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Nacev BA, Dabas Y, Paul MR, Pacheco C, Mitchener M, Perez Y, Fang Y, Soshnev AA, Barrows D, Carroll T, Socci ND, St Jean SC, Tiwari S, Gruss MJ, Monette S, Tap WD, Garcia BA, Muir T, Allis CD. Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation. Nat Commun 2024; 15:5155. [PMID: 38886411 PMCID: PMC11183192 DOI: 10.1038/s41467-024-49486-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Dysregulated epigenetic states are a hallmark of cancer and often arise from genetic alterations in epigenetic regulators. This includes missense mutations in histones, which, together with associated DNA, form nucleosome core particles. However, the oncogenic mechanisms of most histone mutations are unknown. Here, we demonstrate that cancer-associated histone mutations at arginines in the histone H3 N-terminal tail disrupt repressive chromatin domains, alter gene regulation, and dysregulate differentiation. We find that histone H3R2C and R26C mutants reduce transcriptionally repressive H3K27me3. While H3K27me3 depletion in cells expressing these mutants is exclusively observed on the minor fraction of histone tails harboring the mutations, the same mutants recurrently disrupt broad H3K27me3 domains in the chromatin context, including near developmentally regulated promoters. H3K27me3 loss leads to de-repression of differentiation pathways, with concordant effects between H3R2 and H3R26 mutants despite different proximity to the PRC2 substrate, H3K27. Functionally, H3R26C-expressing mesenchymal progenitor cells and murine embryonic stem cell-derived teratomas demonstrate impaired differentiation. Collectively, these data show that cancer-associated H3 N-terminal arginine mutations reduce PRC2 activity and disrupt chromatin-dependent developmental functions, a cancer-relevant phenotype.
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Affiliation(s)
- Benjamin A Nacev
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA.
| | - Yakshi Dabas
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Christian Pacheco
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Michelle Mitchener
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Yekaterina Perez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yan Fang
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Samantha C St Jean
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sagarika Tiwari
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
| | - Michael J Gruss
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tom Muir
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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Machado JPD, de Almeida V, Zuardi AW, Hallak JEC, Crippa JA, Vieira AS. Cannabidiol modulates hippocampal genes involved in mitochondrial function, ribosome biogenesis, synapse organization, and chromatin modifications. Acta Neuropsychiatr 2024:1-7. [PMID: 38528655 DOI: 10.1017/neu.2024.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
BACKGROUND Cannabidiol (CBD) is one of the main cannabinoids present in Cannabis sativa female flowers. Previous investigation has already provided insights into the CBD molecular mechanism; however, there is no transcriptome data for CBD effects on hippocampal subfields. Here, we investigate transcriptomic changes in dorsal and ventral CA1 of adult mice hippocampus after 100 mg/kg of CBD administration (i.p.) for one or seven consecutive days. METHODS C57BL/6JUnib mice were treated with either vehicle or CBD for 1 or 7 days. The collected brains were sectioned, and the hippocampal sub-regions were laser microdissected for RNA-Seq analysis. RESULTS The transcriptome analysis following 7 days of CBD administration indicates the differential expression of 1559 genes in dCA1 and 2924 genes in vCA1. Furthermore, GO/KEGG analysis identified 88 significantly enriched biological process and 26 significantly enriched pathways for dCBD7, whereas vCBD7 revealed 128 enriched BPs and 24 pathways. CONCLUSION This dataset indicates a widespread decrease of electron transport chain and ribosome biogenesis transcripts in CA1, while chromatin modifications and synapse organization transcripts were increased following CBD administration for 7 days.
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Affiliation(s)
- João P D Machado
- Laboratory of Electrophysiology, Neurobiology and Behaviour, Dept Functional and Structural Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Valéria de Almeida
- Laboratory of Neuroproteomics,, Dept Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinsas, São Paulo, Brazil
| | - Antonio W Zuardi
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute for Science and Technology - Translational Medicine, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jaime E C Hallak
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute for Science and Technology - Translational Medicine, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José A Crippa
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute for Science and Technology - Translational Medicine, Rio de Janeiro, Rio de Janeiro, Brazil
| | - André S Vieira
- Laboratory of Electrophysiology, Neurobiology and Behaviour, Dept Functional and Structural Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
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Bhat GR, Sethi I, Sadida HQ, Rah B, Mir R, Algehainy N, Albalawi IA, Masoodi T, Subbaraj GK, Jamal F, Singh M, Kumar R, Macha MA, Uddin S, Akil ASAS, Haris M, Bhat AA. Cancer cell plasticity: from cellular, molecular, and genetic mechanisms to tumor heterogeneity and drug resistance. Cancer Metastasis Rev 2024; 43:197-228. [PMID: 38329598 PMCID: PMC11016008 DOI: 10.1007/s10555-024-10172-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
Cancer is a complex disease displaying a variety of cell states and phenotypes. This diversity, known as cancer cell plasticity, confers cancer cells the ability to change in response to their environment, leading to increased tumor diversity and drug resistance. This review explores the intricate landscape of cancer cell plasticity, offering a deep dive into the cellular, molecular, and genetic mechanisms that underlie this phenomenon. Cancer cell plasticity is intertwined with processes such as epithelial-mesenchymal transition and the acquisition of stem cell-like features. These processes are pivotal in the development and progression of tumors, contributing to the multifaceted nature of cancer and the challenges associated with its treatment. Despite significant advancements in targeted therapies, cancer cell adaptability and subsequent therapy-induced resistance remain persistent obstacles in achieving consistent, successful cancer treatment outcomes. Our review delves into the array of mechanisms cancer cells exploit to maintain plasticity, including epigenetic modifications, alterations in signaling pathways, and environmental interactions. We discuss strategies to counteract cancer cell plasticity, such as targeting specific cellular pathways and employing combination therapies. These strategies promise to enhance the efficacy of cancer treatments and mitigate therapy resistance. In conclusion, this review offers a holistic, detailed exploration of cancer cell plasticity, aiming to bolster the understanding and approach toward tackling the challenges posed by tumor heterogeneity and drug resistance. As articulated in this review, the delineation of cellular, molecular, and genetic mechanisms underlying tumor heterogeneity and drug resistance seeks to contribute substantially to the progress in cancer therapeutics and the advancement of precision medicine, ultimately enhancing the prospects for effective cancer treatment and patient outcomes.
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Affiliation(s)
- Gh Rasool Bhat
- Advanced Centre for Human Genetics, Sher-I-Kashmir Institute of Medical Sciences, Soura, Srinagar, Jammu and Kashmir, India
| | - Itty Sethi
- Institute of Human Genetics, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Hana Q Sadida
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Bilal Rah
- Iron Biology Group, Research Institute of Medical and Health Science, University of Sharjah, Sharjah, UAE
| | - Rashid Mir
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Prince Fahad Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | - Naseh Algehainy
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Prince Fahad Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Tariq Masoodi
- Laboratory of Cancer Immunology and Genetics, Sidra Medicine, Doha, Qatar
| | | | - Farrukh Jamal
- Dr. Rammanohar, Lohia Avadh University, Ayodhya, India
| | - Mayank Singh
- Department of Medical Oncology (Lab.), Institute of Medical Sciences (AIIMS), Dr. BRAIRCH, All India, New Delhi, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Jammu and Kashmir, India
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- Laboratory Animal Research Centre, Qatar University, Doha, Qatar
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Mohammad Haris
- Laboratory Animal Research Centre, Qatar University, Doha, Qatar.
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar.
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Lin YZ, Liu WH, Wu YP, Cai H, Zheng QS, Wei Y, Xu N, Xue XY. Revealing the potential of solute carrier family 31 (copper transporters), member 1: Insights into its role in bladder cancer progression and therapeutic implications. Int J Immunopathol Pharmacol 2024; 38:3946320241240706. [PMID: 38712735 PMCID: PMC11080779 DOI: 10.1177/03946320241240706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/26/2024] [Indexed: 05/08/2024] Open
Abstract
Introduction: Bladder cancer represents a significant public health concern with diverse genetic alterations influencing disease onset, progression, and therapy response. In this study, we explore the multifaceted role of Solute Carrier Family 31 Member 1 (SLC31A1) in bladder cancer, a pivotal gene involved in copper homeostasis. Methods: Our research involved analyzing the SLC31A1 gene expression via RT-qPCR, promoter methylation via targeted bisulfite sequencing, and mutational status via Next Generation Sequencing (NGS) using the clinical samples sourced by the local bladder cancer patients. Later on, The Cancer Genome Atlas (TCGA) datasets were utilized for validation purposes. Moreover, prognostic significance, gene enrichment terms, and therapeutic drugs of SLC31A1 were also explored using KM Plotter, DAVID, and DrugBank databases. Results: We observed that SLC31A1 was significantly up-regulated at both the mRNA and protein levels in bladder cancer tissue samples, suggesting its potential involvement in bladder cancer development and progression. Furthermore, our investigation into the methylation status revealed that SLC31A1 was significantly hypomethylated in bladder cancer tissues, which may contribute to its overexpression. The ROC analysis of the SLC31A1 gene indicated promising diagnostic potential, emphasizing its relevance in distinguishing bladder cancer patients from normal individuals. However, it is crucial to consider other factors such as cancer stage, metastasis, and recurrence for a more accurate evaluation in the clinical context. Interestingly, mutational analysis of SLC31A1 demonstrated only benign mutations, indicating their unknown role in the SLC31A1 disruption. In addition to its diagnostic value, high SLC31A1 expression was associated with poorer overall survival (OS) in bladder cancer patients, shedding light on its prognostic relevance. Gene enrichment analysis indicated that SLC31A1 could influence metabolic and copper-related processes, further underscoring its role in bladder cancer. Lastly, we explored the DrugBank database to identify potential therapeutic agents capable of reducing SLC31A1 expression. Our findings unveiled six important drugs with the potential to target SLC31A1 as a treatment strategy. Conclusion: Our comprehensive investigation highlights SLC31A1 as a promising biomarker for bladder cancer development, progression, and therapy.
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Affiliation(s)
- Yun-Zhi Lin
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wei-hui Liu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yu-Peng Wu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Hai Cai
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qing-Shui Zheng
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yong Wei
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ning Xu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xue-Yi Xue
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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Alfaro-Murillo JA, Townsend JP. Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis. Math Biosci 2023; 366:109091. [PMID: 37996064 PMCID: PMC10847963 DOI: 10.1016/j.mbs.2023.109091] [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: 05/02/2023] [Revised: 09/21/2023] [Accepted: 10/20/2023] [Indexed: 11/25/2023]
Abstract
Cancer occurs as a consequence of multiple somatic mutations that lead to uncontrolled cell growth. Mutual exclusivity and co-occurrence of mutations imply-but do not prove-that mutations exert synergistic or antagonistic epistatic effects on oncogenesis. Knowledge of these interactions, and the consequent trajectories of mutation and selection that lead to cancer has been a longstanding goal within the cancer research community. Recent research has revealed mutation rates and scaled selection coefficients for specific recurrent variants across many cancer types. However, there are no current methods to quantify the strength of selection incorporating pairwise and higher-order epistatic effects on selection within the trajectory of likely cancer genotoypes. Therefore, we have developed a continuous-time Markov chain model that enables the estimation of mutation origination and fixation (flux), dependent on somatic cancer genotype. Coupling this continuous-time Markov chain model with a deconvolution approach provides estimates of underlying mutation rates and selection across the trajectory of oncogenesis. We demonstrate computation of fluxes and selection coefficients in a somatic evolutionary model for the four most frequently variant driver genes (TP53, LRP1B, KRAS and STK11) from 565 cases of lung adenocarcinoma. Our analysis reveals multiple antagonistic epistatic effects that reduce the possible routes of oncogenesis, and inform cancer research regarding viable trajectories of somatic evolution whose progression could be forestalled by precision medicine. Synergistic epistatic effects are also identified, most notably in the somatic genotype TP53 LRP1B for mutations in the KRAS gene, and in somatic genotypes containing KRAS or TP53 mutations for mutations in the STK11 gene. Large positive fluxes of KRAS variants were driven by large selection coefficients, whereas the flux toward LRP1B mutations was substantially aided by a large mutation rate for this gene. The approach enables inference of the most likely routes of site-specific variant evolution and estimation of the strength of selection operating on each step along the route, a key component of what we need to know to develop and implement personalized cancer therapies.
