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Hinrichs AK, Koch A, Richter AM. Dual-Luciferase Reporter Assay for Prescreening CRISPR (d)Cas9-Mediated Epigenetic Editing on a Plant Promoter Using Human Cells. Methods Mol Biol 2024; 2788:273-285. [PMID: 38656520 DOI: 10.1007/978-1-0716-3782-1_16] [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] [Indexed: 04/26/2024]
Abstract
Epigenetic editing, also known as EpiEdit, offers an exciting way to control gene expression without altering the DNA sequence. In this study, we evaluate the application of EpiEdit to plant promoters, specifically the MLO (mildew locus o) gene promoter. We use a modified CRISPR-(d)Cas9 system, in which the nuclease-deficient Cas9 (dCas9) is fused to an epigenetic modifier, to experimentally demonstrate the utility of this tool for optimizing epigenetic engineering of a plant promoter prior to in vivo plant epigenome editing. Guide RNAs are used to deliver the dCas9-epigenetic modifier fusion protein to the target gene sequence, where it induces modification of MLO gene expression. We perform preliminary experiments using a plant promoter cloned into the luciferase reporter system, which is transfected into a human system and analyzed using the dual-luciferase reporter assay. The results suggest that this approach may be useful in the early stages of plant epigenome editing, as it can aid in the selection of appropriate modifications to the plant promoter prior to conducting in vivo experiments under plant system conditions. Overall, the results demonstrate the potential of CRISPR (d)Cas9-based EpiEdit for precise and controlled regulation of gene expression.
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Affiliation(s)
- Ann-Kathrin Hinrichs
- Institute of Plant Sciences, Department of Cell Biology and Plant Biochemistry, Plant RNA Transport, University of Regensburg, Regensburg, Germany
| | - Aline Koch
- Institute of Plant Sciences, Department of Cell Biology and Plant Biochemistry, Plant RNA Transport, University of Regensburg, Regensburg, Germany
| | - Antje M Richter
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany.
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Ramundo V, Palazzo ML, Aldieri E. TGF-β as Predictive Marker and Pharmacological Target in Lung Cancer Approach. Cancers (Basel) 2023; 15:cancers15082295. [PMID: 37190223 DOI: 10.3390/cancers15082295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Lung cancer (LC) represents the leading cause of cancer incidence and mortality worldwide. LC onset is strongly related to genetic mutations and environmental interactions, such as tobacco smoking, or pathological conditions, such as chronic inflammation. Despite advancement in knowledge of the molecular mechanisms involved in LC, this tumor is still characterized by an unfavorable prognosis, and the current therapeutic options are unsatisfactory. TGF-β is a cytokine that regulates different biological processes, particularly at the pulmonary level, and its alteration has been demonstrated to be associated with LC progression. Moreover, TGF-β is involved in promoting invasiveness and metastasis, via epithelial to mesenchymal transition (EMT) induction, where TGF-β is the major driver. Thus, a TGF-β-EMT signature may be considered a potential predictive marker in LC prognosis, and TGF-β-EMT inhibition has been demonstrated to prevent metastasis in various animal models. Concerning a LC therapeutic approach, some TGF-β and TGF-β-EMT inhibitors could be used in combination with chemo- and immunotherapy without major side effects, thereby improving cancer therapy. Overall, targeting TGF-β may be a valid possibility to fight LC, both in improving LC prognosis and cancer therapy, via a novel approach that could open up new effective strategies against this aggressive cancer.
