1
|
Karakatsanis NM, Hamey JJ, Wilkins MR. Taking Me away: the function of phosphorylation on histone lysine demethylases. Trends Biochem Sci 2024; 49:257-276. [PMID: 38233282 DOI: 10.1016/j.tibs.2023.12.004] [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: 07/27/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024]
Abstract
Histone lysine demethylases (KDMs) regulate eukaryotic gene transcription by catalysing the removal of methyl groups from histone proteins. These enzymes are intricately regulated by the kinase signalling system in response to internal and external stimuli. Here, we review the mechanisms by which kinase-mediated phosphorylation influence human histone KDM function. These include the changing of histone KDM subcellular localisation or chromatin binding, the altering of protein half-life, changes to histone KDM complex formation that result in histone demethylation, non-histone demethylation or demethylase-independent effects, and effects on histone KDM complex dissociation. We also explore the structural context of phospho-sites on histone KDMs and evaluate how this relates to function.
Collapse
Affiliation(s)
- Nicola M Karakatsanis
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, Australia
| | - Joshua J Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, Australia.
| |
Collapse
|
2
|
Ibrahim IH. Metalloproteins and metalloproteomics in health and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:123-176. [PMID: 38960472 DOI: 10.1016/bs.apcsb.2023.12.013] [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: 07/05/2024]
Abstract
Metalloproteins represents more than one third of human proteome, with huge variation in physiological functions and pathological implications, depending on the metal/metals involved and tissue context. Their functions range from catalysis, bioenergetics, redox, to DNA repair, cell proliferation, signaling, transport of vital elements, and immunity. The human metalloproteomic studies revealed that many families of metalloproteins along with individual metalloproteins are dysregulated under several clinical conditions. Also, several sorts of interaction between redox- active or redox- inert metalloproteins are observed in health and disease. Metalloproteins profiling shows distinct alterations in neurodegenerative diseases, cancer, inflammation, infection, diabetes mellitus, among other diseases. This makes metalloproteins -either individually or as families- a promising target for several therapeutic approaches. Inhibitors and activators of metalloenzymes, metal chelators, along with artificial metalloproteins could be versatile in diagnosis and treatment of several diseases, in addition to other biomedical and industrial applications.
Collapse
Affiliation(s)
- Iman Hassan Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt.
| |
Collapse
|
3
|
Huang Y, Tang M, Hu Z, Cai B, Chen G, Jiang L, Xia Y, Guan P, Li X, Mao Z, Wan X, Lu W. SMYD3 promotes endometrial cancer through epigenetic regulation of LIG4/XRCC4/XLF complex in non-homologous end joining repair. Oncogenesis 2024; 13:3. [PMID: 38191478 PMCID: PMC10774296 DOI: 10.1038/s41389-023-00503-0] [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: 01/22/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Endometrial cancer (EC) stands as one of the most prevalent malignancies affecting the female genital tract, witnessing a rapid surge in incidence globally. Despite the well-established association of histone methyltransferase SMYD3 with the development and progression of various cancers, its specific oncogenic role in endometrial cancer remains unexplored. In the present study, we report that the expression level of SMYD3 is significantly upregulated in EC samples and associated with EC progression. Through meticulous in vivo and in vitro experiments, we reveal that depletion of SMYD3 curtails cell proliferation, migration, and invasion capabilities, leading to compromised non-homologous end joining repair (NHEJ) and heightened sensitivity of EC cells to radiation. Furthermore, our pathway enrichment analysis underscores the pivotal involvement of the DNA damage repair pathway in regulating EC progression. Mechanistically, in response to DNA damage, SMYD3 is recruited to these sites in a PARP1-dependent manner, specifically methylating LIG4. This methylation sets off a sequential assembly of the LIG4/XRCC4/XLF complex, actively participating in the NHEJ pathway and thereby fostering EC progression. Notably, our findings highlight the promise of SMYD3 as a crucial player in NHEJ repair and its direct correlation with EC progression. Intriguingly, pharmacological intervention targeting SMYD3 with its specific inhibitor, BCI-121, emerges as a potent strategy, markedly suppressing the tumorigenicity of EC cells and significantly enhancing the efficacy of radiotherapy. Collectively, our comprehensive data position SMYD3 as a central factor in NHEJ repair and underscore its potential as a promising pharmacological target for endometrial cancer therapy, validated through both in vitro and in vivo systems.
Collapse
Affiliation(s)
- Yujia Huang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ming Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Zhiyi Hu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Bailian Cai
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Guofang Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Lijun Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yan Xia
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Pujun Guan
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaoqi Li
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xiaoping Wan
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Wen Lu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| |
Collapse
|
4
|
Chen JS, Teng YN, Chen CY, Chen JY. A novel STAT3/ NFκB p50 axis regulates stromal-KDM2A to promote M2 macrophage-mediated chemoresistance in breast cancer. Cancer Cell Int 2023; 23:237. [PMID: 37821959 PMCID: PMC10568766 DOI: 10.1186/s12935-023-03088-1] [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: 08/11/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Lysine Demethylase 2A (KDM2A) plays a crucial role in cancer cell growth, differentiation, metastasis, and the maintenance of cancer stemness. Our previous study found that cancer-secreted IL-6 can upregulate the expression of KDM2A to promote further the transition of cells into cancer-associated fibroblasts (CAFs). However, the molecular mechanism by which breast cancer-secreted IL-6 regulates the expression of KDM2A remains unclear. Therefore, this study aimed to elucidate the underlying molecular mechanism of IL-6 in regulating KDM2A expression in CAFs and KDM2A-mediated paclitaxel resistance in breast cancer. METHODS The ectopic vector expression and biochemical inhibitor were used to analyze the KDM2A expression regulated by HS-578 T conditioned medium or IL-6 in mammary fibroblasts. Immunoprecipitation and chromatin immunoprecipitation assays were conducted to examine the interaction between STAT3 and NFκB p50. M2 macrophage polarization was assessed by analyzing M2 macrophage-specific markers using flow cytometry and RT-PCR. ESTIMATE algorithm was used to analyze the tumor microenvironment-dominant breast cancer samples from the TCGA database. The correlation between stromal KDM2A and CD163 + M2 macrophages was analyzed using the Pearson correlation coefficient. Cell viability was determined using trypan blue exclusion assay. RESULTS IL-6 regulates gene expression via activation and dimerization of STAT3 or collaboration of STAT3 and NFκB. However, STAT3, a downstream transcription factor of the IL-6 signaling pathway, was directly complexed with NFκB p50, not NFκB p65, to upregulate the expression of KDM2A in CAFs. Enrichment analysis of immune cells/stromal cells using TCGA-breast cancer RNA-seq data unveiled a positive correlation between stromal KDM2A and the abundance of M2 macrophages. CXCR2-associated chemokines secreted by KDM2A-expressing CAFs stimulated M2 macrophage polarization, which in turn secreted CCL2 to increase paclitaxel resistance in breast cancer cells by activating CCR2 signaling. CONCLUSION This study revealed the non-canonical molecular mechanism of IL-6 secreted by breast cancer upregulated KDM2A expression in CAFs via a novel STAT3/NFκB p50 axis, which STAT3 complexed with NFκB p50 in NFκB p50 binding motif of KDM2A promoter. KDM2A-expressing CAFs dominantly secreted the CXCR2-associated chemokines to promote M2 macrophage polarization and enhance paclitaxel resistance in breast cancer. These findings underscore the therapeutic potential of targeting the CXCR2 or CCR2 pathway as a novel strategy for paclitaxel-resistant breast cancer.
Collapse
Affiliation(s)
- Jia-Shing Chen
- School of Medicine for International Students, College of Medicine, I-Shou University, No.8, Yida Road, Jiaosu Village, Yanchao District, Kaohsiung, 82425, Taiwan
| | - Yu-Ning Teng
- School of Medicine, College of Medicine, I-Shou University, 8 Yida Road, Kaohsiung, 82445, Taiwan ROC
- Department of Pharmacy, E-Da Cancer Hospital, 21 Yida Road, Kaohsiung, 82445, Taiwan ROC
| | - Cheng-Yi Chen
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan ROC
| | - Jing-Yi Chen
- School of Medicine for International Students, College of Medicine, I-Shou University, No.8, Yida Road, Jiaosu Village, Yanchao District, Kaohsiung, 82425, Taiwan.
- Department of Medical Laboratory Science, College of Medical Science and Technology, I-Shou University, No.8, Yida Road, Jiaosu Village, Yanchao District, Kaohsiung, 82425, Taiwan ROC.
| |
Collapse
|
5
|
Xiong X, Huang X, Zhu Y, Hai Z, Fei X, Pan B, Yang Q, Xiong Y, Fu W, Lan D, Zhang X, Li J. Testis-specific knockout of Kdm2a reveals nonessential roles in male fertility but partially compromises spermatogenesis. Theriogenology 2023; 209:9-20. [PMID: 37354760 DOI: 10.1016/j.theriogenology.2023.06.008] [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: 12/27/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/26/2023]
Abstract
Lysine-specific histone demethylase 2 (Kdm2a) is a regulatory factor of histone modifications that participates in gametogenesis and embryonic development. The mis-regulation of Kdm2a can lead to aberrant gene expression, thereby contributing to abnormal cell proliferation, differentiation, apoptosis, and tumorigenesis. However, due to the potential confounding effects that are secondary to the loss of Kdm2a function from the soma in existing whole-animal mutants, the in vivo function of Kdm2a in spermatogenesis for male fertility remains unknown. Herein, we focus on exploring the spatiotemporal expression profile and biological functions of Kdm2a in the spermatogenesis and fertility of male mice. A testis-specific knockout Kdm2a model (Kdm2a cKO) was established by using the Stra8-Cre/loxP recombinase system to explore the roles of Kdm2a in male fertility. Our results showed that Kdm2a was ubiquitously expressed and dynamically distributed in multiple tissues and cell types in the testis of mice. Surprisingly, Kdm2a-deficient adult males were completely fertile and comparable with their control (Kdm2aflox/flox) counterparts. Despite the significantly reduced total number of sperm and density of seminiferous tubules in Kdm2a cKO testis accompanied by the degeneration of spermatogenesis, the fertilization ability and embryonic developmental competence of the Kdm2a cKO were comparable with those of their control littermates, suggesting that Kdm2a disruption did not markedly affect male fertility, at least during younger ages. Furthermore, Kdm2a homozygous mutants exhibited a lower total number and motility of sperm than the control group and showed notably affected serum 17β-estradiol concentration. Interestingly, the transcriptome sequencing revealed that the loss of Kdm2a remarkably upregulated the expression level of Kdm2b. This effect, in turn, may induce compensative effects in the case of Kdm2a deficiency to maintain normal male reproduction. Together, our results reveal that Kdm2a shows spatiotemporal expression during testicular development and that its loss is insufficient to compromise the production of spermatozoa completely. The homologous Kdm2b gene might compensate for the loss of Kdm2a. Our work provides a novel Kdm2a cKO mouse allowing for the efficient deletion of Kdm2a in a testis-specific manner, and further investigated the biological function of Kdm2a and the compensatory effects of Kdm2b. Our study will advance our understanding of underlying mechanisms in spermatogenesis and male fertility.