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Affiliation(s)
- Jorge A Alfaro-Murillo
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States of America
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States of America; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States of America.
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Lee SW, Frankston CM, Kim J. Epigenome editing in cancer: Advances and challenges for potential therapeutic options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:191-230. [PMID: 38359969 DOI: 10.1016/bs.ircmb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cancers are diseases caused by genetic and non-genetic environmental factors. Epigenetic alterations, some attributed to non-genetic factors, can lead to cancer development. Epigenetic changes can occur in tumor suppressors or oncogenes, or they may contribute to global cell state changes, making cells abnormal. Recent advances in gene editing technology show potential for cancer treatment. Herein, we will discuss our current knowledge of epigenetic alterations occurring in cancer and epigenetic editing technologies that can be applied to developing therapeutic options.
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Affiliation(s)
- Seung-Won Lee
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Connor Mitchell Frankston
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Biomedical Engineering Graduate Program, Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Jungsun Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States; Cancer Biology Research Program, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States.
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8
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Navickas SM, Giles KA, Brettingham-Moore KH, Taberlay PC. The role of chromatin remodeler SMARCA4/BRG1 in brain cancers: a potential therapeutic target. Oncogene 2023:10.1038/s41388-023-02773-9. [PMID: 37433987 PMCID: PMC10374441 DOI: 10.1038/s41388-023-02773-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/16/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
The chromatin remodeler SMARCA4/BRG1 is a key epigenetic regulator with diverse roles in coordinating the molecular programs that underlie brain tumour development. BRG1 function in brain cancer is largely specific to the tumour type and varies further between tumour subtypes, highlighting its complexity. Altered SMARCA4 expression has been linked to medulloblastoma, low-grade gliomas such as oligodendroglioma, high-grade gliomas such as glioblastoma and atypical/teratoid rhabdoid tumours. SMARCA4 mutations in brain cancer predominantly occur in the crucial catalytic ATPase domain, which is associated with tumour suppressor activity. However, SMARCA4 is opposingly seen to promote tumourigenesis in the absence of mutation and through overexpression in other brain tumours. This review explores the multifaceted interaction between SMARCA4 and various brain cancer types, highlighting its roles in tumour pathogenesis, the pathways it regulates, and the advances that have been made in understanding the functional relevance of mutations. We discuss developments made in targeting SMARCA4 and the potential to translate these to adjuvant therapies able to enhance current methods of brain cancer treatment.
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Affiliation(s)
- Sophie M Navickas
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Katherine A Giles
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Kate H Brettingham-Moore
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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9
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Craddock J, Jiang J, Patrick SM, Mutambirwa SBA, Stricker PD, Bornman MSR, Jaratlerdsiri W, Hayes VM. Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities. Cancers (Basel) 2023; 15:3462. [PMID: 37444571 DOI: 10.3390/cancers15133462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Prostate cancer is driven by acquired genetic alterations, including those impacting the epigenetic machinery. With African ancestry as a significant risk factor for aggressive disease, we hypothesize that dysregulation among the roughly 656 epigenetic genes may contribute to prostate cancer health disparities. Investigating prostate tumor genomic data from 109 men of southern African and 56 men of European Australian ancestry, we found that African-derived tumors present with a longer tail of epigenetic driver gene candidates (72 versus 10). Biased towards African-specific drivers (63 versus 9 shared), many are novel to prostate cancer (18/63), including several putative therapeutic targets (CHD7, DPF3, POLR1B, SETD1B, UBTF, and VPS72). Through clustering of all variant types and copy number alterations, we describe two epigenetic PCa taxonomies capable of differentiating patients by ancestry and predicted clinical outcomes. We identified the top genes in African- and European-derived tumors representing a multifunctional "generic machinery", the alteration of which may be instrumental in epigenetic dysregulation and prostate tumorigenesis. In conclusion, numerous somatic alterations in the epigenetic machinery drive prostate carcinogenesis, but African-derived tumors appear to achieve this state with greater diversity among such alterations. The greater novelty observed in African-derived tumors illustrates the significant clinical benefit to be derived from a much needed African-tailored approach to prostate cancer healthcare aimed at reducing prostate cancer health disparities.
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Affiliation(s)
- Jenna Craddock
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa 0208, South Africa
| | - Phillip D Stricker
- Department of Urology, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Vanessa M Hayes
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
- Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
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10
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Ashcroft CR, Penney SW, Whiteway SL. Treatment Refractory Soft Tissue Myoepithelial Carcinoma With an ARID1A Mutation. J Pediatr Hematol Oncol 2023; 45:e539-e542. [PMID: 37083274 DOI: 10.1097/mph.0000000000002650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/02/2023] [Indexed: 04/22/2023]
Abstract
Soft tissue myoepithelial carcinoma is a rare tumor first reported in the salivary gland. There is considerable tumor heterogeneity between pathology findings, tumor aggressiveness, and response to treatment. Recent molecular testing has identified recurrent genetic changes with PLAG mutations in salivary gland primary tumors and loss of SMARCB1 and EWSR1/FUS gene changes in myoepithelial carcinoma. SMARCB1 is a component of the switch/sucrose nonfermentable (SWI/SNF) complex, an essential cellular regulator. ARID1A is another SWI/SNF complex subunit and is a potent oncogenic driver in other tumor types. In this case, we describe the case of an adolescent/young adult patient with treatment refractory soft tissue myoepithelial carcinoma and a previously unreported ARID1A mutation.
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Affiliation(s)
| | - Scott W Penney
- Pediatrics, Brooke Army Medical Center, Fort Sam Houston, TX
| | - Susan L Whiteway
- Department of Pediatrics, Walter Reed National Military Medical Center, Bethesda, MD
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11
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Szczepanek J, Skorupa M, Jarkiewicz-Tretyn J, Cybulski C, Tretyn A. Harnessing Epigenetics for Breast Cancer Therapy: The Role of DNA Methylation, Histone Modifications, and MicroRNA. Int J Mol Sci 2023; 24:ijms24087235. [PMID: 37108398 PMCID: PMC10138995 DOI: 10.3390/ijms24087235] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/24/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Breast cancer exhibits various epigenetic abnormalities that regulate gene expression and contribute to tumor characteristics. Epigenetic alterations play a significant role in cancer development and progression, and epigenetic-targeting drugs such as DNA methyltransferase inhibitors, histone-modifying enzymes, and mRNA regulators (such as miRNA mimics and antagomiRs) can reverse these alterations. Therefore, these epigenetic-targeting drugs are promising candidates for cancer treatment. However, there is currently no effective epi-drug monotherapy for breast cancer. Combining epigenetic drugs with conventional therapies has yielded positive outcomes and may be a promising strategy for breast cancer therapy. DNA methyltransferase inhibitors, such as azacitidine, and histone deacetylase inhibitors, such as vorinostat, have been used in combination with chemotherapy to treat breast cancer. miRNA regulators, such as miRNA mimics and antagomiRs, can alter the expression of specific genes involved in cancer development. miRNA mimics, such as miR-34, have been used to inhibit tumor growth, while antagomiRs, such as anti-miR-10b, have been used to inhibit metastasis. The development of epi-drugs that target specific epigenetic changes may lead to more effective monotherapy options in the future.
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Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Monika Skorupa
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
| | | | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-204 Szczecin, Poland
| | - Andrzej Tretyn
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
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12
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Johnson ML, Strauss J, Patel MR, Garon EB, Eaton KD, Neskorik T, Morin J, Chao R, Halmos B. Mocetinostat in Combination With Durvalumab for Patients With Advanced NSCLC: Results From a Phase I/II Study. Clin Lung Cancer 2023; 24:218-227. [PMID: 36890020 DOI: 10.1016/j.cllc.2023.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023]
Abstract
BACKGROUND Histone deacetylase (HDAC) inhibitors have potential to augment the effectiveness of immune checkpoint inhibitors and overcome treatment resistance. This dose-escalation/expansion study (NCT02805660) investigated mocetinostat (class I/IV HDAC inhibitor) plus durvalumab in patients with advanced non-small cell lung cancer (NSCLC) across cohorts defined by tumor programmed death-ligand 1 (PD-L1) expression and prior experience with anti-programmed cell death protein-1 (anti-PD-1) or anti-PD-L1 regimens. PATIENTS AND METHODS Sequential cohorts of patients with solid tumors received mocetinostat (starting dose: 50 mg TIW) plus durvalumab at a standard dose (1500 mg Q4W) to determine the recommended phase II dose (RP2D: phase I primary endpoint), based on the observed safety profile. RP2D was administered to patients with advanced NSCLC across 4 cohorts grouped by tumor PD-L1 expression (none or low/high) and prior experience with anti-PD-L1 /anti-PD-1 agents (naïve, clinical benefit: yes/no). The phase II primary endpoint was objective response rate (ORR, RECIST v1.1). RESULTS Eighty-three patients were enrolled (phase I [n = 20], phase II [n = 63]). RP2D was mocetinostat 70 mg TIW plus durvalumab. ORR was 11.5% across the phase II cohorts, and responses were durable (median 329 days). Clinical activity was observed in NSCLC patients with disease refractory to prior checkpoint inhibitor treatment: ORR 23.1%. Across all patients, fatigue (41%), nausea (40%), and diarrhea (31%) were the most frequent treatment-related adverse events. CONCLUSION Mocetinostat 70 mg TIW plus durvalumab at the standard dose was generally well tolerated. Clinical activity was observed in patients with NSCLC unresponsive to prior anti-PD-(L)1 therapy.
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Affiliation(s)
| | | | - Manish R Patel
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis, MN
| | - Edward B Garon
- Department of Medicine, David Geffen School of Medicine at UCLA, Santa Monica, CA
| | - Keith D Eaton
- Department of Medicine, Division of Medical Oncology, University of Washington and Fred Hutchinson Cancer Center, Seattle WA
| | - Tavette Neskorik
- Innovative Medicines Development, Mirati Therapeutics Inc., San Diego, CA
| | - Josée Morin
- Innovative Medicines Development, Mirati Therapeutics Inc., San Diego, CA
| | - Richard Chao
- Innovative Medicines Development, Mirati Therapeutics Inc., San Diego, CA
| | - Balazs Halmos
- Department of Oncology, Montefiore Medical Center, Bronx, NY.
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13
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Urwanisch L, Unger MS, Sieberer H, Dang HH, Neuper T, Regl C, Vetter J, Schaller S, Winkler SM, Kerschbamer E, Weichenberger CX, Krenn PW, Luciano M, Pleyer L, Greil R, Huber CG, Aberger F, Horejs-Hoeck J. The Class IIA Histone Deacetylase (HDAC) Inhibitor TMP269 Downregulates Ribosomal Proteins and Has Anti-Proliferative and Pro-Apoptotic Effects on AML Cells. Cancers (Basel) 2023; 15:cancers15041039. [PMID: 36831382 PMCID: PMC9953883 DOI: 10.3390/cancers15041039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by altered myeloid progenitor cell proliferation and differentiation. As in many other cancers, epigenetic transcriptional repressors such as histone deacetylases (HDACs) are dysregulated in AML. Here, we investigated (1) HDAC gene expression in AML patients and in different AML cell lines and (2) the effect of treating AML cells with the specific class IIA HDAC inhibitor TMP269, by applying proteomic and comparative bioinformatic analyses. We also analyzed cell proliferation, apoptosis, and the cell-killing capacities of TMP269 in combination with venetoclax compared to azacitidine plus venetoclax, by flow cytometry. Our results demonstrate significantly overexpressed class I and class II HDAC genes in AML patients, a phenotype which is conserved in AML cell lines. In AML MOLM-13 cells, TMP269 treatment downregulated a set of ribosomal proteins which are overexpressed in AML patients at the transcriptional level. TMP269 showed anti-proliferative effects and induced additive apoptotic effects in combination with venetoclax. We conclude that TMP269 exerts anti-leukemic activity when combined with venetoclax and has potential as a therapeutic drug in AML.