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Affiliation(s)
- Valeria Ramundo
- Department of Oncology, University of Torino, 10126 Torino, Italy
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Huo Y, Cao K, Kou B, Chai M, Dou S, Chen D, Shi Y, Liu X. TP53BP2: Roles in suppressing tumorigenesis and therapeutic opportunities. Genes Dis 2022. [PMID: 37492707 PMCID: PMC10363587 DOI: 10.1016/j.gendis.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
Malignant tumor is still a major problem worldwide. During tumorigenesis or tumor development, tumor suppressor p53-binding protein 2 (TP53BP2), also known as apoptosis stimulating protein 2 of p53 (ASPP2), plays a critical role in p53 dependent and independent manner. Expression of TP53BP2 is highly correlated with the prognosis and survival rate of malignant tumor patients. TP53BP2 can interact with p53, NF-κB p65, Bcl-2, HCV core protein, PP1, YAP, CagA, RAS, PAR3, and other proteins to regulate cell function. Moreover, TP53BP2 can also regulate the proliferation, apoptosis, autophagy, migration, EMT and drug resistance of tumor cells through downstream signaling pathways, such as NF-κB, RAS/MAPK, mevalonate, TGF-β1, PI3K/AKT, aPKC-ι/GLI1 and autophagy pathways. As a potential therapeutic target, TP53BP2 has been attracted more attention. We review the role of TP53BP2 in tumorigenesis or tumor development and the signal pathway involved in TP53BP2, which may provide more deep insight and strategies for tumor treatment.
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Farooqi AA, Kapanova G, Kussainov AZ, Datkhayeva Z, Raganina K, Sadykov BN. Regulation of RASSF by non-coding RNAs in different cancers. Noncoding RNA Res 2022; 7:123-131. [PMID: 35702574 PMCID: PMC9163590 DOI: 10.1016/j.ncrna.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 11/25/2022] Open
Abstract
Ras-association domain family (RASSF) proteins are tumor suppressors and have gained phenomenal limelight because of their mechanistic role in the prevention/inhibition of carcinogenesis and metastasis. Decades of research have demystified wide ranging activities of RASSF molecules in multiple stages of cancers. Although major fraction of RASSF molecules has tumor suppressive roles, yet there is parallel existence of proof-of-concept about moonlighting activities of RASSF proteins as oncogenes. RASSF proteins tactfully rewire signaling cascades for prevention of cancer and metastasis but circumstantial evidence also illuminates oncogenic role of different RASSF proteins in different cancers. In this review we have attempted to provide readers an overview of the complex interplay between non-coding RNAs and RASSF proteins and how these versatile regulators shape the landscape of carcinogenesis and metastasis.
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Kumar VE, Nambiar R, De Souza C, Nguyen A, Chien J, Lam KS. Targeting Epigenetic Modifiers of Tumor Plasticity and Cancer Stem Cell Behavior. Cells 2022; 11:cells11091403. [PMID: 35563709 PMCID: PMC9102449 DOI: 10.3390/cells11091403] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 02/01/2023] Open
Abstract
Tumor heterogeneity poses one of the greatest challenges to a successful treatment of cancer. Tumor cell populations consist of different subpopulations that have distinct phenotypic and genotypic profiles. Such variability poses a challenge in successfully targeting all tumor subpopulations at the same time. Relapse after treatment has been previously explained using the cancer stem cell model and the clonal evolution model. Cancer stem cells are an important subpopulation of tumor cells that regulate tumor plasticity and determine therapeutic resistance. Tumor plasticity is controlled by genetic and epigenetic changes of crucial genes involved in cancer cell survival, growth and metastasis. Targeting epigenetic modulators associated with cancer stem cell survival can unlock a promising therapeutic approach in completely eradicating cancer. Here, we review various factors governing epigenetic dysregulation of cancer stem cells ranging from the role of epigenetic mediators such as histone and DNA methyltransferases, histone deacetylases, histone methyltransferases to various signaling pathways associated with cancer stem cell regulation. We also discuss current treatment regimens targeting these factors and other promising inhibitors in clinical trials.
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Affiliation(s)
- Vigneshwari Easwar Kumar
- Department of Biochemistry and Molecular Medicine, UC Davis Medical Center, Sacramento, CA 95817, USA; (V.E.K.); (R.N.); (C.D.S.); (A.N.); (K.S.L.)
| | - Roshni Nambiar
- Department of Biochemistry and Molecular Medicine, UC Davis Medical Center, Sacramento, CA 95817, USA; (V.E.K.); (R.N.); (C.D.S.); (A.N.); (K.S.L.)
| | - Cristabelle De Souza
- Department of Biochemistry and Molecular Medicine, UC Davis Medical Center, Sacramento, CA 95817, USA; (V.E.K.); (R.N.); (C.D.S.); (A.N.); (K.S.L.)
