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Amatori S, Tavolaro S, Gambardella S, Fanelli M. The dark side of histones: genomic organization and role of oncohistones in cancer. Clin Epigenetics 2021; 13:71. [PMID: 33827674 PMCID: PMC8025322 DOI: 10.1186/s13148-021-01057-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Background The oncogenic role of histone mutations is one of the most relevant discovery in cancer epigenetics. Recurrent mutations targeting histone genes have been described in pediatric brain tumors, chondroblastoma, giant cell tumor of bone and other tumor types. The demonstration that mutant histones can be oncogenic and drive the tumorigenesis in pediatric tumors, led to the coining of the term “oncohistones.” The first identified histone mutations were localized at or near residues normally targeted by post-translational modifications (PTMs) in the histone N-terminal tails and suggested a possible interference with histone PTMs regulation and reading. Main body In this review, we describe the peculiar organization of the multiple genes that encode histone proteins, and the latter advances in both the identification and the biological role of histone mutations in cancer. Recent works show that recurrent somatic mutations target both N-terminal tails and globular histone fold domain in diverse tumor types. Oncohistones are often dominant-negative and occur at higher frequencies in tumors affecting children and adolescents. Notably, in many cases the mutations target selectively only some of the genes coding the same histone protein and are frequently associated with specific tumor types or, as documented for histone variant H3.3 in pediatric glioma, with peculiar tumors arising from specific anatomic locations. Conclusion The overview of the most recent advances suggests that the oncogenic potential of histone mutations can be exerted, together with the alteration of histone PTMs, through the destabilization of nucleosome and DNA–nucleosome interactions, as well as through the disruption of higher-order chromatin structure. However, further studies are necessary to fully elucidate the mechanism of action of oncohistones, as well as to evaluate their possible application to cancer classification, prognosis and to the identification of new therapies.
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Affiliation(s)
- Stefano Amatori
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
| | - Simona Tavolaro
- Fredis Associazione, Via Edoardo Jenner 30, 00151, Rome, Italy
| | - Stefano Gambardella
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.,IRCCS Neuromed, Via Atinense 18, 86077, Pozzilli, IS, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
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Histone H3G34 Mutation in Brain and Bone Tumors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33155138 DOI: 10.1007/978-981-15-8104-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
H3G34 mutations occur in both pediatric non-brainstem high-grade gliomas (G34R/V) and giant cell tumors of bone (G34W/L). Glioblastoma patients with G34R/V mutation have a generally adverse prognosis, whereas giant cell tumors of bone are rarely metastatic benign tumors. G34 mutations possibly disrupt the epigenome by altering H3K36 modifications, which may involve attenuating the function of SETD2 at methyltransferase. H3K36 methylation change may further lead to genomic instability, dysregulated gene expression pattern, and more mutations. In this chapter, we summarize the pathological features of each mutation type in its respective cancer, as well as the potential mechanism of their disruption on the epigenome and genomic instability. Understanding each mutation type would provide a thorough background for a thorough understanding of the cancers and would bring new insights for future investigations and the development of new precise therapies.
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Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation. Nat Genet 2020; 52:1271-1281. [PMID: 33257899 DOI: 10.1038/s41588-020-00736-4] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/08/2020] [Indexed: 12/14/2022]
Abstract
Histone-modifying enzymes are implicated in the control of diverse DNA-templated processes including gene expression. Here, we outline historical and current thinking regarding the functions of histone modifications and their associated enzymes. One current viewpoint, based largely on correlative evidence, posits that histone modifications are instructive for transcriptional regulation and represent an epigenetic 'code'. Recent studies have challenged this model and suggest that histone marks previously associated with active genes do not directly cause transcriptional activation. Additionally, many histone-modifying proteins possess non-catalytic functions that overshadow their enzymatic activities. Given that much remains unknown regarding the functions of these proteins, the field should be cautious in interpreting loss-of-function phenotypes and must consider both cellular and developmental context. In this Perspective, we focus on recent progress relating to the catalytic and non-catalytic functions of the Trithorax-COMPASS complexes, Polycomb repressive complexes and Clr4/Suv39 histone-modifying machineries.
