manish Yadav
- Department of Pharmacy, G.D. Goenka University, Sohna Road, Gurugram, 122103, India
| | - Manish Kumar
- School of Pharmaceutical Sciences, CT University, Ludhiana, 142024, Punjab, India
| | - Priti Tagde
- Bhabha Pharmacy Research Institute, Bhabha University Bhopal, 462026, Madhya Pradesh, India
- PRISAL Foundation, Pharmaceutical Royal International Society, New Dehli, India
| | - P S Rajinikanth
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Amebdkar University, Lucknow, India
| | - Abhishek Tiwari
- Pharmacy Academy, IFTM University, Lodhipur Rajput, Moradabad, U.P., 244102, India
| | - Varsha Tiwari
- Pharmacy Academy, IFTM University, Lodhipur Rajput, Moradabad, U.P., 244102, India
| | - Diksha Nagpal
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Vineet Mittal
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Deepak Kaushik
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
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17
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Waykar R, Kumarapillai S. Breast cancer histopathology, classification and clinical management: Current perspectives. Bioinformation 2024; 20:2069-2079. [PMID: 40230896 PMCID: PMC11993385 DOI: 10.6026/9732063002002069] [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: 12/01/2024] [Revised: 12/31/2024] [Accepted: 12/31/2024] [Indexed: 04/16/2025] Open
Abstract
Breast cancer (BC) manifests as a diverse group of malignancies and presents as a wide array of tumors with distinct morphological, biological and clinical characteristics. Molecular classification of BC serves as the basis for current precision-oriented therapeutic strategies. Upcoming therapeutic strategies will emphasize personalized medicine and tailoring treatments according to each patient's specific needs. These approaches will involve modulating the therapy intensity based on the biological characteristics of tumours and early predictive indicators, allowing for more precise and adaptable care in oncology. Additionally, there remains an unfulfilled requirement for the creation of new medications to treat breast cancer in its early stages, as well as in advanced cases. This review article presents an extensive examination of breast cancer, delving into its prevalence, contributing factors, molecular and cellular features and therapeutic interventions.
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Affiliation(s)
- Ravindra Waykar
- Department of Pharmacy, Lincoln University College, Wisma Lincoln, Jalan SS 6/12, 47301 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Srinivasakumar Kumarapillai
- Department of Pharmacy, Lincoln University College, Wisma Lincoln, Jalan SS 6/12, 47301 Petaling Jaya, Selangor Darul Ehsan, Malaysia
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18
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Ichimura N, Urata Y, Kobayashi T, Ebata R, Matsumoto H, Hibi H. Mutational landscape of Japanese patients with oral squamous cell carcinoma from comprehensive genomic profiling tests. Oral Oncol 2024; 159:107079. [PMID: 39432990 DOI: 10.1016/j.oraloncology.2024.107079] [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: 08/27/2024] [Revised: 10/08/2024] [Accepted: 10/13/2024] [Indexed: 10/23/2024]
Abstract
OBJECTIVES Oral squamous cell carcinoma (OSCC) is the most common subtype of head and neck squamous cell carcinoma (HNSCC). Treatment options for OSCC are currently limited owing to the lack of identified therapeutic targets. In this study, we aimed to analyze the genomic profiles of Japanese patients with OSCC and compare them to those of patients with HNSCC to identify potential therapeutic targets. MATERIALS AND METHODS We extracted the clinical and genomic information of patients with OSCC (n = 242) and those with other HNSCC (n = 402) who underwent comprehensive genomic profiling tests under the National Health Insurance between June 2019 and April 2024 from the Center for Cancer Genomics and Therapeutics database. RESULTS The most frequent genomic alterations identified in OSCC were TP53 (85.5 %), followed by TERT (62.4 %), CDKN2A (41.3 %), FGF19 (24.9 %), and CCND1 (23.6 %). FGF19 and CCND1 were co-amplified, and CDKN2A and CDKN2B were co-deleted. The frequencies of TERT, HRAS, and CASP8 alterations were the highest in OSCC among all HNSCC subtypes. The frequency of EGFR alterations was substantially higher in adolescent and young adults than older patients with OSCC. Genes associated with genomic integrity and the RTK-RAS pathway were frequently altered in OSCC. CONCLUSION This study analyzed the genomic profiles of patients with OSCC in Japan and the genetic differences between OSCC and other HNSCC subtypes. This analysis offers insights into the development of personalized therapeutics for OSCC.
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Affiliation(s)
- Norihisa Ichimura
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Yusuke Urata
- Department of Oral and Maxillofacial Surgery, Nagoya University Hospital, Nagoya, Japan
| | - Takeru Kobayashi
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryo Ebata
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroya Matsumoto
- Department of Oral and Maxillofacial Surgery, Nagoya University Hospital, Nagoya, Japan
| | - Hideharu Hibi
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Oral and Maxillofacial Surgery, Nagoya University Hospital, Nagoya, Japan
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19
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Vu THN, Morozkina SN, Olekhnovich RO, Podshivalov AV, Uspenskaya MV. Study on Fabrication and Properties of Polyvinyl Alcohol/Chitosan Nanofibers Created from Aqueous Solution with Acetic Acid and Ethanol by the Electrospinning Method. Polymers (Basel) 2024; 16:3393. [PMID: 39684138 DOI: 10.3390/polym16233393] [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: 11/11/2024] [Revised: 11/26/2024] [Accepted: 11/28/2024] [Indexed: 12/18/2024] Open
Abstract
The development of nanofibers with incorporated biologically active molecules with a targeted mode of action is a current research trend. Potential materials for the development of such systems include poly(vinyl alcohol) (PVA) and chitosan (CS) nanofibers, which are traditionally fabricated by the electrospinning of aqueous solutions of these polymers with acetic acid. To improve drug integration, ethanol was added to the binary-solvent system. This results in several important data: noticeable shifts in the solvent system's solubility parameter, the interaction of the various component forces, and optical and rheological properties of the PVA-CS solution. The use of ethanol in the electrospun solution also contributes to adjusting the solubility parameters of the solution in the Teas graph, maintaining the "fh - fd" in the optimal region for the fabrication of PVA-CS nanofibers. Increasing the efficiency of PVA-CS nanofiber fabrication by electrospinning is quite difficult due to the requirements of solution parameters, technological parameters, and environmental parameters; however, this efficiency was increased in this work by 2 to 3 times with a more optimal PVA-CS nanofiber morphology. These results demonstrate that aqueous solution containing 4% PVA, 3% CS, 15% ethanol, and 45% acetic acid is optimal for increasing the nanofiber fabrication productivity, improving the morphology and diameter of PVA-CS nanofibers without changing in chemical bonds. The XRD spectrum revealed that the alterations in the crystal lattice and diameter of the PVA-CS nanofibers led to the variation in their thermal and tensile properties.
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Affiliation(s)
- Thi Hong Nhung Vu
- Faculty of Basic Sciences, Vietnam National University of Forestry at Dong Nai, Trang Bom 76000, Dong Nai Province, Vietnam
| | - Svetlana N Morozkina
- Kabardino-Balkarian State University, Chernyshevskogo 173, 360004 Nalchik, Russia
- Center for Chemical Engineering, ITMO University, Kronverkskiy Prospekt, 49A, 197101 St. Petersburg, Russia
| | - Roman O Olekhnovich
- Civil Engineering Institute, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29 B, 195251 St. Petersburg, Russia
- Institute of Chemistry, St. Petersburg State University, 7-9 Universitetskaya Embankment, 199034 St. Petersburg, Russia
| | - Aleksandr V Podshivalov
- Center for Chemical Engineering, ITMO University, Kronverkskiy Prospekt, 49A, 197101 St. Petersburg, Russia
| | - Mayya V Uspenskaya
- Civil Engineering Institute, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29 B, 195251 St. Petersburg, Russia
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20
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Ni D, Chen X, Wang H, Shen T, Li X, Liang B, Zhang R, Liu R, Xiao W. Design, synthesis and biological evaluation of 4,6-diarylquinoxaline-based KDM4D inhibitors. Bioorg Med Chem 2024; 114:117945. [PMID: 39454559 DOI: 10.1016/j.bmc.2024.117945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/18/2024] [Accepted: 10/06/2024] [Indexed: 10/28/2024]
Abstract
Histone lysine demethylase 4D (KDM4D) is a critical player in the regulation of tumorigenesis, emerging as a potential target for developing anti-tumor agents. In this study, a series of KDM4D inhibitors containing the 4,6-diarylquinoxaline scaffold were prepared based on the previously discovered hit compound QD-1. Among these inhibitors, 33a was the most potent compound, with an IC50 value of 0.62 μM. In an in vitro assay, 33a showed a superior ability to inhibit the viability of liver cancer Huh-7 cells with IC50 = 5.23 μM. 33a exhibits significant effects in inhibiting cell cycle progression and proliferation of liver cancer cells, as well as suppressing cell migration. This work provided a promising scaffold for developing KDM4D inhibitors, as well as a lead compound for the development of anti-tumor drugs targeting KDM4D.
