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Kołat D, Zhao LY, Kciuk M, Płuciennik E, Kałuzińska-Kołat Ż. AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization. Cells 2022; 11:cells11244124. [PMID: 36552887 PMCID: PMC9776946 DOI: 10.3390/cells11244124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/26/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Formerly hailed as "undruggable" proteins, transcription factors (TFs) are now under investigation for targeted therapy. In cancer, this may alter, inter alia, immune evasion or replicative immortality, which are implicated in genome organization, a process that accompanies multi-step tumorigenesis and which frequently develops in a non-random manner. Still, targeting-related research on some TFs is scarce, e.g., among AP-2 proteins, which are known for their altered functionality in cancer and prognostic importance. Using public repositories, bioinformatics tools, and RNA-seq data, the present study examined the ligandability of all AP-2 members, selecting the best one, which was investigated in terms of mutations, targets, co-activators, correlated genes, and impact on genome organization. AP-2 proteins were found to have the conserved "TF_AP-2" domain, but manifested different binding characteristics and evolution. Among them, AP-2δ has not only the highest number of post-translational modifications and extended strands but also contains a specific histidine-rich region and cleft that can receive a ligand. Uterine, colon, lung, and stomach tumors are most susceptible to AP-2δ mutations, which also co-depend with cancer hallmark genes and drug targets. Considering AP-2δ targets, some of them were located proximally in the spatial genome or served as co-factors of the genes regulated by AP-2δ. Correlation and functional analyses suggested that AP-2δ affects various processes, including genome organization, via its targets; this has been eventually verified in lung adenocarcinoma using expression and immunohistochemistry data of chromosomal conformation-related genes. In conclusion, AP-2δ affects chromosomal conformation and is the most appropriate target for cancer therapy focused on the AP-2 family.
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Affiliation(s)
- Damian Kołat
- Department of Experimental Surgery, Medical University of Lodz, 90-136 Lodz, Poland
- Correspondence:
| | - Lin-Yong Zhao
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu 610041, China
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, 90-752 Lodz, Poland
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Poreba E, Lesniewicz K, Durzynska J. Histone-lysine N-methyltransferase 2 (KMT2) complexes - a new perspective. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108443. [PMID: 36154872 DOI: 10.1016/j.mrrev.2022.108443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/25/2022] [Accepted: 09/19/2022] [Indexed: 01/01/2023]
Abstract
Histone H3 Lys4 (H3K4) methylation is catalyzed by the Histone-Lysine N-Methyltransferase 2 (KMT2) protein family, and its members are required for gene expression control. In vertebrates, the KMT2s function in large multisubunit complexes known as COMPASS or COMPASS-like complexes (COMplex of Proteins ASsociated with Set1). The activity of these complexes is critical for proper development, and mutation-induced defects in their functioning have frequently been found in human cancers. Moreover, inherited or de novo mutations in KMT2 genes are among the etiological factors in neurodevelopmental disorders such as Kabuki and Kleefstra syndromes. The canonical role of KMT2s is to catalyze H3K4 methylation, which results in a permissive chromatin environment that drives gene expression. However, current findings described in this review demonstrate that these enzymes can regulate processes that are not dependent on methylation: noncatalytic functions of KMT2s include DNA damage response, cell division, and metabolic activities. Moreover, these enzymes may also methylate non-histone substrates and play a methylation-dependent function in the DNA damage response. In this review, we present an overview of the new, noncanonical activities of KMT2 complexes in a variety of cellular processes. These discoveries may have crucial implications for understanding the functions of these methyltransferases in developmental processes, disease, and epigenome-targeting therapeutic strategies in the future.