Collapse
Affiliation(s)
- Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Xiangyue Huang
- Key Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Yanjin Zhu
- Key Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Zhuo Hai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Xixi Fei
- Key Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Bangting Pan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Qinhui Yang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Yan Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Wei Fu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Daoliang Lan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China
| | - Xiaojian Zhang
- Center for Assisted Reproduction, Sichuan Academy of Medical Science, Sichuan Provincial People's Hospital, Chengdu, 610072, PR China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China; Key Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, Sichuan, 610041, PR China.
| |
Collapse
|
6
|
Malik KK, Sridhara SC, Lone KA, Katariya PD, Pulimamidi D, Tyagi S. MLL methyltransferases regulate H3K4 methylation to ensure CENP-A assembly at human centromeres. PLoS Biol 2023; 21:e3002161. [PMID: 37379335 PMCID: PMC10335677 DOI: 10.1371/journal.pbio.3002161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 07/11/2023] [Accepted: 05/12/2023] [Indexed: 06/30/2023] Open
Abstract
The active state of centromeres is epigenetically defined by the presence of CENP-A interspersed with histone H3 nucleosomes. While the importance of dimethylation of H3K4 for centromeric transcription has been highlighted in various studies, the identity of the enzyme(s) depositing these marks on the centromere is still unknown. The MLL (KMT2) family plays a crucial role in RNA polymerase II (Pol II)-mediated gene regulation by methylating H3K4. Here, we report that MLL methyltransferases regulate transcription of human centromeres. CRISPR-mediated down-regulation of MLL causes loss of H3K4me2, resulting in an altered epigenetic chromatin state of the centromeres. Intriguingly, our results reveal that loss of MLL, but not SETD1A, increases co-transcriptional R-loop formation, and Pol II accumulation at the centromeres. Finally, we report that the presence of MLL and SETD1A is crucial for kinetochore maintenance. Altogether, our data reveal a novel molecular framework where both the H3K4 methylation mark and the methyltransferases regulate stability and identity of the centromere.
Collapse
Affiliation(s)
- Kausika Kumar Malik
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Sreerama Chaitanya Sridhara
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Kaisar Ahmad Lone
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, India
| | - Payal Deepakbhai Katariya
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Deepshika Pulimamidi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| |
Collapse
|
7
|
Affandi T, Haas A, Ohm AM, Wright GM, Black JC, Reyland ME. PKCδ regulates chromatin remodeling and DNA repair through SIRT6. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.541991. [PMID: 37292592 PMCID: PMC10245827 DOI: 10.1101/2023.05.24.541991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein kinase C delta (PKCδ) is a ubiquitous kinase whose function is defined in part by localization to specific cellular compartments. Nuclear PKCδ is both necessary and sufficient for IR-induced apoptosis, while inhibition of PKCδ activity provides radioprotection in vivo. How nuclear PKCδ regulates DNA-damage induced cell death is poorly understood. Here we show that PKCδ regulates histone modification, chromatin accessibility, and double stranded break (DSB) repair through a mechanism that requires SIRT6. Overexpression of PKCδ promotes genomic instability and increases DNA damage and apoptosis. Conversely, depletion of PKCδ increases DNA repair via non-homologous end joining (NHEJ) and homologous recombination (HR) as evidenced by more rapid formation of NHEJ (DNA-PK) and HR (Rad51) DNA damage foci, increased expression of repair proteins, and increased repair of NHEJ and HR fluorescent reporter constructs. Nuclease sensitivity indicates that PKCδ depletion is associated with more open chromatin, while overexpression of PKCδ reduces chromatin accessibility. Epiproteome analysis revealed that PKCδ depletion increases chromatin associated H3K36me2, and reduces ribosylation of KDM2A and chromatin bound KDM2A. We identify SIRT6 as a downstream mediator of PKCδ. PKCδ-depleted cells have increased expression of SIRT6, and depletion of SIRT6 reverses the changes in chromatin accessibility, histone modification and NHEJ and HR DNA repair seen with PKCδ-depletion. Furthermore, depletion of SIRT6 reverses radioprotection in PKCδ-depleted cells. Our studies describe a novel pathway whereby PKCδ orchestrates SIRT6-dependent changes in chromatin accessibility to increase DNA repair, and define a mechanism for regulation of radiation-induced apoptosis by PKCδ.
Collapse
Affiliation(s)
- Trisiani Affandi
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ami Haas
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angela M. Ohm
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Gregory M. Wright
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joshua C. Black
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mary E. Reyland
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| |
Collapse
|
8
|
Cao Y, Chen S, Lu J, Zhang M, Shi L, Qin J, Lv J, Li D, Ma L, Zhang Y. BPA induces placental trophoblast proliferation inhibition and fetal growth restriction by inhibiting the expression of SRB1. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:60805-60819. [PMID: 37037937 DOI: 10.1007/s11356-023-26850-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/03/2023] [Indexed: 04/12/2023]
Abstract
Bisphenol-A (BPA) is a common environmental toxicant that is known to be associated with fetal growth restriction (FGR). However, the mechanisms of how BPA induce FGR is poorly characterized. We conducted proteomics to identify the abnormal expression of SRB1 in female placental tissues with high BPA-induced FGR and further verified its decreased expression in human placenta and BeWo cells. Next, the effect of BPA on fetal development was further confirmed in pregnant C57BL/6 mice. The expression of SRB1 was consistently downregulated in human FGR placentas, BPA-exposed trophoblasts and mouse placentas. In addition, we found that SRB1 interacted with PCNA, and BPA exposure indirectly reduced the expression of PCNA and further inhibited placental proliferation. In vitro studies showed that BPA exposure reduced the expression of CDK1, CDK2, cyclin B and phosphorylated Rb in placental trophoblast cells, indicating cell cycle arrest after exposure to BPA. In addition, the expression of γ-H2AX and phosphorylated ATM was upregulated in BPA-exposed trophoblasts, indicating increased DNA damage. Our results indicate that BPA-induced FGR is achieved by reducing the expression of SRB1, inhibiting placental proliferation and increasing DNA damage. Our findings not only explain the mechanism of BPA-associated developmental toxicity but also shed light upon developing novel therapeutic targets.
Collapse
Affiliation(s)
- Yuming Cao
- Department of Gynaecology and Obstetrics, Zhongnan Hospital of Wuhan University, No 169 of Donghu Road, Wuhan, 430071, Hubei, China
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Gynaecology and Obstetrics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, People's Republic of China
| | - Sihan Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jing Lu
- Department of Gynaecology and Obstetrics, Zhongnan Hospital of Wuhan University, No 169 of Donghu Road, Wuhan, 430071, Hubei, China
| | - Ming Zhang
- Department of Gynaecology and Obstetrics, Zhongnan Hospital of Wuhan University, No 169 of Donghu Road, Wuhan, 430071, Hubei, China
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lei Shi
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Juling Qin
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jing Lv
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Danyang Li
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ling Ma
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yuanzhen Zhang
- Department of Gynaecology and Obstetrics, Zhongnan Hospital of Wuhan University, No 169 of Donghu Road, Wuhan, 430071, Hubei, China.
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Department of Gynaecology and Obstetrics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, People's Republic of China.
| |
Collapse
|
9
|
Xiong X, Zhang X, Yang M, Zhu Y, Yu H, Fei X, Mastuda F, Lan D, Xiong Y, Fu W, Yin S, Li J. Oocyte-Specific Knockout of Histone Lysine Demethylase KDM2a Compromises Fertility by Blocking the Development of Follicles and Oocytes. Int J Mol Sci 2022; 23:ijms231912008. [PMID: 36233308 PMCID: PMC9570323 DOI: 10.3390/ijms231912008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022] Open
Abstract
The methylation status of histones plays a crucial role in many cellular processes, including follicular and oocyte development. Lysine-specific demethylase 2a (KDM2a) has been reported to be closely associated with gametogenesis and reproductive performance, but the specific function and regulatory mechanism have been poorly characterized in vivo. We found KDM2a to be highly expressed in growing follicles and oocytes of mice in this study. To elucidate the physiological role of Kdm2a, the zona pellucida 3-Cre (Zp3-Cre)/LoxP system was used to generate an oocyte Kdm2a conditional knockout (Zp3-Cre; Kdm2aflox/flox, termed Kdm2a cKO) model. Our results showed that the number of pups was reduced by approximately 50% in adult Kdm2a cKO female mice mating with wildtype males than that of the control (Kdm2aflox/flox) group. To analyze the potential causes, the ovaries of Kdm2a cKO mice were subjected to histological examination, and results indicated an obvious difference in follicular development between Kdm2a cKO and control female mice and partial arrest at the primary antral follicle stage. The GVBD and matured rates of oocytes were also compromised after conditional knockout Kdm2a, and the morphological abnormal oocytes increased. Furthermore, the level of 17β-estradiol of Kdm2a cKO mice was only 60% of that in the counterparts, and hormone sensitivity decreased as the total number of ovulated and matured oocytes decreased after superovulation. After deletion of Kdm2a, the patterns of H3K36me2/3 in GVBD-stage oocytes were remarkedly changed. Transcriptome sequencing showed that the mRNA expression profiles in Kdm2a cKO oocytes were significantly different, and numerous differentially expressed genes were involved in pathways regulating follicular and oocyte development. Taken together, these results indicated that the oocyte-specific knockout Kdm2a gene led to female subfertility, suggesting the crucial role of Kdm2a in epigenetic modification and follicular and oocyte development.
