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Zhao B, Zhang D, Sun Y, Lei M, Zeng P, Wang Y, Hong Y, Jiao Y, Cai C. Explore the effect of LLY-283 on the ototoxicity of auditory cells caused by cisplatin: A bioinformatic analysis based on RNA-seq. J Clin Lab Anal 2022; 36:e24176. [PMID: 34997776 PMCID: PMC8842247 DOI: 10.1002/jcla.24176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Cisplatin is a commonly used chemotherapeutic drug in clinics, and long-term application will lead to hearing impairment. LLY-283, an inhibitor of PRMT5, has not been reported in deafness. Our study aimed to explore the mechanism of LLY-283 in hearing impairment. MATERIALS AND METHODS First, we performed RNA-seq (cisplatin in the experimental group and DMSO in the control group) to obtain the biological processes mainly involved in differentially expressed genes (DEGs). CCK-8 and LDH experiments were used to observe the effect of LLY-283 on cisplatin-induced auditory cell injury. ROS experiment was used to monitor the impact of LLY-283 on oxidative damage of auditory cells. Effect of LLY-283 on apoptosis of auditory cells detected by TUNEL experiment. PCR and Western blotting were used to detect the expression of genes and proteins related to auditory cell apoptosis in LLY-283 cells. Meanwhile, we explored the effect of LLY-283 on the expression of PRMT5 in cisplatin-induced hearing impaired cells at RNA and protein levels. RESULTS Biological process analysis showed that DEGs were mainly enriched in the apoptotic process involved in morphogenesis (-Log10 P = 3.71). CCK-8 and LDH experiments confirmed that LLY-283 could save cisplatin-induced auditory cell injury. ROS experiments confirmed that LLY-283 could rescue cisplatin-induced oxidative damage to auditory cells. TUNEL experiments confirmed that LLY-283 could protect cisplatin-induced apoptosis of auditory cells. Meanwhile, LLY-283 could inhibit the expression of PRMT5 in auditory cells induced by cisplatin. CONCLUSION LLY-283 can rescue cisplatin-induced auditory cell apoptosis injury. LLY-283 can inhibit the increase in PRMT5 expression induced by cisplatin.
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Affiliation(s)
- Bin Zhao
- Xiamen Health and Medical Big Data CenterXiamenChina
- School of MedicineXiamen UniversityXiamenChina
| | - Dongdong Zhang
- School of MedicineXiamen UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryTeaching Hospital of Fujian Medical UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryZhongshan HospitalSchool of MedicineXiamen UniversityXiamenChina
| | - Yixin Sun
- School of MedicineXiamen UniversityXiamenChina
| | - Min Lei
- School of MedicineXiamen UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryTeaching Hospital of Fujian Medical UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryZhongshan HospitalSchool of MedicineXiamen UniversityXiamenChina
| | - Peiji Zeng
- Department of Otolaryngology‐Head and Neck SurgeryTeaching Hospital of Fujian Medical UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryZhongshan HospitalSchool of MedicineXiamen UniversityXiamenChina
| | - Yue Wang
- School of MedicineXiamen UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryTeaching Hospital of Fujian Medical UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryZhongshan HospitalSchool of MedicineXiamen UniversityXiamenChina
| | - Yongjun Hong
- Department of Otolaryngology‐Head and Neck SurgeryTeaching Hospital of Fujian Medical UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryZhongshan HospitalSchool of MedicineXiamen UniversityXiamenChina
| | - Yanchao Jiao
- Department of Otolaryngology‐Head and Neck SurgeryTeaching Hospital of Fujian Medical UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryZhongshan HospitalSchool of MedicineXiamen UniversityXiamenChina
| | - Chengfu Cai
- School of MedicineXiamen UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryTeaching Hospital of Fujian Medical UniversityXiamenChina
- Department of Otolaryngology‐Head and Neck SurgeryZhongshan HospitalSchool of MedicineXiamen UniversityXiamenChina
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Maron MI, Casill AD, Gupta V, Roth JS, Sidoli S, Query CC, Gamble MJ, Shechter D. Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation. eLife 2022; 11:e72867. [PMID: 34984976 PMCID: PMC8765754 DOI: 10.7554/elife.72867] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/03/2022] [Indexed: 12/26/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) are required for the regulation of RNA processing factors. Type I PRMT enzymes catalyze mono- and asymmetric dimethylation; Type II enzymes catalyze mono- and symmetric dimethylation. To understand the specific mechanisms of PRMT activity in splicing regulation, we inhibited Type I and II PRMTs and probed their transcriptomic consequences. Using the newly developed Splicing Kinetics and Transcript Elongation Rates by Sequencing (SKaTER-seq) method, analysis of co-transcriptional splicing demonstrated that PRMT inhibition resulted in altered splicing rates. Surprisingly, co-transcriptional splicing kinetics did not correlate with final changes in splicing of polyadenylated RNA. This was particularly true for retained introns (RI). By using actinomycin D to inhibit ongoing transcription, we determined that PRMTs post-transcriptionally regulate RI. Subsequent proteomic analysis of both PRMT-inhibited chromatin and chromatin-associated polyadenylated RNA identified altered binding of many proteins, including the Type I substrate, CHTOP, and the Type II substrate, SmB. Targeted mutagenesis of all methylarginine sites in SmD3, SmB, and SmD1 recapitulated splicing changes seen with Type II PRMT inhibition, without disrupting snRNP assembly. Similarly, mutagenesis of all methylarginine sites in CHTOP recapitulated the splicing changes seen with Type I PRMT inhibition. Examination of subcellular fractions further revealed that RI were enriched in the nucleoplasm and chromatin. Taken together, these data demonstrate that, through Sm and CHTOP arginine methylation, PRMTs regulate the post-transcriptional processing of nuclear, detained introns.