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Affiliation(s)
- Elzbieta Poreba
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Julia Durzynska
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
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Kettler L, Sid H, Schaub C, Lischka K, Klinger R, Moser M, Schusser B, Luksch H. AP-2δ Expression Kinetics in Multimodal Networks in the Developing Chicken Midbrain. Front Neural Circuits 2021; 15:756184. [PMID: 34744640 PMCID: PMC8568317 DOI: 10.3389/fncir.2021.756184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
AP-2 is a family of transcription factors involved in many aspects of development, cell differentiation, and regulation of cell growth and death. AP-2δ is a member of this group and specific gene expression patterns are required in the adult mouse brain for the development of parts of the inferior colliculus (IC), as well as the cortex, dorsal thalamus, and superior colliculus. The midbrain is one of the central areas in the brain where multimodal integration, i.e., integration of information from different senses, occurs. Previous data showed that AP-2δ-deficient mice are viable but due to increased apoptosis at the end of embryogenesis, lack part of the posterior midbrain. Despite the absence of the IC in AP-2δ-deficient mice, these animals retain at least some higher auditory functions. Neuronal responses to tones in the neocortex suggest an alternative auditory pathway that bypasses the IC. While sufficient data are available in mammals, little is known about AP-2δ in chickens, an avian model for the localization of sounds and the development of auditory circuits in the brain. Here, we identified and localized AP-2δ expression in the chicken midbrain during embryogenesis. Our data confirmed the presence of AP-2δ in the inferior colliculus and optic tectum (TeO), specifically in shepherd's crook neurons, which are an essential component of the midbrain isthmic network and involved in multimodal integration. AP-2δ expression in the chicken midbrain may be related to the integration of both auditory and visual afferents in these neurons. In the future, these insights may allow for a more detailed study of circuitry and computational rules of auditory and multimodal networks.
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Affiliation(s)
- Lutz Kettler
- Chair of Zoology, Technical University of Munich, Freising, Germany
| | - Hicham Sid
- Reproductive Biotechnology, Technical University of Munich, Freising, Germany
| | - Carina Schaub
- Chair of Zoology, Technical University of Munich, Freising, Germany
| | - Katharina Lischka
- Institute for Biology I, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Romina Klinger
- Reproductive Biotechnology, Technical University of Munich, Freising, Germany
| | - Markus Moser
- TranslaTUM, Technical University of Munich, Munich, Germany
| | - Benjamin Schusser
- Reproductive Biotechnology, Technical University of Munich, Freising, Germany
| | - Harald Luksch
- Chair of Zoology, Technical University of Munich, Freising, Germany
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Aberrant Activity of Histone-Lysine N-Methyltransferase 2 (KMT2) Complexes in Oncogenesis. Int J Mol Sci 2020; 21:ijms21249340. [PMID: 33302406 PMCID: PMC7762615 DOI: 10.3390/ijms21249340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
KMT2 (histone-lysine N-methyltransferase subclass 2) complexes methylate lysine 4 on the histone H3 tail at gene promoters and gene enhancers and, thus, control the process of gene transcription. These complexes not only play an essential role in normal development but have also been described as involved in the aberrant growth of tissues. KMT2 mutations resulting from the rearrangements of the KMT2A (MLL1) gene at 11q23 are associated with pediatric mixed-lineage leukemias, and recent studies demonstrate that KMT2 genes are frequently mutated in many types of human cancers. Moreover, other components of the KMT2 complexes have been reported to contribute to oncogenesis. This review summarizes the recent advances in our knowledge of the role of KMT2 complexes in cell transformation. In addition, it discusses the therapeutic targeting of different components of the KMT2 complexes.