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Affiliation(s)
- Dongxuan Ni
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, School of Chemical Science and Technology, School of Pharmacy, School of Life Sciences, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Research & Development Center for Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xuechun Chen
- Translational Cancer Research Center, Peking University First Hospital, Beijing 100034, China
| | - Hairong Wang
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, School of Chemical Science and Technology, School of Pharmacy, School of Life Sciences, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Research & Development Center for Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Tianze Shen
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, School of Chemical Science and Technology, School of Pharmacy, School of Life Sciences, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Research & Development Center for Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; Southwest United Graduate School, Kunming 650092, China
| | - Xiaoli Li
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, School of Chemical Science and Technology, School of Pharmacy, School of Life Sciences, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Research & Development Center for Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Bin Liang
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, School of Chemical Science and Technology, School of Pharmacy, School of Life Sciences, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Research & Development Center for Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ruihan Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, School of Chemical Science and Technology, School of Pharmacy, School of Life Sciences, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Research & Development Center for Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
| | - Rong Liu
- Translational Cancer Research Center, Peking University First Hospital, Beijing 100034, China; Southwest United Graduate School, Kunming 650092, China.
| | - Weilie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, School of Chemical Science and Technology, School of Pharmacy, School of Life Sciences, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Research & Development Center for Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; Southwest United Graduate School, Kunming 650092, China.
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21
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Pollard CA, Saito ER, Burns JM, Hill JT, Jenkins TG. Considering Biomarkers of Neurodegeneration in Alzheimer's Disease: The Potential of Circulating Cell-Free DNA in Precision Neurology. J Pers Med 2024; 14:1104. [PMID: 39590596 PMCID: PMC11595805 DOI: 10.3390/jpm14111104] [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: 10/10/2024] [Revised: 10/30/2024] [Accepted: 11/06/2024] [Indexed: 11/28/2024] Open
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD), are a growing public health crisis, exacerbated by an aging global population and the lack of effective early disease-modifying therapies. Early detection of neurodegenerative disorders is critical to delaying symptom onset and mitigating disease progression, but current diagnostic tools often rely on detecting pathology once clinical symptoms have emerged and significant neuronal damage has already occurred. While disease-specific biomarkers, such as amyloid-beta and tau in AD, offer precise insights, they are too limited in scope for broader neurodegeneration screening for these conditions. Conversely, general biomarkers like neurofilament light chain (NfL) provide valuable staging information but lack targeted insights. Circulating cell-free DNA (cfDNA), released during cell death, is emerging as a promising biomarker for early detection. Derived from dying cells, cfDNA can capture both general neurodegenerative signals and disease-specific insights, offering multi-layered genomic and epigenomic information. Though its clinical potential remains under investigation, advances in cfDNA detection sensitivity, standardized protocols, and reference ranges could establish cfDNA as a valuable tool for early screening. cfDNA methylation signatures, in particular, show great promise for identifying tissue-of-origin and disease-specific changes, offering a minimally invasive biomarker that could transform precision neurology. However, further research is required to address technological challenges and validate cfDNA's utility in clinical settings. Here, we review recent work assessing cfDNA as a potential early biomarker in AD. With continued advances, cfDNA could play a pivotal role in shifting care from reactive to proactive, improving diagnostic timelines and patient outcomes.
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Affiliation(s)
- Chad A. Pollard
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
- Resonant, Heber, UT 84032, USA
| | | | - Jeffrey M. Burns
- University of Kansas Alzheimer’s Disease Research Center, Fairway, KS 66205, USA
| | - Jonathon T. Hill
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Timothy G. Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
- Resonant, Heber, UT 84032, USA
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22
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Gezer U, Özgür E, Yörüker EE, Polatoglou E, Holdenrieder S, Bronkhorst A. LINE-1 cfDNA Methylation as an Emerging Biomarker in Solid Cancers. Cancers (Basel) 2024; 16:3725. [PMID: 39594682 PMCID: PMC11592170 DOI: 10.3390/cancers16223725] [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: 10/08/2024] [Revised: 11/01/2024] [Accepted: 11/03/2024] [Indexed: 11/28/2024] Open
Abstract
Epigenetic dysregulation is a hallmark of many human malignancies, with DNA methylation being a primary mechanism influencing gene expression and maintaining genomic stability. Genome-wide hypomethylation, characteristic of many cancers, is partly attributed to the demethylation of repetitive elements, including LINE-1, a prevalent non-LTR retrotransposon. The methylation status of LINE-1 is closely associated with overall genomic methylation levels in tumors. cfDNA comprises extracellular DNA fragments found in bodily fluids such as plasma, serum, and urine, offering a dynamic snapshot of the genetic and epigenetic landscape of tumors. This real-time sampling provides a minimally invasive avenue for cancer diagnostics, prognostics, and monitoring. The methylation status of LINE-1 in cfDNA has emerged as a promising biomarker, with several studies highlighting its potential in diagnosing and predicting outcomes in cancer patients. Recent research also suggests that cfDNA-based LINE-1 methylation analysis could serve as a valuable tool in evaluating the efficacy of cancer therapies, including immunotherapy. The growing clinical significance of cfDNA calls for a closer examination of its components, particularly repetitive elements like LINE-1. Despite their importance, the role of LINE-1 elements in cfDNA has not been thoroughly gauged. We aim to address this gap by reviewing the current literature on LINE-1 cfDNA assays, focusing on their potential applications in diagnostics and disease monitoring.
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Affiliation(s)
- Ugur Gezer
- Department of Basic Oncology, Oncology Institute, Istanbul University, 34093 Istanbul, Türkiye; (U.G.); (E.Ö.); (E.E.Y.)
| | - Emre Özgür
- Department of Basic Oncology, Oncology Institute, Istanbul University, 34093 Istanbul, Türkiye; (U.G.); (E.Ö.); (E.E.Y.)
| | - Ebru E. Yörüker
- Department of Basic Oncology, Oncology Institute, Istanbul University, 34093 Istanbul, Türkiye; (U.G.); (E.Ö.); (E.E.Y.)
| | - Eleni Polatoglou
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, 80636 Munich, Germany (S.H.)
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, 80636 Munich, Germany (S.H.)
| | - Abel Bronkhorst
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, 80636 Munich, Germany (S.H.)
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23
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Toma MM, Skorski T. Star wars against leukemia: attacking the clones. Leukemia 2024; 38:2293-2302. [PMID: 39223295 PMCID: PMC11519008 DOI: 10.1038/s41375-024-02369-6] [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: 07/02/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
Leukemia, although most likely starts as a monoclonal genetic/epigenetic anomaly, is a polyclonal disease at manifestation. This polyclonal nature results from ongoing evolutionary changes in the genome/epigenome of leukemia cells to promote their survival and proliferation advantages. We discuss here how genetic and/or epigenetic aberrations alter intracellular microenvironment in individual leukemia clones and how extracellular microenvironment selects the best fitted clones. This dynamic polyclonal composition of leukemia makes designing an effective therapy a challenging task especially because individual leukemia clones often display substantial differences in response to treatment. Here, we discuss novel therapeutic approach employing single cell multiomics to identify and eradicate all individual clones in a patient.
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Affiliation(s)
- Monika M Toma
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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24
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Mahanta CS, Hansdah S, Khuntia K, Jena BB, Swain BR, Acharya S, Dash BP, Debata PR, Satapathy R. Novel carboranyl-BODIPY conjugates: design, synthesis and anti-cancer activity. RSC Adv 2024; 14:34643-34660. [PMID: 39479484 PMCID: PMC11521004 DOI: 10.1039/d4ra07241c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 10/23/2024] [Indexed: 11/02/2024] Open
Abstract
A series of four carboranyl-BODIPY conjugates (o-CB-10, m-CB-15, Me-o-CB-28, and Me-o-CB-35) and one phenylene-BODIPY conjugate (PB-20) were synthesized. The carboranyl-BODIPY conjugates incorporate boron clusters, specifically ortho- and meta-carboranes, covalently linked to BODIPY fluorophores while the phenylene-BODIPY conjugate features a phenylene ring covalently linked to BODIPY fluorophore. The newly synthesized conjugates were characterized by 1H NMR, 13C NMR, 11B NMR, 19F NMR, FT-IR, and high-resolution mass spectral analysis. In vitro cytotoxicity of the synthesized conjugates has been evaluated against the HeLa cervical cancer cell line. The study reveals that o-CB-10 shows a maximum cell death potential at lower concentrations (12.03 μM) and inhibited cell proliferation and migration in cancer (HeLa) cells. Additionally, flow cytometry study reveals that o-CB-10 and Me-o-CB-28 arrest the cell cycle at the S phase. The results indicate that the carboranyl-BODIPY conjugates have the potential to be effective anticancer agents.
