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Sadida HQ, Abdulla A, Marzooqi SA, Hashem S, Macha MA, Akil ASAS, Bhat AA. Epigenetic modifications: Key players in cancer heterogeneity and drug resistance. Transl Oncol 2024; 39:101821. [PMID: 37931371 PMCID: PMC10654239 DOI: 10.1016/j.tranon.2023.101821] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Cancer heterogeneity and drug resistance remain pivotal obstacles in effective cancer treatment and management. One major contributor to these challenges is epigenetic modifications - gene regulation that does not involve changes to the DNA sequence itself but significantly impacts gene expression. As we elucidate these phenomena, we underscore the pivotal role of epigenetic modifications in regulating gene expression, contributing to cellular diversity, and driving adaptive changes that can instigate therapeutic resistance. This review dissects essential epigenetic modifications - DNA methylation, histone modifications, and chromatin remodeling - illustrating their significant yet complex contributions to cancer biology. While these changes offer potential avenues for therapeutic intervention due to their reversible nature, the interplay of epigenetic and genetic changes in cancer cells presents unique challenges that must be addressed to harness their full potential. By critically analyzing the current research landscape, we identify knowledge gaps and propose future research directions, exploring the potential of epigenetic therapies and discussing the obstacles in translating these concepts into effective treatments. This comprehensive review aims to stimulate further research and aid in developing innovative, patient-centered cancer therapies. Understanding the role of epigenetic modifications in cancer heterogeneity and drug resistance is critical for scientific advancement and paves the way towards improving patient outcomes in the fight against this formidable disease.
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Affiliation(s)
- Hana Q Sadida
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Alanoud Abdulla
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sara Al Marzooqi
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sheema Hashem
- Laboratory of Genomic Medicine, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Jammu & Kashmir, India
| | - Ammira S Al-Shabeeb Akil
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar.
| | - Ajaz A Bhat
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar.
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Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
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Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
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Mereuta L, Asandei A, Andricioaei I, Park J, Park Y, Luchian T. Considerable slowdown of short DNA fragment translocation across a protein nanopore using pH-induced generation of enthalpic traps inside the permeation pathway. Nanoscale 2023; 15:14754-14763. [PMID: 37655668 DOI: 10.1039/d3nr03344a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
A pressing challenge in the realm of nanopore-based sensing technologies for nucleic acid characterization has been the cheap and efficient control of analyte translocation. To address this, a plethora of methods were tested, including mutagenesis, molecular motors, enzymes, or the optimization of experimental conditions. Herein, we present a paradigm exploiting the manipulation of electrostatic interactions between 22-mer single-stranded DNAs (22_ssDNA) and low pH-induced charges in the alpha-hemolysin (α-HL) nanopore, to efficiently control the passage of captured molecules. We discovered that in electrolytes buffered at pH = 5 and pH = 4.5 where the nanopore's vestibule and lumen become oppositely charged as compared to that at neutral pH, the electrostatic anchoring at these regions of a 22_ssDNA fragment leads to a dramatic increase of the translocation time, orders of magnitude larger compared to that at neutral pH. This pH-dependent tethering effect is reversible, side invariant, and sensitive to the ionic strength and ssDNA contour length. In the long run, our discovery has the potential to provide a simple read-out of the sequence of bases pertaining to short nucleotide sequences, thus extending the efficacy of current nanopore-based sequencers.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania.
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Ioan Andricioaei
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, CA 92617, USA
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, 61452, Republic of Korea.
| | - Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania.
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Abstract
Epigenetics has transformed our understanding of the molecular basis of complex diseases, including cardiovascular and metabolic disorders. This review offers a comprehensive overview of the current state of knowledge on epigenetic processes implicated in cardiovascular and metabolic diseases, highlighting the potential of DNA methylation as a precision medicine biomarker and examining the impact of social determinants of health, gut bacterial epigenomics, noncoding RNA, and epitranscriptomics on disease development and progression. We discuss challenges and barriers to advancing cardiometabolic epigenetics research, along with the opportunities for novel preventive strategies, targeted therapies, and personalized medicine approaches that may arise from a better understanding of epigenetic processes. Emerging technologies, such as single-cell sequencing and epigenetic editing, hold the potential to further enhance our ability to dissect the complex interplay between genetic, environmental, and lifestyle factors. To translate research findings into clinical practice, interdisciplinary collaborations, technical and ethical considerations, and accessibility of resources and knowledge are crucial. Ultimately, the field of epigenetics has the potential to revolutionize the way we approach cardiovascular and metabolic diseases, paving the way for precision medicine and personalized health care, and improving the lives of millions of individuals worldwide affected by these conditions.
