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Yang Q, Madueke-Laveaux OS, Cun H, Wlodarczyk M, Garcia N, Carvalho KC, Al-Hendy A. Comprehensive Review of Uterine Leiomyosarcoma: Pathogenesis, Diagnosis, Prognosis, and Targeted Therapy. Cells 2024; 13:1106. [PMID: 38994959 PMCID: PMC11240800 DOI: 10.3390/cells13131106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
Uterine leiomyosarcoma (uLMS) is the most common subtype of uterine sarcomas. They have a poor prognosis with high rates of recurrence and metastasis. The five-year survival for uLMS patients is between 25 and 76%, with survival rates approaching 10-15% for patients with metastatic disease at the initial diagnosis. Accumulating evidence suggests that several biological pathways are involved in uLMS pathogenesis. Notably, drugs that block abnormal functions of these pathways remarkably improve survival in uLMS patients. However, due to chemotherapy resistance, there remains a need for novel drugs that can target these pathways effectively. In this review article, we provide an overview of the recent progress in ascertaining the biological functions and regulatory mechanisms in uLMS from the perspective of aberrant biological pathways, including DNA repair, immune checkpoint blockade, protein kinase and intracellular signaling pathways, and the hedgehog pathway. We review the emerging role of epigenetics and epitranscriptome in the pathogenesis of uLMS. In addition, we discuss serum markers, artificial intelligence (AI) combined with machine learning, shear wave elastography, current management and medical treatment options, and ongoing clinical trials for patients with uLMS. Comprehensive, integrated, and deeper insights into the pathobiology and underlying molecular mechanisms of uLMS will help develop novel strategies to treat patients with this aggressive tumor.
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Affiliation(s)
- Qiwei Yang
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
| | | | - Han Cun
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
| | - Marta Wlodarczyk
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland
| | - Natalia Garcia
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Katia Candido Carvalho
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento deObstetricia e Ginecologia, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 05403-010, Brazil
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
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Pandey M, Bhattacharyya J. Gut microbiota and epigenetics in colorectal cancer: implications for carcinogenesis and therapeutic intervention. Epigenomics 2024; 16:403-418. [PMID: 38410915 DOI: 10.2217/epi-2023-0382] [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] [Indexed: 02/28/2024] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. The occurrence of CRC is associated with various genetic and epigenetic mutations in intestinal epithelial cells that transform them into adenocarcinomas. There is increasing evidence indicating the gut microbiota plays a crucial role in the regulation of host physiological processes. Alterations in gut microbiota composition are responsible for initiating carcinogenesis through diverse epigenetic modifications, including histone modifications, ncRNAs and DNA methylation. This work was designed to comprehensively review recent findings to provide insight into the associations between the gut microbiota and CRC at an epigenetic level. These scientific insights can be used in the future to develop effective strategies for early detection and treatment of CRC.
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Affiliation(s)
- Monu Pandey
- Centre for Biomedical Engineering, Indian Institute of Technology, Delhi, 110016, India
- Department of Biomedical Engineering, All India Institute of Medical Science, Delhi, 110608, India
| | - Jayanta Bhattacharyya
- Centre for Biomedical Engineering, Indian Institute of Technology, Delhi, 110016, India
- Department of Biomedical Engineering, All India Institute of Medical Science, Delhi, 110608, India
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3
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Mlodawska OW, Saini P, Parker JB, Wei JJ, Bulun SE, Simon MA, Chakravarti D. Epigenomic and enhancer dysregulation in uterine leiomyomas. Hum Reprod Update 2022; 28:518-547. [PMID: 35199155 PMCID: PMC9247409 DOI: 10.1093/humupd/dmac008] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/16/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Uterine leiomyomas, also known as uterine fibroids or myomas, are the most common benign gynecological tumors and are found in women of reproductive and postmenopausal age. There is an exceptionally high prevalence of this tumor in women by the age of 50 years. Black women are particularly affected, with an increased incidence, earlier age of onset, larger and faster growing fibroids and greater severity of symptoms as compared to White women. Although advances in identifying genetic and environmental factors to delineate these fibroids have already been made, only recently has the role of epigenomics in the pathogenesis of this disease been considered. OBJECTIVE AND RATIONALE Over recent years, studies have identified multiple epigenomic aberrations that may contribute to leiomyoma development and growth. This review will focus on the most recent discoveries in three categories of epigenomic changes found in uterine fibroids, namely aberrant DNA methylation, histone tail modifications and histone variant exchange, and their translation into altered target gene architecture and transcriptional outcome. The findings demonstrating how the altered 3D shape of the enhancer can regulate gene expression from millions of base pairs away will be discussed. Additionally, translational implications of these discoveries and potential roadblocks in leiomyoma treatment will be addressed. SEARCH METHODS A comprehensive PubMed search was performed to identify published articles containing keywords relevant to the focus of the review, such as: uterine leiomyoma, uterine fibroids, epigenetic alterations, epigenomics, stem cells, chromatin modifications, extracellular matrix [ECM] organization, DNA methylation, enhancer, histone post-translational modifications and dysregulated gene expression. Articles until September 2021 were explored and evaluated to identify relevant updates in the field. Most of the articles focused on in the discussion were published between 2015 and 2021, although some key discoveries made before 2015 were included for background information and foundational purposes. We apologize to the authors whose work was not included because of space restrictions or inadvertent omission. OUTCOMES Chemical alterations to the DNA structure and of nucleosomal histones, without changing the underlying DNA sequence, have now been implicated in the phenotypic manifestation of uterine leiomyomas. Genome-wide DNA methylation analysis has revealed subsets of either suppressed or overexpressed genes accompanied by aberrant promoter methylation. Furthermore, differential promoter access resulting from altered 3D chromatin structure and histone modifications plays a role in regulating transcription of key genes thought to be involved in leiomyoma etiology. The dysregulated genes function in tumor suppression, apoptosis, angiogenesis, ECM formation, a variety of cancer-related signaling pathways and stem cell differentiation. Aberrant DNA methylation or histone modification is also observed in altering enhancer architecture, which leads to changes in enhancer-promoter contact strength, producing novel explanations for the overexpression of high mobility group AT-hook 2 and gene dysregulation found in mediator complex subunit 12 mutant fibroids. While many molecular mechanisms and epigenomic features have been investigated, the basis for the racial disparity observed among those in the Black population remains unclear. WIDER IMPLICATIONS A comprehensive understanding of the exact pathogenesis of uterine leiomyoma is lacking and requires attention as it can provide clues for prevention and viable non-surgical treatment. These findings will widen our knowledge of the role epigenomics plays in the mechanisms related to uterine leiomyoma development and highlight novel approaches for the prevention and identification of epigenome targets for long-term non-invasive treatment options of this significantly common disease.