Collapse
Affiliation(s)
- Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory for Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
| | - Xiaojian Zhang
- Center for Assisted Reproduction, Sichuan Academy of Medical Science, Sichuan Provincial People’s Hospital, Chengdu 610072, China
| | - Manzhen Yang
- Key Laboratory for Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
| | - Yanjin Zhu
- Key Laboratory for Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
| | - Hailing Yu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Xixi Fei
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Fuko Mastuda
- Laboratory of Theriogenology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Daoliang Lan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Yan Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Wei Fu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Shi Yin
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
- Key Laboratory for Animal Science of National Ethnic Affairs Commission, Southwest Minzu University, Chengdu 610041, China
- Correspondence:
| |
Collapse
|
10
|
Wang J, Zhang ZY, Jiang J, Tang L, Wang XY, Wang Z, Yang XL, Yu XL, Huang CC, Chen F, Ye SJ, Wan H. KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma. Biochem Biophys Res Commun 2022; 624:53-58. [DOI: 10.1016/j.bbrc.2022.07.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 11/26/2022]
|
11
|
Separovich RJ, Wong MW, Bartolec TK, Hamey JJ, Wilkins MR. Site-specific phosphorylation of histone H3K36 methyltransferase Set2p and demethylase Jhd1p is required for stress responses in Saccharomyces cerevisiae. J Mol Biol 2022; 434:167500. [DOI: 10.1016/j.jmb.2022.167500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
|
12
|
Takatsuka H, Shibata A, Umeda M. Genome Maintenance Mechanisms at the Chromatin Level. Int J Mol Sci 2021; 22:ijms221910384. [PMID: 34638727 PMCID: PMC8508675 DOI: 10.3390/ijms221910384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Genome integrity is constantly threatened by internal and external stressors, in both animals and plants. As plants are sessile, a variety of environment stressors can damage their DNA. In the nucleus, DNA twines around histone proteins to form the higher-order structure “chromatin”. Unraveling how chromatin transforms on sensing genotoxic stress is, thus, key to understanding plant strategies to cope with fluctuating environments. In recent years, accumulating evidence in plant research has suggested that chromatin plays a crucial role in protecting DNA from genotoxic stress in three ways: (1) changes in chromatin modifications around damaged sites enhance DNA repair by providing a scaffold and/or easy access to DNA repair machinery; (2) DNA damage triggers genome-wide alterations in chromatin modifications, globally modulating gene expression required for DNA damage response, such as stem cell death, cell-cycle arrest, and an early onset of endoreplication; and (3) condensed chromatin functions as a physical barrier against genotoxic stressors to protect DNA. In this review, we highlight the chromatin-level control of genome stability and compare the regulatory systems in plants and animals to find out unique mechanisms maintaining genome integrity under genotoxic stress.
Collapse
Affiliation(s)
- Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-Machi, Kanazawa 920-1192, Japan;
| | - Atsushi Shibata
- Signal Transduction Program, Gunma University Initiative for Advanced Research (GIAR), 3-39-22, Showa-Machi, Maebashi 371-8511, Japan;
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
- Correspondence:
| |
Collapse
|
13
|
DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
Collapse
|
14
|
SETD2-mediated H3K14 trimethylation promotes ATR activation and stalled replication fork restart in response to DNA replication stress. Proc Natl Acad Sci U S A 2021; 118:2011278118. [PMID: 34074749 PMCID: PMC8201831 DOI: 10.1073/pnas.2011278118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ataxia telangiectasia and Rad3 related (ATR) activation after replication stress involves a cascade of reactions, including replication protein A (RPA) complex loading onto single-stranded DNA and ATR activator loading onto chromatin. The contribution of histone modifications to ATR activation, however, is unclear. Here, we report that H3K14 trimethylation responds to replication stress by enhancing ATR activation. First, we confirmed that H3K14 monomethylation, dimethylation, and trimethylation all exist in mammalian cells, and that both SUV39H1 and SETD2 methyltransferases can catalyze H3K14 trimethylation in vivo and in vitro. Interestingly, SETD2-mediated H3K14 trimethylation markedly increases in response to replication stress induced with hydroxyurea, a replication stress inducer. Under these conditions, SETD2-mediated H3K14me3 recruited the RPA complex to chromatin via a direct interaction with RPA70. The increase in H3K14me3 levels was abolished, and RPA loading was attenuated when SETD2 was depleted or H3K14 was mutated. Rather, the cells were sensitive to replication stress such that the replication forks failed to restart, and cell-cycle progression was delayed. These findings help us understand how H3K14 trimethylation links replication stress with ATR activation.
Collapse
|
15
|
Sterling J, Menezes SV, Abbassi RH, Munoz L. Histone lysine demethylases and their functions in cancer. Int J Cancer 2021; 148:2375-2388. [PMID: 33128779 DOI: 10.1002/ijc.33375] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022]
Abstract
Histone lysine demethylases (KDMs) are enzymes that remove the methylation marks on lysines in nucleosomes' histone tails. These changes in methylation marks regulate gene transcription during both development and malignant transformation. Depending on which lysine residue is targeted, the effect of a given KDM on gene transcription can be either activating or repressing, and KDMs can regulate the expression of both oncogenes and tumour suppressors. Thus, the functions of KDMs can be regarded as both oncogenic and tumour suppressive, contingent on cell context and the enzyme isoform. Finally, KDMs also demethylate nonhistone proteins and have a variety of demethylase-independent functions. These epigenetic and other mechanisms that KDMs control make them important regulators of malignant tumours. Here, we present an overview of eight KDM subfamilies, their most-studied lysine targets and selected recent data on their roles in cancer stem cells, tumour aggressiveness and drug tolerance.
Collapse
Affiliation(s)
- Jayden Sterling
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharleen V Menezes
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ramzi H Abbassi
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Lenka Munoz
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
16
|
DNA double-strand break repair: Putting zinc fingers on the sore spot. Semin Cell Dev Biol 2021; 113:65-74. [DOI: 10.1016/j.semcdb.2020.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/22/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022]
|
17
|
Control of the chromatin response to DNA damage: Histone proteins pull the strings. Semin Cell Dev Biol 2021; 113:75-87. [DOI: 10.1016/j.semcdb.2020.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022]
|
18
|
Di Nisio E, Lupo G, Licursi V, Negri R. The Role of Histone Lysine Methylation in the Response of Mammalian Cells to Ionizing Radiation. Front Genet 2021; 12:639602. [PMID: 33859667 PMCID: PMC8042281 DOI: 10.3389/fgene.2021.639602] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/11/2021] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic genomes are wrapped around nucleosomes and organized into different levels of chromatin structure. Chromatin organization has a crucial role in regulating all cellular processes involving DNA-protein interactions, such as DNA transcription, replication, recombination and repair. Histone post-translational modifications (HPTMs) have a prominent role in chromatin regulation, acting as a sophisticated molecular code, which is interpreted by HPTM-specific effectors. Here, we review the role of histone lysine methylation changes in regulating the response to radiation-induced genotoxic damage in mammalian cells. We also discuss the role of histone methyltransferases (HMTs) and histone demethylases (HDMs) and the effects of the modulation of their expression and/or the pharmacological inhibition of their activity on the radio-sensitivity of different cell lines. Finally, we provide a bioinformatic analysis of published datasets showing how the mRNA levels of known HMTs and HDMs are modulated in different cell lines by exposure to different irradiation conditions.
Collapse
Affiliation(s)
- Elena Di Nisio
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Lupo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Counsil (IBPM-CNR), Rome, Italy
| |
Collapse
|
19
|
Separovich RJ, Wong MWM, Chapman TR, Slavich E, Hamey JJ, Wilkins MR. Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential. J Biol Chem 2021; 296:100192. [PMID: 33334889 PMCID: PMC7948420 DOI: 10.1074/jbc.ra120.015995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/06/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
Histone methylation is central to the regulation of eukaryotic transcription. In Saccharomyces cerevisiae, it is controlled by a system of four methyltransferases (Set1p, Set2p, Set5p, and Dot1p) and four demethylases (Jhd1p, Jhd2p, Rph1p, and Gis1p). While the histone targets for these enzymes are well characterized, the connection of the enzymes with the intracellular signaling network and thus their regulation is poorly understood; this also applies to all other eukaryotes. Here we report the detailed characterization of the eight S. cerevisiae enzymes and show that they carry a total of 75 phosphorylation sites, 92 acetylation sites, and two ubiquitination sites. All enzymes are subject to phosphorylation, although demethylases Jhd1p and Jhd2p contained one and five sites respectively, whereas other enzymes carried 14 to 36 sites. Phosphorylation was absent or underrepresented on catalytic and other domains but strongly enriched for regions of disorder on methyltransferases, suggesting a role in the modulation of protein-protein interactions. Through mutagenesis studies, we show that phosphosites within the acidic and disordered N-terminus of Set2p affect H3K36 methylation levels in vivo, illustrating the functional importance of such sites. While most kinases upstream of the yeast histone methylation enzymes remain unknown, we model the possible connections between the cellular signaling network and the histone-based gene regulatory system and propose an integrated regulatory structure. Our results provide a foundation for future, detailed exploration of the role of specific kinases and phosphosites in the regulation of histone methylation.