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Affiliation(s)
| | - Sunitee Hansdah
- Department of Zoology Maharaja Sriram Chandra Bhanja Deo University Sri Ram Chandra Vihar, Takatpur, Mayurbhanj Baripada 757003 Odisha India
| | - Kabita Khuntia
- Department of Zoology Maharaja Sriram Chandra Bhanja Deo University Sri Ram Chandra Vihar, Takatpur, Mayurbhanj Baripada 757003 Odisha India
| | - Bibhuti Bhusan Jena
- Department of Chemistry Ravenshaw University College Square Cuttack 753003 Odisha India
| | - Biswa Ranjan Swain
- Department of Chemistry Ravenshaw University College Square Cuttack 753003 Odisha India
| | - Subhadeep Acharya
- Department of Chemistry Ravenshaw University College Square Cuttack 753003 Odisha India
| | | | - Priya Ranjan Debata
- Department of Zoology Maharaja Sriram Chandra Bhanja Deo University Sri Ram Chandra Vihar, Takatpur, Mayurbhanj Baripada 757003 Odisha India
| | - Rashmirekha Satapathy
- Department of Chemistry Ravenshaw University College Square Cuttack 753003 Odisha India
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Overs A, Peixoto P, Hervouet E, Molimard C, Monnien F, Durand J, Guittaut M, Vienot A, Viot J, Herfs M, Borg C, Feugeas JP, Selmani Z. COL25A1 and METAP1D DNA methylation are promising liquid biopsy epigenetic biomarkers of colorectal cancer using digital PCR. Clin Epigenetics 2024; 16:146. [PMID: 39425144 PMCID: PMC11490026 DOI: 10.1186/s13148-024-01748-1] [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: 07/08/2024] [Accepted: 09/16/2024] [Indexed: 10/21/2024] Open
Abstract
BACKGROUND Colorectal cancer is a public health issue and was the third leading cause of cancer-related death worldwide in 2022. Early diagnosis can improve prognosis, making screening a central part of colorectal cancer management. Blood-based screening, diagnosis and follow-up of colorectal cancer patients are possible with the study of cell-free circulating tumor DNA. This study aimed to identify novel DNA methylation biomarkers of colorectal cancer that can be used for the follow-up of patients with colorectal cancer. METHODS A DNA methylation profile was established in the Gene Expression Omnibus (GEO) database (n = 507) using bioinformatics analysis and subsequently confirmed using The Cancer Genome Atlas (TCGA) database (n = 348). The in silico profile was then validated on local tissue and cell-free DNA samples using methylation-specific digital PCR in colorectal cancer patients (n = 35) and healthy donors (n = 35). RESULTS The DNA methylation of COL25A1 and METAP1D was predicted to be a colorectal cancer biomarker by bioinformatics analysis (ROC AUC = 1, 95% CI [0.999-1]). The two biomarkers were confirmed with tissue samples, and the combination of COL25A1 and METAP1D yielded 49% sensitivity and 100% specificity for cell-free DNA. CONCLUSION Bioinformatics analysis of public databases revealed COL25A1 and METAP1D DNA methylation as clinically applicable liquid biopsies DNA methylation biomarkers. The specificity implies an excellent positive predictive value for follow-up, and the high sensitivity and relative noninvasiveness of a blood-based test make these biomarkers compatible with colorectal cancer screening. However, the clinical impact of these biomarkers in colorectal cancer screening and follow-up needs to be established in further prospective studies.
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Affiliation(s)
- Alexis Overs
- Department of Oncobiology, University Hospital of Besançon, 3 Boulevard Alexandre Fleming, 25000, Besançon, France.
- UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France.
| | - Paul Peixoto
- UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France
| | - Eric Hervouet
- UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France
| | - Chloé Molimard
- Department of Pathology, University Hospital of Besançon, 25000, Besancon, France
| | - Franck Monnien
- Department of Pathology, University Hospital of Besançon, 25000, Besancon, France
| | - Jules Durand
- UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France
| | - Michael Guittaut
- UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France
| | - Angélique Vienot
- Department of Oncology, University Hospital of Besançon, 25000, Besancon, France
| | - Julien Viot
- Department of Oncology, University Hospital of Besançon, 25000, Besancon, France
| | - Michael Herfs
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, Liège, Belgium
| | - Christophe Borg
- UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France
- Department of Oncology, University Hospital of Besançon, 25000, Besancon, France
| | - Jean-Paul Feugeas
- Department of Oncobiology, University Hospital of Besançon, 3 Boulevard Alexandre Fleming, 25000, Besançon, France
- UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France
| | - Zohair Selmani
- Department of Oncobiology, University Hospital of Besançon, 3 Boulevard Alexandre Fleming, 25000, Besançon, France
- UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France
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26
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Li Y, Li W, Deng J, Yin M. PER3 promoter hypermethylation correlates to the progression of pan-cancer. Clin Epigenetics 2024; 16:140. [PMID: 39402618 PMCID: PMC11476066 DOI: 10.1186/s13148-024-01760-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 10/07/2024] [Indexed: 10/19/2024] Open
Abstract
BACKGROUND Malignant cells exhibit reduced period circadian regulator 3 (PER3) expression. However, the underlying mechanisms of variations in PER3 expression in cancers and the specific function of PER3 in tumor progression remain poorly understood. RESULTS We explored multiple public databases, conducted bioinformatics analyses, and performed in vitro and in vivo experiments for validation. We found PER3 expression was decreased in most types of cancers, and PER3 downregulation was associated with a poor prognosis in 8 types of cancer. PER3 promoter methylation levels were increased in 11 types of cancer. Promoter hypermethylation (CpG islands [CGIs] cg12258811 and cg14204433) correlated with decreased PER3 expression in six cancers (breast invasive carcinoma, colon adenocarcinoma, head and neck squamous cell carcinoma, kidney renal papillary cell carcinoma [KIRP], lung adenocarcinoma [LUAD], and uterine corpus endometrial carcinoma). CGI cg12258811 hypermethylation was associated with reduced survival time and advanced cancer stages. Moreover, the bisulfite pyrosequencing assay confirmed CGI cg12258811 hypermethylation and its negative correlation with PER3 expression. In vitro and in vivo experiments demonstrated that PER3 inhibited KIRP and LUAD progression. Decitabine enhanced PER3 expression and inhibited KIRP cell functions by reducing promoter (cg12258811) methylation level. CONCLUSIONS Our findings advanced the mechanistic understanding of variations in PER3 expression in cancers and confirmed the tumor-associated function of PER3 hypermethylation and downregulation.
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Affiliation(s)
- Yaoxu Li
- Department of Stomatology, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Wanzhou District, Chongqing, 404100, China
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Wanzhou District, Chongqing, 404100, China
| | - Wenjuan Li
- Department of Emergency and Critical Care Medicine, The First Afliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jinhai Deng
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Wanzhou District, Chongqing, 404100, China
| | - Mingzhu Yin
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Wanzhou District, Chongqing, 404100, China.
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Wanzhou District, Chongqing, 404100, China.
- Three Gorges Hospital & Academy for Advanced Interdisciplinary Technology, CQU-Ferenc Krausz Nobel Laureate Scientific Workstation, Chongqing University, Chongqing, China.
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Yadav P, Jain R, Yadav RK. Emerging roles of cancer-associated histone mutations in genomic instabilities. Front Cell Dev Biol 2024; 12:1455572. [PMID: 39439908 PMCID: PMC11494296 DOI: 10.3389/fcell.2024.1455572] [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: 06/27/2024] [Accepted: 09/10/2024] [Indexed: 10/25/2024] Open
Abstract
Epigenetic mechanisms often fuel the quick evolution of cancer cells from normal cells. Mutations or aberrant expressions in the enzymes of DNA methylation, histone post-translational modifications, and chromatin remodellers have been extensively investigated in cancer pathogenesis; however, cancer-associated histone mutants have gained momentum in recent decades. Next-generation sequencing of cancer cells has identified somatic recurrent mutations in all the histones (H3, H4, H2A, H2B, and H1) with different frequencies for various tumour types. Importantly, the well-characterised H3K27M, H3G34R/V, and H3K36M mutations are termed as oncohistone mutants because of their wide roles, from defects in cellular differentiation, transcriptional dysregulation, and perturbed epigenomic profiles to genomic instabilities. Mechanistically, these histone mutants impart their effects on histone modifications and/or on irregular distributions of chromatin complexes. Recent studies have identified the crucial roles of the H3K27M and H3G34R/V mutants in the DNA damage response pathway, but their impacts on chemotherapy and tumour progression remain elusive. In this review, we summarise the recent developments in their functions toward genomic instabilities and tumour progression. Finally, we discuss how such a mechanistic understanding can be harnessed toward the potential treatment of tumours harbouring the H3K27M, H3G34R/V, and H3K36M mutations.