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Luo X, Xia Y, Li XD, Wang JY. The effect of AP-2δ on transcription of the Prestin gene in HEI-OC1 cells upon oxidative stress. Cell Mol Biol Lett 2019; 24:45. [PMID: 31297132 PMCID: PMC6595603 DOI: 10.1186/s11658-019-0170-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/07/2019] [Indexed: 12/18/2022] Open
Abstract
Background The study aimed to investigate the effect of oxidative stress on Prestin expression, and explore the transcription factors (TFs) that are involved in regulating the expression of Prestin in House Ear Institute-Organ of Corti 1 (HEI-OC1) cells upon oxidative stress. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were used to detect the expression level of Prestin. Reverse chromatin immunoprecipitation (reverse ChIP) assay was performed to identify proteins that could bind to the Prestin gene. Small interfering RNA (siRNA) and chromatin immunoprecipitation (ChIP) experiments were used to further verify the results. HEI-OC1 cells were incubated with four different concentrations of tert-butyl hydroperoxide (t-BHP) for 24 h or 48 h to construct the oxidative stress model. Results Oxidative stress induced Prestin increase at the mRNA level but with a concomitant decrease at the protein level. TF activating enhancer binding protein-2δ (AP-2δ) screened by reverse ChIP assay was demonstrated to bind to transcriptional start site 1441 of the Prestin promoter region and negatively regulate the expression of Prestin by siRNA and ChIP experiments. Furthermore, AP-2δ was down-regulated under oxidative stress. Conclusions In conclusion, oxidative stress inhibits the expression of Prestin protein, and the transcription mechanism is triggered to compensate for the loss of Prestin protein. AP-2δ is one of the important TFs that suppresses transcription of the Prestin gene, and AP-2δ suppression further boosted Prestin mRNA activation under oxidative stress. Electronic supplementary material The online version of this article (10.1186/s11658-019-0170-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuan Luo
- 1Department of Labor Health and Environmental Hygiene, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510310 China
| | - Yun Xia
- 2Department of Labor Health and Environmental Hygiene, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510310 China
| | - Xu-Dong Li
- Key Laboratory, Occupational Disease Prevention and Control of Hospital of Guangdong Province, Guangzhou, 510300 China
| | - Jun-Yi Wang
- 1Department of Labor Health and Environmental Hygiene, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510310 China
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6
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Hicks EA, Zaveri M, Deschamps PA, Noseworthy MD, Ball A, Williams T, West-Mays JA. Conditional Deletion of AP-2α and AP-2β in the Developing Murine Retina Leads to Altered Amacrine Cell Mosaics and Disrupted Visual Function. Invest Ophthalmol Vis Sci 2019; 59:2229-2239. [PMID: 29715367 PMCID: PMC5931233 DOI: 10.1167/iovs.17-23283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The combined action of the activating protein-2 (AP-2) transcription factors, AP-2α and AP-2β, is important in early retinal development, specifically in the formation of horizontal cells. However, in previous studies, it was not possible to analyze postnatal development and function of additional retinal subtypes. Methods We used a double conditional deletion of AP-2α and AP-2β from the retina to further examine the combinatory role of these genes in retinal cell patterning and function in postnatal adult mice as measured by Voronoi domain area and nearest-neighbor distance spatial analyses and ERGs, respectively. Results Conditional deletion of both AP-2α and AP-2β from the retina resulted in a variety of abnormalities, including the absence of horizontal cells, defects in the photoreceptor ribbons in which synapses failed to form, along with evidence of aberrant amacrine cell arrangement. Although no significant changes in amacrine cell population numbers were observed in the double mutants, significant irregularities in the mosaic patterning of amacrine cells was observed as demonstrated by both Voronoi domain areas and nearest-neighbor distances analyses. These changes were further accompanied by an alteration in the retinal response to light as recorded by ERGs. In particular, in the double-mutant mice lacking AP-2α and AP-2β, the b-wave amplitude, representative of interneuron signal processing, was significantly reduced compared with control littermates. Conclusions Together these findings demonstrate the requirement for both AP-2α and AP-2β in proper amacrine mosaic patterning and a normal functional light response in the retina.
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Affiliation(s)
- Emily Anne Hicks
- McMaster School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Mizna Zaveri
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Paula A Deschamps
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michael D Noseworthy
- McMaster School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada.,Department of Electrical and Computer Engineering, McMaster University, Hamilton, Ontario, Canada.,Department of Radiology, McMaster University, Hamilton, Ontario, Canada
| | - Alexander Ball
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Trevor Williams
- Department of Craniofacial Biology and Department of Cell and Developmental Biology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, United States
| | - Judith A West-Mays
- McMaster School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018; 7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation.