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Yoon S, Wu X, Armstrong B, Habib N, Rossi JJ. An RNA Aptamer Targeting the Receptor Tyrosine Kinase PDGFRα Induces Anti-tumor Effects through STAT3 and p53 in Glioblastoma. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:131-141. [PMID: 30594071 PMCID: PMC6307106 DOI: 10.1016/j.omtn.2018.11.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/02/2023]
Abstract
Human glioblastoma (GBM) is the most aggressive malignancy of the CNS, with less than 5% survival. Despite great efforts to find effective therapeutics, current options remain very limited. To develop a targeted cancer therapeutic, we selected RNA aptamers against platelet-derived growth factor receptor α (PDGFRα), which is a receptor tyrosine kinase. One RNA aptamer (PDR3) with high affinity (0.25 nM) showed PDGFRα specificity and was internalized in U251-MG cells. Following treatment with the PDR3 aptamer, expression of the transcription factor STAT3 (signal transducer and activator of transcription 3) was inhibited, whereas the expression of the histone demethylase JMJD3 and the tumor suppressor p53 were upregulated. PDR3 also upregulated serine phosphorylation of p53, which subsequently mediated apoptosis through the death receptors: tumor necrosis factor (TNF)-related apoptosis-inducing ligand receptors 1/2 (TRAIL-R1/R2), Fas-associated via death domain (FADD), and Fas. PDR3 significantly decreased cell viability in a dose-dependent manner. Furthermore, translocation of PDR3 into the nucleus induced hypomethylation at the promoters of cyclin D2. To assess the feasibility of targeted delivery, we conjugated PDR3 aptamer with STAT3-siRNA for a chimera. The PDR3-siSTAT3 chimera successfully inhibited the expression of target genes and showed significant inhibition of cell viability. In summary, our results show that well-tailored RNA aptamers targeting the PDGFRα-STAT3 axis have the potential to act as anti-cancer therapeutics in GBM.
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Affiliation(s)
- Sorah Yoon
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Xiwei Wu
- Integrative Genomic Core, City of Hope, Duarte, CA 91010, USA
| | | | - Nagy Habib
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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Qiu L, Hu X, Jing Q, Zeng X, Chan KM, Han J. Mechanism of cancer: Oncohistones in action. J Genet Genomics 2018; 45:227-236. [PMID: 29804713 DOI: 10.1016/j.jgg.2018.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 02/06/2023]
Abstract
Oncohistones are histones with high-frequency point mutations that are associated with tumorigenesis. Although each histone variant is encoded by multiple genes, a single mutation in one allele of one gene seems to have a dominant effect over global histone H3 methylation level at the relevant amino acid residue. These oncohistones are highly tumor type specific. For example, H3K27M and H3G34V/R mutations occur only in pediatric brain cancers, whereas H3K36M and H3G34W/L have only been found in pediatric bone tumors. H1 mutations also seem to be exclusively linked to lymphomas. In this review, we discuss the occurrence, frequency and potential functional mechanisms of each oncohistone in tumorigenesis of its relevant cancer. We believe that further investigation into the mechanism regarding their tumor type specificity and cancer-related functions will shed new light on their application in cancer diagnosis and targeted therapy development.
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Affiliation(s)
- Lei Qiu
- Department of Abdominal Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Xiaoyan Hu
- Department of Abdominal Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Qian Jing
- Department of Abdominal Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Xinyi Zeng
- Department of Abdominal Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Kui-Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong 999077, China
| | - Junhong Han
- Department of Abdominal Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China.
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Morera L, Lübbert M, Jung M. Targeting histone methyltransferases and demethylases in clinical trials for cancer therapy. Clin Epigenetics 2016; 8:57. [PMID: 27222667 PMCID: PMC4877953 DOI: 10.1186/s13148-016-0223-4] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022] Open
Abstract
The term epigenetics is defined as heritable changes in gene expression that are not due to alterations of the DNA sequence. In the last years, it has become more and more evident that dysregulated epigenetic regulatory processes have a central role in cancer onset and progression. In contrast to DNA mutations, epigenetic modifications are reversible and, hence, suitable for pharmacological interventions. Reversible histone methylation is an important process within epigenetic regulation, and the investigation of its role in cancer has led to the identification of lysine methyltransferases and demethylases as promising targets for new anticancer drugs. In this review, we describe those enzymes and their inhibitors that have already reached the first stages of clinical trials in cancer therapy, namely the histone methyltransferases DOT1L and EZH2 as well as the demethylase LSD1.
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Affiliation(s)
- Ludovica Morera
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology and Oncology, University of Freiburg Medical Center, Hugstetter Straße 55, 79106 Freiburg, Germany ; German Cancer Consortium (DKTK), Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany ; German Cancer Consortium (DKTK), Freiburg, Germany
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Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. Genome Biol 2015; 16:263. [PMID: 26607552 PMCID: PMC4659173 DOI: 10.1186/s13059-015-0827-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0827-6) contains supplementary material, which is available to authorized users.
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Feng J, Hao S, Pan C, Wang Y, Wu Z, Zhang J, Yan H, Zhang L, Wan H. The H3.3 K27M mutation results in a poorer prognosis in brainstem gliomas than thalamic gliomas in adults. Hum Pathol 2015; 46:1626-32. [DOI: 10.1016/j.humpath.2015.07.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/23/2015] [Accepted: 07/01/2015] [Indexed: 12/31/2022]
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