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Affiliation(s)
- Laura Urwanisch
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Michael Stefan Unger
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Helene Sieberer
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Hieu-Hoa Dang
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Theresa Neuper
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Christof Regl
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Julia Vetter
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg im Muehlkreis, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg im Muehlkreis, Austria
| | - Stephan M. Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg im Muehlkreis, Austria
| | - Emanuela Kerschbamer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via A. Volta 21, 39100 Bolzano, Italy
| | - Christian X. Weichenberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via A. Volta 21, 39100 Bolzano, Italy
| | - Peter W. Krenn
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Michela Luciano
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Lisa Pleyer
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- IIIrd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, 5020 Salzburg, Austria
| | - Richard Greil
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- IIIrd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Fritz Aberger
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Jutta Horejs-Hoeck
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Correspondence: ; Tel.: +43-(0)662-8044-5709
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The Role of Epigenetics in Brain and Spinal Cord Tumors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1394:119-136. [PMID: 36587385 DOI: 10.1007/978-3-031-14732-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Identification of distinct genetic and epigenetic profiles in various neuroepithelial tumors has improved the classification and uncovered novel diagnostic, prognostic, and predictive molecular biomarkers for improved prediction of treatment response and outcome. Especially, in pediatric high-grade brain tumors, such as diffuse midline glioma, H3K27M-altered and posterior fossa group A-ependymoma, epigenetic changes predominate, along with changes in expression of known oncogenes and tumor suppressor genes induced by histone modifications and DNA methylation. The precise role of epigenetic abnormalities is important for understanding tumorigenesis and the establishment of brain tumor treatment strategies. Using powerful epigenetic-based therapies for cancer cells, the aberrantly regulated epigenome can be restored to a more normal state through epigenetic reprogramming. Combinations of agents targeting DNA methylation and/or other epigenetic modifications may be a promising cancer treatment. Therefore, the integration of multi-omics data including epigenomics is now important for classifying primary brain tumors and predicting their biological behavior. Recent advances in molecular genetics and epigenetic integrated diagnostics of brain tumors influence new strategies for targeted therapy.
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15
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McCornack C, Woodiwiss T, Hardi A, Yano H, Kim AH. The function of histone methylation and acetylation regulators in GBM pathophysiology. Front Oncol 2023; 13:1144184. [PMID: 37205197 PMCID: PMC10185819 DOI: 10.3389/fonc.2023.1144184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/29/2023] [Indexed: 05/21/2023] Open
Abstract
Glioblastoma (GBM) is the most common and lethal primary brain malignancy and is characterized by a high degree of intra and intertumor cellular heterogeneity, a starkly immunosuppressive tumor microenvironment, and nearly universal recurrence. The application of various genomic approaches has allowed us to understand the core molecular signatures, transcriptional states, and DNA methylation patterns that define GBM. Histone posttranslational modifications (PTMs) have been shown to influence oncogenesis in a variety of malignancies, including other forms of glioma, yet comparatively less effort has been placed on understanding the transcriptional impact and regulation of histone PTMs in the context of GBM. In this review we discuss work that investigates the role of histone acetylating and methylating enzymes in GBM pathogenesis, as well as the effects of targeted inhibition of these enzymes. We then synthesize broader genomic and epigenomic approaches to understand the influence of histone PTMs on chromatin architecture and transcription within GBM and finally, explore the limitations of current research in this field before proposing future directions for this area of research.
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Affiliation(s)
- Colin McCornack
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, United States
| | - Timothy Woodiwiss
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa, IA, United States
| | - Angela Hardi
- Bernard Becker Medical Library, Washington University School of Medicine, St. Louis, MO, United States
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Albert H. Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, United States
- *Correspondence: Albert H. Kim,
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16
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The R736H cancer mutation in DNMT3A modulates the properties of the FF-subunit interface. Biochimie 2022; 208:66-74. [PMID: 36528185 DOI: 10.1016/j.biochi.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
The DNMT3A DNA methyltransferase is an important epigenetic enzyme that is frequently mutated in cancers, particularly in AML. The heterozygous R736H mutation in the FF-interface of the tetrameric enzyme is the second most frequently observed DNMT3A cancer mutation, but its pathogenic mechanism is unclear. We show here that R736H leads to a moderate reduction in catalytic activity of 20-40% depending on the substrate, but no changes in CpG specificity, flanking sequence preferences and subnuclear localization. Strikingly, R736H showed a very strong stimulation by DNMT3L and the R736H/DNMT3L complex was 3-fold more active than WT/DNMT3L. Similarly, formation of mixed R736H/DNMT3A WT FF-interfaces led to an increased activity. R736H/DNMT3L and mixed R736H/DNMT3A WT FF-interfaces were less stable than interfaces not involving R736H, suggesting that an increased flexibility of the mixed interfaces stimulates catalytic activity. Our data suggest that aberrant activity of DNMT3A R736H may lead to DNA hypermethylation in cancer cells which could cause changes in gene expression.
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17
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Qi L, Zhang W, Ren X, Xu R, Yang Z, Chen R, Tu C, Li Z. Cross-Talk of Multiple Types of RNA Modification Regulators Uncovers the Tumor Microenvironment and Immune Infiltrates in Soft Tissue Sarcoma. Front Immunol 2022; 13:921223. [PMID: 35860263 PMCID: PMC9289169 DOI: 10.3389/fimmu.2022.921223] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/02/2022] [Indexed: 01/10/2023] Open
Abstract
BackgroundSoft-tissue sarcoma (STS) represents a rare and diverse cohort of solid tumors, and encompasses over 100 various histologic and molecular subtypes. In recent years, RNA modifications including m6A, m5C, m1A, and m7G have been demonstrated to regulate immune response and tumorigenesis. Nevertheless, the cross-talk among these RNA modification regulators and related effects upon the tumor microenvironment (TME), immune infiltrates, and immunotherapy in STS remain poorly understood.MethodsIn this study, we comprehensively investigated transcriptional and genetic alterations of 32 RNA modification regulators in STS patients from The Cancer Genome Atlas (TCGA) cohort and validated them in the Gene Expression Omnibus (GEO) cohort. Single-cell transcriptomes were introduced to identify regulators within specific cell types, with own sequencing data and RT-qPCR conducted for biological validation. Distinct regulator clusters and regulator gene subtypes were identified by using unsupervised consensus clustering analysis. We further built the regulator score model based on the prognostic regulator-related differentially expressed genes (DEGs), which could be used to quantitatively assess the risk for individual STS patients. The clinical and biological characteristics of different regulator score groups were further examined.ResultsA total of 455 patients with STS were included in this analysis. The network of 32 RNA modification regulators demonstrated significant correlations within multiple different RNA modification types. Distinct regulator clusters and regulator gene subtypes were characterized by markedly different prognoses and TME landscapes. The low regulator score group in the TCGA-SARC cohort was characterized by poor prognosis. The robustness of the scoring model was further confirmed by the external validation in GSE30929 and GSE17674. The regulator score was negatively correlated with CD4+ T cell, Th2 cell, and Treg cell recruitment and most immunotherapy-predicted pathways, and was also associated with immunotherapy efficacy.ConclusionsOverall, our study is the first to demonstrate the cross-talk of RNA modification regulators and the potential roles in TME and immune infiltrates in STS. The individualized assessment based on the regulator score model could facilitate and optimize personalized treatment.
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Affiliation(s)
- Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Wenchao Zhang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Xiaolei Ren
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Ruiling Xu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Zhimin Yang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
- Department of Microbiology, Immunology & Molecular Genetics, UT Health Science Center, University of Texas Long School of Medicine, San Antonio, TX, United States
| | - Ruiqi Chen
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Chao Tu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
- *Correspondence: Zhihong Li, ; Chao Tu,
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
- *Correspondence: Zhihong Li, ; Chao Tu,
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18
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Zhang Z, Weng Z, Yao J, Liu D, Zhang L, Zhang L, Xie G. Toehold-mediated nonenzymatic DNA strand displacement coupling UDG mediated PCR and multi-code magnetic beads for DNA genotyping. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Intravesical delivery of KDM6A-mRNA via mucoadhesive nanoparticles inhibits the metastasis of bladder cancer. Proc Natl Acad Sci U S A 2022; 119:2112696119. [PMID: 35131941 PMCID: PMC8851555 DOI: 10.1073/pnas.2112696119] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2021] [Indexed: 12/24/2022] Open
Abstract
This study provides proof-of-principle evidence for intravesical delivery of messenger RNA (mRNA) via a mucoadhesive nanoparticle (NP) strategy and reveals the therapeutic potential of KDM6A in treating bladder cancer metastasis, which remains difficult due to the physiological bladder barriers. The mucoadhesive NPs could protect loaded mRNA, prolong exposure of mRNA in disease sites, and benefit the penetration and effective expression, which all represent challenging hurdles for intravesical delivery of mRNA therapeutics. mRNA local delivery can also avoid potential toxicity issues via systemic delivery and unwanted protein expression throughout the body. We expect this mucoadhesive mRNA nanotechnology can be useful for the effective up-regulation of targeted proteins in bladder tissues in situ for both mechanistic understanding and translational study of bladder-related diseases. Lysine-specific demethylase 6A (KDM6A), also named UTX, is frequently mutated in bladder cancer (BCa). Although known as a tumor suppressor, KDM6A’s therapeutic potential in the metastasis of BCa remains elusive. It also remains difficult to fulfill the effective up-regulation of KDM6A levels in bladder tumor tissues in situ to verify its potential in treating BCa metastasis. Here, we report a mucoadhesive messenger RNA (mRNA) nanoparticle (NP) strategy for the intravesical delivery of KDM6A-mRNA in mice bearing orthotopic Kdm6a-null BCa and show evidence of KDM6A’s therapeutic potential in inhibiting the metastasis of BCa. Through this mucoadhesive mRNA NP strategy, the exposure of KDM6A-mRNA to the in situ BCa tumors can be greatly prolonged for effective expression, and the penetration can be also enhanced by adhering to the bladder for sustained delivery. This mRNA NP strategy is also demonstrated to be effective for combination cancer therapy with other clinically approved drugs (e.g., elemene), which could further enhance therapeutic outcomes. Our findings not only report intravesical delivery of mRNA via a mucoadhesive mRNA NP strategy but also provide the proof-of-concept for the usefulness of these mRNA NPs as tools in both mechanistic understanding and translational study of bladder-related diseases.
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20
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Li Z, Zhang J, Zhou M, Li JL, Qiu QC, Fu JH, Xue SL, Qiu HY. Epigenetic therapy with chidamide alone or combined with 5‑azacitidine exerts antitumour effects on acute myeloid leukaemia cells in vitro. Oncol Rep 2022; 47:66. [PMID: 35103292 PMCID: PMC8848469 DOI: 10.3892/or.2022.8277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/04/2022] [Indexed: 11/06/2022] Open
Abstract
Chidamide, a selective histone deacetylase inhibitor, has antitumour effects. 5‑azacitidine (5‑AZA), a hypomethylating agent, is effective in treating acute myeloid leukaemia (AML) and myelodysplastic syndrome. However, to the best of our knowledge, the effect of chidamide and 5‑AZA on AML cell lines has not been fully investigated. In the present study, the antileukaemia activity of chidamide, alone and in combination with 5‑AZA, was assessed on different subtypes of AML cell lines (M1‑M5) and primary samples from several patients with AML in vitro. The results indicated that the proliferation of leukaemia cells was significantly and dose‑dependently inhibited by chidamide and 5‑AZA alone or in combination. The combination also had marked synergistic effects to induce apoptosis of AML cells. The apoptosis of leukaemia cells was induced via downregulation of BCL‑2 and myeloid‑cell leukemia 1 (MCL‑1) levels. Of note, chidamide also degraded the MCL‑1 protein in venetoclax‑resistant U937 cells, in which the MCL‑1 protein is upregulated. In addition, chidamide was able to induce myeloid differentiation (with CD11b upregulation) of AML cell lines or monocytic/dendritic differentiation (with CD86 upregulation) of primary cultured cells from several patients with AML. Chidamide was also able to promote the differentiation of the venetoclax‑resistant U937 cell line by upregulating CD11b expression. In conclusion, chidamide alone or combined with 5‑AZA may be an effective therapy for AML.