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Affiliation(s)
| | | | - J Brandon Parker
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jian-Jun Wei
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA
| | - Serdar E Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Melissa A Simon
- Department of Obstetrics and Gynecology, Center for Health Equity Transformation, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Debabrata Chakravarti
- Correspondence address. Department of Obstetrics and Gynecology, Northwestern University, Feinberg School of Medicine, 303 E Superior Street, Lurie 4-119, Chicago, IL 60611, USA. E-mail:
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Mahmoud AM. An Overview of Epigenetics in Obesity: The Role of Lifestyle and Therapeutic Interventions. Int J Mol Sci 2022; 23:ijms23031341. [PMID: 35163268 PMCID: PMC8836029 DOI: 10.3390/ijms23031341] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 02/06/2023] Open
Abstract
Obesity has become a global epidemic that has a negative impact on population health and the economy of nations. Genetic predispositions have been demonstrated to have a substantial role in the unbalanced energy metabolism seen in obesity. However, these genetic variations cannot entirely explain the massive growth in obesity over the last few decades. Accumulating evidence suggests that modern lifestyle characteristics such as the intake of energy-dense foods, adopting sedentary behavior, or exposure to environmental factors such as industrial endocrine disruptors all contribute to the rising obesity epidemic. Recent advances in the study of DNA and its alterations have considerably increased our understanding of the function of epigenetics in regulating energy metabolism and expenditure in obesity and metabolic diseases. These epigenetic modifications influence how DNA is transcribed without altering its sequence. They are dynamic, reflecting the interplay between the body and its surroundings. Notably, these epigenetic changes are reversible, making them appealing targets for therapeutic and corrective interventions. In this review, I discuss how these epigenetic modifications contribute to the disordered energy metabolism in obesity and to what degree lifestyle and weight reduction strategies and pharmacological drugs can restore energy balance by restoring normal epigenetic profiles.
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Affiliation(s)
- Abeer M Mahmoud
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
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5
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Alternative Splicing, Epigenetic Modifications and Cancer: A Dangerous Triangle, or a Hopeful One? Cancers (Basel) 2022; 14:cancers14030560. [PMID: 35158828 PMCID: PMC8833605 DOI: 10.3390/cancers14030560] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Epigenetics studies the alteration of gene expression without changing DNA sequence and very often, epigenetic dysregulation causes cancer. Alternative splicing is a mechanism that results in the production of several mRNA isoforms from a single gene and aberrant splicing is also a frequent cause of cancer. The present review is built on the interrelations of epigenetics and alternative splicing. In an intuitive way, we say that epigenetic modifications and alternative splicing are at two vertices of a triangle, the third vertex being occupied by cancer. Interconnection between alternative splicing and epigenetic modifications occurs backward and forward and the mechanisms involved are widely reviewed. These connections also provide novel diagnostic or prognostic tools, which are listed. Finally, as epigenetic alterations are reversible and aberrant alternative splicing may be corrected, the therapeutic possibilities to break the triangle are discussed. Abstract The alteration of epigenetic modifications often causes cancer onset and development. In a similar way, aberrant alternative splicing may result in oncogenic products. These issues have often been individually reviewed, but there is a growing body of evidence for the interconnection of both causes of cancer. Actually, aberrant splicing may result from abnormal epigenetic signalization and epigenetic factors may be altered by alternative splicing. In this way, the interrelation between epigenetic marks and alternative splicing form the base of a triangle, while cancer may be placed at the vertex. The present review centers on the interconnections at the triangle base, i.e., between alternative splicing and epigenetic modifications, which may result in neoplastic transformations. The effects of different epigenetic factors, including DNA and histone modifications, the binding of non-coding RNAs and the alterations of chromatin organization on alternative splicing resulting in cancer are first considered. Other less-frequently considered questions, such as the epigenetic regulation of the splicing machinery, the aberrant splicing of epigenetic writers, readers and erasers, etc., are next reviewed in their connection with cancer. The knowledge of the above-mentioned relationships has allowed increasing the collection of biomarkers potentially useful as cancer diagnostic and/or prognostic tools. Finally, taking into account on one hand that epigenetic changes are reversible, and some epigenetic drugs already exist and, on the other hand, that drugs intended for reversing aberrations in alternative splicing, therapeutic possibilities for breaking the mentioned cancer-related triangle are discussed.
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Deshpande N, Jordan R, Henderson Pozzi M, Bryk M. Histone 3 lysine 4 monomethylation supports activation of transcription in S. cerevisiae during nutrient stress. Curr Genet 2022; 68:181-194. [PMID: 35041077 PMCID: PMC8976815 DOI: 10.1007/s00294-022-01226-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/17/2021] [Accepted: 12/31/2021] [Indexed: 12/11/2022]
Abstract
Mono-methylation of the fourth lysine on the N-terminal tail of histone H3 was found to support the induction of RNA polymerase II transcription in S. cerevisiae during nutrient stress. In S. cerevisiae, the mono-, di- and tri-methylation of lysine 4 on histone H3 (H3K4) is catalyzed by the protein methyltransferase, Set1. The three distinct methyl marks on H3K4 act in discrete ways to regulate transcription. Nucleosomes enriched with tri-methylated H3K4 are usually associated with active transcription whereas di-methylated H3K4 is associated with gene repression. Mono-methylated H3K4 has been shown to repress gene expression in S. cerevisiae and is detected at enhancers and promoters in eukaryotes. S. cerevisiae set1Δ mutants unable to methylate H3K4 exhibit growth defects during histidine starvation. The growth defects are rescued by either a wild-type allele of SET1 or partial-function alleles of set1, including a mutant that predominantly generates H3K4me1 and not H3K4me3. Rescue of the growth defect is associated with induction of the HIS3 gene. Growth defects observed when set1Δ cultures were starved for isoleucine and valine were also rescued by wild-type SET1 or partial-function set1 alleles. The results show that H3K4me1, in the absence of H3K4me3, supports transcription of the HIS3 gene and expression of one or more of the genes required for biosynthesis of isoleucine and valine during nutrient stress. Set1-like methyltransferases are evolutionarily conserved, and research has linked their functions to developmental gene regulation and several cancers in higher eukaryotes. Identification of mechanisms of H3K4me1-mediated activation of transcription in budding yeast will provide insight into gene regulation in all eukaryotes.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Rachel Jordan
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
- iBio, 8800 HSC Blvd, Bryan, TX, 77807, USA
| | - Michelle Henderson Pozzi
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA.