Collapse
Affiliation(s)
- Ryan J Separovich
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mandy W M Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Tyler R Chapman
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Eve Slavich
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| |
Collapse
|
20
|
Zhou Y, Shao C. Histone methylation can either promote or reduce cellular radiosensitivity by regulating DNA repair pathways. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108362. [PMID: 34083050 DOI: 10.1016/j.mrrev.2020.108362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
Radiotherapy is one of the primary modalities for cancer treatment, and its efficiency usually relies on cellular radiosensitivity. DNA damage repair is a core content of cellular radiosensitivity, and the primary mechanism of which includes non-homologous end-joining (NHEJ) and homologous recombination (HR). By affecting DNA damage repair, histone methylation regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs) participates in the regulation of cellular radiosensitivity via three mechanisms: (a) recruiting DNA repair-related proteins, (b) regulating the expressions of DNA repair genes, and (c) mediating the dynamic change of chromatin. Interestingly, both aberrantly high and low levels of histone methylation could impede DNA repair processes. Here we reviewed the mechanisms of the dual effects of histone methylation on cell response to radiation. Since some inhibitors of HMTs and HDMs are reported to increase cellular radiosensitivity, understanding their molecular mechanisms may be helpful in developing new drugs for the therapy of radioresistant tumors.
Collapse
Affiliation(s)
- Yuchuan Zhou
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai, 200032, China
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai, 200032, China.
| |
Collapse
|
21
|
Controlling the Controllers: Regulation of Histone Methylation by Phosphosignalling. Trends Biochem Sci 2020; 45:1035-1048. [DOI: 10.1016/j.tibs.2020.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/23/2020] [Accepted: 08/07/2020] [Indexed: 01/05/2023]
|
22
|
Tanaka Y, Obinata H, Konishi A, Yamagiwa N, Tsuneoka M. Production of ROS by Gallic Acid Activates KDM2A to Reduce rRNA Transcription. Cells 2020; 9:E2266. [PMID: 33050392 PMCID: PMC7601038 DOI: 10.3390/cells9102266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
Metformin, which is suggested to have anti-cancer effects, activates KDM2A to reduce rRNA transcription and proliferation of cancer cells. Thus, the specific activation of KDM2A may be applicable to the treatment of cancers. In this study, we screened a food-additive compound library to identify compounds that control cell proliferation. We found that gallic acid activated KDM2A to reduce rRNA transcription and cell proliferation in breast cancer MCF-7 cells. Gallic acid accelerated ROS production and activated AMPK. When ROS production or AMPK activity was inhibited, gallic acid did not activate KDM2A. These results suggest that both ROS production and AMPK activation are required for activation of KDM2A by gallic acid. Gallic acid did not reduce the succinate level, which was required for KDM2A activation by metformin. Metformin did not elevate ROS production. These results suggest that the activation of KDM2A by gallic acid includes mechanisms distinct from those by metformin. Therefore, signals from multiple intracellular conditions converge in KDM2A to control rRNA transcription. Gallic acid did not induce KDM2A-dependent anti-proliferation activity in non-tumorigenic MCF10A cells. These results suggest that the mechanism of KDM2A activation by gallic acid may be applicable to the treatment of breast cancers.
Collapse
Affiliation(s)
- Yuji Tanaka
- Laboratory of Molecular and Cellular Biology, Faculty of Pharmacy, Takasaki University of Health and Welfare, Takasaki 370-0033, Japan;
| | - Hideru Obinata
- Education and Research Support Center, Gunma University Graduate School of Medicine, Maebashi 371-8511, Japan;
| | - Akimitsu Konishi
- Department of Biochemistry, Gunma University Graduate School of Medicine, Maebashi 371-8511, Japan;
| | - Noriyuki Yamagiwa
- Laboratory of Molecular Design Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, Takasaki 370-0033, Japan;
| | - Makoto Tsuneoka
- Laboratory of Molecular and Cellular Biology, Faculty of Pharmacy, Takasaki University of Health and Welfare, Takasaki 370-0033, Japan;
| |
Collapse
|
23
|
Rezazadeh S, Yang D, Biashad SA, Firsanov D, Takasugi M, Gilbert M, Tombline G, Bhanu NV, Garcia BA, Seluanov A, Gorbunova V. SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair. Aging (Albany NY) 2020; 12:11165-11184. [PMID: 32584788 PMCID: PMC7343504 DOI: 10.18632/aging.103567] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/09/2020] [Indexed: 01/06/2023]
Abstract
When transcribed DNA is damaged, the transcription and DNA repair machineries must interact to ensure successful DNA repair. The mechanisms of this interaction in the context of chromatin are still being elucidated. Here we show that the SIRT6 protein enhances non-homologous end joining (NHEJ) DNA repair by transiently repressing transcription. Specifically, SIRT6 mono-ADP ribosylates the lysine demethylase JHDM1A/KDM2A leading to rapid displacement of KDM2A from chromatin, resulting in increased H3K36me2 levels. Furthermore, we found that through HP1α binding, H3K36me2 promotes subsequent H3K9 tri-methylation. This results in transient suppression of transcription initiation by RNA polymerase II and recruitment of NHEJ factors to DNA double-stranded breaks (DSBs). These data reveal a mechanism where SIRT6 mediates a crosstalk between transcription and DNA repair machineries to promote DNA repair. SIRT6 functions in multiple pathways related to aging, and its novel function coordinating DNA repair and transcription is yet another way by which SIRT6 promotes genome stability and longevity.
Collapse
Affiliation(s)
- Sarallah Rezazadeh
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - David Yang
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Seyed Ali Biashad
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Denis Firsanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Masaki Takasugi
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Michael Gilbert
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Natarajan V. Bhanu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| |
Collapse
|
24
|
de Krijger I, van der Torre J, Peuscher MH, Eder M, Jacobs JJL. H3K36 dimethylation by MMSET promotes classical non-homologous end-joining at unprotected telomeres. Oncogene 2020; 39:4814-4827. [PMID: 32472076 PMCID: PMC7299843 DOI: 10.1038/s41388-020-1334-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022]
Abstract
The epigenetic environment plays an important role in DNA damage recognition and repair, both at DNA double-strand breaks and at deprotected telomeres. To increase understanding on how DNA damage responses (DDR) at deprotected telomeres are regulated by modification and remodeling of telomeric chromatin we screened 38 methyltransferases for their ability to promote telomere dysfunction-induced genomic instability. As top hit we identified MMSET, a histone methyltransferase (HMT) causally linked to multiple myeloma and Wolf-Hirschhorn syndrome. We show that MMSET promotes non-homologous end-joining (NHEJ) at deprotected telomeres through Ligase4-dependent classical NHEJ, and does not contribute to Ligase3-dependent alternative NHEJ. Moreover, we show that this is dependent on the catalytic activity of MMSET, enabled by its SET-domain. Indeed, in absence of MMSET H3K36-dimethylation (H3K36me2) decreases, both globally and at subtelomeric regions. Interestingly, the level of MMSET-dependent H3K36me2 directly correlates with NHEJ-efficiency. We show that MMSET depletion does not impact on recognition of deprotected telomeres by the DDR-machinery or on subsequent recruitment of DDR-factors acting upstream or at the level of DNA repair pathway choice. Our data are most consistent with an important role for H3K36me2 in more downstream steps of the DNA repair process. Moreover, we find additional H3K36me2-specific HMTs to contribute to NHEJ at deprotected telomeres, further emphasizing the importance of H3K36me2 in DNA repair.
Collapse
Affiliation(s)
- Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jaco van der Torre
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Marieke H Peuscher
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Mathias Eder
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| |
Collapse
|
25
|
Liu K, Min J. Structural Basis for the Recognition of Non-methylated DNA by the CXXC Domain. J Mol Biol 2020:S0022-2836(19)30591-1. [DOI: 10.1016/j.jmb.2019.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023]
|
26
|
Lu X, Tang M, Zhu Q, Yang Q, Li Z, Bao Y, Liu G, Hou T, Lv Y, Zhao Y, Wang H, Yang Y, Cheng Z, Wen H, Liu B, Xu X, Gu L, Zhu WG. GLP-catalyzed H4K16me1 promotes 53BP1 recruitment to permit DNA damage repair and cell survival. Nucleic Acids Res 2019; 47:10977-10993. [PMID: 31612207 PMCID: PMC6868394 DOI: 10.1093/nar/gkz897] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/29/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022] Open
Abstract
The binding of p53-binding protein 1 (53BP1) to damaged chromatin is a critical event in non-homologous DNA end joining (NHEJ)-mediated DNA damage repair. Although several molecular pathways explaining how 53BP1 binds damaged chromatin have been described, the precise underlying mechanisms are still unclear. Here we report that a newly identified H4K16 monomethylation (H4K16me1) mark is involved in 53BP1 binding activity in the DNA damage response (DDR). During the DDR, H4K16me1 rapidly increases as a result of catalyzation by the histone methyltransferase G9a-like protein (GLP). H4K16me1 shows an increased interaction level with 53BP1, which is important for the timely recruitment of 53BP1 to DNA double-strand breaks. Differing from H4K16 acetylation, H4K16me1 enhances the 53BP1-H4K20me2 interaction at damaged chromatin. Consistently, GLP knockdown markedly attenuates 53BP1 foci formation, leading to impaired NHEJ-mediated repair and decreased cell survival. Together, these data support a novel axis of the DNA damage repair pathway based on H4K16me1 catalysis by GLP, which promotes 53BP1 recruitment to permit NHEJ-mediated DNA damage repair.