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Affiliation(s)
- Zheng Li
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jian Zhang
- Department of Blood Transfusion, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Min Zhou
- Department of Hematology, Changshu Affiliated Hospital of Soochow University, The First People's Hospital of Changshu, Changshu, Jiangsu 215500, P.R. China
| | - Jin-Li Li
- State Key Laboratory of Radiation Medicine and Protection, Oncology Radiotherapy Department, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Qiao-Cheng Qiu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jian-Hong Fu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Sheng-Li Xue
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Hui-Ying Qiu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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21
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Mack A, Emperle M, Schnee P, Adam S, Pleiss J, Bashtrykov P, Jeltsch A. Preferential self-interaction of DNA methyltransferase DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence preferences. J Mol Biol 2022; 434:167482. [DOI: 10.1016/j.jmb.2022.167482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022]
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23
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Xiang XS, Li PC, Wang WQ, Liu L. Histone deacetylases: A novel class of therapeutic targets for pancreatic cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188676. [PMID: 35016922 DOI: 10.1016/j.bbcan.2022.188676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic cancer is the seventh leading cause of cancer death worldwide, with a low 5-year survival rate. Novel agents are urgently necessary to treat the main pathological type, known as pancreatic ductal carcinoma (PDAC). The dysregulation of histone deacetylases (HDACs) has been identified in association with PDAC, which can be more easily targeted by small molecular inhibitors than gene mutations and may represent a therapeutic breakthrough for PDAC. However, the contributions of HDACs to PDAC remain controversial, and pharmacokinetic challenges have limited the application of HDAC inhibitors (HDACis) in PDAC. This review summarizes the mechanisms associated with success and failure of HDACis in PDAC and discusses the recent progress made in HDACi development and application, such as combination therapies designed to enhance efficacy. More precise strategies involving HDACis might eventually improve the outcomes of PDAC treatment.
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Affiliation(s)
- Xue-Song Xiang
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peng-Cheng Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Quan Wang
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Liang Liu
- Department of Pancreatic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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24
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Wang HC, Shih HY, Wu CC, Chen LT, Luo CW, Liu YC, Du JS, Huang MC, Su YY, Chen HD, Hsiao HH, Moi SH, Pan MR. Clustering of Chromatin Remodeling Enzymes Predicts Prognosis and Clinical Benefit of Therapeutic Strategy in Pancreatic Cancer. Int J Med Sci 2022; 19:1615-1627. [PMID: 36185333 PMCID: PMC9515693 DOI: 10.7150/ijms.73800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
In recent years, translational research and pharmacological targeting of epigenetic modifications have become the focus of personalized therapy for patients with pancreatic cancer. Preclinical and clinical trials targeting post-translational modifications have been evaluated as monotherapy or in combination with standard chemotherapy. In this study, we selected 43 genes from seven families of chromatin-modifying enzymes and investigated the influences of epigenetic modifications and their interactions on pancreatic ductal adenocarcinoma (PDAC) using hierarchical clustering analysis. Our analysis also evaluated their effects on treatment modalities and regimens of chemotherapy for PDAC. RNA-seq data for a total of 177 patients with pancreatic cancer, obtained from The Cancer Genome Atlas database, were analyzed. Our results suggested that high-risk patients of survival significant chromatin remodeling-associated gene cluster (gene cluster 2), composed of histone methyltransferases, histone acetyltransferases, histone deacetylases, histone demethylases, and 10-11 translocation family, demonstrated inferior progression-free survival and overall survival in patients with PDAC, especially in men. Our novel biomarker, survival significant chromatin remodeling-associated gene cluster, showed superior prediction performance compared with the conventional TNM system. Overall, these findings suggest that epigenetic modifications and interactions play an important role in the prognosis and therapeutic response of patients with PDAC.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hsiang-Yao Shih
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Chi-Wen Luo
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Yi-Chang Liu
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jeng-Shiun Du
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Min-Chin Huang
- Specialist Nurse and Surgical Nurse Practitioner Office, Kaohsiung Medical University Chung-Ho Memorial Hospital
| | - Yung-Yeh Su
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Huan-Da Chen
- Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hui-Hua Hsiao
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Sin-Hua Moi
- Center of Cancer Program Development, E-Da Cancer Hospital, I-Shou University, Kaohsiung 807, Taiwan
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital
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25
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Van der Mude A. A proposed Information-Based modality for the treatment of cancer. Biosystems 2021; 211:104587. [PMID: 34915101 DOI: 10.1016/j.biosystems.2021.104587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 11/20/2021] [Accepted: 12/01/2021] [Indexed: 11/02/2022]
Abstract
Treatment modalities for cancer involve physical manipulations such as surgery, immunology, radiation, chemotherapy or gene editing. This is a proposal for an information-based modality. This modality does not change the internal state of the cancer cell directly - instead, the cancer cell is manipulated by giving it information to instruct the cell to perform an action. This modality is based on a theory of Structure Encoding in DNA, where information about body part structure controls the epigenetic state of cells in the process of development from pluripotent cells to fully differentiated cells. It has been noted that cancer is often due to errors in morphogenetic differentiation accompanied by associated epigenetic processes. This implies a model of cancer called the Epigenetic Differentiation Model. A major feature of the Structure Encoding Theory is that the characteristics of the differentiated cell are affected by inter-cellular information passed in the tissue microenvironment, which specifies the exact location of a cell in a body part structure. This is done by exosomes that carry fragments of long non-coding RNA and transposons, which convey structure information. In the normal process of epigenetic differentiation, the information passed may lead to apoptosis due to the constraints of a particular body part structure. The proposed treatment involves determining what structure information is being passed in a particular tumor, then adding artificial exosomes that overwhelm the current information with commands for the cells to go into apoptosis.
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26
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Bagal SK, Gregson C, O' Donovan DH, Pike KG, Bloecher A, Barton P, Borodovsky A, Code E, Fillery SM, Hsu JHR, Kawatkar SP, Li C, Longmire D, Nai Y, Nash SC, Pike A, Robinson J, Read JA, Rawlins PB, Shen M, Tang J, Wang P, Woods H, Williamson B. Diverse, Potent, and Efficacious Inhibitors That Target the EED Subunit of the Polycomb Repressive Complex 2 Methyltransferase. J Med Chem 2021; 64:17146-17183. [PMID: 34807608 DOI: 10.1021/acs.jmedchem.1c01161] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aberrant activity of the histone methyltransferase polycomb repressive complex 2 (PRC2) has been linked to several cancers, with small-molecule inhibitors of the catalytic subunit of the PRC2 enhancer of zeste homologue 2 (EZH2) being recently approved for the treatment of epithelioid sarcoma (ES) and follicular lymphoma (FL). Compounds binding to the EED subunit of PRC2 have recently emerged as allosteric inhibitors of PRC2 methyltransferase activity. In contrast to orthosteric inhibitors that target EZH2, small molecules that bind to EED retain their efficacy in EZH2 inhibitor-resistant cell lines. In this paper we disclose the discovery of potent and orally bioavailable EED ligands with good solubilities. The solubility of the EED ligands was optimized through a variety of design tactics, with the resulting compounds exhibiting in vivo efficacy in EZH2-driven tumors.
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Affiliation(s)
- Sharan K Bagal
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Clare Gregson
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Daniel H O' Donovan
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Kurt G Pike
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Andrew Bloecher
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Peter Barton
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | | | - Erin Code
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Shaun M Fillery
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Jessie Hao-Ru Hsu
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sameer P Kawatkar
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Chengzhi Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - David Longmire
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Youfeng Nai
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Samuel C Nash
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Andrew Pike
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - James Robinson
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Jon A Read
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Phillip B Rawlins
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
| | - Minhui Shen
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jia Tang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Peng Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Haley Woods
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Beth Williamson
- AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, United Kingdom
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Li G, Li D, Yuan F, Cheng C, Chen L, Wei X. Synergistic effect of chidamide and venetoclax on apoptosis in acute myeloid leukemia cells and its mechanism. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1575. [PMID: 34790781 PMCID: PMC8576699 DOI: 10.21037/atm-21-5066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/16/2021] [Indexed: 01/02/2023]
Abstract
Background Acute myeloid leukemia (AML) is a hematological malignancy with a low remission rate and high recurrence rate. Overexpression of the antiapoptotic protein Bcl-2 is associated with a lower overall survival rate in AML patients. Venetoclax (ABT199) is a selective inhibitor of Bcl-2 that has a significant effect in AML, but single-drug resistance often occurs due to the high expression of Mcl-1 protein. Studies have confirmed that chidamide can downregulate the expression levels of Bcl-2 and Mcl-1 and induce apoptosis. Methods This study aimed to use AML cell lines and primary cells to study the effects of venetoclax and chidamide combination therapy on AML cell apoptosis, the cell cycle, and changes in related signaling pathways in vitro; establish an AML mouse model to observe the efficacy and survival time of combination therapy in vivo; and analyze the drug effects with multi-omics sequencing technology. The changes in gene and protein expression before and after treatment were examined to clarify the molecular mechanism driving the synergistic effect of the two drugs. Results (I) Both venetoclax and chidamide promoted apoptosis in AML cell lines and primary cells in a time- and concentration-dependent manner. The effect was further enhanced when the two drugs were combined, and a synergistic effect was observed (combination index <1). (II) At both the mRNA and protein levels, the expression of Mcl-1 was upregulated by venetoclax and downregulated by chidamide, and the expression of Mcl-1 decreased further after combination treatment. (III) Transcriptome sequencing showed that differentially expressed genes in the combination group compared with the venetoclax monotherapy group were mainly enriched in the PI3K-AKT pathway and JAK2/STAT3 pathway. Moreover, qRT-PCR and Western blot confirmed these results. (IV) The combination therapy group exhibited significantly inhibited disease progression and a prolonged survival time among AML mice. Conclusions Chidamide combined with venetoclax synergistically promoted apoptosis in AML cell lines and primary cells by inhibiting activation of the PI3K/AKT pathway and JAK2/STAT3 pathway.
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Affiliation(s)
- Gangping Li
- Department of Hematopathy, Henan Institute of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongbei Li
- Department of Hematopathy, Henan Institute of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Fangfang Yuan
- Department of Hematopathy, Henan Institute of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Cheng Cheng
- Department of Hematopathy, Henan Institute of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Lin Chen
- Department of Hematopathy, Henan Institute of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Xudong Wei
- Department of Hematopathy, Henan Institute of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
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Kdm6a deficiency restricted to mouse hematopoietic cells causes an age- and sex-dependent myelodysplastic syndrome-like phenotype. PLoS One 2021; 16:e0255706. [PMID: 34780480 PMCID: PMC8592440 DOI: 10.1371/journal.pone.0255706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022] Open
Abstract
Kdm6a/Utx, a gene on the X chromosome, encodes a histone H3K27me3 demethylase that has an orthologue on the Y chromosome (Uty) (Zheng et al. 2018). We previously identified inactivating mutations of Kdm6a in approximately 50% of mouse acute promyelocytic leukemia samples; however, somatic mutations of KDM6A are more rare in human AML samples, ranging in frequency from 2–15% in different series of patients, where their role in pathogenesis is not yet clear. In this study, we show that female Kdm6aflox/flox mice (with allele inactivation initiated by Vav1-Cre in hematopoietic stem and progenitor cells (HSPCs) have a sex-specific phenotype that emerges with aging, with features resembling a myelodysplastic syndrome (MDS). Female Kdm6a-knockout (KO) mice have an age-dependent expansion of their HSPCs with aberrant self-renewal, but they did not differentiate normally into downstream progeny. These mice became mildly anemic and thrombocytopenic, but did not develop overt leukemia, or die from these cytopenias. ChIP-seq and ATAC-seq studies showed only minor changes in H3K27me3, H3K27ac, H3K4me, H3K4me3 and chromatin accessibility between Kdm6a-WT and Kdm6a-KO mice. Utilizing scRNA-seq, Kdm6a loss was linked to the transcriptional repression of genes that mediate hematopoietic cell fate determination. These data demonstrate that Kdm6a plays an important role in normal hematopoiesis, and that its inactivation may contribute to AML pathogenesis.