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Affiliation(s)
- Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, New York (A.A.B.)
| | - José Ordovás
- Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, at Tufts University, Boston, MA (J.O.)
- IMDEA Food Institute, CEI UAM + CSIC, Madrid, Spain (J.O.)
- Consortium CIBERObn, Instituto de Salud Carlos III (ISCIII), Madrid, Spain (J.O.)
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Nicolì V, Coppedè F. Epigenetics of Thymic Epithelial Tumors. Cancers (Basel) 2023; 15. [PMID: 36672310 DOI: 10.3390/cancers15020360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/08/2023] Open
Abstract
Thymic epithelial tumors (TETs) arise from the epithelial cells of the thymus and consist in the 1% of all adult malignancies, despite the fact that they are the most common lesions of the anterior mediastinum. TETs can be divided mainly into thymomas, thymic carcinomas, and the rarest ad aggressive neuroendocrine forms. Despite the surgical resection is quite resolving, the diagnosis of TETs is complicated by the absence of symptoms and the clinical presentation aggravated by several paraneoplastic disorders, including myasthenia gravis. Thus, the heterogeneity of TETs prompts the search for molecular biomarkers that could be helpful for tumor characterization and clinical outcomes prediction. With these aims, several researchers investigated the epigenetic profiles of TETs. In this manuscript, we narratively review the works investigating the deregulation of epigenetic mechanisms in TETs, highlighting the need for further studies combining genetic, epigenetic, and expression data to better characterize the different molecular subtypes and identify, for each of them, the most relevant epigenetic biomarkers of clinical utility.
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Li S. Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns. Cancer Treat Res 2023; 190:375-393. [PMID: 38113008 DOI: 10.1007/978-3-031-45654-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Tumor cells evolve through space and time, generating genetically and phenotypically diverse cancer cell populations that are continually subjected to the selection pressures of their microenvironment and cancer treatment.
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Affiliation(s)
- Sheng Li
- The Jackson Laboratory for Genomic Medicine and Cancer Center, Farmington, USA.
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Gisina A, Kholodenko I, Kim Y, Abakumov M, Lupatov A, Yarygin K. Glioma Stem Cells: Novel Data Obtained by Single-Cell Sequencing. Int J Mol Sci 2022; 23. [PMID: 36430704 DOI: 10.3390/ijms232214224] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/04/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Glioma is the most common type of primary CNS tumor, composed of cells that resemble normal glial cells. Recent genetic studies have provided insight into the inter-tumoral heterogeneity of gliomas, resulting in the updated 2021 WHO classification of gliomas. Thorough understanding of inter-tumoral heterogeneity has already improved the prognosis and treatment outcomes of some types of gliomas. Currently, the challenge for researchers is to study the intratumoral cell heterogeneity of newly defined glioma subtypes. Cancer stem cells (CSCs) present in gliomas and many other tumors are an example of intratumoral heterogeneity of great importance. In this review, we discuss the modern concept of glioma stem cells and recent single-cell sequencing-driven progress in the research of intratumoral glioma cell heterogeneity. The particular emphasis was placed on the recently revealed variations of the cell composition of the subtypes of the adult-type diffuse gliomas, including astrocytoma, oligodendroglioma and glioblastoma. The novel data explain the inconsistencies in earlier glioma stem cell research and also provide insight into the development of more effective targeted therapy and the cell-based immunotherapy of gliomas. Separate sections are devoted to the description of single-cell sequencing approach and its role in the development of cell-based immunotherapies for glioma.
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