- Department of Stem Cell Research and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Audrey Nguyen
- Department of Biochemistry and Molecular Medicine, UC Davis Medical Center, Sacramento, CA 95817, USA; (V.E.K.); (R.N.); (C.D.S.); (A.N.); (K.S.L.)
| | - Jeremy Chien
- Department of Biochemistry and Molecular Medicine, UC Davis Medical Center, Sacramento, CA 95817, USA; (V.E.K.); (R.N.); (C.D.S.); (A.N.); (K.S.L.)
- Department of Obstetrics and Gynecology, UC Davis Medical Center, Sacramento, CA 95817, USA
- Correspondence:
| | - Kit S. Lam
- Department of Biochemistry and Molecular Medicine, UC Davis Medical Center, Sacramento, CA 95817, USA; (V.E.K.); (R.N.); (C.D.S.); (A.N.); (K.S.L.)
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Guo Q, Li L, Gao G, Liu R, Einaga Y, Zhi J. Nanodiamonds Inhibit Cancer Cell Migration by Strengthening Cell Adhesion: Implications for Cancer Treatment. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9620-9629. [PMID: 33595291 DOI: 10.1021/acsami.0c21332] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanodiamonds (NDs) are a type of biocompatible nanomaterial with easily modified surfaces and are considered as promising candidates in biomedicine. In this work, the inhibition of tumor cell migration by carboxylated nanodiamonds (cNDs) was investigated. AFM-based single cell adhesion and F-actin staining experiments demonstrated that cNDs treatment could enhance cell adhesion and impair assembly of the cytoskeleton. The mechanism analysis of the regulatory protein expression level also proved that cNDs could inhibit the migration of Hela cells by preventing the epithelial-mesenchymal transition (EMT) process through the transforming growth factor β (TGF-β) signaling pathway. The in vivo pulmonary metastasis model also showed that cNDs effectively reduced the metastasis of murine B16 melanoma cells. In summary, cNDs have been demonstrated to inhibit cancer cell migration in vitro and decrease tumor metastasis in vivo. Therefore, cNDs might have potential utility for specific cancer treatment.
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Affiliation(s)
- Qingyue Guo
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Lei Li
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Guanyue Gao
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Runze Liu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yasuaki Einaga
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Jinfang Zhi
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100190, P. R. China
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Deutschmeyer VE, Richter AM. The ZAR1 protein in cancer; from epigenetic silencing to functional characterisation and epigenetic therapy of tumour suppressors. Biochim Biophys Acta Rev Cancer 2020; 1874:188417. [PMID: 32828887 DOI: 10.1016/j.bbcan.2020.188417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
ZAR1, zygote arrest 1, is a zinc finger protein (C-terminus), which was initially identified in mouse oocytes. Later it was found that its expression is present in various human tissues e.g. lung and kidney. Interestingly, it was observed that in various tumour types the ZAR1 transcript is missing due to hypermethylation of its CpG island promoter, but not ZAR2. Since methylation of the ZAR1 promoter is described as a frequent event in tumourigenesis, ZAR1 could serve as a useful diagnostic marker in cancer screens. ZAR1 was described as a useful prognostic/diagnostic cancer marker for lung cancer, kidney cancer, melanoma and possibly liver carcinoma. Furthermore, ZAR1 was reactivated as a tumour suppressor by epigenetic therapy using CRISPR-dCas9 method. This method holds the potential to precisely target not only ZAR1 and reactivate tumour suppressors in a tailored cancer therapy. ZAR1 is highly conserved amongst vertebrates, especially its zinc finger, which is the relevant domain for its protein and RNA binding ability. ZAR1 is implicated in various cellular mechanisms including regulation of oocyte/embryo development, cell cycle control and mRNA binding, though little was known about the underlying mechanisms. ZAR1 was reported to regulate and activate translation through the binding to TCS translation control sequences in the 3'UTRs of its target mRNA the kinase WEE1. ZAR1 has a tumour suppressing function by inhibiting cell cycle progression. Here we review the current literature on ZAR1 focusing on structural, functional and epigenetic aspects. Characterising the cellular mechanisms that regulate the signalling pathways ZAR1 is involved in, could lead to a deeper understanding of tumour development and, furthermore, to new strategies in cancer treatment.