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Integrative analysis of DNA methylation and gene expression profiles to identify biomarkers of glioblastoma. Cancer Genet 2021; 258-259:135-150. [PMID: 34773808 DOI: 10.1016/j.cancergen.2021.10.008] [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] [Received: 06/24/2021] [Revised: 09/21/2021] [Accepted: 10/31/2021] [Indexed: 12/26/2022]
Abstract
Glioblastoma multiforme (GBM) is the most common, most invasive, and malignant type of primary brain tumor with poor prognosis and poor survival rate. Using GSE22891 the expression and methylation status of same GBM patients was evaluated to identify key epigenetic genes in GBM. Using |log2FC| > 1 and FDR 〈 0.05 as the threshold, DEGs including 4910 downregulated and 2478 upregulated were screened and by |log2FC| 〉 0.2 and p-value < 0.05, 3223 DMCs were detected. By merging the results of DEGs and DMCs, 643 genes were selected for network analysis by WGCNA, and based on expression values three modules and by methylation values, one module was selected. Using STRING and Cytoscape databases, PPI network of genes of all modules were constructed separately. According to the PPI network, core genes were picked out. The expression status of core genes was evaluated using GSE77043, GSE42656, GSE30563, GSE22891, GSE15824, and GSE122498, and 50 genes were validated. The methylation status of 50 genes was explored using GSE50923, GSE22891, and GSE36245, and finally, 12 hub genes including ARHGEF7, RAB11FIP4, PPP1R16B, OLFM1, CLDN10, BCAT1, C1QB, C1QC, IFI16, NUP37, PARP9, and PCLAF were selected. Using GEPIA database, the expression and by cBioportal the survival plot and also scatterplot of methylation versus expression of 12 hub genes were extracted based on TCGA. To determine the diagnostic values of the hub genes, the receiver operating characteristic (ROC) curve and the area under the curve (AUC) were extracted based on GSE22891 and GSE122498. Finally, we evaluated the expression level of the genes in tissue of 83 GBM patients and also non-tumoral adjacent (as control) tissues.
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Sahara S, Herzog AE, Nör JE. Systemic therapies for salivary gland adenoid cystic carcinoma. Am J Cancer Res 2021; 11:4092-4110. [PMID: 34659878 PMCID: PMC8493384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023] Open
Abstract
Adenoid cystic carcinoma (ACC) is a slow growing, but relentless cancer. Due to its rarity and lack of understanding of its molecular etiology, no standard chemotherapy for ACC currently exists and many patients suffer from recurrent and/or metastatic disease. As such, development of safe and effective therapies is imperative. To describe and summarize existing clinical trial studies and preclinical discoveries, we surveyed the PubMed on developmental therapeutics for ACC. Objective response rates to monotherapy with cytotoxic agents were approximately 10% with cisplatin, 5-FU, gemcitabine, mitoxantrone, epirubicin, vinorelbine and paclitaxel. The most studied combination therapies were cyclophosphamide-doxorubicin-cisplatin (CAP) and cisplatin-vinorelbine, with an objective response rate of 18-31%. Among molecularly targeted drugs, the most studied drugs are inhibitors targeting the vascular endothelial growth factor receptor (VEGFR) to inhibit tumor angiogenesis. Among those, lenvatinib and axitinib showed a relatively high objective response rate of 11-16% and 9-17%, respectively. Given high recurrence rates and chemoresistance of ACC, treatments targeting cancer stem cells (CSC), which function as tumor-initiating cells and drive chemoresistance, may be particularly valuable. CSC have been shown to be targetable via MYB, Notch1, p53 and epigenetic mechanisms. Myb overexpression is characteristic in ACC but was previously thought to present a difficult target due to its nature as a transcription factor. However, due to the development Myb-targeted inhibitors and an ongoing clinical trial of MYB-targeted cancer vaccine therapy, MYB is becoming an increasingly attractive therapeutic target. Drugs targeting NOTCH signaling demonstrated 5-17% response rate in phase I clinical trials. Within the field of epigenetics, treatment with PRMT5 inhibitors has shown 21% partial response rate in phase I clinical trial. Immunotherapies, such as PD-1 inhibitors, are also associated with CSC, but have not been effective against ACC. However, clinical trials of cancer vaccine therapies are actively being conducted. In addition to conventional chemotherapies and inhibitors of angiogenesis, the emergence of new therapies such as immunotherapy and those targeting cancer stemness is expected to bring clinical benefits to patients in the future.
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Affiliation(s)
- Sosuke Sahara
- Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of DentistryAnn Arbor, Michigan 48109-1078, USA
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of MedicineHamamatsu 431-3192, Japan
| | - Alexandra E Herzog
- Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of DentistryAnn Arbor, Michigan 48109-1078, USA
| | - Jacques E Nör
- Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of DentistryAnn Arbor, Michigan 48109-1078, USA
- Department of Otolaryngology-Head & Neck Surgery, University of Michigan School of MedicineAnn Arbor, Michigan 48109-1078, USA
- Department of Biomedical Engineering, University of Michigan College of EngineeringAnn Arbor, Michigan 48109, USA
- University of Michigan Rogel Cancer CenterAnn Arbor, Michigan 48109, USA
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Mehrpouri M, Pourbagheri-Sigaroodi A, Bashash D. The contributory roles of histone deacetylases (HDACs) in hematopoiesis regulation and possibilities for pharmacologic interventions in hematologic malignancies. Int Immunopharmacol 2021; 100:108114. [PMID: 34492531 DOI: 10.1016/j.intimp.2021.108114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 12/17/2022]
Abstract
Although the definitive role of epigenetic modulations in a wide range of hematologic malignancies, spanning from leukemia to lymphoma and multiple myeloma, has been evidenced, few articles reviewed the task. Given the high accessibility of histone deacetylase (HDACs) to necessary transcription factors involved in hematopoiesis, this review aims to outline physiologic impacts of these enzymes in normal hematopoiesis, and also to outline the original data obtained from international research laboratories on their regulatory role in the differentiation and maturation of different hematopoietic lineages. Questions on how aberrant expression of HDACs contributes to the formation of hematologic malignancies are also responded, because these classes of enzymes have a respectable share in the development, progression, and recurrence of leukemia, lymphoma, and multiple myeloma. The last section provides a special focus on the therapeutic perspectiveof HDACs inhibitors, either as single agents or in a combined-modal strategy, in these neoplasms. In conclusion, optimizing the dose and the design of more patient-tailored inhibitors, while maintaining low toxicity against normal cells, will help improve clinical outcomes of HDAC inhibitors in hematologic malignancies.
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Affiliation(s)
- Mahdieh Mehrpouri
- Department of Laboratory Sciences, School of Allied Medical Sciences, Alborz University of Medical Sciences, Karaj, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Nandi S, Dey R, Dey S, Samadder A, Saxena A. Naturally Sourced CDK Inhibitors and Current Trends in Structure-Based Synthetic Anticancer Drug Design by Crystallography. Anticancer Agents Med Chem 2021; 22:485-498. [PMID: 34503422 DOI: 10.2174/1871520621666210908101751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 06/12/2021] [Accepted: 07/12/2021] [Indexed: 11/22/2022]
Abstract
Cyclin-dependent kinases (CDKs) are the chief regulators in cell proliferation; the kinase activities are largely regulated by their interactions with CDK inhibitors (CKIs) and Cyclins. The association of different CDKs with CDKIs and Cyclins at the cell-cycle checkpoints of different stages of mitotic cell cycle function act more likely as the molecular switches that regulate different transcriptional events required for progression through the cell cycle. A fine balance in response to extracellular and intracellular signals is highly maintained in the orchestrated function of CDKs along with Cyclins and CDKIs for normal cell proliferation. This fine-tuning in mitotic cell cycle progression sometimes gets lost due to dysregulation of CDKs. The aberrant functioning of the CDKIs is therefore studied for its contributions as a vital hallmark of cancers. It has attracted our focus to maneuver cancer therapy. Hence, several synthetic CDKIs and their crystallography-based drug design have been explained to understand their mode of action with CDKs. Since most of the synthetic drugs function by inhibiting the CDK4/6 kinases by competitively binding to their ATP binding cleft, these synthetic drugs are reported to attack the normal, healthy growing cells adjacent to the cancer cells leading to the decrease in the life span of the cancer patients. The quest for traditional natural medicines may have a great impact on the treatment of cancer. Therefore, in the present studies, a search for naturally sourced CDK inhibitors has been briefly focused. Additionally, some synthetic crystallography-based drug design has been explained to elucidate different avenues to develop better anticancer chemotherapeutics, converting natural scaffolds into inhibitors of the CDK mediated abnormal signal transduction with lesser side effects.
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Affiliation(s)
- Sisir Nandi
- Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713. India
| | - Rishita Dey
- Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713. India
| | - Sudatta Dey
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235. India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235. India
| | - Anil Saxena
- Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713. India
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33
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Belikov AV, Vyatkin A, Leonov SV. The Erlang distribution approximates the age distribution of incidence of childhood and young adulthood cancers. PeerJ 2021; 9:e11976. [PMID: 34434669 PMCID: PMC8351573 DOI: 10.7717/peerj.11976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/24/2021] [Indexed: 11/20/2022] Open
Abstract
Background It is widely believed that cancers develop upon acquiring a particular number of (epi) mutations in driver genes, but the law governing the kinetics of this process is not known. We have previously shown that the age distribution of incidence for the 20 most prevalent cancers of old age is best approximated by the Erlang probability distribution. The Erlang distribution describes the probability of several successive random events occurring by the given time according to the Poisson process, which allows an estimate for the number of critical driver events. Methods Here we employ a computational grid search method to find global parameter optima for five probability distributions on the CDC WONDER dataset of the age distribution of childhood and young adulthood cancer incidence. Results We show that the Erlang distribution is the only classical probability distribution we found that can adequately model the age distribution of incidence for all studied childhood and young adulthood cancers, in addition to cancers of old age. Conclusions This suggests that the Poisson process governs driver accumulation at any age and that the Erlang distribution can be used to determine the number of driver events for any cancer type. The Poisson process implies the fundamentally random timing of driver events and their constant average rate. As waiting times for the occurrence of the required number of driver events are counted in decades, and most cells do not live this long, it suggests that driver mutations accumulate silently in the longest-living dividing cells in the body—the stem cells.
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Affiliation(s)
- Aleksey V Belikov
- Laboratory of Innovative Medicine, School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alexey Vyatkin
- Laboratory of Innovative Medicine, School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Sergey V Leonov
- Laboratory of Innovative Medicine, School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
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Bussey KJ, Davies PCW. Reverting to single-cell biology: The predictions of the atavism theory of cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:49-55. [PMID: 34371024 DOI: 10.1016/j.pbiomolbio.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Cancer or cancer-like phenomena pervade multicellular life, implying deep evolutionary roots. Many of the hallmarks of cancer recapitulate unicellular modalities, suggesting that cancer initiation and progression represent a systematic reversion to simpler ancestral phenotypes in response to a stress or insult. This so-called atavism theory may be tested using phylostratigraphy, which can be used to assign ages to genes. Several research groups have confirmed that cancer cells tend to over-express evolutionary older genes, and rewire the architecture linking unicellular and multicellular gene networks. In addition, some of the elevated mutation rate - a well-known hallmark of cancer - is actually self-inflicted, driven by genes found to be homologs of the ancient SOS genes activated in stressed bacteria, and employed to evolve biological workarounds. These findings have obvious implications for therapy.
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Affiliation(s)
- Kimberly J Bussey
- Precision Medicine, Midwestern University, Glendale, AZ, USA; The BEYOND Center for Fundamental Concepts in Science, Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Paul C W Davies
- The BEYOND Center for Fundamental Concepts in Science, Department of Physics, Arizona State University, Tempe, AZ, USA.
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Karol D, McKinnon M, Mukhtar L, Awan A, Lo B, Wheatley-Price P. The Impact of Foundation Medicine Testing on Cancer Patients: A Single Academic Centre Experience. Front Oncol 2021; 11:687730. [PMID: 34381713 PMCID: PMC8350441 DOI: 10.3389/fonc.2021.687730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The use of Next-Generation Sequencing (NGS) has recently allowed significant improvements in cancer treatment. Foundation Medicine® (FM) provides a genomic profiling test based on NGS for a variety of cancers. However, it is unclear if the Foundation Medicine test would result in a better outcome than the standard on-site molecular testing. In this retrospective chart review, we identified the FM cases from an academic Canadian hospital and determined whether these test results improved treatment options for those patients. MATERIALS AND METHODS A retrospective analysis was performed on patients with solid tumors who had FM testing between May 1, 2014 and May 1, 2018. Clinical factors and outcomes were measured using descriptive statistics using Microsoft Excel® Software. RESULTS Out of 66 FM tests, eight patients (= 12%) had a direct change in therapy based on the FM tests. Identified were 285 oncogenic mutations (median 1, range 0-31); where TP53 (n = 31, 10.9%), CDKN2A (n = 19, 6.7%), KRAS (n = 16, 5.6%) and APC (n = 9, 3.2%) were the most common FM mutations identified. CONCLUSION A small proportion of FM reports identified actionable mutations and led to direct treatment change. FM testing is expensive and a few of the identified mutations are now part of routine on-site testing. NGS testing is likely to become more widespread, but this research suggests that its true clinical impact may be restricted to a minority of patients.