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Esteller M, Dawson MA, Kadoch C, Rassool FV, Jones PA, Baylin SB. The Epigenetic Hallmarks of Cancer. Cancer Discov 2024; 14:1783-1809. [PMID: 39363741 DOI: 10.1158/2159-8290.cd-24-0296] [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: 02/29/2024] [Revised: 05/08/2024] [Accepted: 06/24/2024] [Indexed: 10/05/2024]
Abstract
Cancer is a complex disease in which several molecular and cellular pathways converge to foster the tumoral phenotype. Notably, in the latest iteration of the cancer hallmarks, "nonmutational epigenetic reprogramming" was newly added. However, epigenetics, much like genetics, is a broad scientific area that deserves further attention due to its multiple roles in cancer initiation, progression, and adaptive nature. Herein, we present a detailed examination of the epigenetic hallmarks affected in human cancer, elucidating the pathways and genes involved, and dissecting the disrupted landscapes for DNA methylation, histone modifications, and chromatin architecture that define the disease. Significance: Cancer is a disease characterized by constant evolution, spanning from its initial premalignant stages to the advanced invasive and disseminated stages. It is a pathology that is able to adapt and survive amidst hostile cellular microenvironments and diverse treatments implemented by medical professionals. The more fixed setup of the genetic structure cannot fully provide transformed cells with the tools to survive but the rapid and plastic nature of epigenetic changes is ready for the task. This review summarizes the epigenetic hallmarks that define the ecological success of cancer cells in our bodies.
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Affiliation(s)
- Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Cigall Kadoch
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Feyruz V Rassool
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Peter A Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Stephen B Baylin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
- Department of Oncology, The Johns Hopkins School of Medicine, The Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
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29
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Di Marco T, Mazzoni M, Greco A, Cassinelli G. Non-oncogene dependencies: Novel opportunities for cancer therapy. Biochem Pharmacol 2024; 228:116254. [PMID: 38704100 DOI: 10.1016/j.bcp.2024.116254] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Targeting oncogene addictions have changed the history of subsets of malignancies and continues to represent an excellent therapeutic opportunity. Nonetheless, alternative strategies are required to treat malignancies driven by undruggable oncogenes or loss of tumor suppressor genes and to overcome drug resistance also occurring in cancers addicted to actionable drivers. The discovery of non-oncogene addiction (NOA) uncovered novel therapeutically exploitable "Achilles' heels". NOA refers to genes/pathways not oncogenic per sé but essential for the tumor cell growth/survival while dispensable for normal cells. The clinical success of several classes of conventional and molecular targeted agents can be ascribed to their impact on both tumor cell-associated intrinsic as well as microenvironment-related extrinsic NOA. The integration of genetic, computational and pharmacological high-throughput approaches led to the identification of an expanded repertoire of synthetic lethality interactions implicating NOA targets. Only a few of them have been translated into the clinics as most NOA vulnerabilities are not easily druggable or appealing targets. Nonetheless, their identification has provided in-depth knowledge of tumor pathobiology and suggested novel therapeutic opportunities. Here, we summarize conceptual framework of intrinsic and extrinsic NOA providing exploitable vulnerabilities. Conventional and emerging methodological approaches used to disclose NOA dependencies are reported together with their limits. We illustrate NOA paradigmatic and peculiar examples and outline the functional/mechanistic aspects, potential druggability and translational interest. Finally, we comment on difficulties in exploiting the NOA-generated knowledge to develop novel therapeutic approaches to be translated into the clinics and to fully harness the potential of clinically available drugs.
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Affiliation(s)
- Tiziana Di Marco
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Mara Mazzoni
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Angela Greco
- Integrated Biology of Rare Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
| | - Giuliana Cassinelli
- Molecular Pharmacology Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy.
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John E, Lesluyes T, Baker TM, Tarabichi M, Gillenwater A, Wang JR, Van Loo P, Zhao X. Reconstructing oral cavity tumor evolution through brush biopsy. Sci Rep 2024; 14:22591. [PMID: 39343812 PMCID: PMC11439926 DOI: 10.1038/s41598-024-72946-3] [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: 02/11/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024] Open
Abstract
Oral potentially malignant disorders (OPMDs) with genomic alterations have a heightened risk of evolving into oral squamous cell carcinoma (OSCC). Currently, genomic data are typically obtained through invasive tissue biopsy. However, brush biopsy is a non-invasive method that has been utilized for identifying dysplastic cells in OPMD but its effectiveness in reflecting the genomic landscape of OPMDs remains uncertain. This pilot study investigates the potential of brush biopsy samples in accurately reconstructing the genomic profile and tumor evolution in a patient with both OPMD and OSCC. We analyzed single nucleotide variants (SNVs), copy number aberrations (CNAs), and subclonal architectures in paired tissue and brush biopsy samples. The results showed that brush biopsy effectively captured 90% of SNVs and had similar CNA profiles as those seen in its paired tissue biopsies in all lesions. It was specific, as normal buccal mucosa did not share these genomic alterations. Interestingly, brush biopsy revealed shared SNVs and CNAs between the distinct OPMD and OSCC lesions from the same patient, indicating a common ancestral origin. Subclonal reconstruction confirmed this shared ancestry, followed by divergent evolution of the lesions. These findings highlight the potential of brush biopsies in accurately representing the genomic profile of OPL and OSCC, proving insight into reconstructing tumor evolution.
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Affiliation(s)
- Evit John
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, FCT 10.6008, 77030, TX, Houston, USA
| | | | - Toby M Baker
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, FCT 10.6008, 77030, TX, Houston, USA
- The Francis Crick Institute, London, UK
| | - Maxime Tarabichi
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Ann Gillenwater
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, TX, Houston, USA
| | - Jennifer R Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, TX, Houston, USA
| | - Peter Van Loo
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, FCT 10.6008, 77030, TX, Houston, USA
- The Francis Crick Institute, London, UK
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, TX, Houston, USA
| | - Xiao Zhao
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1400 Pressler St, FCT 10.6008, 77030, TX, Houston, USA.
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, TX, Houston, USA.
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31
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Low JT, Chan MWY, Shen CH, Wei KL. Immunological hide-and-seek: epigenetically reprogrammed cancer cells and the dynamics of CD8 + T cells. Mol Biol Rep 2024; 51:959. [PMID: 39230620 DOI: 10.1007/s11033-024-09882-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: 06/13/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024]
Abstract
Cancer remains a global health burden, shaped by both genetic mutations and epigenetic dysregulation. Epigenetic alteration plays a pivotal role in tumorigenesis, immune response modulation, and the emergence of treatment resistance. This review emphasizes the intricate interplay between epigenetically reprogrammed cancer cells and the tumor microenvironment (TME), a relationship central to the immunoediting concept, which encompasses elimination, equilibrium, and escape phases. This review highlights the significance of CD8+ T cells as potent anticancer agents and discusses the mechanisms by which tumor cells evade immune surveillance and evolve resistance to immunotherapy. Such evasion entails the regulation of inhibitory molecules, antigen presentation machinery, and cytokine milieu. Furthermore, this review explores the complex dynamics culminating in CD8+ T cell dysfunction within the TME. In summary, this work offers insights into the indispensable role of epigenetic mechanisms in bolstering cancer cell survival amidst immunological challenges within the TME.
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Affiliation(s)
- Jie-Ting Low
- Department of Biomedical Sciences, National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan
- Epigenomics and Human Diseases Research Center, National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan.
- Epigenomics and Human Diseases Research Center, National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan.
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan.
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi, Taiwan.
| | - Kuo-Liang Wei
- Division of Gastroenterology, Chang Gung Memorial Hospital, Chiayi, Taiwan.