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Kanapeckaitė A, Burokienė N, Mažeikienė A, Cottrell GS, Widera D. Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies. BIOPHYSICAL REPORTS 2021; 1:100028. [PMID: 36425454 PMCID: PMC9680810 DOI: 10.1016/j.bpr.2021.100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/24/2021] [Indexed: 06/16/2023]
Abstract
Epigenetic research holds great promise to advance our understanding of biomarkers and regulatory processes in health and disease. An increasing number of new approaches, ranging from molecular to biophysical analyses, enable identifying epigenetic changes on the level of a single gene or the whole epigenome. The aim of this review is to highlight how the field is shifting from completely molecular-biology-driven solutions to multidisciplinary strategies including more reliance on biophysical analysis tools. Biophysics not only offers technical advancements in imaging or structure analysis but also helps to explore regulatory interactions. New computational methods are also being developed to meet the demand of growing data volumes and their processing. Therefore, it is important to capture these new directions in epigenetics from a biophysical perspective and discuss current challenges as well as multiple applications of biophysical methods and tools. Specifically, we gradually introduce different biophysical research methods by first considering the DNA-level information and eventually higher-order chromatin structures. Moreover, we aim to highlight that the incorporation of bioinformatics, machine learning, and artificial intelligence into biophysical analysis allows gaining new insights into complex epigenetic processes. The gained understanding has already proven useful in translational and clinical research providing better patient stratification options or new therapeutic insights. Together, this offers a better readiness to transform bench-top experiments into industrial high-throughput applications with a possibility to employ developed methods in clinical practice and diagnostics.
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Affiliation(s)
- Austė Kanapeckaitė
- Algorithm379, Laisvės g. 7, LT 12007, Vilnius, Lithuania
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
| | - Neringa Burokienė
- Clinics of Internal Diseases, Family Medicine and Oncology, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | - Asta Mažeikienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | | | - Darius Widera
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
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Zhang Z, Chen B, Zhu Y, Zhang T, Yuan Y, Zhang X, Xu Y. The Jumonji Domain-Containing Histone Demethylase Homolog 1D/lysine Demethylase 7A (JHDM1D/KDM7A) Is an Epigenetic Activator of RHOJ Transcription in Breast Cancer Cells. Front Cell Dev Biol 2021; 9:664375. [PMID: 34249916 PMCID: PMC8262595 DOI: 10.3389/fcell.2021.664375] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
The small GTPase RHOJ is a key regulator of breast cancer metastasis by promoting cell migration and invasion. The prometastatic stimulus TGF-β activates RHOJ transcription via megakaryocytic leukemia 1 (MKL1). The underlying epigenetic mechanism is not clear. Here, we report that MKL1 deficiency led to disrupted assembly of the RNA polymerase II preinitiation complex on the RHOJ promoter in breast cancer cells. This could be partially explained by histone H3K9/H3K27 methylation status. Further analysis confirmed that the H3K9/H3K27 dual demethylase JHDM1D/KDM7A was essential for TGF-β-induced RHOJ transcription in breast cancer cells. MKL1 interacted with and recruited KDM7A to the RHOJ promoter to cooperatively activate RHOJ transcription. KDM7A knockdown attenuated migration and invasion of breast cancer cells in vitro and mitigated the growth and metastasis of breast cancer cells in nude mice. KDM7A expression level, either singularly or in combination with that of RHOJ, could be used to predict prognosis in breast cancer patients. Of interest, KDM7A appeared to be a direct transcriptional target of TGF-β signaling. A SMAD2/SMAD4 complex bound to the KDM7A promoter and mediated TGF-β-induced KDM7A transcription. In conclusion, our data unveil a novel epigenetic mechanism whereby TGF-β regulates the transcription of the prometastatic small GTPase RHOJ. Screening for small-molecule inhibitors of KDM7A may yield effective therapeutic solutions to treat malignant breast cancers.
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Affiliation(s)
- Ziyu Zhang
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China
| | - Baoyu Chen
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yuwen Zhu
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Tianyi Zhang
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yibiao Yuan
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xiaoling Zhang
- School of Medicine, Nanchang University, Nanchang, China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China
| | - Yong Xu
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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9
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Holt MV, Wang T, Young NL. Expeditious Extraction of Histones from Limited Cells or Tissue Samples and Quantitative Top-Down Proteomic Analysis. Curr Protoc 2021; 1:e26. [PMID: 33534192 DOI: 10.1002/cpz1.26] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Histones are the primary protein component of chromatin and are involved in virtually all DNA-templated processes. Histones are abundantly post-translationally modified by a variety of chromatin-modifying machinery. These post-translational modifications (PTMs) are recognized by a range of "reader" proteins, which recruit additional proteins to specific locations on chromatin and impart precise and powerful effects on gene regulation. Each PTM typically exerts a positive or negative effect on transcription, and recent studies have shown that histone PTMs function in a combinatorial histone code: that is, histone PTMs function in combination to exert precise DNA-templated regulation. Thus, there is a need to identify and understand proteoforms, or unambiguously defined single protein molecules with all combinations of modifications. Top-down proteomics is currently the only viable approach for identifying and quantitating histone proteoforms, and mass spectrometry instruments have become sufficiently powerful to perform these quantitative analyses in a robust and high-throughput fashion. These recent innovations have enabled new experimental directions in chromatin research but have also introduced temporal and other constraints. This has led us to develop the protocols described here, which increase throughput, reduce sample requirements, and maintain robust quantitation. Although originally designed for high-throughput quantitative top-down proteomics, the protocols described here are useful for a wide range of chromatin biology applications. Starting with small amounts of cells or tissue, we describe two basic protocols for exceptionally rapid and efficient nuclei isolation, acid extraction of histones, and high-performance liquid chromatography fractionation of histones into histone families. We additionally describe the quantitative top-down proteomic analysis of histone H4 proteoforms. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Nuclei isolation and acid extraction of histones from mammalian cells in culture/tissues Basic Protocol 2: HPLC fractionation of histones and histone H4 HPLC-MS/MS Support Protocol: Preparation of intact H3 histone tails by Glu-C digestion.