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Affiliation(s)
- Dalia Karol
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | | | - Lenah Mukhtar
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Arif Awan
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Medicine, Division of Medical Oncology, The Ottawa Hospital Cancer Centre, Ottawa, ON, Canada
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Bryan Lo
- Department of Anatomical Pathology, The Ottawa Hospital, Ottawa, ON, Canada
| | - Paul Wheatley-Price
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Medicine, Division of Medical Oncology, The Ottawa Hospital Cancer Centre, Ottawa, ON, Canada
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
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de Guillebon E, Jimenez M, Mazzarella L, Betsou F, Stadler P, Peták I, Jeannot E, Chanas L, Servant N, Marret G, Duso BA, Legrand F, Kornerup KN, Bernhart SH, Balogh G, Dóczi R, Filotás P, Curigliano G, Bièche I, Guérin J, Dirner A, Neuzillet C, Girard N, Borcoman E, Larbi Chérif L, Tresca P, Roufai DB, Dupain C, Scholl S, André F, Fernandez X, Filleron T, Kamal M, Le Tourneau C. Combining immunotherapy with an epidrug in squamous cell carcinomas of different locations: rationale and design of the PEVO basket trial. ESMO Open 2021; 6:100106. [PMID: 33865192 PMCID: PMC8066350 DOI: 10.1016/j.esmoop.2021.100106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/12/2021] [Accepted: 03/06/2021] [Indexed: 12/25/2022] Open
Abstract
Squamous cell carcinomas (SCCs) are among the most frequent solid tumors in humans. SCCs, related or not to the human papillomavirus, share common molecular features. Immunotherapies, and specifically immune checkpoint inhibitors, have been shown to improve overall survival in multiple cancer types, including SCCs. However, only a minority of patients experience a durable response with immunotherapy. Epigenetic modulation plays a major role in escaping tumor immunosurveillance and confers resistance to immune checkpoint inhibitors. Preclinical evidence suggests that modulating the epigenome might improve the efficacy of immunotherapy. We herein review the preclinical and the clinical rationale for combining immunotherapy with an epidrug, and detail the design of PEVOsq, a basket clinical trial combining pembrolizumab with vorinostat, a histone deacetylase inhibitor, in patients with SCCs of different locations. Sequential blood and tumor sampling will be collected in order to identify predictive and pharmacodynamics biomarkers of efficacy of the combination. We also present how clinical and biological data will be managed with the aim to enable the development of a prospective integrative platform to allow secure and controlled access to the project data as well as further exploitations.
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Affiliation(s)
- E de Guillebon
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France; Inserm U932 Research Unit - Immunite et cancer, Paris, France
| | | | - L Mazzarella
- Department of Experimental Oncology, European Institute of Oncology - IRCCS, Milan, Italy; Division of Innovative Therapies, European Institute of Oncology - IRCCS, Milan, Italy
| | - F Betsou
- Integrated Biobank of Luxembourg, Dudelange, Luxembourg
| | - P Stadler
- Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany
| | - I Peták
- Oncompass Medicine Ltd, Budapest, Hungary; Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, USA
| | - E Jeannot
- Department of Genetics, Institut Curie, Paris, France; Department of Pathology, Institut Curie, Paris, France
| | - L Chanas
- Data Direction, Institut Curie, Paris, France
| | - N Servant
- Inserm U900 Research Unit, Saint Cloud, France
| | - G Marret
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - B A Duso
- Department of Experimental Oncology, European Institute of Oncology - IRCCS, Milan, Italy
| | | | - K N Kornerup
- Integrated Biobank of Luxembourg, Dudelange, Luxembourg
| | - S H Bernhart
- Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany
| | - G Balogh
- Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany
| | - R Dóczi
- Oncompass Medicine Ltd, Budapest, Hungary
| | - P Filotás
- Oncompass Medicine Ltd, Budapest, Hungary
| | - G Curigliano
- Division of Innovative Therapies, European Institute of Oncology - IRCCS, Milan, Italy; Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary; University of Milano, Milan, Italy
| | - I Bièche
- Department of Genetics, Institut Curie, Paris, France
| | - J Guérin
- Data Direction, Institut Curie, Paris, France
| | - A Dirner
- Oncompass Medicine Ltd, Budapest, Hungary
| | - C Neuzillet
- Department of Medical Oncology, Institut Curie, Paris, France; Paris-Saclay University, Paris, France
| | - N Girard
- Department of Medical Oncology, Institut Curie, Paris, France; Paris-Saclay University, Paris, France
| | - E Borcoman
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - L Larbi Chérif
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - P Tresca
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - D B Roufai
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - C Dupain
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - S Scholl
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - F André
- Department of Medical Oncology, Gustave Roussy, Villejuif; INSERM, Gustave Roussy Cancer Campus, UMR981, Villejuif; University of Paris-Sud, Orsay, France
| | - X Fernandez
- Data Direction, Institut Curie, Paris, France
| | - T Filleron
- Biostatistics Unit, Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - M Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France.
| | - C Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France; Inserm U900 Research Unit, Saint Cloud, France; Paris-Saclay University, Paris, France.
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Chen X, Lin X, Pang G, Deng J, Xie Q, Zhang Z. Significance of KDM6A mutation in bladder cancer immune escape. BMC Cancer 2021; 21:635. [PMID: 34051747 PMCID: PMC8164329 DOI: 10.1186/s12885-021-08372-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/06/2021] [Indexed: 12/14/2022] Open
Abstract
Background Bladder cancer (BC) is the fourth most prevalent neoplasm in men and is associated with high tumour recurrence rates, leading to major treatment challenges. Lysine-specific demethylase 6A (KDM6A) is frequently mutated in several cancer types; however, its effects on tumour progression and clinical outcome in BC remain unclear. Here, we explored the potential role of KDM6A in regulating the antitumor immune response. Methods We mined The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases for somatic mutation and clinical data in patients with BC. Results We found frequent mutations in 12 genes in both cohorts, including TP53, KDM6A, CSMD3, MUC16, STAG2, PIK3CA, ARID1A, RB1, EP300, ERBB2, ERBB3, and FGFR3. The frequency o KDM6A mutations in the TCGA and ICGC datasets was 25.97 and 24.27%, respectively. In addition, KDM6A mutation was associated with a lower number of tumour-infiltrating immune cells (TIICs) and indicated a state of immune tolerance. KDM6A mutation was associated with lower KDM6A mRNA level compared with that in samples carrying the wild-type gene. Further, survival analysis showed that the prognosis of patients with low KDM6A expression was worse than that with high KDM6A expression. Using the CIBERSORT algorithm, Tumor Immune Estimation Resource site, and Gene Set Enrichment Analysis, we found that KDM6A mutation downregulated nine signalling pathways that participate in the immune system and attenuated the tumour immune response. Conclusion Overall, we conclude that KDM6A mutation is frequent in BC and promotes tumour immune escape, which may serve as a novel biomarker to predict the immune response. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08372-9.
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Affiliation(s)
- Xingxing Chen
- Department of Urology, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Kangning Road No.79, in Zhuhai city, Guang Dong Province, Zhuhai, People's Republic of China
| | - Xuehua Lin
- Department of Urology, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Kangning Road No.79, in Zhuhai city, Guang Dong Province, Zhuhai, People's Republic of China
| | - Guofu Pang
- Department of Urology, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Kangning Road No.79, in Zhuhai city, Guang Dong Province, Zhuhai, People's Republic of China
| | - Jian Deng
- Department of Urology, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Kangning Road No.79, in Zhuhai city, Guang Dong Province, Zhuhai, People's Republic of China
| | - Qun Xie
- Department of Urology, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Kangning Road No.79, in Zhuhai city, Guang Dong Province, Zhuhai, People's Republic of China
| | - Zhengrong Zhang
- Department of Urology, Zhuhai People's Hospital, Zhuhai Hospital affiliated with Jinan University, Kangning Road No.79, in Zhuhai city, Guang Dong Province, Zhuhai, People's Republic of China.
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Giles KA, Gould CM, Achinger-Kawecka J, Page SG, Kafer GR, Rogers S, Luu PL, Cesare AJ, Clark SJ, Taberlay PC. BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer. Clin Epigenetics 2021; 13:37. [PMID: 33596994 PMCID: PMC7888175 DOI: 10.1186/s13148-021-01023-7] [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: 08/24/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Background BRG1 (encoded by SMARCA4) is a catalytic component of the SWI/SNF chromatin remodelling complex, with key roles in modulating DNA accessibility. Dysregulation of BRG1 is observed, but functionally uncharacterised, in a wide range of malignancies. We have probed the functions of BRG1 on a background of prostate cancer to investigate how BRG1 controls gene expression programmes and cancer cell behaviour. Results Our investigation of SMARCA4 revealed that BRG1 is over-expressed in the majority of the 486 tumours from The Cancer Genome Atlas prostate cohort, as well as in a complementary panel of 21 prostate cell lines. Next, we utilised a temporal model of BRG1 depletion to investigate the molecular effects on global transcription programmes. Depleting BRG1 had no impact on alternative splicing and conferred only modest effect on global expression. However, of the transcriptional changes that occurred, most manifested as down-regulated expression. Deeper examination found the common thread linking down-regulated genes was involvement in proliferation, including several known to increase prostate cancer proliferation (KLK2, PCAT1 and VAV3). Interestingly, the promoters of genes driving proliferation were bound by BRG1 as well as the transcription factors, AR and FOXA1. We also noted that BRG1 depletion repressed genes involved in cell cycle progression and DNA replication, but intriguingly, these pathways operated independently of AR and FOXA1. In agreement with transcriptional changes, depleting BRG1 conferred G1 arrest. Conclusions Our data have revealed that BRG1 promotes cell cycle progression and DNA replication, consistent with the increased cell proliferation associated with oncogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01023-7.
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Affiliation(s)
- Katherine A Giles
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia.,Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, TAS, Hobart, 7000, Australia
| | - Cathryn M Gould
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Joanna Achinger-Kawecka
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Scott G Page
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Georgia R Kafer
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Samuel Rogers
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Phuc-Loi Luu
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Susan J Clark
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, TAS, Hobart, 7000, Australia.
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Lowe BR, Yadav RK, Henry RA, Schreiner P, Matsuda A, Fernandez AG, Finkelstein D, Campbell M, Kallappagoudar S, Jablonowski CM, Andrews AJ, Hiraoka Y, Partridge JF. Surprising phenotypic diversity of cancer-associated mutations of Gly 34 in the histone H3 tail. eLife 2021; 10:e65369. [PMID: 33522486 PMCID: PMC7872514 DOI: 10.7554/elife.65369] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/30/2021] [Indexed: 12/11/2022] Open
Abstract
Sequencing of cancer genomes has identified recurrent somatic mutations in histones, termed oncohistones, which are frequently poorly understood. Previously we showed that fission yeast expressing only the H3.3G34R mutant identified in aggressive pediatric glioma had reduced H3K36 trimethylation and acetylation, increased genomic instability and replicative stress, and defective homology-dependent DNA damage repair. Here we show that surprisingly distinct phenotypes result from G34V (also in glioma) and G34W (giant cell tumors of bone) mutations, differentially affecting H3K36 modifications, subtelomeric silencing, genomic stability; sensitivity to irradiation, alkylating agents, and hydroxyurea; and influencing DNA repair. In cancer, only 1 of 30 alleles encoding H3 is mutated. Whilst co-expression of wild-type H3 rescues most G34 mutant phenotypes, G34R causes dominant hydroxyurea sensitivity, homologous recombination defects, and dominant subtelomeric silencing. Together, these studies demonstrate the complexity associated with different substitutions at even a single residue in H3 and highlight the utility of genetically tractable systems for their analysis.
