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Jeremias G, Muñiz-González AB, Mendes Gonçalves FJ, Martínez-Guitarte JL, Asselman J, Luísa Pereira J. History of exposure to copper influences transgenerational gene expression responses in Daphnia magna. Epigenetics 2024; 19:2296275. [PMID: 38154067 PMCID: PMC10761054 DOI: 10.1080/15592294.2023.2296275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023] Open
Abstract
The establishment of transgenerational effects following chemical exposure is a powerful phenomenon, capable of modulating ecosystem health beyond exposure periods. This study assessed the transgenerational effects occurring due to copper exposure in the invertebrate D. magna at the transcriptional level, while evaluating the role of exposure history on such responses. Thus, daphnids acclimated for several generations in a copper vs. clean medium were then exposed for one generation (F0) to this metal, and monitored for the following non-exposed generations (F1, F2 and F3). Organisms differing in exposure histories showed remarkably different transcriptional profiles at the F0, with naïve organisms being more profoundly affected. These trends were confirmed for F3 treatments, which presented different transcriptional patterns for genes involved in detoxification, oxidative stress, DNA damage repair, circadian clock functioning and epigenetic regulation. Furthermore, regardless of exposure history, a great number of histone modifier genes were always found transcriptionally altered, thus suggesting the involvement of histone modifications in the response of Daphnia to metal exposure. Lastly, remarkably distinct transgenerational transcriptional responses were found between naïve and non-naïve organisms, thereby highlighting the influence of exposure history on gene expression and confirming the capacity of metals to determine transgenerational transcriptional effects across non-exposed generations.
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Affiliation(s)
- Guilherme Jeremias
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Ana-Belén Muñiz-González
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
- Biology & Toxicology Group, Department of Mathematics, Physics, and Fluids, National Distance Education University (UNED), Madrid, Spain
| | | | - José-Luis Martínez-Guitarte
- Biology & Toxicology Group, Department of Mathematics, Physics, and Fluids, National Distance Education University (UNED), Madrid, Spain
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Ostend, Belgium
| | - Joana Luísa Pereira
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
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Tinsley E, Bredin P, Toomey S, Hennessy BT, Furney SJ. KMT2C and KMT2D aberrations in breast cancer. Trends Cancer 2024:S2405-8033(24)00029-3. [PMID: 38453563 DOI: 10.1016/j.trecan.2024.02.003] [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: 11/10/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
KMT2C and KMT2D are histone lysine methyltransferases responsible for the monomethylation of histone 3 lysine 4 (H3K4) residues at gene enhancer sites. KMT2C/D are the most frequently mutated histone methyltransferases (HMTs) in breast cancer, occurring at frequencies of 10-20% collectively. Frequent damaging and truncating somatic mutations indicate a tumour-suppressive role of KMT2C/D in breast oncogenesis. Recent studies using cell lines and mouse models to replicate KMT2C/D loss show that these genes contribute to oestrogen receptor (ER)-driven transcription in ER+ breast cancers through the priming of gene enhancer regions. This review provides an overview of the functions of KMT2C/D and outlines the recent clinical and experimental evidence of the roles of KMT2C and KMT2D in breast cancer development.
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Affiliation(s)
- Emily Tinsley
- Genomic Oncology Research Group, Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Philip Bredin
- Medical Oncology Group, Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Sinead Toomey
- Medical Oncology Group, Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Bryan T Hennessy
- Medical Oncology Group, Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Dublin, Ireland; Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland.