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AP-2ε Expression in Developing Retina: Contributing to the Molecular Diversity of Amacrine Cells. Sci Rep 2018; 8:3386. [PMID: 29467543 PMCID: PMC5821864 DOI: 10.1038/s41598-018-21822-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/12/2018] [Indexed: 02/04/2023] Open
Abstract
AP-2 transcription factors play important roles in the regulation of gene expression during development. Four of the five members of the AP-2 family (AP-2α, AP-2β, AP-2γ and AP-2δ) have previously been shown to be expressed in developing retina. Mouse knockouts have revealed roles for AP-2α, AP-2β and AP-2δ in retinal cell specification and function. Here, we show that the fifth member of the AP-2 family, AP-2ε, is also expressed in amacrine cells in developing mammalian and chicken retina. Our data indicate that there are considerably fewer AP-2ε-positive cells in the developing mouse retina compared to AP-2α, AP-2β and AP-2γ-positive cells, suggesting a specialized role for AP-2ε in a subset of amacrine cells. AP-2ε, which is restricted to the GABAergic amacrine lineage, is most commonly co-expressed with AP-2α and AP-2β, especially at early stages of retinal development. Co-expression of AP-2ε and AP-2γ increases with differentiation. Analysis of previously published Drop-seq data from single retinal cells supports co-expression of multiple AP-2s in the same cell. Since AP-2s bind to their target sequences as either homodimers or heterodimers, our work suggests spatially- and temporally-coordinated roles for combinations of AP-2 transcription factors in amacrine cells during retinal development.
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Li X, Gaillard F, Monckton EA, Glubrecht DD, Persad ARL, Moser M, Sauvé Y, Godbout R. Loss of AP-2delta reduces retinal ganglion cell numbers and axonal projections to the superior colliculus. Mol Brain 2016; 9:62. [PMID: 27259519 PMCID: PMC4893287 DOI: 10.1186/s13041-016-0244-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/29/2016] [Indexed: 11/10/2022] Open
Abstract
Background AP-2δ is the most divergent member of the Activating Protein-2 (TFAP2) family of transcription factors. AP-2δ is restricted to specific regions of the CNS, including a subset of ganglion cells in the retina. Retinal ganglion cells (RGCs), the only output neurons of the retina, are responsible for transmitting the visual signal to the brain. Results AP-2δ knockout results in loss of Brn3c (Pou4f3) expression in AP-2δ -positive RGCs. While AP-2δ-/- mice have morphologically normal retinas at birth, there is a significant reduction in retinal ganglion cell numbers by P21, after eye opening. Chromatin immunoprecipitation indicates that Brn3c is a target of AP-2δ in the retina. Using fluorochrome-conjugated cholera toxin subunit B to trace ganglion cell axons from the eye to the major visual pathways in the brain, we found 87 % and 32 % decreases in ipsilateral and contralateral projections, respectively, to the superior colliculus in AP-2δ-/- mice. In agreement with anatomical data, visually evoked responses recorded from the brain confirmed that retinal outputs to the brain are compromised. Conclusions AP-2δ is important for the maintenance of ganglion cell numbers in the retina. Loss of AP-2δ alters retinal axonal projections to visual centers of the brain, with ipsilaterial projections to the superior colliculus being the most dramatically affected. Our results have important implications for integration of the visual signal at the superior colliculus. Electronic supplementary material The online version of this article (doi:10.1186/s13041-016-0244-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaodong Li
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada
| | - Frédéric Gaillard
- Department of Physiology, University of Alberta, 11560 University Avenue, Edmonton, AB, Canada.,Department of Ophthalmology, University of Alberta, 11560 University Avenue, Edmonton, AB, Canada
| | - Elizabeth A Monckton
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada
| | - Darryl D Glubrecht
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada
| | - Amit R L Persad
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada
| | - Markus Moser
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Yves Sauvé
- Department of Physiology, University of Alberta, 11560 University Avenue, Edmonton, AB, Canada.,Department of Ophthalmology, University of Alberta, 11560 University Avenue, Edmonton, AB, Canada
| | - Roseline Godbout
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada.
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