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Affiliation(s)
| | - Antje M Richter
- Institute for Genetics, University of Giessen, 35392 Giessen, Germany; Max-Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.
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RASSF10 regulates bone invasion of growth hormone-secreting adenomas via exosomes. Biochem Biophys Res Commun 2020; 527:603-610. [PMID: 32423821 DOI: 10.1016/j.bbrc.2020.04.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/26/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUND Invasion of pituitary growth hormone-secreting adenoma into surrounding tissues poses a challenge for complete resection in surgery, which is the main reason for recurrence of this type of cancer. Studies have shown that abnormal methylation of RASSF10 can promote the expression of MDM2 and regulate the tumor microenvironment by affecting the secretion of exosomes. In the present study, we aim to uncover the specific underlying mechanism of this effect. METHOD Transwell co-culture assays was performed using GT1.1 cells or exosomes and RAW264.7 cells. RAW264.7 cells were collected for invasion, proliferation and apoptosis assays, RT-qPCR and western blotting. RNA-seq was performed and used to assess the potential molecular pathways of the effect of GT1.1 cell-exosomes on RAW264.7 cells. RESULTS GT1.1 cells with reduced RASSF10 expression could promote the proliferation and migration of RAW264.7 cells, and promote their expression of osteoclast markers TRAP and CK. The effect of GT1.1 cell exosomes on the RAW264.7-cell phenotype was shown to be achieved through the RASSF10-MDM2 pathway. RNA-seq allowed the identification of PI3K-AKT, MAPK, and calcium signaling as important in this regulation system of RASSF10-MDM2. CONCLUSION Our results indicate that GT1.1 cells activate PI3K-AKT, MAPK and calcium signaling via the RASSF10-MDM2 pathway, and promote the differentiation of RAW264.7 cells into osteoclasts through exosomes. This study may provide new ideas to aid in early diagnosis, prognostic assessment and treatment of aggressive pituitary adenomas.
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Richter AM, Woods ML, Küster MM, Walesch SK, Braun T, Boettger T, Dammann RH. RASSF10 is frequently epigenetically inactivated in kidney cancer and its knockout promotes neoplasia in cancer prone mice. Oncogene 2020; 39:3114-3127. [PMID: 32047266 PMCID: PMC7142015 DOI: 10.1038/s41388-020-1195-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/22/2022]
Abstract
Kidney cancer incidences are rising globally, thereby fueling the demand for targeted therapies and precision medicine. In our previous work, we have identified and characterized the Ras-Association Domain Family encoding ten members that are often aberrantly expressed in human cancers. In this study, we created and analyzed the Rassf10 knockout mice. Here we show that Rassf10 haploinsufficiency promotes neoplasia formation in two established mouse cancer models (Rassf1A-/- and p53-/-). Haploinsufficient Rassf10 knockout mice were significantly prone to various diseases including lymphoma (Rassf1A-/- background) and thymoma (p53-/- background). Especially Rassf10-/- and p53-deficient mice exhibited threefold increased rates of kidney cysts compared with p53-/- controls. Moreover, we observed that in human kidney cancer, RASSF10 is frequently epigenetically inactivated by its CpG island promoter hypermethylation. Primary tumors of renal clear cell and papillary cell carcinoma confirmed that RASSF10 methylation is associated with decreased expression in comparison to normal kidney tissue. In independent data sets, we could validate that RASSF10 inactivation clinically correlated with decreased survival and with progressed disease state of kidney cancer patients and polycystic kidney size. Functionally, we revealed that the loss of Rassf10 was significantly associated with upregulation of KRAS signaling and MYC expression. In summary, we could show that Rassf10 functions as a haploinsufficient tumor suppressor. In combination with other markers, RASSF10 silencing can serve as diagnostic and prognostic cancer biomarker in kidney diseases.
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Affiliation(s)
- Antje M Richter
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany. .,Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
| | - Michelle L Woods
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany
| | - Miriam M Küster
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany
| | - Sara K Walesch
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany
| | - Thomas Braun
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center, 35392, Giessen, Germany
| | - Thomas Boettger
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Reinhard H Dammann
- Institute for Genetics, University of Giessen, 35392, Giessen, Germany. .,German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center, 35392, Giessen, Germany.
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