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Affiliation(s)
- Brandon R Lowe
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Rajesh K Yadav
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer CenterPhiladelphiaUnited States
| | - Patrick Schreiner
- Department of Bioinformatics, St. Jude Children’s Research HospitalMemphisUnited States
| | - Atsushi Matsuda
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications TechnologyKobeJapan
- Graduate School of Frontier Biosciences, Osaka UniversitySuitaJapan
| | - Alfonso G Fernandez
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | - David Finkelstein
- Department of Bioinformatics, St. Jude Children’s Research HospitalMemphisUnited States
| | - Margaret Campbell
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | | | | | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer CenterPhiladelphiaUnited States
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications TechnologyKobeJapan
- Graduate School of Frontier Biosciences, Osaka UniversitySuitaJapan
| | - Janet F Partridge
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
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Taylor EL, Westendorf JJ. Histone Mutations and Bone Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:53-62. [PMID: 33155137 DOI: 10.1007/978-981-15-8104-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Primary bone tumors are rare cancers that cause significant morbidity and mortality. The recent identification of recurrent mutations in histone genes H3F3A and H3F3B within specific bone cancers, namely, chondroblastomas and giant cell tumors of bone (GCTB), has provided insights into the cellular and molecular origins of these neoplasms and enhanced understanding of how histone variants control chromatin function. Somatic mutations in H3F3A and H3F3B produce oncohistones, H3.3G34W and H3.3K36M, in more than nine of ten GCTB and chondroblastomas, respectively. Incorporation of the mutant histones into nucleosomes inhibits histone methyltransferases NSD2 and SETD2 to alter the chromatin landscape and change gene expression patterns that control cell proliferation, survival, and differentiation, as well as DNA repair and chromosome stability. The discovery of these histone mutations has facilitated more accurate diagnoses of these diseases and stratification of malignant tumors from benign tumors so that appropriate care can be delivered. The broad-scale epigenomic and transcriptomic changes that arise from incorporation of mutant histones into chromatin provide opportunities to develop new and disease-specific therapies. In this chapter, we review how mutant histones inhibit SETD2 and NSD2 function in bone tumors and discuss how this information could lead to better treatments for these cancers.
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Affiliation(s)
- Earnest L Taylor
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
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Tong Z, Yan C, Dong YA, Yao M, Zhang H, Liu L, Zheng Y, Zhao P, Wang Y, Fang W, Zhang F, Jiang W. Whole-exome sequencing reveals potential mechanisms of drug resistance to FGFR3-TACC3 targeted therapy and subsequent drug selection: towards a personalized medicine. BMC Med Genomics 2020; 13:138. [PMID: 32957974 PMCID: PMC7507681 DOI: 10.1186/s12920-020-00794-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/08/2020] [Indexed: 12/31/2022] Open
Abstract
Background Drug resistance is a major obstacle to effective cancer therapy. In order to detect the change in tumor genomic states under drug selection pressure, we use next-generation sequencing technology to investigate the underlying potential mechanisms of drug resistance. Methods In our study, we presented a bladder cancer patient who had been a bona fide responder to first-line gemcitabine plus cisplatin regimen and second-line pazopanib (tyrosine kinase inhibitor (TKI) for FGFR3-TACC3 fusion) but finally had disease progression as an ideal case for showing genomic alteration during drug resistance. We applied whole-exome sequencing and ultra-deep target sequencing to the patient pre- and post- pazopanib resistance. Protein-protein interaction (PPI) network and Gene Ontology (GO) analyses were used to analysis protein interactions and genomic alterations. Patient-derived xenograft (PDX) model was built to test drug sensitivity. Results Twelve mutations scattered in 12 genes were identified by WES pre- pazopanib resistance, while 63 mutations in 50 genes arose post- pazopanib resistance. PPI network showed proteins from multiple epigenetic regulator families were involved post- pazopanib resistance, including subunits of chromatin remodeler SWI/SNF complex ARID1A/1B and SMARCA4, histone acetylation writers CREBBP, histone methylation writer NSD1 and erasers KDM6A/5A. GO enrichment analysis showed pazopanib resistance genes were prominently tagged for chromatin modification, transcription, as well as gland development, leaving genes with the best adaptive FGFR TKI-coping mechanisms. In addition, significantly elevated tumor mutational burden suggested possible utility of immunotherapy. Intriguingly, PDX model suggested that, sensitivity to original chemotherapy regimen (cisplatin) was restored in patient tumor post-pazopanib. Conclusions Epigenetic regulation may play a role in acquired TKI resistance. Our study traced the complete tumor genomic variation course from chemo-resistant but TKI-sensitive to TKI-resistant but chemo-(re) sensitive, revealing the potential complex dynamic drug-driven mechanisms of resistance.
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Affiliation(s)
- Zhou Tong
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Cong Yan
- Department of Medical Oncology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
| | - Yu-An Dong
- OrigiMed, Building 3, 115 Xinjun Huan Rd. Minghang, Shanghai, 201114, China
| | - Ming Yao
- OrigiMed, Building 3, 115 Xinjun Huan Rd. Minghang, Shanghai, 201114, China
| | - Hangyu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Lulu Liu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yi Zheng
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yimin Wang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Provincial Key Laboratory of Pancreatic Disease, Hangzhou, 310003, China
| | - Feifei Zhang
- Shanghai LIDE Biotech Co.LTD, Shanghai, 201203, China
| | - Weiqin Jiang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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Wang L, Luo J, Chen G, Fang M, Wei X, Li Y, Liu Z, Zhang Y, Gao S, Shen J, Wang X, Gao X, Zhou W, Ma Y, Liu H, Li X, Yang L, Sun K, Yu L. Chidamide, decitabine, cytarabine, aclarubicin, and granulocyte colony-stimulating factor (CDCAG) in patients with relapsed/refractory acute myeloid leukemia: a single-arm, phase 1/2 study. Clin Epigenetics 2020; 12:132. [PMID: 32873343 PMCID: PMC7466805 DOI: 10.1186/s13148-020-00923-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/19/2020] [Indexed: 01/08/2023] Open
Abstract
Background Epigenetic mechanisms play an important role in the chemoresistance of acute myeloid leukemia (AML). The clinical response to epigenetic modifier-based chemotherapy in patients with relapsed/refractory AML (r/r AML) is unclear. This multicenter clinical trial evaluated the safety and efficacy of epigenetic modifiers (chidamide and decitabine) in combination with aclarubicin, cytarabine, and granulocyte colony-stimulating factor (G-CSF) in patients with r/r AML. Results Adult patients with r/r AML were treated with chidamide, decitabine, cytarabine, aclarubicin, and G-CSF (CDCAG). The primary measures were overall response (OR), overall survival (OS), and safety. Next-generation sequencing was performed to analyze the correlation between gene mutations and response. A total of 93 patients with r/r AML were enrolled. Overall, 24 patients had a complete remission (CR) and 19 patients achieved CR with incomplete blood count recovery (CRi). The overall response rate (ORR) was 46.2%. The overall survival of these 43 patients who achieved CR/CRi was significantly longer than that of patients who failed to achieve remission (563 vs 152 days, P < 0.0001). Of the patients with mutations in epigenetic and transcription factor-related genes, but without internal tandem duplications in FMS-like tyrosine kinase3 (FLT3-ITDs), 55.6% achieved CR/CRi, whereas the ORR was 28.2% for patients with mutations in other genes. Conclusions The CDCAG regimen was well tolerated and effective in r/r AML. Patients with epigenetic and transcription factor-related gene mutations, but without FLT3-ITD mutations, may benefit from this regimen. Trial registration Clinical Trials, NCT02886559. Registered 01 September 2016
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Affiliation(s)
- Lixin Wang
- Department of Hematology-Oncology, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, China.,Department of Hematology, The Sixth Medical Center, Chinese General Hospital of PLA, Beijing, China
| | - Jianmin Luo
- Department of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Guofeng Chen
- Department of Endoscopy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,School of Medicine, Nankai University, Tianjin, China.,Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Meiyun Fang
- Department of Hematology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xudong Wei
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yinghua Li
- Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhuogang Liu
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yin Zhang
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Sujun Gao
- Department of Hematology, The First Hospital, Jilin University, Changchun, China
| | - Jianliang Shen
- Department of Hematology, The Sixth Medical Center, Chinese General Hospital of PLA, Beijing, China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Xiaoning Gao
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Wei Zhou
- School of Medicine, Nankai University, Tianjin, China
| | - Yigai Ma
- Department of Hematology, China-Japan Friendship Hospital, Beijing, China
| | - Hui Liu
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Xinquan Li
- Department of Hematology, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, China
| | - Linhua Yang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Kai Sun
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Li Yu
- Department of Hematology-Oncology, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, China. .,Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
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Neganova ME, Klochkov SG, Aleksandrova YR, Aliev G. Histone modifications in epigenetic regulation of cancer: Perspectives and achieved progress. Semin Cancer Biol 2020; 83:452-471. [PMID: 32814115 DOI: 10.1016/j.semcancer.2020.07.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic changes associated with histone modifications play an important role in the emergence and maintenance of the phenotype of various cancer types. In contrast to direct mutations in the main DNA sequence, these changes are reversible, which makes the development of inhibitors of enzymes of post-translational histone modifications one of the most promising strategies for the creation of anticancer drugs. To date, a wide variety of histone modifications have been found that play an important role in the regulation of chromatin state, gene expression, and other nuclear events. This review examines the main features of the most common and studied epigenetic histone modifications with a proven role in the pathogenesis of a wide range of malignant neoplasms: acetylation / deacetylation and methylation / demethylation of histone proteins, as well as the role of enzymes of the HAT / HDAC and HMT / HDMT families in the development of oncological pathologies. The data on the relationship between histone modifications and certain types of cancer are presented and discussed. Special attention is devoted to the consideration of various strategies for the development of epigenetic inhibitors. The main directions of the development of inhibitors of histone modifications are analyzed and effective strategies for their creation are identified and discussed. The most promising strategy is the use of multitarget drugs, which will affect multiple molecular targets of cancer. A critical analysis of the current status of approved epigenetic anticancer drugs has also been performed.
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Affiliation(s)
- Margarita E Neganova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Sergey G Klochkov
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Yulia R Aleksandrova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Gjumrakch Aliev
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation.,I. M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow, 119991, Russian Federation.,Laboratory of Cellular Pathology, Federal State Budgetary Institution «Research Institute of Human Morphology», 3, Tsyurupy Str., Moscow, 117418, Russian Federation.,GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA.
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Chen KY, Bush K, Klein RH, Cervantes V, Lewis N, Naqvi A, Carcaboso AM, Lechpammer M, Knoepfler PS. Reciprocal H3.3 gene editing identifies K27M and G34R mechanisms in pediatric glioma including NOTCH signaling. Commun Biol 2020; 3:363. [PMID: 32647372 PMCID: PMC7347881 DOI: 10.1038/s42003-020-1076-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
Histone H3.3 mutations are a hallmark of pediatric gliomas, but their core oncogenic mechanisms are not well-defined. To identify major effectors, we used CRISPR-Cas9 to introduce H3.3K27M and G34R mutations into previously H3.3-wildtype brain cells, while in parallel reverting the mutations in glioma cells back to wildtype. ChIP-seq analysis broadly linked K27M to altered H3K27me3 activity including within super-enhancers, which exhibited perturbed transcriptional function. This was largely independent of H3.3 DNA binding. The K27M and G34R mutations induced several of the same pathways suggesting key shared oncogenic mechanisms including activation of neurogenesis and NOTCH pathway genes. H3.3 mutant gliomas are also particularly sensitive to NOTCH pathway gene knockdown and drug inhibition, reducing their viability in culture. Reciprocal editing of cells generally produced reciprocal effects on tumorgenicity in xenograft assays. Overall, our findings define common and distinct K27M and G34R oncogenic mechanisms, including potentially targetable pathways. Kuang-Yui Chen et al. show that histone H3.3 K27M and G34R mutations share key oncogenic mechanisms such as activation of neurogenesis and NOTCH pathway genes. They find that H3.3 mutant gliomas are sensitive to inhibition of the NOTCH pathway, suggesting a potentially targetable pathway in pediatric gliomas.