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Affiliation(s)
- Matthew V Holt
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Tao Wang
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas.,Current Address: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
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10
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Zappacosta F, Wagner CD, Della Pietra A, Gerhart SV, Keenan K, Korenchuck S, Quinn CJ, Barbash O, McCabe MT, Annan RS. A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling. Mol Cell Proteomics 2021; 20:100067. [PMID: 33775892 PMCID: PMC8138768 DOI: 10.1016/j.mcpro.2021.100067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Histones are highly posttranslationally modified proteins that regulate gene expression by modulating chromatin structure and function. Acetylation and methylation are the most abundant histone modifications, with methylation occurring on lysine (mono-, di-, and trimethylation) and arginine (mono- and dimethylation) predominately on histones H3 and H4. In addition, arginine dimethylation can occur either symmetrically (SDMA) or asymmetrically (ADMA) conferring different biological functions. Despite the importance of histone methylation on gene regulation, characterization and quantitation of this modification have proven to be quite challenging. Great advances have been made in the analysis of histone modification using both bottom-up and top-down mass spectrometry (MS). However, MS-based analysis of histone posttranslational modifications (PTMs) is still problematic, due both to the basic nature of the histone N-terminal tails and to the combinatorial complexity of the histone PTMs. In this report, we describe a simplified MS-based platform for histone methylation analysis. The strategy uses chemical acetylation with d0-acetic anhydride to collapse all the differently acetylated histone forms into one form, greatly reducing the complexity of the peptide mixture and improving sensitivity for the detection of methylation via summation of all the differently acetylated forms. We have used this strategy for the robust identification and relative quantitation of H4R3 methylation, for which stoichiometry and symmetry status were determined, providing an antibody-independent evidence that H4R3 is a substrate for both Type I and Type II PRMTs. Additionally, this approach permitted the robust detection of H4K5 monomethylation, a very low stoichiometry methylation event (0.02% methylation). In an independent example, we developed an in vitro assay to profile H3K27 methylation and applied it to an EZH2 mutant xenograft model following small-molecule inhibition of the EZH2 methyltransferase. These specific examples highlight the utility of this simplified MS-based approach to quantify histone methylation profiles. Simplification of histone complexity for analysis of lysine and arginine methylation. Improved sensitivity for the analysis of dimethylarginine symmetry. Accurate ratio of symmetric and asymmetric H4R3 dimethylarginine in cancer cells. Catalog of accessible histone methyl marks to facilitate assay development.
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Affiliation(s)
- Francesca Zappacosta
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Craig D Wagner
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Sarah V Gerhart
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Kathryn Keenan
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Chad J Quinn
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Olena Barbash
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Roland S Annan
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA.
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11
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Wardowska A. m6A RNA Methylation in Systemic Autoimmune Diseases-A New Target for Epigenetic-Based Therapy? Pharmaceuticals (Basel) 2021; 14:ph14030218. [PMID: 33807762 PMCID: PMC8001529 DOI: 10.3390/ph14030218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/17/2022] Open
Abstract
The general background of autoimmune diseases is a combination of genetic, epigenetic and environmental factors, that lead to defective immune reactions. This erroneous immune cell activation results in an excessive production of autoantibodies and prolonged inflammation. During recent years epigenetic mechanisms have been extensively studied as potential culprits of autoreactivity. Alike DNA and proteins, also RNA molecules are subjected to an extensive repertoire of chemical modifications. N6-methyladenosine is the most prevalent form of internal mRNA modification in eukaryotic cells and attracts increasing attention due to its contribution to human health and disease. Even though m6A is confirmed as an essential player in immune response, little is known about its role in autoimmunity. Only few data have been published up to date in the field of RNA methylome. Moreover, only selected autoimmune diseases have been studied in respect of m6A role in their pathogenesis. In this review, I attempt to present all available research data regarding m6A alterations in autoimmune disorders and appraise its role as a potential target for epigenetic-based therapies.
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Affiliation(s)
- Anna Wardowska
- Department of Embryology, Medical University of Gdansk, 80-210 Gdansk, Poland
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12
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Pontelo TP, Franco MM, Kawamoto TS, Caixeta FMC, de Oliveira Leme L, Kussano NR, Zangeronimo MG, Dode MAN. Histone deacetylase inhibitor during in vitro maturation decreases developmental capacity of bovine oocytes. PLoS One 2021; 16:e0247518. [PMID: 33667248 PMCID: PMC7935280 DOI: 10.1371/journal.pone.0247518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
This study aimed to evaluate the effect of scriptaid during pre-maturation (PIVM) and/or maturation (IVM) on developmental competence of bovine oocytes. Cumulus-oocyte complexes (COCs) were submitted to PIVM for 6 h in the presence or absence of scriptaid. COCs were distributed into five groups: T1-IVM for 22 h, T2-PIVM for 6 h and IVM for 22 h, T3-PIVM with scriptaid for 6 h and IVM for 22 h, T4-PIVM for 6 h and IVM with scriptaid for 22 h, and T5-PIVM with scriptaid for 6 h and IVM with scriptaid for 22 h. Nuclear maturation, gene expression, cumulus cells (CCs) expansion, and embryo development and quality were evaluated. At the end of maturation, all groups presented the majority of oocytes in MII (P>0.05). Only HAT1 gene was differentially expressed (P<0.01) in oocytes with different treatments. Regarding embryo development at D7, T4 (23%) and T5 (18%) had lower blastocyst rate (P<0.05) than the other treatments (T1 = 35%, T2 = 37% and T3 = 32%). No effect was observed when scriptaid in PIVM was used in less competent oocytes (P>0.05). In conclusion, presence of scriptaid in PIVM and/or IVM did not improve developmental competence or embryo quality.
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Affiliation(s)
| | - Mauricio Machaim Franco
- Federal University Uberlândia, Animal Science, Uberlândia, Minas Gerais, Brazil
- Institute of Genetics and Biochemistry of Federal, University of Uberlandia, Uberlândia, Minas Gerais, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | | | | | | | | | | | - Margot Alves Nunes Dode
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- University of Brasilia, Animal Science, Brasilia, Distrito Federal, Brazil
- University of Brasilia, Institute of Biology, Brasilia, Distrito Federal, Brazil
- * E-mail:
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13
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Fellows R, Varga-Weisz P. Chromatin dynamics and histone modifications in intestinal microbiota-host crosstalk. Mol Metab 2020; 38:100925. [PMID: 31992511 PMCID: PMC7300386 DOI: 10.1016/j.molmet.2019.12.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The microbiota in the human gut are an important component of normal physiology that has co-evolved from the earliest multicellular organisms. Therefore, it is unsurprising that there is intimate crosstalk between the microbial world in the gut and the host. Genome regulation through microbiota-host interactions not only affects the host's immunity, but also metabolic health and resilience against cancer. Chromatin dynamics of the host epithelium involving histone modifications and other facets of the epigenetic machinery play an important role in this process. SCOPE OF REVIEW This review discusses recent findings relevant to how chromatin dynamics shape the crosstalk between the microbiota and its host, with a special focus on the role of histone modifications. MAJOR CONCLUSIONS Host-microbiome interactions are important evolutionary drivers and are thus expected to be hardwired into and mould the epigenetic machinery in multicellular organisms. Microbial-derived short-chain fatty acids (SCFA) are dominant determinants of microbiome-host interactions, and the inhibition of histone deacetylases (HDACs) by SCFA is a key mechanism in this process. The discovery of alternative histone acylations, such as crotonylation, in addition to the canonical histone acetylation reveals a new layer of complexity in this crosstalk.