Collapse
Affiliation(s)
- Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
- Key laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Ming Tang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200032, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Qiaoyan Yang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Zhiming Li
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
- Key laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Yantao Bao
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Ge Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Tianyun Hou
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
- Key laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Yafei Lv
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Ying Zhao
- Key laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Haiying Wang
- Key laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Key laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab Co. Ltd., Hangzhou Economic and Technological Development Area, Hangzhou 310018, China
| | - He Wen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Baohua Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Luo Gu
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China
- Key laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
- International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China
| |
Collapse
|
27
|
Bayo J, Tran TA, Wang L, Peña-Llopis S, Das AK, Martinez ED. Jumonji Inhibitors Overcome Radioresistance in Cancer through Changes in H3K4 Methylation at Double-Strand Breaks. Cell Rep 2019; 25:1040-1050.e5. [PMID: 30355483 PMCID: PMC6245670 DOI: 10.1016/j.celrep.2018.09.081] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/17/2018] [Accepted: 09/25/2018] [Indexed: 01/10/2023] Open
Abstract
We have uncovered a role for Jumonji inhibitors in overcoming radioresistance through KDM5B inhibition. Pharmacological blockade of Jumonji demethy-lases with JIB-04 leads to specific accumulation of H3K4me3 at sites marked by γH2AX and impaired recruitment of DNA repair factors, preventing resolution of damage and resulting in robust sensitization to radiation therapy. In DNA-repair-proficient cancer cells, knockdown of the H3K4me3 demethylase KDM5B, but not other Jumonji enzymes, mimics pharmacological inhibition, and KDM5B overexpression rescues this phenotype and increases radioresistance. The H3K4me3 demethylase inhibitor PBIT also sensitizes cancer cells to radiation, while an H3K27me3 demethylase inhibitor does not. In vivo co-administration of radiation with JIB-04 significantly prolongs the survival of mice with tumors even long after cessation of treatment. In human patients, lung squamous cell carcinomas highly ex-pressing KDM5B respond poorly to radiation. Thus, we propose the use of Jumonji KDM inhibitors as potent radiosensitizers. Radioresistance is an obstacle to lung cancer cures. Bayo et al. reveal that JARID1B removes H3K4me3 marks at sites of DNA damage. Genetic or pharmacological inhibition of JARID1B robustly radiosensitizes cancers in vitro and in vivo through defects in DNA repair, providing a therapeutic option for radioresistant tumors.
Collapse
Affiliation(s)
- Juan Bayo
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA; Instituto de Investigaciones en Medicina Traslacional, CONICET, Universidad Austral, Argentina
| | - Tram Anh Tran
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lei Wang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel Peña-Llopis
- Division of Translational Oncology, Essen University Hospital, German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amit K Das
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Elisabeth D Martinez
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
28
|
Vacík T, Lađinović D, Raška I. KDM2A/B lysine demethylases and their alternative isoforms in development and disease. Nucleus 2019; 9:431-441. [PMID: 30059280 PMCID: PMC7000146 DOI: 10.1080/19491034.2018.1498707] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aberrant levels of histone modifications lead to chromatin malfunctioning and consequently to various developmental defects and human diseases. Therefore, the proteins bearing the ability to modify histones have been extensively studied and the molecular mechanisms of their action are now fairly well understood. However, little attention has been paid to naturally occurring alternative isoforms of chromatin modifying proteins and to their biological roles. In this review, we focus on mammalian KDM2A and KDM2B, the only two lysine demethylases whose genes have been described to produce also an alternative isoform lacking the N-terminal demethylase domain. These short KDM2A/B-SF isoforms arise through alternative promoter usage and seem to play important roles in development and disease. We hypothesise about the biological significance of these alternative isoforms, which might represent a more common evolutionarily conserved regulatory mechanism.
Collapse
Affiliation(s)
- Tomáš Vacík
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Dijana Lađinović
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Ivan Raška
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| |
Collapse
|
29
|
Zhang Q, Riddle RC, Yang Q, Rosen CR, Guttridge DC, Dirckx N, Faugere MC, Farber CR, Clemens TL. The RNA demethylase FTO is required for maintenance of bone mass and functions to protect osteoblasts from genotoxic damage. Proc Natl Acad Sci U S A 2019; 116:17980-17989. [PMID: 31434789 PMCID: PMC6731662 DOI: 10.1073/pnas.1905489116] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fat mass and obesity-associated gene (FTO) encodes an m6A RNA demethylase that controls mRNA processing and has been linked to both obesity and bone mineral density in humans by genome-wide association studies. To examine the role of FTO in bone, we characterized the phenotype of mice lacking Fto globally (FtoKO ) or selectively in osteoblasts (FtoOcKO ). Both mouse models developed age-related reductions in bone volume in both the trabecular and cortical compartments. RNA profiling in osteoblasts following acute disruption of Fto revealed changes in transcripts of Hspa1a and other genes in the DNA repair pathway containing consensus m6A motifs required for demethylation by FtoFto KO osteoblasts were more susceptible to genotoxic agents (UV and H2O2) and exhibited increased rates of apoptosis. Importantly, forced expression of Hspa1a or inhibition of NF-κB signaling normalized the DNA damage and apoptotic rates in Fto KO osteoblasts. Furthermore, increased metabolic stress induced in mice by feeding a high-fat diet induced greater DNA damage in osteoblast of FtoOc KO mice compared to controls. These data suggest that FTO functions intrinsically in osteoblasts through Hspa1a-NF-κB signaling to enhance the stability of mRNA of proteins that function to protect cells from genotoxic damage.
Collapse
Affiliation(s)
- Qian Zhang
- Department of Orthopaedic Surgery, The Johns Hopkins University, Baltimore, MD 21287
| | - Ryan C Riddle
- Department of Orthopaedic Surgery, The Johns Hopkins University, Baltimore, MD 21287
- Baltimore Veterans Administration Medical Center, Baltimore, MD 21201
| | - Qian Yang
- Department of Orthopaedic Surgery, The Johns Hopkins University, Baltimore, MD 21287
| | - Clifford R Rosen
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME 04074
| | - Denis C Guttridge
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC 29425
| | - Naomi Dirckx
- Department of Orthopaedic Surgery, The Johns Hopkins University, Baltimore, MD 21287
| | | | - Charles R Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908
| | - Thomas L Clemens
- Department of Orthopaedic Surgery, The Johns Hopkins University, Baltimore, MD 21287;
- Baltimore Veterans Administration Medical Center, Baltimore, MD 21201
| |
Collapse
|
30
|
Li Y, Li Z, Dong L, Tang M, Zhang P, Zhang C, Cao Z, Zhu Q, Chen Y, Wang H, Wang T, Lv D, Wang L, Zhao Y, Yang Y, Wang H, Zhang H, Roeder RG, Zhu WG. Histone H1 acetylation at lysine 85 regulates chromatin condensation and genome stability upon DNA damage. Nucleic Acids Res 2019; 46:7716-7730. [PMID: 29982688 PMCID: PMC6125638 DOI: 10.1093/nar/gky568] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022] Open
Abstract
Linker histone H1 has a key role in maintaining higher order chromatin structure and genome stability, but how H1 functions in these processes is elusive. Here, we report that acetylation of lysine 85 (K85) within the H1 globular domain is a critical post-translational modification that regulates chromatin organization. H1K85 is dynamically acetylated by the acetyltransferase PCAF in response to DNA damage, and this effect is counterbalanced by the histone deacetylase HDAC1. Notably, an acetylation-mimic mutation of H1K85 (H1K85Q) alters H1 binding to the nucleosome and leads to condensed chromatin as a result of increased H1 binding to core histones. In addition, H1K85 acetylation promotes heterochromatin protein 1 (HP1) recruitment to facilitate chromatin compaction. Consequently, H1K85 mutation leads to genomic instability and decreased cell survival upon DNA damage. Together, our data suggest a novel model whereby H1K85 acetylation regulates chromatin structure and preserves chromosome integrity upon DNA damage.
Collapse
Affiliation(s)
- Yinglu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Zhiming Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Liping Dong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ping Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chaohua Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ziyang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yongcan Chen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China.,Peking University-Tsinghua University Center for Life Sciences, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Tianzhuo Wang
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Danyu Lv
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Lina Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Haiying Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Hongquan Zhang
- Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing 100191, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China.,Peking University-Tsinghua University Center for Life Sciences, Beijing 100871, China
| |
Collapse
|
31
|
Duchatel RJ, Jackson ER, Alvaro F, Nixon B, Hondermarck H, Dun MD. Signal Transduction in Diffuse Intrinsic Pontine Glioma. Proteomics 2019; 19:e1800479. [DOI: 10.1002/pmic.201800479] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/03/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Ryan J. Duchatel
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
| | - Evangeline R. Jackson
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
| | - Frank Alvaro
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
- John Hunter Children's Hospital Faculty of Health and Medicine University of Newcastle New Lambton Heights NSW 2305 Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Science School of Environmental and Life Sciences University of Newcastle Callaghan NSW 2308 Australia
| | - Hubert Hondermarck
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
- Cancer Neurobiology Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
| | - Matthew D. Dun
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
| |
Collapse
|
32
|
Li Z, Chen Y, Tang M, Li Y, Zhu WG. Regulation of DNA damage-induced ATM activation by histone modifications. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42764-019-00004-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
33
|
Li Y, Li Z, Zhu WG. Molecular Mechanisms of Epigenetic Regulators as Activatable Targets in Cancer Theranostics. Curr Med Chem 2019; 26:1328-1350. [PMID: 28933282 DOI: 10.2174/0929867324666170921101947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/24/2017] [Accepted: 06/09/2017] [Indexed: 12/11/2022]
Abstract
Epigenetics is defined as somatically inheritable changes that are not accompanied by alterations in DNA sequence. Epigenetics encompasses DNA methylation, covalent histone modifications, non-coding RNA as well as nucleosome remodeling. Notably, abnormal epigenetic changes play a critical role in cancer development including malignant transformation, metastasis, prognosis, drug resistance and tumor recurrence, which can provide effective targets for cancer prognosis, diagnosis and therapy. Understanding these changes provide effective means for cancer diagnosis and druggable targets for better clinical applications. Histone modifications and related enzymes have been found to correlate well with cancer incidence and prognosis in recent years. Dysregulated expression or mutation of histone modification enzymes and histone modification status abnormalities have been considered to play essential roles in tumorigenesis and clinical outcomes of cancer treatment. Some of the histone modification inhibitors have been extensively employed in clinical practice and many others are still under laboratory research or pre-clinical assessment. Here we summarize the important roles of epigenetics, especially histone modifications in cancer diagnostics and therapeutics, and also discuss the developmental implications of activatable epigenetic targets in cancer theranostics.