| | - Simon J Furney
- Genomic Oncology Research Group, Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
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Wang DX, Long JY, Li RZ, Zhang DL, Liu H, Liu J, Tian JC, Li H, Liu J, Zhao HT, Li T. Mutation status of the KMT2 family associated with immune checkpoint inhibitors (ICIs) therapy and implicating diverse tumor microenvironments. Mol Cancer 2024; 23:15. [PMID: 38225603 PMCID: PMC10789049 DOI: 10.1186/s12943-023-01930-8] [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: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024] Open
Abstract
Mounting evidence suggests a strong association between tumor immunity and epigenetic regulation. The histone-lysine N-methyltransferase 2 (KMT2) family plays a crucial role in the methylation of histone H3 at lysine 4. By influencing chromatin structure and DNA accessibility, this modification serves as a key regulator of tumor progression and immune tolerance across various tumors. These findings highlight the potential significance of the KMT2 family in determining response to immune checkpoint inhibitor (ICI) therapy, which warrants further exploration. In this study, we integrated four ICI-treated cohorts (n = 2069) across 10 cancer types and The Cancer Genome Atlas pan-cancer cohort and conducted a comprehensive clinical and bioinformatic analysis. Our study indicated that patients with KMT2 family gene mutations benefited more from ICI therapy in terms of overall survival (P < 0.001, hazard ratio [HR] = 0.733 [95% confidence interval (CI): 0.632-0.850]), progression-free survival (P = 0.002, HR = 0.669 [95% CI: 0.518-0.864]), durable clinical benefit (P < 0.001, 54.1% vs. 32.6%), and objective response rate (P < 0.001, 40.6% vs. 22.0%). Through a comprehensive analysis of the tumor microenvironment across different KMT2 mutation statuses, we observed that tumors harboring the KMT2 mutation exhibited enhanced immunogenicity, increased infiltration of immune cells, and higher levels of immune cell cytotoxicity, suggesting a propensity towards a "hot tumor" phenotype. Therefore, our study indicates a potential association between KMT2 mutations and a more favorable response to ICI therapy and implicates different tumor microenvironments associated with ICI therapy response.
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Affiliation(s)
- Dong-Xu Wang
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Jun-Yu Long
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Rui-Zhe Li
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Dao-Lin Zhang
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Hui Liu
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Jingru Liu
- Department of Radiation Oncology, Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Shandong University Cancer Center, Jinan, Shandong, China
| | - Jin-Cheng Tian
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Han Li
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Jie Liu
- Department of Radiation Oncology, Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Shandong University Cancer Center, Jinan, Shandong, China.
| | - Hai-Tao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China.
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, Shandong, 250012, People's Republic of China.
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Amin HM, Abukhairan R, Szabo B, Jacksi M, Varady G, Lozsa R, Schad E, Tantos A. KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing. Protein Sci 2024; 33:e4847. [PMID: 38058280 PMCID: PMC10731558 DOI: 10.1002/pro.4847] [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: 04/19/2023] [Revised: 10/30/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Histone lysine methyltransferases (HKMTs) perform vital roles in cellular life by controlling gene expression programs through the posttranslational modification of histone tails. Since many of them are intimately involved in the development of different diseases, including several cancers, understanding the molecular mechanisms that control their target recognition and activity is vital for the treatment and prevention of such conditions. RNA binding has been shown to be an important regulatory factor in the function of several HKMTs, such as the yeast Set1 and the human Ezh2. Moreover, many HKMTs are capable of RNA binding in the absence of a canonical RNA binding domain. Here, we explored the RNA binding capacity of KMT2D, one of the major H3K4 monomethyl transferases in enhancers, using RNA immunoprecipitation followed by sequencing. We identified a broad range of coding and non-coding RNAs associated with KMT2D and confirmed their binding through RNA immunoprecipitation and quantitative PCR. We also showed that a separated RNA binding region within KMT2D is capable of binding a similar RNA pool, but differences in the binding specificity indicate the existence of other regulatory elements in the sequence of KMT2D. Analysis of the bound mRNAs revealed that KMT2D preferentially binds co-transcriptionally to the mRNAs of the genes under its control, while also interacting with super enhancer- and splicing-related non-coding RNAs. These observations, together with the nuclear colocalization of KMT2D with differentially phosphorylated forms of RNA Polymerase II suggest a so far unexplored role of KMT2D in the RNA processing of the nascent transcripts.