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Affiliation(s)
| | - Patrick Varga-Weisz
- Babraham Institute, Babraham, Cambridge, CB22 3AT, UK; School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
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14
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Kumar A, Kono H. Heterochromatin protein 1 (HP1): interactions with itself and chromatin components. Biophys Rev 2020; 12:387-400. [PMID: 32144738 PMCID: PMC7242596 DOI: 10.1007/s12551-020-00663-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/23/2020] [Indexed: 12/12/2022] Open
Abstract
Isoforms of heterochromatin protein 1 (HP1) have been known to perform a multitude of functions ranging from gene silencing, gene activation to cell cycle regulation, and cell differentiation. This functional diversity arises from the dissimilarities coded in protein sequence which confers different biophysical and biochemical properties to individual structural elements of HP1 and thereby different behavior and interaction patterns. Hence, an understanding of various interactions of the structural elements of HP1 will be of utmost importance to better elucidate chromatin dynamics in its presence. In this review, we have gathered available information about interactions of HP1 both within and with itself as well as with chromatin elements. Also, the possible implications of these interactions are discussed.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan.
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15
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The epigenetic face of lupus: Focus on antigen-presenting cells. Int Immunopharmacol 2020; 81:106262. [PMID: 32045873 DOI: 10.1016/j.intimp.2020.106262] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022]
Abstract
In recent years, epigenetic mechanisms became widely known due to their ability to regulate and maintain physiological processes such as cell growth, development, differentiation and genomic stability. When dysregulated, epigenetic mechanisms, may introduce gene expression changes and disturbance in immune homeostasis leading to autoimmune diseases. Systemic lupus erythematosus (SLE), the most extensively studied autoimmune disorder, has already been correlated with epigenetic modifications, especially in T cells. Since these cell rely on antigen presentation, it may be assumed that erroneous activity of antigen-presenting cells (APCs), culminates in T cell abnormalities. In this review we summarize and discuss the epigenetic modifications in SLE affected APCs, with the focus on dendritic cells (DCs), B cells and monocytes. Unravelling this aspect of SLE pathogenesis, might result in identification of new disease biomarkers and putative therapeutic approaches.
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16
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Xu X, Yu H. Ras-PI3K pathway promotes osteosarcoma progression via regulating VRK1-mediated H2A phosphorylation at threonine 120. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:4274-4283. [PMID: 31810390 DOI: 10.1080/21691401.2019.1687506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: Ras-PI3K pathway aberrant activation plays an important role in the occurrence and development of osteosarcoma. This study investigated the functions of Ras-PI3K pathway specific activation on histone H2A phosphorylation at threonine 120 (H2AT120ph) in osteosarcoma cells, along with the possible internal molecular mechanisms.Methods: Cell transfection was done to alter RasG12V/Y40C, H2AT120ph and vaccinia-related kinase 1 (VRK1) expression. Then, cell viability, proliferation, migration and cell cycle distribution were assessed, respectively. qRT-PCR was utilized to measure the VRK1 and Ras-PI3K pathway downstream genes (CYR61, IGFBP3, WNT16B, NT5E, GDF15 and CARD16) expression. Chromatin immunoprecipitation (ChIP) was conducted to evaluate the input levels of H2AT120ph and VRK1 in the promoter regions of Ras-PI3K pathway downstream genes.Results: Ras-PI3K specific activation promoted histone H2AT120ph. H2AT120ph participated in the oncogenic functions of Ras-PI3K pathway on osteosarcoma by modulating the transcription of Ras-PI3K-targeted genes. Moreover, VRK1 contributed to the Ras-PI3K specific activation-induced up-regulation of H2AT120ph and osteosarcoma progression. Ras-PI3K pathway-specific activation-induced up-regulation of H2AT120ph was achieved by up-regulation of VRK1.Conclusions: Ras-PI3K pathway activation promoted osteosarcoma progression might be via up-regulating VRK1-mediated H2AT120ph. We proposed that VRK1 and H2AT120ph could be the potential targets for osteosarcoma diagnosis and treatment.HighlightsH2AT120ph is specifically promoted by Ras-PI3K pathway activation.H2AT120ph joins in the oncogenic effects of Ras-PI3K pathway on osteosarcoma.H2AT120ph regulates the transcription of Ras-PI3K-targeted genes.VRK1 takes part in the regulatory function of Ras-PI3K pathway on H2AT120ph.
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Affiliation(s)
- Xianlun Xu
- Department of Traumatology, Jining No.1 People's Hospital, Jining, Shandong, China.,Affiliated Jining No. 1 People's Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Hao Yu
- Department of Traumatology, Jining No.1 People's Hospital, Jining, Shandong, China.,Affiliated Jining No. 1 People's Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
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17
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Ge Y, Liu BL, Cui JP, Li SQ. Livin Regulates H2A.X Y142 Phosphorylation and Promotes Autophagy in Colon Cancer Cells via a Novel Kinase Activity. Front Oncol 2019; 9:1233. [PMID: 31799193 PMCID: PMC6868062 DOI: 10.3389/fonc.2019.01233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022] Open
Abstract
Objective: To investigate Livin-mediated regulation of H2A.XY142 phosphorylation via a novel kinase activity and its effect on autophagy in colon cancer cells. Methods: The interaction between Livin and H2A.X was tested by immunoprecipitation. H2A.X–/– HCT116 cells were transfected with human influenza hemagglutinin (HA)-tagged WT or Y142F phospho-dead mutantH2A.X plasmids. GST-tagged recombinant Livin protein was used to perform in vitro pull-down experiment and kinase assay. H2A.X–/–Livin+/+ SW480 cells were co-transfected with H2A.XWT/H2A.XY142F plasmid and LC3 EGFP-tagged plasmid to explore whether H2A.XY142F was involved in Livin-mediated autophagy induced by starvation in colon cancer cells. Results: Co-immunoprecipitation studies confirmed that Livin interacted with H2A.X and that it was phosphorylation dependent. In vitro kinase assay confirmed that Livin could phosphorylate H2A.X. Knockdown of Livin (Livin–/–) in SW480 cells or HCT116 cells canceled the starvation-induced autophagy in colon cancer cells; H2A.X–/–Livin+/+ SW480 cells transfected with H2A.XWT activated autophagy induced by starvation while cells transfected with H2A.XY142F had no significant difference; Livin-H2A.XY142F axis activated autophagy in colon cancer cells through transcriptionally regulating ATG5 and ATG7. Conclusion: Livin promotes autophagy in colon cancer cells via regulating the phosphorylation of H2A.XY142.
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Affiliation(s)
- Yang Ge
- The Six Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Bao-Lin Liu
- The Six Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jun-Peng Cui
- The Six Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shu-Qiang Li
- The Six Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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18
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Lung Microbiome in Asthma: Current Perspectives. J Clin Med 2019; 8:jcm8111967. [PMID: 31739446 PMCID: PMC6912699 DOI: 10.3390/jcm8111967] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 12/20/2022] Open
Abstract
A growing body of evidence implicates the human microbiome as a potentially influential player actively engaged in shaping the pathogenetic processes underlying the endotypes and phenotypes of chronic respiratory diseases, particularly of the airways. In this article, we specifically review current evidence on the characteristics of lung microbiome, and specifically the bacteriome, the modes of interaction between lung microbiota and host immune system, the role of the “lung–gut axis”, and the functional effects thereof on asthma pathogenesis. We also attempt to explore the possibilities of therapeutic manipulation of the microbiome, aiming at the establishment of asthma prevention strategies and the optimization of asthma treatment.