Collapse
Affiliation(s)
- Yinglu Li
- Shenzhen University School of Medicine, Shenzhen 518060, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Zhiming Li
- Shenzhen University School of Medicine, Shenzhen 518060, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Wei-Guo Zhu
- Shenzhen University School of Medicine, Shenzhen 518060, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| |
Collapse
|
34
|
Tellier M, Chalmers R. The roles of the human SETMAR (Metnase) protein in illegitimate DNA recombination and non-homologous end joining repair. DNA Repair (Amst) 2019; 80:26-35. [PMID: 31238295 PMCID: PMC6715855 DOI: 10.1016/j.dnarep.2019.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
Full length SETMAR expression has no effect on DNA repair and integration in vivo. SETMAR putative nuclease activity is not required in vivo. Separate expression of the SET and MAR domains affects DNA repair and integration. SETMAR isoform with a truncated SET-domain is specific to species containing the MAR domain.
SETMAR is a fusion between a SET-domain methyltransferase gene and a mariner-family transposase gene, which is specific to anthropoid primates. However, the ancestral SET gene is present in all other mammals and birds. SETMAR is reported to be involved in transcriptional regulation and a diverse set of reactions related to DNA repair. Since the transcriptional effects of SETMAR depend on site-specific DNA binding, and are perturbed by inactivating the methyltransferase, we wondered whether we could differentiate the effects of the SET and MAR domains in DNA repair assays. We therefore generated several stable U2OS cell lines expressing either wild type SETMAR or truncation or point mutant variants. We tested these cell lines with in vivo plasmid-based assays to determine the relevance of the different domains and activities of SETMAR in DNA repair. Contrary to previous reports, we found that wild type SETMAR had little to no effect on the rate of cell division, DNA integration into the genome or non-homologous end joining. Also contrary to previous reports, we failed to detect any effect of a strong active-site mutation that should have knocked out the putative nuclease activity of SETMAR.
Collapse
Affiliation(s)
- Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
| |
Collapse
|
35
|
Herberg M, Siebert S, Quaas M, Thalheim T, Rother K, Hussong M, Altmüller J, Kerner C, Galle J, Schweiger MR, Aust G. Loss of Msh2 and a single-radiation hit induce common, genome-wide, and persistent epigenetic changes in the intestine. Clin Epigenetics 2019; 11:65. [PMID: 31029155 PMCID: PMC6486978 DOI: 10.1186/s13148-019-0639-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background Mismatch repair (MMR)-deficiency increases the risk of colorectal tumorigenesis. To determine whether the tumors develop on a normal or disturbed epigenetic background and how radiation affects this, we quantified genome-wide histone H3 methylation profiles in macroscopic normal intestinal tissue of young radiated and untreated MMR-deficient VCMsh2LoxP/LoxP (Msh2−/−) mice months before tumor onset. Results Histone H3 methylation increases in Msh2−/− compared to control Msh2+/+ mice. Activating H3K4me3 and H3K36me3 histone marks frequently accumulate at genes that are H3K27me3 or H3K4me3 modified in Msh2+/+ mice, respectively. The genes recruiting H3K36me3 enrich in gene sets associated with DNA repair, RNA processing, and ribosome biogenesis that become transcriptionally upregulated in the developing tumors. A similar epigenetic effect is present in Msh2+/+ mice 4 weeks after a single-radiation hit, whereas radiation of Msh2−/− mice left their histone methylation profiles almost unchanged. Conclusions MMR deficiency results in genome-wide changes in histone H3 methylation profiles preceding tumor development. Similar changes constitute a persistent epigenetic signature of radiation-induced DNA damage. Electronic supplementary material The online version of this article (10.1186/s13148-019-0639-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Maria Herberg
- Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, Leipzig, Germany
| | - Susann Siebert
- Laboratory for Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Graduate School for Biological Sciences (GSfBS), University of Cologne, Cologne, Germany
| | - Marianne Quaas
- Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, Leipzig, Germany.,Department of Surgery, Research Laboratories, Leipzig University, Liebigstr. 19, D-04103, Leipzig, Germany
| | - Torsten Thalheim
- Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, Leipzig, Germany
| | - Karen Rother
- Department of Surgery, Research Laboratories, Leipzig University, Liebigstr. 19, D-04103, Leipzig, Germany.,Laboratory for Clinical and Experimental Hepatology (LCEHep) Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Michelle Hussong
- Laboratory for Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Christiane Kerner
- Department of Surgery, Research Laboratories, Leipzig University, Liebigstr. 19, D-04103, Leipzig, Germany
| | - Joerg Galle
- Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, Leipzig, Germany
| | - Michal R Schweiger
- Laboratory for Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Gabriela Aust
- Department of Surgery, Research Laboratories, Leipzig University, Liebigstr. 19, D-04103, Leipzig, Germany.
| |
Collapse
|
36
|
Iuchi S, Paulo JA. Lysine-specific demethylase 2A enhances binding of various nuclear factors to CpG-rich genomic DNAs by action of its CXXC-PHD domain. Sci Rep 2019; 9:5496. [PMID: 30940825 PMCID: PMC6445129 DOI: 10.1038/s41598-019-41896-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/19/2019] [Indexed: 02/08/2023] Open
Abstract
The lysine-specific demethylase 2A gene (KDM2A) is ubiquitously expressed and its transcripts consist of several alternatively spliced forms, including KDM2A and the shorter form N782 that lacks the 3' end encoding F-box and LRR. KDM2A binds to numerous CpG-rich genomic loci and regulates various cellular activities; however, the mechanism of the pleiotropic function is unknown. Here, we identify the mechanism of KDM2A played by its CXXC-PHD domain. KDM2A is necessary for a rapid proliferation of post-natal keratinocytes while its 3' end eclipses the stimulatory effect. EGFP-N782 binds to chromatin together with the XRCC5/6 complex, and the CXXC-PHD domain regulates the CpG-rich IGFBPL1 promoter. In vitro, CXXC-PHD enhances binding of nuclear extract ORC3 to the CpG-rich promoter, but not to the AT-rich DIP2B promoter to which ORC3 binds constitutively. Furthermore, CXXC-PHD recruits 94 nuclear factors involved in replication, ribosome synthesis, and mitosis, including POLR1A to the IGFBPL1 promoter. This recruitment is unprecedented; however, the result suggests that these nuclear factors bind to their cognate loci, as substantiated by the result that CXXC-PHD recruits POLR1A to the rDNA promoter. We propose that CXXC-PHD promotes permissiveness for nuclear factors to interact, but involvement of the XRCC5/6 complex in the recruitment is undetermined.
Collapse
Affiliation(s)
- Shiro Iuchi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 20115, USA.
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 20115, USA
| |
Collapse
|
37
|
Kerns SL, Chuang KH, Hall W, Werner Z, Chen Y, Ostrer H, West C, Rosenstein B. Radiation biology and oncology in the genomic era. Br J Radiol 2018; 91:20170949. [PMID: 29888979 PMCID: PMC6475928 DOI: 10.1259/bjr.20170949] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/25/2022] Open
Abstract
Radiobiology research is building the foundation for applying genomics in precision radiation oncology. Advances in high-throughput approaches will underpin increased understanding of radiosensitivity and the development of future predictive assays for clinical application. There is an established contribution of genetics as a risk factor for radiotherapy side effects. An individual's radiosensitivity is an inherited polygenic trait with an architecture that includes rare mutations in a few genes that confer large effects and common variants in many genes with small effects. Current thinking is that some will be tissue specific, and future tests will be tailored to the normal tissues at risk. The relationship between normal and tumor cell radiosensitivity is poorly understood. Data are emerging suggesting interplay between germline genetic variation and epigenetic modification with growing evidence that changes in DNA methylation regulate the radiosensitivity of cancer cells and histone acetyltransferase inhibitors have radiosensitizing effects. Changes in histone methylation can also impair DNA damage response signaling and alter radiosensitivity. An important effort to advance radiobiology in the genomic era was establishment of the Radiogenomics Consortium to enable the creation of the large radiotherapy cohorts required to exploit advances in genomics. To address challenges in harmonizing data from multiple cohorts, the consortium established the REQUITE project to collect standardized data and genotyping for ~5,000 patients. The collection of detailed dosimetric data is important to produce validated multivariable models. Continued efforts will identify new genes that impact on radiosensitivity to generate new knowledge on toxicity pathogenesis and tests to incorporate into the clinical decision-making process.
Collapse
Affiliation(s)
| | - Kuang-Hsiang Chuang
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - William Hall
- Department of Radiation Oncology, Medical College of Wisconsin and Clement J Zablocki VA Medical Center Milwaukee, Milwaukee, WI, USA
| | | | - Yuhchyau Chen
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, NY, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Catharine West
- Division of Cancer Sciences, University of Manchester, Christie Hospital, Manchester, UK
| | - Barry Rosenstein
- Departments of Radiation Oncology, Genetics and Genomic Sciences, and Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
38
|
Lim K, Nguyen T, Li AY, Yeo Y, Chen E. Histone H3 lysine 36 methyltransferase mobilizes NER factors to regulate tolerance against alkylation damage in fission yeast. Nucleic Acids Res 2018; 46:5061-5074. [PMID: 29635344 PMCID: PMC6007430 DOI: 10.1093/nar/gky245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 03/17/2018] [Accepted: 03/22/2018] [Indexed: 11/30/2022] Open
Abstract
The Set2 methyltransferase and its target, histone H3 lysine 36 (H3K36), affect chromatin architecture during the transcription and repair of DNA double-stranded breaks. Set2 also confers resistance against the alkylating agent, methyl methanesulfonate (MMS), through an unknown mechanism. Here, we show that Schizosaccharomyces pombe (S. pombe) exhibit MMS hypersensitivity when expressing a set2 mutant lacking the catalytic histone methyltransferase domain or a H3K36R mutant (reminiscent of a set2-null mutant). Set2 acts synergistically with base excision repair factors but epistatically with nucleotide excision repair (NER) factors, and determines the timely nuclear accumulation of the NER initiator, Rhp23, in response to MMS. Set2 facilitates Rhp23 recruitment to chromatin at the brc1 locus, presumably to repair alkylating damage and regulate the expression of brc1+ in response to MMS. Set2 also show epistasis with DNA damage checkpoint proteins; regulates the activation of Chk1, a DNA damage response effector kinase; and acts in a similar functional group as proteins involved in homologous recombination. Consistently, Set2 and H3K36 ensure the dynamicity of Rhp54 in DNA repair foci formation after MMS treatment. Overall, our results indicate a novel role for Set2/H3K36me in coordinating the recruitment of DNA repair machineries to timely manage alkylating damage.