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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32
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Peedicayil J. Editorial: Epigenetics and neurodevelopment in psychiatry. Front Genet 2024; 15:1473521. [PMID: 39224862 PMCID: PMC11366571 DOI: 10.3389/fgene.2024.1473521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, India
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33
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Kulikova DA, Bespalova AV, Zelentsova ES, Evgen'ev MB, Funikov SY. Epigenetic Phenomenon of Paramutation in Plants and Animals. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1429-1450. [PMID: 39245454 DOI: 10.1134/s0006297924080054] [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: 03/28/2024] [Revised: 06/17/2024] [Accepted: 06/27/2024] [Indexed: 09/10/2024]
Abstract
The phenomenon of paramutation describes the interaction between two alleles, in which one allele initiates inherited epigenetic conversion of another allele without affecting the DNA sequence. Epigenetic transformations due to paramutation are accompanied by the change in DNA and/or histone methylation patterns, affecting gene expression. Studies of paramutation in plants and animals have identified small non-coding RNAs as the main effector molecules required for the initiation of epigenetic changes in gene loci. Due to the fact that small non-coding RNAs can be transmitted across generations, the paramutation effect can be inherited and maintained in a population. In this review, we will systematically analyze examples of paramutation in different living systems described so far, highlighting common and different molecular and genetic aspects of paramutation between organisms, and considering the role of this phenomenon in evolution.
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Affiliation(s)
- Dina A Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alina V Bespalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Elena S Zelentsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mikhail B Evgen'ev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Sergei Yu Funikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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34
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Ivancevic A, Simpson DM, Joyner OM, Bagby SM, Nguyen LL, Bitler BG, Pitts TM, Chuong EB. Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer. SCIENCE ADVANCES 2024; 10:eado1218. [PMID: 39018396 PMCID: PMC466953 DOI: 10.1126/sciadv.ado1218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
Abstract
Cancer cells exhibit rewired transcriptional regulatory networks that promote tumor growth and survival. However, the mechanisms underlying the formation of these pathological networks remain poorly understood. Through a pan-cancer epigenomic analysis, we found that primate-specific endogenous retroviruses (ERVs) are a rich source of enhancers displaying cancer-specific activity. In colorectal cancer and other epithelial tumors, oncogenic MAPK/AP1 signaling drives the activation of enhancers derived from the primate-specific ERV family LTR10. Functional studies in colorectal cancer cells revealed that LTR10 elements regulate tumor-specific expression of multiple genes associated with tumorigenesis, such as ATG12 and XRCC4. Within the human population, individual LTR10 elements exhibit germline and somatic structural variation resulting from a highly mutable internal tandem repeat region, which affects AP1 binding activity. Our findings reveal that ERV-derived enhancers contribute to transcriptional dysregulation in response to oncogenic signaling and shape the evolution of cancer-specific regulatory networks.
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Affiliation(s)
- Atma Ivancevic
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - David M. Simpson
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Olivia M. Joyner
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Stacey M. Bagby
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lily L. Nguyen
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ben G. Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Todd M. Pitts
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Edward B. Chuong
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
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35
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Shu M, Huang L, Chen Y, Wang Y, Xie Z, Li S, Zhou J, Wei L, Fu T, Liu B, Chen H, Tang K, Ke Z. Identification of a DNA-methylome-based signature for prognosis prediction in driver gene-negative lung adenocarcinoma. Cancer Lett 2024; 593:216835. [PMID: 38548216 DOI: 10.1016/j.canlet.2024.216835] [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: 11/30/2023] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 06/01/2024]
Abstract
"Driver gene-negative" lung adenocarcinoma (LUAD) was of rare treatment options and a poor prognosis. Presently, for them, few biomarkers are available for stratification analysis to make appropriate treatment strategy. This study aimed to develop a DNA-methylome-based signature to realize the precise risk-stratifying. Here, an Illumina MethylationEPIC Beadchip was applied to obtain differentially methylated CpG sites (DMCs). A four-CpG-based signature, named as TLA, was successfully established, whose prognosis-predicting power was well verified in one internal (n = 78) and other external (n = 110) validation cohorts. Patients with high-risk scores had shorter overall survival (OS) in all cohorts [hazard ratio (HR): 11.79, 5.16 and 2.99, respectively]. Additionally, it can effectively divide patients into low-risk and high-risk groups, with significantly different OS in the diverse subgroups stratified by the standard clinical parameters. As an independent prognostic factor, TLA may assist in improving the nomogram's 5-year OS-predicting ability (AUC 0.756, 95% CI:0.695-0.816), superior to TNM alone (AUC 0.644, 95% CI: 0.590-0.698). Additionally, the relationship of TLA-related genes, TAC1, LHX9, and ALX1, with prognosis and tumour invasion made them serve as potential therapy targets for driver gene-negative LUAD.
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Affiliation(s)
- Man Shu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Leilei Huang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Yu Chen
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, PR China
| | - Yanxia Wang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Zhongpeng Xie
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Shuhua Li
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Jianwen Zhou
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Lihong Wei
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Tongze Fu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Bixia Liu
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Honglei Chen
- Department of Pathology, School of Basic Medical Science, Wuhan University, Wuhan, Hubei, PR China.
| | - Kejing Tang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, PR China.
| | - Zunfu Ke
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China.
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36
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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37
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Ahn SI, Choi SK, Kim MJ, Wie J, You JS. Mdivi-1: Effective but complex mitochondrial fission inhibitor. Biochem Biophys Res Commun 2024; 710:149886. [PMID: 38581953 DOI: 10.1016/j.bbrc.2024.149886] [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: 01/19/2024] [Revised: 03/19/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
Mdivi-1, Mitochondrial DIVIsion inhibitor 1, has been widely employed in research under the assumption that it exclusively influences mitochondrial fusion, but effects other than mitochondrial dynamics have been underinvestigated. This paper provides transcriptome and DNA methylome-wide analysis for Mdivi-1 treated SH-SY5Y human neuroblastoma cells using RNA sequencing (RNA-seq) and methyl capture sequencing (MC-seq) methods. Gene ontology analysis of RNA sequences revealed that p53 transcriptional gene network and DNA replication initiation-related genes were significantly up and down-regulated, respectively, showing the correlation with the arrest cell cycle in the G1 phase. MC-seq, a powerful sequencing method for capturing DNA methylation status in CpG sites, revealed that although Mdivi-1 does not induce dramatic DNA methylation change, the subtle alterations were concentrated within the CpG island. Integrative analysis of both sequencing data disclosed that the p53 transcriptional network was activated while the Parkinson's disease pathway was halted. Next, we investigated several changes in mitochondria in response to Mdivi-1. Copy number and transcription of mitochondrial DNA were suppressed. ROS levels increased, and elevated ROS triggered mitochondrial retrograde signaling rather than inducing direct DNA damage. In this study, we could better understand the molecular network of Mdivi-1 by analyzing DNA methylation and mRNA transcription in the nucleus and further investigating various changes in mitochondria, providing inspiration for studying nuclear-mitochondrial communications.
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Affiliation(s)
- Seor I Ahn
- Department of Biochemistry, School of Medicine, Konkuk University, Chungju, Republic of Korea
| | - Sung Kyung Choi
- Department of Biochemistry, School of Medicine, Konkuk University, Chungju, Republic of Korea
| | - Myoung Jun Kim
- Department of Biochemistry, School of Medicine, Konkuk University, Chungju, Republic of Korea
| | - Jinhong Wie
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jueng Soo You
- Department of Biochemistry, School of Medicine, Konkuk University, Chungju, Republic of Korea; KU Open Innovation Center, Research Institute of Medical Science, Konkuk University, Republic of Korea.
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38
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Boughanem H, Pilo J, García-Flores LA, Arranz I, Ramos-Fernandez M, Ortega-Castan M, Crujeiras AB, Sandoval J, Macias-Gonzalez M. Identification of epigenetic silencing of the SFRP2 gene in colorectal cancer as a clinical biomarker and molecular significance. J Transl Med 2024; 22:509. [PMID: 38802858 PMCID: PMC11129357 DOI: 10.1186/s12967-024-05329-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: 11/13/2023] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Several studies have suggested secreted frizzled-related protein 2 (SFRP2) gene as a potential clinical biomarker in colorectal cancer (CRC). However, its diagnostic role remains unclear. In this study, we aimed to investigate the significance of SFRP2 methylation levels in a large cohort of biological specimens (including blood, adipose and colonic tissues) from patients with CRC, thereby potentially identifying new biomarker utility. METHODS We examined the expression (by qPCR) and methylation status (by 450 K DNA array and DNA pyrosequencing) of the SFRP2 gene in healthy participants (N = 110, aged as 53.7 (14.2), 48/62 males/females) and patients with CRC (N = 85, aged 67.7 (10.5), 61/24 males/females), across different biological tissues, and assessing its potential as a biomarker for CRC. Additionally, we investigated the effect of recombinant human SFRP2 (rhSFRP2) as a therapeutic target, on cell proliferation, migration, and the expression of key genes related to carcinogenesis and the Wnt pathway. RESULTS Our findings revealed that SFRP2 promoter methylation in whole blood could predict cancer stage (I + II vs. III + IV) (AUC = 0.653), lymph node invasion (AUC = 0.692), and CRC recurrence (AUC = 0.699) in patients with CRC (all with p < 0.05). Furthermore, we observed a global hypomethylation of SFRP2 in tumors compared to the adjacent area (p < 0.001). This observation was validated in the TCGA-COAD and TCGA-READ cohorts, demonstrating overall hypermethylation (both with p < 0.001) and low expression (p < 0.001), as shown in publicly available scRNA-Seq data. Notably, neoadjuvant-treated CRC patients exhibited lower SFRP2 methylation levels compared to untreated patients (p < 0.05) and low promoter SFRP2 methylation in untreated patients was associated with poor overall survival (p < 0.05), when compared to high methylation. Finally, treatment with 5 µg of rhSFRP2 treatment in CRC cells (HCT116 cells) inhibited cell proliferation (p < 0.001) and migration (p < 0.05), and downregulated the expression of AXIN2 (p < 0.01), a gene involved in Wnt signaling pathway. CONCLUSIONS These findings establish promoter methylation of the SFRP2 gene as a prognostic candidate in CRC when assessed in blood, and as a therapeutic prognostic candidate in tumors, potentially valuable in clinical practice. SFRP2 also emerges as a therapeutic option, providing new clinical and therapeutical avenues.