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19
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Sasse SK, Gruca M, Allen MA, Kadiyala V, Song T, Gally F, Gupta A, Pufall MA, Dowell RD, Gerber AN. Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression. Genome Res 2019; 29:1753-1765. [PMID: 31519741 PMCID: PMC6836729 DOI: 10.1101/gr.248187.119] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022]
Abstract
The glucocorticoid receptor (NR3C1, also known as GR) binds to specific DNA sequences and directly induces transcription of anti-inflammatory genes that contribute to cytokine repression, frequently in cooperation with NF-kB. Whether inflammatory repression also occurs through local interactions between GR and inflammatory gene regulatory elements has been controversial. Here, using global run-on sequencing (GRO-seq) in human airway epithelial cells, we show that glucocorticoid signaling represses transcription within 10 min. Many repressed regulatory regions reside within "hyper-ChIPable" genomic regions that are subject to dynamic, yet nonspecific, interactions with some antibodies. When this artifact was accounted for, we determined that transcriptional repression does not require local GR occupancy. Instead, widespread transcriptional induction through canonical GR binding sites is associated with reciprocal repression of distal TNF-regulated enhancers through a chromatin-dependent process, as evidenced by chromatin accessibility and motif displacement analysis. Simultaneously, transcriptional induction of key anti-inflammatory effectors is decoupled from primary repression through cooperation between GR and NF-kB at a subset of regulatory regions. Thus, glucocorticoids exert bimodal restraints on inflammation characterized by rapid primary transcriptional repression without local GR occupancy and secondary anti-inflammatory effects resulting from transcriptional cooperation between GR and NF-kB.
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Affiliation(s)
- Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Margaret Gruca
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Vineela Kadiyala
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Tengyao Song
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Fabienne Gally
- Department of Biomedical Research, National Jewish Health, Denver, Colorado 80206, USA
| | - Arnav Gupta
- Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
- Computer Science, University of Colorado, Boulder, Colorado 80309, USA
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
- Department of Biomedical Research, National Jewish Health, Denver, Colorado 80206, USA
- Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
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20
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Patsouras MD, Vlachoyiannopoulos PG. Evidence of epigenetic alterations in thrombosis and coagulation: A systematic review. J Autoimmun 2019; 104:102347. [PMID: 31607428 DOI: 10.1016/j.jaut.2019.102347] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
Thrombosis in the context of Cardiovascular disease (CVD) affects mainly the blood vessels supplying the heart, brain and peripheries and it is the leading cause of death worldwide. The pathophysiological thrombotic mechanisms are largely unknown. Heritability contributes to a 30% of the incidence of CVD. The remaining variation can be explained by life style factors such as smoking, dietary and exercise habits, environmental exposure to toxins, and drug usage and other comorbidities. Epigenetic variation can be acquired or inherited and constitutes an interaction between genes and the environment. Epigenetics have been implicated in atherosclerosis, ischemia/reperfusion damage and the cardiovascular response to hypoxia. Epigenetic regulators of gene expression are mainly the methylation of CpG islands, histone post translational modifications (PTMs) and microRNAs (miRNAs). These epigenetic regulators control gene expression either through activation or silencing. Epigenetic control is mostly dynamic and can potentially be manipulated to prevent or reverse the uncontrolled expression of genes, a trait that renders them putative therapeutic targets. In the current review, we systematically studied and present available data on epigenetic alterations implicated in thrombosis derived from human studies. Evidence of epigenetic alterations is observed in several thrombotic diseases such as Coronary Artery Disease and Cerebrovascular Disease, Preeclampsia and Antiphospholipid Syndrome. Differential CpG methylation and specific histone PTMs that control transcription of prothrombotic and proinflammatory genes have also been associated with predisposing factors of thrombosis and CVD, such us smoking, air pollution, hypertriglyceridemia, occupational exposure to particulate matter and comorbidities including cancer, Chronic Obstructive Pulmonary Disease and Chronic Kidney Disease. These clinical observations are further supported by in vitro experiments and indicate that epigenetic regulation affects the pathophysiology of thrombotic disorders with potential diagnostic or therapeutic utility.
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Affiliation(s)
- M D Patsouras
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - P G Vlachoyiannopoulos
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Greece.
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21
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Vincent D, Binos S, Rochfort S, Spangenberg G. Top-Down Proteomics of Medicinal Cannabis. Proteomes 2019; 7:proteomes7040033. [PMID: 31554318 PMCID: PMC6958505 DOI: 10.3390/proteomes7040033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/06/2019] [Accepted: 09/20/2019] [Indexed: 02/02/2023] Open
Abstract
The revised legislation on medicinal cannabis has triggered a surge of research studies in this space. Yet, cannabis proteomics is lagging. In a previous study, we optimised the protein extraction of mature buds for bottom-up proteomics. In this follow-up study, we developed a top-down mass spectrometry (MS) proteomics strategy to identify intact denatured protein from cannabis apical buds. After testing different source-induced dissociation (SID), collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron transfer dissociation (ETD) parameters on infused known protein standards, we devised three LC-MS/MS methods for top-down sequencing of cannabis proteins. Different MS/MS modes produced distinct spectra, albeit greatly overlapping between SID, CID, and HCD. The number of fragments increased with the energy applied; however, this did not necessarily translate into greater sequence coverage. Some precursors were more amenable to fragmentation than others. Sequence coverage decreased as the mass of the protein increased. Combining all MS/MS data maximised amino acid (AA) sequence coverage, achieving 73% for myoglobin. In this experiment, most cannabis proteins were smaller than 30 kD. A total of 46 cannabis proteins were identified with 136 proteoforms bearing different post-translational modifications (PTMs), including the excision of N-terminal M, the N-terminal acetylation, methylation, and acetylation of K resides, and phosphorylation. Most identified proteins are involved in photosynthesis, translation, and ATP production. Only one protein belongs to the phytocannabinoid biosynthesis, olivetolic acid cyclase.