Collapse
Affiliation(s)
- Kim Kiat Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Adelicia Yongling Li
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee Phan Yeo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore
| |
Collapse
|
39
|
Wei S, Li C, Yin Z, Wen J, Meng H, Xue L, Wang J. Histone methylation in DNA repair and clinical practice: new findings during the past 5-years. J Cancer 2018; 9:2072-2081. [PMID: 29937925 PMCID: PMC6010677 DOI: 10.7150/jca.23427] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 03/31/2018] [Indexed: 12/12/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can impair cellular homeostasis and genome stability to result in tumorigenesis for inappropriate repair. Although DSBs are repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ), the related mechanisms are still incompletely unclear. Indeed, more and more evidences indicate that the methylation of histone lysine has an important role in choosing the pathways of DNA repair. For example, tri-methylated H3K36 is required for HR repair, while di-methylated H4K20 can recruit 53BP1 for NHEJ repair. Here, we reviewed the recent progress in the molecular mechanisms by which histone methylation functions in DNA double-strand breaks repair (DSBR). The insight into the mechanisms of histone methylation repairing DNA damage will supply important cues for clinical cancer treatment.
Collapse
Affiliation(s)
- Shuhua Wei
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Chunxiao Li
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Zhongnan Yin
- Medical Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Jie Wen
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Hui Meng
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Lixiang Xue
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China.,Medical Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Junjie Wang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| |
Collapse
|
40
|
Wilson MD, Durocher D. Reading chromatin signatures after DNA double-strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0280. [PMID: 28847817 DOI: 10.1098/rstb.2016.0280] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are DNA lesions that must be accurately repaired in order to preserve genomic integrity and cellular viability. The response to DSBs reshapes the local chromatin environment and is largely orchestrated by the deposition, removal and detection of a complex set of chromatin-associated post-translational modifications. In particular, the nucleosome acts as a central signalling hub and landing platform in this process by organizing the recruitment of repair and signalling factors, while at the same time coordinating repair with other DNA-based cellular processes. While current research has provided a descriptive overview of which histone marks affect DSB repair, we are only beginning to understand how these marks are interpreted to foster an efficient DSB response. Here we review how the modified chromatin surrounding DSBs is read, with a focus on the insights gleaned from structural and biochemical studies.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
Collapse
Affiliation(s)
- Marcus D Wilson
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| |
Collapse
|
41
|
Cao LL, Du C, Liu H, Pei L, Qin L, Jia M, Wang H. Lysine-specific demethylase 2A expression is associated with cell growth and cyclin D1 expression in colorectal adenocarcinoma. Int J Biol Markers 2018; 33:1724600818764069. [PMID: 29683067 DOI: 10.1177/1724600818764069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Lysine-specific demethylase 2A (KDM2A), a specific H3K36me1/2 demethylase, has been reported to be closely associated with several types of cancer. In this study, we aimed to investigate the expression and function of KDM2A in colorectal adenocarcinoma. METHODS A total of 215 colorectal adenocarcinoma specimens were collected, and then subjected to immunohistochemistry assay to evaluate the expression levels of KDM2A, cyclin D1 and other proteins in colorectal adenocarcinoma tissues. Real-time polymerase chain reaction, Western blot, and other molecular biology methods were used to explore the role of KDM2A in colorectal adenocarcinoma cells. RESULTS In this study, we report that the expression level of KDM2A is high in colorectal adenocarcinoma tissues, and this high expression promotes the proliferation and colony formation of colorectal adenocarcinoma cells, as demonstrated by KDM2A knockdown experiments. In addition, the expression of KDM2A is closely associated with cyclin D1 expression in colorectal adenocarcinoma tissues and cell lines. CONCLUSIONS Our study reveals a novel role for high-expressed KDM2A in colorectal adenocarcinoma cell growth, and that the expression of KDM2A is associated with that of cyclin D1 in colorectal adenocarcinoma.
Collapse
Affiliation(s)
- Lin-Lin Cao
- 1 Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Changzheng Du
- 2 Department of Colorectal Surgery, Beijing Cancer Hospital, Beijing, China
| | - Hangqi Liu
- 1 Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Lin Pei
- 1 Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Li Qin
- 1 Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Mei Jia
- 1 Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hui Wang
- 1 Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| |
Collapse
|
42
|
Recruitment of lysine demethylase 2A to DNA double strand breaks and its interaction with 53BP1 ensures genome stability. Oncotarget 2018; 9:15915-15930. [PMID: 29662616 PMCID: PMC5882307 DOI: 10.18632/oncotarget.24636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/27/2018] [Indexed: 12/21/2022] Open
Abstract
Lysine demethylase 2A (KDM2A) functions in transcription as a demethylase of lysine 36 on histone H3. Herein, we characterise a role for KDM2A in the DNA damage response in which KDM2A stimulates conjugation of ubiquitin to 53BP1. Impaired KDM2A-mediated ubiquitination negatively affects the recruitment of 53BP1 to DSBs. Notably, we show that KDM2A itself is recruited to DSBs in a process that depends on its demethylase activity and zinc finger domain. Moreover, we show that KDM2A plays an important role in ensuring genomic stability upon DNA damage. Depletion of KDM2A or disruption of its zinc finger domain results in the accumulation of micronuclei following ionizing radiation (IR) treatment. In addition, IR-treated cells depleted of KDM2A display premature exit from the G2/M checkpoint. Interestingly, loss of the zinc finger domain also resulted in 53BP1 focal distribution in condensed mitotic chromosomes. Overall, our data indicates that KDM2A plays an important role in modulating the recruitment of 53BP1 to DNA breaks and is crucial for the preservation of genome integrity following DNA damage.
Collapse
|
43
|
Vilas CK, Emery LE, Denchi EL, Miller KM. Caught with One's Zinc Fingers in the Genome Integrity Cookie Jar. Trends Genet 2018; 34:313-325. [PMID: 29370947 DOI: 10.1016/j.tig.2017.12.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 12/27/2022]
Abstract
Zinc finger (ZnF) domains are present in at least 5% of human proteins. First characterized as binding to DNA, ZnFs display extraordinary binding plasticity and can bind to RNA, lipids, proteins, and protein post-translational modifications (PTMs). The diverse binding properties of ZnFs have made their functional characterization challenging. While once confined to large and poorly characterized protein families, proteomic, cellular, and molecular studies have begun to shed light on their involvement as protectors of the genome. We focus here on the emergent roles of ZnF domain-containing proteins in promoting genome integrity, including their involvement in telomere maintenance and DNA repair. These findings have highlighted the need for further characterization of ZnF proteins, which can reveal the functions of this large gene class in normal cell function and human diseases, including those involving genome instability such as aging and cancer.
Collapse
Affiliation(s)
- Caroline K Vilas
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Lara E Emery
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Eros Lazzerini Denchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA.
| |
Collapse
|
44
|
Hou T, Li Z, Zhao Y, Zhu WG. Mechanisms controlling the anti-neoplastic functions of FoxO proteins. Semin Cancer Biol 2017; 50:101-114. [PMID: 29155239 DOI: 10.1016/j.semcancer.2017.11.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/18/2017] [Accepted: 11/14/2017] [Indexed: 02/06/2023]
Abstract
The Forkhead box O (FoxO) proteins comprise a family of evolutionarily conserved transcription factors that predominantly function as tumor suppressors. These proteins assume diverse roles in the cellular anti-neoplastic response, including regulation of apoptosis and autophagy, cancer metabolism, cell-cycle arrest, oxidative stress and the DNA damage response. More recently, FoxO proteins have been implicated in cancer immunity and cancer stem-cell (CSC) homeostasis. Interestingly, in some sporadic sub-populations, FoxO protein function may also be manipulated by factors such as β-catenin whereby they instead can facilitate cancer progression via maintenance of CSC properties or promoting drug resistance or metastasis and invasion. This review highlights the essential biological functions of FoxOs and explores the areas that may be exploited in FoxO protein signaling pathways in the development of novel cancer therapeutic agents.
Collapse
Affiliation(s)
- Tianyun Hou
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhiming Li
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| |
Collapse
|
45
|
Cassandri M, Smirnov A, Novelli F, Pitolli C, Agostini M, Malewicz M, Melino G, Raschellà G. Zinc-finger proteins in health and disease. Cell Death Discov 2017; 3:17071. [PMID: 29152378 PMCID: PMC5683310 DOI: 10.1038/cddiscovery.2017.71] [Citation(s) in RCA: 438] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 02/07/2023] Open
Abstract
Zinc-finger proteins (ZNFs) are one of the most abundant groups of proteins and have a wide range of molecular functions. Given the wide variety of zinc-finger domains, ZNFs are able to interact with DNA, RNA, PAR (poly-ADP-ribose) and other proteins. Thus, ZNFs are involved in the regulation of several cellular processes. In fact, ZNFs are implicated in transcriptional regulation, ubiquitin-mediated protein degradation, signal transduction, actin targeting, DNA repair, cell migration, and numerous other processes. The aim of this review is to provide a comprehensive summary of the current state of knowledge of this class of proteins. Firstly, we describe the actual classification of ZNFs, their structure and functions. Secondly, we focus on the biological role of ZNFs in the development of organisms under normal physiological and pathological conditions.