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Affiliation(s)
- Kuang-Yui Chen
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA, 95817, USA
| | - Kelly Bush
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA, 95817, USA
| | - Rachel Herndon Klein
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA, 95817, USA
| | - Vanessa Cervantes
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA, 95817, USA
| | - Nichole Lewis
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA, 95817, USA
| | - Aasim Naqvi
- Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA, 95817, USA
| | | | | | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616, USA. .,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, CA, 95817, USA. .,Department Pathology and Laboratory Medicine, University of California, Davis, CA, USA.
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Differential methylation landscape of pancreatic ductal adenocarcinoma and its precancerous lesions. Hepatobiliary Pancreat Dis Int 2020; 19:205-217. [PMID: 32312637 DOI: 10.1016/j.hbpd.2020.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 03/18/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pancreatic cancer is one of the most lethal diseases with an incidence almost equal to the mortality. In addition to having genetic causes, cancer can also be considered an epigenetic disease. DNA methylation is the premier epigenetic modification and patterns of aberrant DNA methylation are recognized to be a common hallmark of human tumor. In the multistage carcinogenesis of pancreas starting from precancerous lesions to pancreatic ductal adenocarcinoma (PDAC), the epigenetic changes play a significant role. DATA SOURCES Relevant studies for this review were derived via an extensive literature search in PubMed via using various keywords such as pancreatic ductal adenocarcinoma, precancerous lesions, methylation profile, epigenetic biomarkers that are relevant directly or closely associated with the concerned area of our interest. The literature search was intensively done considering a time frame of 20 years (1998-2018). RESULT In this review we have highlighted the hypermethylation and hypomethylation of the precancerous PDAC lesions (pancreatic intra-epithelial neoplasia, intraductal papillary mucinous neoplasm, mucinous cystic neoplasm and chronic pancreatitis) and PDAC along with the potential biomarkers. We have also achieved the early epigenetic driver that leads to progression from precancerous lesions to PDAC. A bunch of epigenetic driver genes leads to progression of precancerous lesions to PDAC (ppENK, APC, p14/5/16/17, hMLH1 and MGMT) are also documented. We summarized the importance of these observations in therapeutics and diagnosis of PDAC hence identifying the potential use of epigenetic biomarkers in epigenetic targeted therapy. Epigenetic inactivation occurs by hypermethylation of CpG islands in the promoter regions of tumor suppressor genes. We listed all hyper- and hypomethylation of CpG islands of several genes in PDAC including its precancerous lesions. CONCLUSIONS The concept of the review would help to understand their biological effects, and to determine whether they may be successfully combined with other epigenetic drugs. However, we need to continue our research to develop more specific DNA-demethylating agents, which are the targets for hypermethylated CpG methylation sites.
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Li R, Li P, Xing W, Qiu H. Heterogeneous genomic aberrations in esophageal squamous cell carcinoma: a review. Am J Transl Res 2020; 12:1553-1568. [PMID: 32509161 PMCID: PMC7269976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Esophageal cancer (EC) causes hundreds of thousands of deaths a year worldwide, especially the major subtype esophageal squamous cell carcinoma (ESCC). With the advent of next-generation sequencing and the availability of commercial microarrays, abnormities in genetic levels have been revealed in various independent researches. High frequencies of structure variations (SVs), single nucleotide variations (SNVs) and copy-number alterations (CNAs) in ESCCs are uncovered, and ESCC shows high levels of inter- and intratumor heterogeneity, implying diverse evolutionary trajectories. This review tries to explain the pathogenesis of ESCC on the scope of most often mutated genes based on prior studies, hopes to offer some hints for diagnosis and therapy in clinic.
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Affiliation(s)
- Renling Li
- Quality and Standards Academy, Shenzhen Technology UniversityShenzhen 518060, China
| | - Peng Li
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer HospitalZhengzhou 450008, China
| | - Wenqun Xing
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer HospitalZhengzhou 450008, China
| | - Huiling Qiu
- Quality and Standards Academy, Shenzhen Technology UniversityShenzhen 518060, China
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Shenoy S. Cell plasticity in cancer: A complex interplay of genetic, epigenetic mechanisms and tumor micro-environment. Surg Oncol 2020; 34:154-162. [PMID: 32891322 DOI: 10.1016/j.suronc.2020.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/13/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
Abstract
Cell plasticity, also known as lineage plasticity is defined as the ability of a cell to reprogram and change its phenotype identity. Cell plasticity is context dependent and occurs during the development of an embryo, tissue regeneration, wound healing. However when deregulated and aberrant it also contributes to cancer initiation, progression, metastases and resistance to therapies. Tumors cells exhibit varying forms of cell plasticity in each stage of the disease to evade normal regulation as would have occurred in normal cell division and homeostasis. Current evidence demonstrates complex interplay between the genes, epigenes, tumor microenvironment and the EMT in cell reprogramming and cancer cell plasticity. Herein we present experimental evidence and evolving new developments in cell plasticity in cancer cells. Additionally "Deregulated/aberrant/hijacked cell plasticity" could be considered as an additional hallmark of a cancer. In the future, combining the advances in next generation sequencing and single cell RNA techniques with evolving AI (artificial intelligence) technologies such as deep learning techniques may predict the trajectories of cancer cells and assist in navigating through the complex intricacies of the cancers. A durable, precise, personalized oncologic treatment could be a reality.
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Affiliation(s)
- Santosh Shenoy
- Clinical Associate Professor of Surgery, Department of Surgery, Kansas City VA Medical Center, University of Missouri Kansas City, USA; Cancer Biology and Therapeutics, HMS High-Impact Cancer Research (HI-CR) Program, Harvard Medical School 2018-2019, USA.
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Yu Z, Feng J, Wang W, Deng Z, Zhang Y, Xiao L, Wang Z, Liu C, Liu Q, Chen S, Wu M. The EGFR-ZNF263 signaling axis silences SIX3 in glioblastoma epigenetically. Oncogene 2020; 39:3163-3178. [PMID: 32051553 PMCID: PMC7142014 DOI: 10.1038/s41388-020-1206-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/28/2020] [Accepted: 02/03/2020] [Indexed: 12/15/2022]
Abstract
The homeotic protein SIX3 is a transcription factor vital for neurogenesis and has a bivalent promoter. We previously showed that SIX3 can be transcriptionally silenced by DNA hypermethylation, functions as a tumor suppressor gene, and inhibits human glioblastoma transcriptionally. Here, we show that the activation of epidermal growth factor (EGFR) induces DNA methylation of SIX3 promoter through the MAPK pathway. ERK, when activated, binds with ZNF263, consequently abrogating the ubiquitination of ZNF263 and leading to its stabilization. ZNF263 binds to the core promoter region of SIX3 and recruits the KAP1/HATS/DNMT corepressor complex to induce transcriptional silencing of SIX3 through H3K27me3 and methylation of SIX3 promoter. Activation of the EGFR-ZNF263 signaling axis in phenotypically normal astrocytes or glioblastoma cells triggers or enhances tumorigenic activities, while elevated expression of the EGFR-ZNF263 signaling components in glioblastoma tissues is associated with poor prognosis of the patients. Together, our findings demonstrate that epigenetic silencing of SIX3 is controlled by a sophisticated and highly ordered oncogenic signaling pathway and therefore provide new insights into initiation and progression of glioblastoma.
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Affiliation(s)
- Zhibin Yu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, 410078, Hunan, China
- Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianbo Feng
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, 410078, Hunan, China
| | - Wei Wang
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, 272000, Shandong, China
| | - Zhiyong Deng
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
| | - Yan Zhang
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, 410078, Hunan, China
| | - Lan Xiao
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, 410078, Hunan, China
| | - Zeyou Wang
- Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Changhong Liu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, 410078, Hunan, China
| | - Qing Liu
- Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Shuai Chen
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.
| | - Minghua Wu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, 410078, Hunan, China.
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Masoodi T, Siraj AK, Siraj S, Azam S, Qadri Z, Albalawy WN, Parvathareddy SK, Al-Sobhi SS, Al-Dayel F, Alkuraya FS, Al-Kuraya KS. Whole-Exome Sequencing of Matched Primary and Metastatic Papillary Thyroid Cancer. Thyroid 2020; 30:42-56. [PMID: 31668133 PMCID: PMC6983753 DOI: 10.1089/thy.2019.0052] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Background: Distant metastasis is a rare occurrence in thyroid cancer, and it can be associated with poor prognosis. The genomic repertoires of various solid malignancies have previously been reported but remain underexplored in metastatic papillary thyroid cancer (PTC). Furthermore, whether distant metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. Methods: We performed whole-exome sequencing on 14 matched distant metastases, primary PTC tumors, and normal tissues. Point mutations, copy number alterations, cancer cell fractions, and mutational signatures were defined using the state-of-the-art bioinformatics methods. All likely deleterious variants were validated by orthogonal methods. Results: Genomic differences were observed between primary and distant metastatic deposits, with a median of 62% (range 21-92%) of somatic mutations detected in metastatic tissues, but absent from the corresponding primary tumor sample. Mutations in known driver genes including BRAF, NRAS, and HRAS were shared and preferentially clonal in both sites. However, likely deleterious variants affecting DNA methylation and transcriptional repression signaling genes including SIN3A, RBBP1, and CHD4 were found to be restricted in the metastatic lesions. Moreover, a mutational signature shift was observed between the mutations that are specific or enriched in the metastatic and primary lesions. Conclusions: Primary PTC and distant metastases differ in their range of somatic alterations. Genomic analysis of distant metastases provides an opportunity to identify potentially clinically informative alterations not detected in primary tumors, which might influence decisions for personalized therapy in PTC patients with distant metastasis.
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Affiliation(s)
- Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sarah Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Wafaa N. Albalawy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | - Saif S. Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Fowzan S. Alkuraya, MD, Department of Genetics, King Faisal Specialist Hospital and Research Centre, MBC-03, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Address correspondence to: Khawla S. Al-Kuraya, MD, Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, MBC#98-16, PO Box 3354, Riyadh 11211, Saudi Arabia
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San José-Enériz E, Gimenez-Camino N, Agirre X, Prosper F. HDAC Inhibitors in Acute Myeloid Leukemia. Cancers (Basel) 2019; 11:cancers11111794. [PMID: 31739588 PMCID: PMC6896008 DOI: 10.3390/cancers11111794] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by uncontrolled proliferation, differentiation arrest, and accumulation of immature myeloid progenitors. Although clinical advances in AML have been made, especially in young patients, long-term disease-free survival remains poor, making this disease an unmet therapeutic challenge. Epigenetic alterations and mutations in epigenetic regulators contribute to the pathogenesis of AML, supporting the rationale for the use of epigenetic drugs in patients with AML. While hypomethylating agents have already been approved in AML, the use of other epigenetic inhibitors, such as histone deacetylases (HDAC) inhibitors (HDACi), is under clinical development. HDACi such as Panobinostat, Vorinostat, and Tricostatin A have been shown to promote cell death, autophagy, apoptosis, or growth arrest in preclinical AML models, yet these inhibitors do not seem to be effective as monotherapies, but rather in combination with other drugs. In this review, we discuss the rationale for the use of different HDACi in patients with AML, the results of preclinical studies, and the results obtained in clinical trials. Although so far the results with HDACi in clinical trials in AML have been modest, there are some encouraging data from treatment with the HDACi Pracinostat in combination with DNA demethylating agents.
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Affiliation(s)
- Edurne San José-Enériz
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IDISNA), Universidad de Navarra, 31008 Pamplona, Spain; (E.S.J.-E.); (N.G.-C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Naroa Gimenez-Camino
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IDISNA), Universidad de Navarra, 31008 Pamplona, Spain; (E.S.J.-E.); (N.G.-C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Xabier Agirre
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IDISNA), Universidad de Navarra, 31008 Pamplona, Spain; (E.S.J.-E.); (N.G.-C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence: (X.A.); (F.P.); Tel.: +34-948-194700 (ext. 1002) (X.A.); +34-948-255400 (ext. 5807) (F.P.)
| | - Felipe Prosper
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IDISNA), Universidad de Navarra, 31008 Pamplona, Spain; (E.S.J.-E.); (N.G.-C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, 31008 Pamplona, Spain
- Correspondence: (X.A.); (F.P.); Tel.: +34-948-194700 (ext. 1002) (X.A.); +34-948-255400 (ext. 5807) (F.P.)
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