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Affiliation(s)
- Delphine Vincent
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - Steve Binos
- Thermo Fisher Scientific, Bio21 Institute, The University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia.
| | - Simone Rochfort
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - German Spangenberg
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
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22
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Identifying the culprits in neurological autoimmune diseases. J Transl Autoimmun 2019; 2:100015. [PMID: 32743503 PMCID: PMC7388404 DOI: 10.1016/j.jtauto.2019.100015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022] Open
Abstract
The target organ of neurological autoimmune diseases (NADs) is the central or peripheral nervous system. Multiple sclerosis (MS) is the most common NAD, whereas Guillain-Barré syndrome (GBS), myasthenia gravis (MG), and neuromyelitis optica (NMO) are less common NADs, but the incidence of these diseases has increased exponentially in the last few years. The identification of a specific culprit in NADs is challenging since a myriad of triggering factors interplay with each other to cause an autoimmune response. Among the factors that have been associated with NADs are genetic susceptibility, epigenetic mechanisms, and environmental factors such as infection, microbiota, vitamins, etc. This review focuses on the most studied culprits as well as the mechanisms used by these to trigger NADs. Neurological autoimmune diseases are caused by a complex interaction between genes, environmental factors, and epigenetic deregulation. Infectious agents can cause an autoimmune reaction to myelin epitopes through molecular mimicry and/or bystander activation. Gut microbiota dysbiosis contributes to neurological autoimmune diseases. Smoking increases the risk of NADs through inflammatory signaling pathways, oxidative stress, and Th17 differentiation. Deficiency in vitamin D favors NAD development through direct damage to the central and peripheral nervous system.
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23
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García-Giménez JL, Romá-Mateo C, Pallardó FV. Oxidative post-translational modifications in histones. Biofactors 2019; 45:641-650. [PMID: 31185139 DOI: 10.1002/biof.1532] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/12/2019] [Indexed: 01/12/2023]
Abstract
Epigenetic regulation is attracting much attention because it explains many of the effects that the external environment induces in organisms. Changes in the cellular redox status and even more specifically in its nuclear redox compartment is one of these examples. Redox changes can induce modulation of the epigenetic regulation in cells. Here we present a few cases where reactive oxygen or nitrogen species induces epigenetic marks in histones. Posttranslational modification of these proteins like histone nitrosylation, carbonylation, or glutathionylation together with other mechanisms not reviewed here are the cornerstones of redox-related epigenetic regulation. We currently face a new field of research with potential important consequences for the treatment of many pathologies.
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Affiliation(s)
- José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Carlos Romá-Mateo
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
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24
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Expression of UTX Indicates Poor Prognosis in Patients With Luminal Breast Cancer and is Associated With MMP-11 Expression. Appl Immunohistochem Mol Morphol 2019; 28:544-550. [DOI: 10.1097/pai.0000000000000795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Gimeno-Valiente F, Riffo-Campos ÁL, Vallet-Sánchez A, Siscar-Lewin S, Gambardella V, Tarazona N, Cervantes A, Franco L, Castillo J, López-Rodas G. ZNF518B gene up-regulation promotes dissemination of tumour cells and is governed by epigenetic mechanisms in colorectal cancer. Sci Rep 2019; 9:9339. [PMID: 31249328 PMCID: PMC6597559 DOI: 10.1038/s41598-019-45411-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 06/04/2019] [Indexed: 12/19/2022] Open
Abstract
Most of colorectal cancer CRC-related death is due to metastasis and the finding of markers for prognosis of invasiveness, constitutes an appealing challenge. Here, after analysing cDNA array containing 43 tumour and 5 normal mucosa samples, we report that the expression of the ZNF518B gene as a whole and that of its two major splicing isoforms are significantly increased in tumours. The canonical isoform was also up-regulated in a patients’ cohort containing 70 tumour and 69 adjacent tissue samples. The effects of silencing ZNF518B on the phenotype of CRC cell lines were then studied. The gene does not affect cell proliferation, but plays a significant role in cell migration and invasiveness and induces changes in the epithelial-to-mesenchymal transition markers, suggesting that ZNF518B favours tumour cell dissemination. To study the regulation of the gene, transcription-related changes in nucleosomal organisation and epigenetic marks around the transcriptional start site were analysed. The positioning of a nucleosome over the transcription start site and the differential presence of the epigenetic marks H3K9ac, H3K27ac, H3K4me3 and H3K9me3 correlate with gene expression. Inhibition of histone deacetylases increases the transcription of ZNF518B, which may be a candidate for invasiveness prognosis in CRC and a target for epigenetic drugs.
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Affiliation(s)
| | - Ángela L Riffo-Campos
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro De Excelencia de Modelación y Computación Científica, Departamento de Anatomía Patológica, Universidad de La Frontera, Temuco, Chile
| | - Azahara Vallet-Sánchez
- Institute of Health Research, INCLIVA, Valencia, Spain.,Department of Cell Biology, Universitat de València, Burjassot, Valencia, Spain
| | - Sofía Siscar-Lewin
- Institute of Health Research, INCLIVA, Valencia, Spain.,Department of Microbial Pathogenicity Mechanisms, Hans-Knoell-Institute, Jena, Germany
| | - Valentina Gambardella
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Oncology, University Hospital, Universitat de València, Valencia, Spain
| | - Noelia Tarazona
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Oncology, University Hospital, Universitat de València, Valencia, Spain
| | - Andrés Cervantes
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Oncology, University Hospital, Universitat de València, Valencia, Spain
| | - Luis Franco
- Institute of Health Research, INCLIVA, Valencia, Spain. .,Department of Biochemistry and Molecular Biology, Universitat de València, Valencia, Spain.
| | - Josefa Castillo
- Institute of Health Research, INCLIVA, Valencia, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Biochemistry and Molecular Biology, Universitat de València, Valencia, Spain
| | - Gerardo López-Rodas
- Institute of Health Research, INCLIVA, Valencia, Spain.,Department of Biochemistry and Molecular Biology, Universitat de València, Valencia, Spain
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Collemare J, Seidl MF. Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? FEMS Microbiol Rev 2019; 43:591-607. [PMID: 31301226 PMCID: PMC8038932 DOI: 10.1093/femsre/fuz018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/07/2023] Open
Abstract
Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.
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Affiliation(s)
| | - Michael F Seidl
- Corresponding author: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands. E-mail: ; Present address: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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Rezapour S, Hosseinzadeh E, Marofi F, Hassanzadeh A. Epigenetic-based therapy for colorectal cancer: Prospect and involved mechanisms. J Cell Physiol 2019; 234:19366-19383. [PMID: 31020647 DOI: 10.1002/jcp.28658] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022]
Abstract
Epigenetic modifications are heritable variations in gene expression not encoded by the DNA sequence. According to reports, a large number of studies have been performed to characterize epigenetic modification during normal development and also in cancer. Epigenetics can be regarded more widely to contain all of the changes in expression of genes that make by adjusted interactions between the regulatory portions of DNA or messenger RNAs that lead to indirect variation in the DNA sequence. In the last decade, epigenetic modification importance in colorectal cancer (CRC) pathogenesis was demonstrated powerfully. Although developments in CRC therapy have been made in the last years, much work is required as it remains the second leading cause of cancer death. Nowadays, epigenetic programs and genetic change have pivotal roles in the CRC incidence as well as progression. While our knowledge about epigenetic mechanism in CRC is not comprehensive, selective histone modifications and resultant chromatin conformation together with DNA methylation most likely regulate CRC pathogenesis that involved genes expression. Undoubtedly, the advanced understanding of epigenetic-based gene expression regulation in the CRC is essential to make epigenetic drugs for CRC therapy. The major aim of this review is to deliver a summary of valuable results that represent evidence of principle for epigenetic-based therapeutic approaches employment in CRC with a focus on the advantages of epigenetic-based therapy in the inhibition of the CRC metastasis and proliferation.