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Affiliation(s)
- Hatim Boughanem
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Malaga, Spain
- Institute of Biomedical Research in Malaga (IBIMA)-Bionand Platform, University of Malaga, 29010, Malaga, Spain
- Spanish Biomedical Research Center in Physiopathology of Obesity and Nutrition (CIBERObn), Instituto de Salud Carlos III, Madrid, Spain
- Unidad de Gestión Clinica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004, Córdoba, Spain
| | - Jesús Pilo
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Malaga, Spain
- Institute of Biomedical Research in Malaga (IBIMA)-Bionand Platform, University of Malaga, 29010, Malaga, Spain
| | - Libia Alejandra García-Flores
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Malaga, Spain
- Institute of Biomedical Research in Malaga (IBIMA)-Bionand Platform, University of Malaga, 29010, Malaga, Spain
| | - Isabel Arranz
- Division of Anatomical Pathology, Hospital Universitario Virgen de la Victoria, 29010, Malaga, Spain.
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010, Malaga, Spain.
| | - María Ramos-Fernandez
- Unidad de Gestion Clinica Cirugía General y del Aparato Digestivo, Virgen de la Victoria University, 29010, Malaga, Spain
| | - María Ortega-Castan
- Unidad de Gestion Clinica Cirugía General y del Aparato Digestivo, Virgen de la Victoria University, 29010, Malaga, Spain
| | - Ana B Crujeiras
- Spanish Biomedical Research Center in Physiopathology of Obesity and Nutrition (CIBERObn), Instituto de Salud Carlos III, Madrid, Spain
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
| | - Juan Sandoval
- Epigenomics Core Facility and Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, 46026, Valencia, Spain
| | - Manuel Macias-Gonzalez
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Malaga, Spain.
- Institute of Biomedical Research in Malaga (IBIMA)-Bionand Platform, University of Malaga, 29010, Malaga, Spain.
- Spanish Biomedical Research Center in Physiopathology of Obesity and Nutrition (CIBERObn), Instituto de Salud Carlos III, Madrid, Spain.
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Gu W, Wang T, Lin Y, Wang Y, Chen Y, Dai Y, Duan H. Particulate polycyclic aromatic hydrocarbons and metals, DNA methylation and DNA methyltransferase among middle-school students in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172087. [PMID: 38561129 DOI: 10.1016/j.scitotenv.2024.172087] [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: 02/05/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
The main components of particulate matter (PM) had been reported to change DNA methylation levels. However, the mixed effect of PM and its constituents on DNA methylation and the underlying mechanism in children has not been well characterized. To investigate the association between single or mixture exposures and global DNA methylation or DNA methyltransferases (DNMTs), 273 children were recruited (110 in low-exposed area and 163 in high-exposed area) in China. Serum benzo[a]pyridin-7,8-dihydroglycol-9, 10-epoxide (BPDE)-albumin adduct and urinary metals were determined as exposure markers. The global DNA methylation (% 5mC) and the mRNA expression of DNMT1, and DNMT3A were measured. The linear regression, quantile-based g-computation (QGC), and mediation analyses were performed to investigate the effects of individual and mixture exposure. We found that significantly lower levels of % 5mC (P < 0.001) and the mRNA expression of DNMT3A in high-PM exposed group (P = 0.031). After adjustment for age, gender, BMI z-score, detecting status of urinary cotinine, serum folate, and white blood cells, urinary arsenic (As) was negatively correlated with the % 5mC. One IQR increase in urinary As (19.97 μmol/mol creatinine) was associated with a 11.06 % decrease in % 5mC (P = 0.026). Serum BPDE-albumin adduct and urinary cadmium (Cd) were negatively correlated with the levels of DNMT1 and DNMT3A (P < 0.05). Mixture exposure was negatively associated with expression of DNMT3A in QGC analysis (β: -0.19, P < 0.001). Mixture exposure was significantly associated with decreased % 5mC in the children with non-detected cotinine or normal serum folate (P < 0.05), which the most contributors were PAHs and As. The mediated effect of hypomethylation through DNMT1 or DNMT3A pathway was not observed. Our findings indicated that individual and mixture exposure PAHs and metal components had negative associations with global DNA methylation and decreased DNMT3A expression significantly in school-age individuals.
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Affiliation(s)
- Wen Gu
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Ting Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Yang Lin
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; Beijing Chaoyang District Center for Disease Prevention and Control, Beijing 100021, China
| | - Yanhua Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; State Key Laboratory of Trauma and Chemical Poisoning, China
| | - Yuanyuan Chen
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Yufei Dai
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Huawei Duan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; State Key Laboratory of Trauma and Chemical Poisoning, China.
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Wang J, Zhao E, Geng B, Zhang W, Li Z, Liu Q, Liu W, Zhang W, Hou W, Zhang N, Liu Z, You B, Wu P, Li X. Downregulation of UBB potentiates SP1/VEGFA-dependent angiogenesis in clear cell renal cell carcinoma. Oncogene 2024; 43:1386-1396. [PMID: 38467852 PMCID: PMC11065696 DOI: 10.1038/s41388-024-03003-6] [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: 10/03/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) presents a unique profile characterized by high levels of angiogenesis and robust vascularization. Understanding the underlying mechanisms driving this heterogeneity is essential for developing effective therapeutic strategies. This study revealed that ubiquitin B (UBB) is downregulated in ccRCC, which adversely affects the survival of ccRCC patients. UBB exerts regulatory control over vascular endothelial growth factor A (VEGFA) by directly interacting with specificity protein 1 (SP1), consequently exerting significant influence on angiogenic processes. Subsequently, we validated that DNA methyltransferase 3 alpha (DNMT3A) is located in the promoter of UBB to epigenetically inhibit UBB transcription. Additionally, we found that an unharmonious UBB/VEGFA ratio mediates pazopanib resistance in ccRCC. These findings underscore the critical involvement of UBB in antiangiogenic therapy and unveil a novel therapeutic strategy for ccRCC.
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Affiliation(s)
- Jinpeng Wang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Enyang Zhao
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Bo Geng
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wei Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Zhuolun Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Qing Liu
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Department of Radiation Oncology, Urology, and Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Weiyang Liu
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wenfu Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wenbin Hou
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Nan Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Zhiming Liu
- Department of Urology, Shanghai Fengxian District Central Hospital, Shanghai, 200233, China
| | - Bosen You
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Pengfei Wu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Anhui Province Key Laboratory of Brain Function and Brain Disease, Hefei, Anhui, 230001, China.
- Anhui Provincial Stereotactic Neurosurgical Institute, Hefei, Anhui, 230001, China.
- Anhui Provincial Clinical Research Center for Neurosurgical Disease, Hefei, Anhui, 230001, China.
- Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui, 233030, China.
| | - Xuedong Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
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Perurena N, Situ L, Cichowski K. Combinatorial strategies to target RAS-driven cancers. Nat Rev Cancer 2024; 24:316-337. [PMID: 38627557 DOI: 10.1038/s41568-024-00679-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 05/01/2024]
Abstract
Although RAS was formerly considered undruggable, various agents that inhibit RAS or specific RAS oncoproteins have now been developed. Indeed, the importance of directly targeting RAS has recently been illustrated by the clinical success of mutant-selective KRAS inhibitors. Nevertheless, responses to these agents are typically incomplete and restricted to a subset of patients, highlighting the need to develop more effective treatments, which will likely require a combinatorial approach. Vertical strategies that target multiple nodes within the RAS pathway to achieve deeper suppression are being investigated and have precedence in other contexts. However, alternative strategies that co-target RAS and other therapeutic vulnerabilities have been identified, which may mitigate the requirement for profound pathway suppression. Regardless, the efficacy of any given approach will likely be dictated by genetic, epigenetic and tumour-specific variables. Here we discuss various combinatorial strategies to treat KRAS-driven cancers, highlighting mechanistic concepts that may extend to tumours harbouring other RAS mutations. Although many promising combinations have been identified, clinical responses will ultimately depend on whether a therapeutic window can be achieved and our ability to prospectively select responsive patients. Therefore, we must continue to develop and understand biologically diverse strategies to maximize our likelihood of success.
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Affiliation(s)
- Naiara Perurena
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lisa Situ
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Karen Cichowski
- Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
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42
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Parreno V, Loubiere V, Schuettengruber B, Fritsch L, Rawal CC, Erokhin M, Győrffy B, Normanno D, Di Stefano M, Moreaux J, Butova NL, Chiolo I, Chetverina D, Martinez AM, Cavalli G. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 2024; 629:688-696. [PMID: 38658752 PMCID: PMC11096130 DOI: 10.1038/s41586-024-07328-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Although cancer initiation and progression are generally associated with the accumulation of somatic mutations1,2, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility3-6, suggesting that genetic mechanisms might not be the only drivers of malignant transformation7. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations has been unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signalling pathway and zfh1, the fly homologue of the ZEB1 oncogene, whose aberrant activation is required for Polycomb perturbation-induced tumorigenesis. These data show that a reversible depletion of Polycomb proteins can induce cancer in the absence of driver mutations, suggesting that tumours can emerge through epigenetic dysregulation leading to inheritance of altered cell fates.
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Affiliation(s)
- V Parreno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - V Loubiere
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - B Schuettengruber
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - L Fritsch
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - C C Rawal
- University of Southern California, Los Angeles, CA, USA
| | - M Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - B Győrffy
- Semmelweis University Department of Bioinformatics, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - D Normanno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - M Di Stefano
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - J Moreaux
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- UFR Medicine, University of Montpellier, Montpellier, France
| | - N L Butova
- University of Southern California, Los Angeles, CA, USA
| | - I Chiolo
- University of Southern California, Los Angeles, CA, USA
| | - D Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - A-M Martinez
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| | - G Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
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Liu Y, Ali H, Khan F, Pang L, Chen P. Epigenetic regulation of tumor-immune symbiosis in glioma. Trends Mol Med 2024; 30:429-442. [PMID: 38453529 PMCID: PMC11081824 DOI: 10.1016/j.molmed.2024.02.004] [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: 11/28/2023] [Revised: 02/01/2024] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
Glioma is a type of aggressive and incurable brain tumor. Patients with glioma are highly resistant to all types of therapies, including immunotherapies. Epigenetic reprogramming is a key molecular hallmark in tumors across cancer types, including glioma. Mounting evidence highlights a pivotal role of epigenetic regulation in shaping tumor biology and therapeutic responses through mechanisms involving both glioma cells and immune cells, as well as their symbiotic interactions in the tumor microenvironment (TME). In this review, we discuss the molecular mechanisms of epigenetic regulation that impacts glioma cell biology and tumor immunity in both a cell-autonomous and non-cell-autonomous manner. Moreover, we provide an overview of potential therapeutic approaches that can disrupt epigenetic-regulated tumor-immune symbiosis in the glioma TME.
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Affiliation(s)
- Yang Liu
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Heba Ali
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Fatima Khan
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lizhi Pang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Peiwen Chen
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Zhang M, Li X, Herman JG, Gao A, Wang Q, Yao Y, Shen F, He K, Guo M. Methylation of NRIP3 Is a Synthetic Lethal Marker for Combined PI3K and ATR/ATM Inhibitors in Colorectal Cancer. Clin Transl Gastroenterol 2024; 15:e00682. [PMID: 38235705 PMCID: PMC10962901 DOI: 10.14309/ctg.0000000000000682] [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: 07/21/2023] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
INTRODUCTION The aim of this study was to investigate the epigenetic regulation and underlying mechanism of NRIP3 in colorectal cancer (CRC). METHODS Eight cell lines (SW480, SW620, DKO, LOVO, HT29, HCT116, DLD1, and RKO), 187 resected margin samples from colorectal cancer tissue, 146 cases with colorectal adenomatous polyps, and 308 colorectal cancer samples were used. Methylation-specific PCR, Western blotting, RNA interference assay, and a xenograft mouse model were used. RESULTS NRIP3 exhibited methylation in 2.7% (5/187) of resected margin samples from colorectal cancer tissue, 32.2% (47/146) of colorectal adenomatous polyps, and 50.6% (156/308) of CRC samples, and the expression of NRIP3 was regulated by promoter region methylation. The methylation of NRIP3 was found to be significantly associated with late onset (at age 50 years or older), poor tumor differentiation, lymph node metastasis, and poor 5-year overall survival in CRC (all P < 0.05). In addition, NRIP3 methylation was an independent poor prognostic marker ( P < 0.05). NRIP3 inhibited cell proliferation, colony formation, invasion, and migration, while induced G1/S arrest. NRIP3 suppressed CRC growth by inhibiting PI3K-AKT signaling both in vitro and in vivo . Methylation of NRIP3 sensitized CRC cells to combined PI3K and ATR/ATM inhibitors. DISCUSSION NRIP3 was frequently methylated in both colorectal adenomatous polyps and CRC. The methylation of NRIP3 may potentially serve as an early detection, late-onset, and poor prognostic marker in CRC. NRIP3 is a potential tumor suppressor. NRIP3 methylation is a potential synthetic lethal marker for combined PI3K and ATR/ATM inhibitors.
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Affiliation(s)
- Meiying Zhang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaoyun Li
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- Department of Gastroenterology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - James G. Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Aiai Gao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qian Wang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yuanxin Yao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fangfang Shen
- Department of Gastroenterology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Kunlun He
- Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital, Beijing, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- National Key Laboratory of Kidney Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, China
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Aghajani Mir M. Vault RNAs (vtRNAs): Rediscovered non-coding RNAs with diverse physiological and pathological activities. Genes Dis 2024; 11:772-787. [PMID: 37692527 PMCID: PMC10491885 DOI: 10.1016/j.gendis.2023.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/16/2023] [Indexed: 04/05/2023] Open
Abstract
The physicochemical characteristics of RNA admit non-coding RNAs to perform a different range of biological acts through various mechanisms and are involved in regulating a diversity of fundamental processes. Notably, some reports of pathological conditions have proved abnormal expression of many non-coding RNAs guides the ailment. Vault RNAs are a class of non-coding RNAs containing stem regions or loops with well-conserved sequence patterns that play a fundamental role in the function of vault particles through RNA-ligand, RNA-RNA, or RNA-protein interactions. Taken together, vault RNAs have been proposed to be involved in a variety of functions such as cell proliferation, nucleocytoplasmic transport, intracellular detoxification processes, multidrug resistance, apoptosis, and autophagy, and serve as microRNA precursors and signaling pathways. Despite decades of investigations devoted, the biological function of the vault particle or the vault RNAs is not yet completely cleared. In this review, the current scientific assertions of the vital vault RNAs functions were discussed.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Health Research Institute, Babol University of Medical Sciences, Babol 47176-4774, Iran
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Kapoor U, Kim YC, Mittal J. Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation. J Chem Theory Comput 2024; 20:1717-1731. [PMID: 37988476 PMCID: PMC10911113 DOI: 10.1021/acs.jctc.3c00525] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/23/2023]
Abstract
Recent advances in coarse-grained (CG) computational models for DNA have enabled molecular-level insights into the behavior of DNA in complex multiscale systems. However, most existing CG DNA models are not compatible with CG protein models, limiting their applications for emerging topics such as protein-nucleic acid assemblies. Here, we present a new computationally efficient CG DNA model. We first use experimental data to establish the model's ability to predict various aspects of DNA behavior, including melting thermodynamics and relevant local structural properties such as the major and minor grooves. We then employ an all-atom hydropathy scale to define nonbonded interactions between protein and DNA sites, to make our DNA model compatible with an existing CG protein model (HPS-Urry), which is extensively used to study protein phase separation, and show that our new model reasonably reproduces the experimental binding affinity for a prototypical protein-DNA system. To further demonstrate the capabilities of this new model, we simulate a full nucleosome with and without histone tails, on a microsecond time scale, generating conformational ensembles and provide molecular insights into the role of histone tails in influencing the liquid-liquid phase separation (LLPS) of HP1α proteins. We find that histone tails interact favorably with DNA, influencing the conformational ensemble of the DNA and antagonizing the contacts between HP1α and DNA, thus affecting the ability of DNA to promote LLPS of HP1α. These findings shed light on the complex molecular framework that fine-tunes the phase transition properties of heterochromatin proteins and contributes to heterochromatin regulation and function. Overall, the CG DNA model presented here is suitable to facilitate micrometer-scale studies with sub-nm resolution in many biological and engineering applications and can be used to investigate protein-DNA complexes, such as nucleosomes, or LLPS of proteins with DNA, enabling a mechanistic understanding of how molecular information may be propagated at the genome level.