Collapse
Affiliation(s)
- Matteo Cassandri
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Artem Smirnov
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Flavia Novelli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Consuelo Pitolli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Massimiliano Agostini
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Michal Malewicz
- Medical Research Council, Toxicology Unit, Leicester University, Leicester LE1 9HN, UK
| | - Gerry Melino
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy.,Medical Research Council, Toxicology Unit, Leicester University, Leicester LE1 9HN, UK
| | - Giuseppe Raschellà
- ENEA Research Center Casaccia, Laboratory of Biosafety and Risk Assessment, Via Anguillarese, Rome, Italy
| |
Collapse
|
46
|
Degryse S, de Bock CE, Demeyer S, Govaerts I, Bornschein S, Verbeke D, Jacobs K, Binos S, Skerrett-Byrne DA, Murray HC, Verrills NM, Van Vlierberghe P, Cools J, Dun MD. Mutant JAK3 phosphoproteomic profiling predicts synergism between JAK3 inhibitors and MEK/BCL2 inhibitors for the treatment of T-cell acute lymphoblastic leukemia. Leukemia 2017; 32:788-800. [PMID: 28852199 PMCID: PMC5843905 DOI: 10.1038/leu.2017.276] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/17/2017] [Accepted: 08/15/2017] [Indexed: 02/06/2023]
Abstract
Mutations in the interleukin-7 receptor (IL7R) or the Janus kinase 3 (JAK3) kinase occur frequently in T-cell acute lymphoblastic leukemia (T-ALL) and both are able to drive cellular transformation and the development of T-ALL in mouse models. However, the signal transduction pathways downstream of JAK3 mutations remain poorly characterized. Here we describe the phosphoproteome downstream of the JAK3(L857Q)/(M511I) activating mutations in transformed Ba/F3 lymphocyte cells. Signaling pathways regulated by JAK3 mutants were assessed following acute inhibition of JAK1/JAK3 using the JAK kinase inhibitors ruxolitinib or tofacitinib. Comprehensive network interrogation using the phosphoproteomic signatures identified significant changes in pathways regulating cell cycle, translation initiation, mitogen-activated protein kinase and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/AKT signaling, RNA metabolism, as well as epigenetic and apoptotic processes. Key regulatory proteins within pathways that showed altered phosphorylation following JAK inhibition were targeted using selumetinib and trametinib (MEK), buparlisib (PI3K) and ABT-199 (BCL2), and found to be synergistic in combination with JAK kinase inhibitors in primary T-ALL samples harboring JAK3 mutations. These data provide the first detailed molecular characterization of the downstream signaling pathways regulated by JAK3 mutations and provide further understanding into the oncogenic processes regulated by constitutive kinase activation aiding in the development of improved combinatorial treatment regimens.
Collapse
Affiliation(s)
- S Degryse
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - C E de Bock
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Demeyer
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - I Govaerts
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Bornschein
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - D Verbeke
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - K Jacobs
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Binos
- Thermo Fisher Scientific, Scoresby, Victoria, Australia
| | - D A Skerrett-Byrne
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - H C Murray
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - N M Verrills
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - P Van Vlierberghe
- Department of Pediatrics and Genetics, Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - J Cools
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - M D Dun
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| |
Collapse
|
47
|
G9a coordinates with the RPA complex to promote DNA damage repair and cell survival. Proc Natl Acad Sci U S A 2017; 114:E6054-E6063. [PMID: 28698370 DOI: 10.1073/pnas.1700694114] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Histone methyltransferase G9a has critical roles in promoting cancer-cell growth and gene suppression, but whether it is also associated with the DNA damage response is rarely studied. Here, we report that loss of G9a impairs DNA damage repair and enhances the sensitivity of cancer cells to radiation and chemotherapeutics. In response to DNA double-strand breaks (DSBs), G9a is phosphorylated at serine 211 by casein kinase 2 (CK2) and recruited to chromatin. The chromatin-enriched G9a can then directly interact with replication protein A (RPA) and promote loading of the RPA and Rad51 recombinase to DSBs. This mechanism facilitates homologous recombination (HR) and cell survival. We confirmed the interaction between RPA and G9a to be critical for RPA foci formation and HR upon DNA damage. Collectively, our findings demonstrate a regulatory pathway based on CK2-G9a-RPA that permits HR in cancer cells and provide further rationale for the use of G9a inhibitors as a cancer therapeutic.
Collapse
|
48
|
5-Fluorouracil targets histone acetyltransferases p300/CBP in the treatment of colorectal cancer. Cancer Lett 2017; 400:183-193. [PMID: 28465257 DOI: 10.1016/j.canlet.2017.04.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/17/2017] [Accepted: 04/21/2017] [Indexed: 12/14/2022]
Abstract
Although 5-fluorouracil (5-FU) is known to interfere with the synthesis of ribonucleic acid and deoxyribonucleic acid, the mechanism underlying its therapeutic efficacy in colorectal cancer (CRC) has not been fully elucidated. We aimed to investigate the influence of 5-FU on histone acetylation, a well-established anti-cancer target, to reveal novel pharmacological effects of 5-FU and their significance for CRC therapy. Results demonstrated that 5-FU induces global histone de-acetylation in multiple CRC cell lines. We identified that 5-FU reduces the binding ability of histone acetyltransferases p300 and CBP to chromatin, and induces their degradation through lysosome. Further work revealed that the degradation of p300/CBP induced by 5-FU was dependent on chaperone-mediated autophagy, mediated by heat-shock cognate protein 70 kDa (hsc70) and lysosomal-associated membrane protein 2A (LAMP2A). Moreover, the degradation of p300/CBP is relevant to cellular resistance to 5-FU, since blocking the degradation enhances 5-FU's cytotoxicity in CRC cells. From clinical data, we demonstrated that low expression of p300/CBP in CRC tissue was closely associated with poor clinical response to 5-FU based-chemotherapy, based on the analysis of 262 colorectal samples from the patients receiving 5-FU treatment: compared to cases with high expression of p300/CBP, those with low expression had lower long-term disease-free survival rate and increased early-progression. These results elucidate a novel pharmacological effect of 5-FU involving global histone de-acetylation by promoting the degradation of p300/CBP, and highlights p300 and CBP as promising predictors of chemo-sensitivity to 5-FU treatment.
Collapse
|
49
|
Amendola PG, Zaghet N, Ramalho JJ, Vilstrup Johansen J, Boxem M, Salcini AE. JMJD-5/KDM8 regulates H3K36me2 and is required for late steps of homologous recombination and genome integrity. PLoS Genet 2017; 13:e1006632. [PMID: 28207814 PMCID: PMC5336306 DOI: 10.1371/journal.pgen.1006632] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 03/03/2017] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
The eukaryotic genome is organized in a three-dimensional structure called chromatin, constituted by DNA and associated proteins, the majority of which are histones. Post-translational modifications of histone proteins greatly influence chromatin structure and regulate many DNA-based biological processes. Methylation of lysine 36 of histone 3 (H3K36) is a post-translational modification functionally relevant during early steps of DNA damage repair. Here, we show that the JMJD-5 regulates H3K36 di-methylation and it is required at late stages of double strand break repair mediated by homologous recombination. Loss of jmjd-5 results in hypersensitivity to ionizing radiation and in meiotic defects, and it is associated with aberrant retention of RAD-51 at sites of double strand breaks. Analyses of jmjd-5 genetic interactions with genes required for resolving recombination intermediates (rtel-1) or promoting the resolution of RAD-51 double stranded DNA filaments (rfs-1 and helq-1) suggest that jmjd-5 prevents the formation of stalled postsynaptic recombination intermediates and favors RAD-51 removal. As these phenotypes are all recapitulated by a catalytically inactive jmjd-5 mutant, we propose a novel role for H3K36me2 regulation during late steps of homologous recombination critical to preserve genome integrity.
Collapse
Affiliation(s)
- Pier Giorgio Amendola
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Nico Zaghet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - João J. Ramalho
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, CH Utrecht, The Netherlands
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Mike Boxem
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, CH Utrecht, The Netherlands
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
50
|
Chen Y, Zhu WG. Biological function and regulation of histone and non-histone lysine methylation in response to DNA damage. Acta Biochim Biophys Sin (Shanghai) 2016; 48:603-16. [PMID: 27217472 DOI: 10.1093/abbs/gmw050] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/21/2016] [Indexed: 02/07/2023] Open
Abstract
DNA damage response (DDR) signaling network is initiated to protect cells from various exogenous and endogenous damage resources. Timely and accurate regulation of DDR proteins is required for distinct DNA damage repair pathways. Post-translational modifications of histone and non-histone proteins play a vital role in the DDR factor foci formation and signaling pathway. Phosphorylation, ubiquitylation, SUMOylation, neddylation, poly(ADP-ribosyl)ation, acetylation, and methylation are all involved in the spatial-temporal regulation of DDR, among which phosphorylation and ubiquitylation are well studied. Studies in the past decade also revealed extensive roles of lysine methylation in response to DNA damage. Lysine methylation is finely regulated by plenty of lysine methyltransferases, lysine demethylases, and can be recognized by proteins with chromodomain, plant homeodomain, Tudor domain, malignant brain tumor domain, or proline-tryptophan-tryptophan-proline domain. In this review, we outline the dynamics and regulation of histone lysine methylation at canonical (H3K4, H3K9, H3K27, H3K36, H3K79, and H4K20) and non-canonical sites after DNA damage, and discuss their context-specific functions in DDR protein recruitment or extraction, chromatin environment establishment, and transcriptional regulation. We also present the emerging advances of lysine methylation in non-histone proteins during DDR.
Collapse
Affiliation(s)
- Yongcan Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China Peking University-Tsinghua University Center for Life Sciences, Beijing 100191, China
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China Peking University-Tsinghua University Center for Life Sciences, Beijing 100191, China School of Medicine, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|