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Affiliation(s)
- Saleheh Rezapour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Hosseinzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faroogh Marofi
- Division of Hematology, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Hassanzadeh
- Division of Hematology, Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Li L, Miao W, Huang M, Williams P, Wang Y. Integrated Genomic and Proteomic Analyses Reveal Novel Mechanisms of the Methyltransferase SETD2 in Renal Cell Carcinoma Development. Mol Cell Proteomics 2019; 18:437-447. [PMID: 30487242 PMCID: PMC6398210 DOI: 10.1074/mcp.ra118.000957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/14/2018] [Indexed: 01/20/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type of RCC in humans. SET domain-containing 2 (SETD2), a lysine methyltransferase for histone and other proteins, has been found to be frequently lost in ccRCC. However, the mechanisms through which deficiency in SETD2 contributes to ccRCC development remain largely unknown. Here, we used a human embryonic kidney epithelial cell line with the SETD2 gene being knocked out using CRISPR/Cas9 technology. Using ChIP-seq analysis, we showed that SETD2 loss leads to diminished occupancy of histone H3K36me3 and H4K16ac on actively transcribed genes. Transcriptome sequencing of the knockout cells revealed diminished expression of genes involved in metabolic pathways and elevated expression of genes involved in regulation of RNA polymerase II-mediated transcription. Quantitative proteomic analysis of chromatin-associated proteins showed that genetic ablation of SETD2 leads to elevated chromatin occupancy of proteins involved in chromatin remodeling and RNA polymerase II transcription regulation, and diminished chromatin binding of proteins involved in translation elongation and RNA splicing. Interestingly, we found that SETD2 depletion attenuates cell proliferation, and this can be rescued by knockdown of CDK1. Taken together, we illustrate multiple SETD2-regulated cellular pathways that suppress cancer development and uncover mechanisms underlying aberrant cell cycle regulation in SETD2-depleted cells.
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Affiliation(s)
- Lin Li
- From the ‡Department of Chemistry, University of California, Riverside, California 92521
| | - Weili Miao
- From the ‡Department of Chemistry, University of California, Riverside, California 92521
| | - Ming Huang
- §Environmental Toxicology Graduate Program, University of California, Riverside, California 92521
| | - Preston Williams
- From the ‡Department of Chemistry, University of California, Riverside, California 92521
| | - Yinsheng Wang
- From the ‡Department of Chemistry, University of California, Riverside, California 92521;
- §Environmental Toxicology Graduate Program, University of California, Riverside, California 92521
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29
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Liu Z, Gao Y, Li X. Cancer epigenetics and the potential of epigenetic drugs for treating solid tumors. Expert Rev Anticancer Ther 2018; 19:139-149. [PMID: 30470148 DOI: 10.1080/14737140.2019.1552139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Epigenetic modification without DNA sequence mutation plays an important role in cancer development. Some small molecular inhibitors targeting key epigenetic molecules have been approved by the Food and Drug Administration to treat hematological malignancies. However, the anticancer effects of these drugs on solid tumors are not satisfactory, and the mechanisms of action remain largely unknown. Areas covered: The review summarizes the latest research on cancer epigenetics and discusses the potentials and limitations of using epigenetic drugs to treat solid tumors. An analysis of possible reasons for epigenetic drug treatment failure in solid tumors in some clinical trials is discussed along with prospects for future development. Expert commentary: Next-generation small molecule inhibitors will target novel epigenetic regulators with high cancer specificity. Combined modalities exploiting epigenetic drugs with chemo-/radiotherapy, molecular-targeting drugs, and immunotherapy will be able to effectively treat solid tumors in the near future.
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Affiliation(s)
- Zhenghui Liu
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Yingxue Gao
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Xiong Li
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
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30
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Fellows R, Varga-Weisz P. In vitro Enzymatic Assays of Histone Decrotonylation on Recombinant Histones. Bio Protoc 2018; 8:e2924. [PMID: 30283810 PMCID: PMC6166789 DOI: 10.21769/bioprotoc.2924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Class I histone deacetylases (HDACs) are efficient histone decrotonylases, broadening the enzymatic spectrum of these important (epi-)genome regulators and drug targets. Here, we describe an in vitro approach to assaying class I HDACs with different acyl-histone substrates, including crotonylated histones and expand this to examine the effect of inhibitors and estimate kinetic constants.
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Affiliation(s)
| | - Patrick Varga-Weisz
- Babraham Institute, Cambridge, UK.,School of Biological Sciences, University of Essex, Colchester, UK
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Role of epigenetic factors in the selection of the alternative splicing isoforms of human KRAS in colorectal cancer cell lines. Oncotarget 2018; 9:20578-20589. [PMID: 29755673 PMCID: PMC5945503 DOI: 10.18632/oncotarget.25016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/17/2018] [Indexed: 01/10/2023] Open
Abstract
Mutation-driven activation of KRAS is crucial to cancer development. The human gene yields four mRNA splicing isoforms, 4A and 4B being translated to protein. Their different properties and oncogenic potential have been studied, but the mechanisms deciding the ratio 4A/4B are not known. To address this issue, the expression of the four KRAS isoforms was determined in 9 human colorectal cancer cell lines. HCT116 and SW48 were further selected because they present the highest difference in the ratio 4A/4B (twice as much in HCT116 than in SW48). Chromatin structure was analysed at the exon 4A, characteristic of isoform 4A, at its intronic borders and at the two flanking exons. The low nucleosome occupancy at exon 4A in both cell lines may result in a fast transcriptional rate, which would explain the general lower abundance of isoform 4A, also found in cells and tissues by other authors, but due to its similarity between both cell lines, chromatin structure does not influence alternative splicing. DNA methylation downstream exon 4A significantly differs in HCT116 and SW48 cells, but the CCCTC-binding factor, which affects the processivity of RNA polymerase and the alternative splicing, does not bind the differentially methylated sequences. Quantitative epigenetic analysis at mononucleosomal level revealed significant differences between both cell lines in H3K4me3, H3K27me3, H3K36me3, H3K9ac, H3K27ac and H4K20me1, and the inhibition of some histone-modifying enzymes alters the ratio 4A/4B. It can be concluded that the epigenetic modification of histones has an influence on the selection of isoforms 4A and 4B.
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