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Affiliation(s)
- Utkarsh Kapoor
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 78743, United States
| | - Young C. Kim
- Center
for Materials Physics and Technology, Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Jeetain Mittal
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 78743, United States
- Department
of Chemistry, Texas A&M University, College Station, Texas 78743, United States
- Interdisciplinary
Graduate Program in Genetics in Genomics, Texas A&M University, College
Station, Texas 78743, United States
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Jafarbeik-Iravani N, Kolahdozan S, Esmaeili R. The role of ASXL1 mutations and ASXL1 CircRNAs in cancer. Biomarkers 2024; 29:1-6. [PMID: 38193494 DOI: 10.1080/1354750x.2024.2304187] [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: 04/27/2023] [Accepted: 01/06/2024] [Indexed: 01/10/2024]
Abstract
BACKGROUND Mutations in the Additional Sex Combs Like 1 (ASXL1) gene were first reported in myelodysplastic syndromes. Recent studies have clarified the relationship between ASXL1 mutations and the development of cancers. OBJECTIVE This study aims to review the roles of ASXL1 and ASXL1 CircRNAs, such as epigenetic regulation, chromatin modification, and transcription factor function in malignancies. METHOD This study is a review of articles related to the role of ASXL1 and ASXL1 CircRNAs in malignancies, retrieved from PubMed and Scopus. RESULTS ASXL1 plays a role in malignancies and is also related to poor overall survival and cancer metastasis. ASXL1 encodes conserved and abundant Circular RNAs (circRNAs) that act as post-transcriptional regulators, regulating tumorigenesis and progression in cancer. ASXL1 circRNA was identified in the top 10% of differentially expressed circRNAs in clinically relevant tissues. Additionally, the role of ASXL1 gene circRNAs in cancer development is reviewed in this study. CONCLUSION ASXL1 and ASXL1circRNA have dual functions in combination with different proteins, being involved in both transcriptional activation and repression in a context-dependent manner. Moreover, studies indicate these genes play an important role in epithelial-mesenchymal transition (EMT) and metastasis. Ongoing research is aimed at determining this gene family's function in biological events.
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Affiliation(s)
- Narges Jafarbeik-Iravani
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Sara Kolahdozan
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Feng Q, Duan H, Zhou X, Wang Y, Zhang J, Zhang H, Chen G, Bao X. DNA Methyltransferase 3A: A Significant Target for the Discovery of Inhibitors as Potent Anticancer Drugs. Mini Rev Med Chem 2024; 24:507-520. [PMID: 37642180 DOI: 10.2174/1389557523666230825100246] [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: 04/20/2023] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
DNA methyltransferase (DNMT) is a conserved family of Cytosine methylases, which plays a crucial role in the regulation of Epigenetics. They have been considered promising therapeutic targets for cancer. Among the DNMT family, mutations in the DNMT3A subtype are particularly important in hematologic malignancies. The development of specific DNMT3A subtype inhibitors to validate the therapeutic potential of DNMT3A in certain diseases is a significant task. In this review, we summarized the small molecule inhibitors of DNMT3A discovered in recent years and their inhibitory activities, and classified them based on their inhibitory mechanisms.
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Affiliation(s)
- Qixun Feng
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Honggao Duan
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinglong Zhou
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuning Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jinda Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Haoge Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Guoliang Chen
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xuefei Bao
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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Zhou Y, Xiao Y, Liu H, Chen Q, Zhu L, Zeng L, Liu X, Pan Y, Zhang J, Fu J, Shao C. Elevation of H3K27me3 level contributes to the radioresistance of nasopharyngeal carcinoma by inhibiting OAS1 expression. Am J Physiol Cell Physiol 2024; 326:C60-C73. [PMID: 38009194 DOI: 10.1152/ajpcell.00358.2023] [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: 08/01/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
Radiotherapy has long been a main treatment option for nasopharyngeal carcinoma (NPC). However, during clinical treatment, NPC is prone to developing radioresistance, resulting in treatment failure. This study aims to examine the role of histone methylation in the induction of radioresistance. It was found that the radioresistance of NPC cells was related to the increase of the level of histone H3 lysine 27 trimethylation (H3K27me3). Treatment of cells with histone methyltransferase inhibitor GSK126 increased the radiosensitivity of NPC cells by triggering Bcl2 apoptosis regulator/BCL2-associated X, apoptosis regulator (Bcl2/BAX) signaling pathway. Bioinformatics analysis indicated that the expression of 2'-5'-oligoadenylate synthetase 1 (OAS1) was reduced in the radioresistant cells but increased in the GSK126-treated cells. Chromatin immunoprecipitation assay confirmed that the decrease of OAS1 expression in radioresistant cells was mainly due to the enrichment of H3K27me3 in its promoter region. Furthermore, downregulation of OAS1 reduced apoptosis due to the inhibition of Bcl2/BAX pathway after irradiation, while OAS1 overexpression increased radiosensitivity. Our findings revealed for the first time that the increase of H3K27me3 level was associated with the decrease of OAS1 expression, leading to the inhibition of apoptosis and ultimately contributing to the radioresistance of NPC cells. Moreover, the histone methyltransferase inhibitor GSK126 could overcome the radioresistance and thus might be a potential therapeutic strategy for NPC.NEW & NOTEWORTHY Our findings revealed for the first time that the increase of H3K27me3 level was associated with the decrease of OAS1 expression, leading to the inhibition of apoptosis and ultimately contributing to the radioresistance of NPC cells. Moreover, we demonstrated that the histone methyltransferase inhibitor GSK126 could be a promising therapeutic strategy for NPC by overcoming radioresistance, providing valuable insights into the clinical treatment of NPC.
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Affiliation(s)
- Yuchuan Zhou
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yuqi Xiao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Hongxia Liu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Qianping Chen
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Lin Zhu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Liang Zeng
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xinglong Liu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yan Pan
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Jianghong Zhang
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Jiamei Fu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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Rezkitha YAA, Panenggak NSR, Lusida MI, Rianda RV, Mahmudah I, Pradana AD, Uchida T, Miftahussurur M. Detecting colorectal cancer using genetic and epigenetic biomarkers: screening and diagnosis. J Med Life 2024; 17:4-14. [PMID: 38737656 PMCID: PMC11080499 DOI: 10.25122/jml-2023-0269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/01/2023] [Indexed: 05/14/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most frequent types of cancer, with high incidence rates and mortality globally. The extended timeframe for developing CRC allows for the potential screening and early identification of the disease. Furthermore, studies have shown that survival rates for patients with cancer are increased when diagnoses are made at earlier stages. Recent research suggests that the development of CRC, including its precancerous lesion, is influenced not only by genetic factors but also by epigenetic variables. Studies suggest epigenetics plays a significant role in cancer development, particularly CRC. While this approach is still in its early stages and faces challenges due to the variability of CRC, it shows promise as a potential method for understanding and addressing the disease. This review examined the current evidence supporting genetic and epigenetic biomarkers for screening and diagnosis. In addition, we also discussed the feasibility of translating these methodologies into clinical settings. Several markers show promising potential, including the methylation of vimentin (VIM), syndecan-2 (SDC2), and septin 9 (SEPT9). However, their application as screening and diagnostic tools, particularly for early-stage CRC, has not been fully optimized, and their effectiveness needs validation in large, multi-center patient populations. Extensive trials and further investigation are required to translate genetic and epigenetic biomarkers into practical clinical use. biomarkers, diagnostic biomarkers.
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Affiliation(s)
- Yudith Annisa Ayu Rezkitha
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Nur Syahadati Retno Panenggak
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Maria Inge Lusida
- Institute of Tropical Disease, Indonesia-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Universitas Airlangga, Surabaya, Indonesia
| | - Raissa Virgy Rianda
- Department of Child Health, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Isna Mahmudah
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Aditya Doni Pradana
- Department of Emergency Services, Kendal Islamic Hospital, Kendal, Indonesia
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
| | - Tomohisa Uchida
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, Indonesia
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