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Affiliation(s)
- Harem Muhamad Amin
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
- Doctoral School of Biology and Institute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
- Department of Biology, College of ScienceUniversity of SulaimaniSulaymaniyahIraq
| | - Rawan Abukhairan
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Beata Szabo
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Mevan Jacksi
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
- Doctoral School of Biology and Institute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Gyorgy Varady
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Rita Lozsa
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Eva Schad
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Agnes Tantos
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
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Golden CS, Williams S, Serrano MA. Molecular insights of KMT2D and clinical aspects of Kabuki syndrome type 1. Birth Defects Res 2023; 115:1809-1824. [PMID: 37158694 PMCID: PMC10845236 DOI: 10.1002/bdr2.2183] [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: 01/25/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Kabuki syndrome type 1 (KS1), a rare multisystem congenital disorder, presents with characteristic facial features, intellectual disability, persistent fetal fingertip pads, skeletal abnormalities, and postnatal growth delays. KS1 results from pathogenic variants in the KMT2D gene, which encodes a histone methyltransferase protein involved in chromatin remodeling, promoter and enhancer regulation, and scaffold formation during early development. KMT2D also mediates cell signaling pathways, responding to external stimuli and organizing effector protein assembly. Research on KMT2D's molecular mechanisms in KS1 has primarily focused on its histone methyltransferase activity, leaving a gap in understanding the methyltransferase-independent roles in KS1 clinical manifestations. METHODS This scoping review examines KMT2D's role in gene expression regulation across various species, cell types, and contexts. We analyzed human pathogenic KMT2D variants using publicly available databases and compared them to research organism models of KS1. We also conducted a systematic search of healthcare and governmental databases for clinical trials, studies, and therapeutic approaches. RESULTS Our review highlights KMT2D's critical roles beyond methyltransferase activity in diverse cellular contexts and conditions. We identified six distinct groups of KMT2D as a cell signaling mediator, including evidence of methyltransferase-dependent and -independent activity. A comprehensive search of the literature, clinical databases, and public registries emphasizes the need for basic research on KMT2D's functional complexity and longitudinal studies of KS1 patients to establish objective outcome measurements for therapeutic development. CONCLUSION We discuss how KMT2D's role in translating external cellular communication can partly explain the clinical heterogeneity observed in KS1 patients. Additionally, we summarize the current molecular diagnostic approaches and clinical trials targeting KS1. This review is a resource for patient advocacy groups, researchers, and physicians to support KS1 diagnosis and therapeutic development.
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Affiliation(s)
- Carly S Golden
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
| | - Saylor Williams
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
| | - Maria A Serrano
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
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Karan D, Singh M, Dubey S, Van Veldhuizen PJ, Saunthararajah Y. DNA Methyltransferase 1 Targeting Using Guadecitabine Inhibits Prostate Cancer Growth by an Apoptosis-Independent Pathway. Cancers (Basel) 2023; 15:2763. [PMID: 37345101 DOI: 10.3390/cancers15102763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023] Open
Abstract
Epigenetic alterations such as DNA methylation and histone modifications are implicated in repressing several tumor suppressor genes in prostate cancer progression. In this study, we determined the anti-prostate cancer effect of a small molecule drug guadecitabine (gDEC) that inhibits/depletes the DNA methylation writer DNA methyltransferase 1 (DNMT1). gDEC inhibited prostate cancer cell growth and proliferation in vitro without activating the apoptotic cascade. Molecular studies confirmed DNMT1 depletion and modulated epithelial-mesenchymal transition markers E-cadherin and β-catenin in several prostate cancer cell lines (LNCaP, 22Rv1, and MDA PCa 2b). gDEC treatment also significantly inhibited prostate tumor growth in vivo in mice (22Rv1, MDA PCa 2b, and PC-3 xenografts) without any observed toxicities. gDEC did not impact the expression of androgen receptor (AR) or AR-variant 7 (AR-V7) nor sensitize the prostate cancer cells to the anti-androgen enzalutamide in vitro. In further investigating the mechanism of cytoreduction by gDEC, a PCR array analyses of 84 chromatin modifying enzymes demonstrated upregulation of several lysine-specific methyltransferases (KMTs: KMT2A, KMT2C, KMT2E, KMT2H, KMT5A), confirmed by additional expression analyses in vitro and of harvested xenografts. Moreover, gDEC treatment increased global histone 3 lysine 4 mono-and di-methylation (H3K4me1 and H3K4me2). In sum, gDEC, in addition to directly depleting the corepressor DNMT1, upregulated KMT activating epigenetic enzymes, activating terminal epithelial program activation, and prostate cancer cell cycling exits independent of apoptosis.
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Affiliation(s)
- Dev Karan
- Department of Pathology, MCW Cancer Center, Prostate Cancer Center of Excellence, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Manohar Singh
- Department of Pathology, MCW Cancer Center, Prostate Cancer Center of Excellence, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Seema Dubey
- Department of Pathology, MCW Cancer Center, Prostate Cancer Center of Excellence, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Peter J Van Veldhuizen
- Department of Internal Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Yogen Saunthararajah
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
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