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Affiliation(s)
- Maxim I Maron
- Department of Biochemistry, Albert Einstein College of MedicineBronxUnited States
| | - Alyssa D Casill
- Department of Molecular Pharmacology, Albert Einstein College of MedicineBronxUnited States
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Jacob S Roth
- Department of Biochemistry, Albert Einstein College of MedicineBronxUnited States
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of MedicineBronxUnited States
| | - Charles C Query
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Matthew J Gamble
- Department of Molecular Pharmacology, Albert Einstein College of MedicineBronxUnited States
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of MedicineBronxUnited States
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Conery AR, Rocnik JL, Trojer P. Small molecule targeting of chromatin writers in cancer. Nat Chem Biol 2021; 18:124-133. [PMID: 34952934 DOI: 10.1038/s41589-021-00920-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 10/13/2021] [Indexed: 01/10/2023]
Abstract
More than a decade after the launch of DNA methyltransferase and histone deacetylase inhibitors for the treatment of cancer, 2020 heralded the approval of the first histone methyltransferase inhibitor, revitalizing the concept that targeted manipulation of the chromatin regulatory landscape can have profound therapeutic impact. Three chromatin regulatory pathways-DNA methylation, histone acetylation and methylation-are frequently implicated in human cancer but hundreds of potentially druggable mechanisms complicate identification of key targets for therapeutic intervention. In addition to human genetics and functional screening, chemical biology approaches have proven critical for the discovery of key nodes in these pathways and in an ever-increasing complexity of molecularly defined human cancer contexts. This review introduces small molecule targeting approaches, showcases chemical probes and drug candidates for epigenetic writer enzymes, illustrates molecular features that may represent epigenetic dependencies and suggests translational strategies to maximize their impact in cancer therapy.
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Alcantara Llaguno S, Parada LF. Cancer stem cells in gliomas: evolving concepts and therapeutic implications. Curr Opin Neurol 2021; 34:868-874. [PMID: 34581301 PMCID: PMC9746696 DOI: 10.1097/wco.0000000000000994] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Cancer stem cells (CSCs) have been implicated in the hierarchical heterogeneity and treatment resistance of hematologic and solid tumor malignancies, including gliomas, for several decades now but their therapeutic targeting has not been fully realized. Recent studies have uncovered deeper layers of CSC complexity, related to developmental origins, plasticity, cellular states, and interface with the microenvironment. RECENT FINDINGS Sequencing and in-vivo lineage-tracing studies in mouse and patient-derived models show evidence of stem and progenitor origin of glioma, at the same time that genomic studies show a relatedness of glioma CSCs with radial glia. The spate of single-cell sequencing analyses demonstrates the diversity of transcriptional cellular states, which are susceptible to transitions, indicating the plasticity of glioma CSCs. The evolution of glioma CSCs and their interactions with niche cells play important roles in CSC treatment resistance and immune evasion, with epigenetic modulation as one of the emerging mechanisms. SUMMARY To harness the potential of CSCs for clinical application, there is urgent need to investigate their complex nature and myriad interactions, to better understand the contribution of these self-renewing, stem-like cancer cells in the pathogenesis and therapy resistance of malignant brain tumors.
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Affiliation(s)
- Sheila Alcantara Llaguno
- Brain Tumor Center, Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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55
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Liu H, Qiu W, Sun T, Wang L, Du C, Hu Y, Liu W, Feng F, Chen Y, Sun H. Therapeutic strtegies of glioblastoma (GBM): The current advances in the molecular targets and bioactive small molecule compounds. Acta Pharm Sin B 2021; 12:1781-1804. [PMID: 35847506 PMCID: PMC9279645 DOI: 10.1016/j.apsb.2021.12.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/02/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is the most common aggressive malignant tumor in brain neuroepithelial tumors and remains incurable. A variety of treatment options are currently being explored to improve patient survival, including small molecule inhibitors, viral therapies, cancer vaccines, and monoclonal antibodies. Among them, the unique advantages of small molecule inhibitors have made them a focus of attention in the drug discovery of glioblastoma. Currently, the most used chemotherapeutic agents are small molecule inhibitors that target key dysregulated signaling pathways in glioblastoma, including receptor tyrosine kinase, PI3K/AKT/mTOR pathway, DNA damage response, TP53 and cell cycle inhibitors. This review analyzes the therapeutic benefit and clinical development of novel small molecule inhibitors discovered as promising anti-glioblastoma agents by the related targets of these major pathways. Meanwhile, the recent advances in temozolomide resistance and drug combination are also reviewed. In the last part, due to the constant clinical failure of targeted therapies, this paper reviewed the research progress of other therapeutic methods for glioblastoma, to provide patients and readers with a more comprehensive understanding of the treatment landscape of glioblastoma.
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56
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Lorenzi C, Barriere S, Arnold K, Luco RF, Oldfield AJ, Ritchie W. IRFinder-S: a comprehensive suite to discover and explore intron retention. Genome Biol 2021; 22:307. [PMID: 34749764 PMCID: PMC8573998 DOI: 10.1186/s13059-021-02515-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available samples, and provides a tested method to detect differential levels of intron retention.
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Affiliation(s)
- Claudio Lorenzi
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Sylvain Barriere
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Katharina Arnold
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Reini F Luco
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Andrew J Oldfield
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - William Ritchie
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France.
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Jensen-Pergakes K, Tatlock J, Maegley KA, McAlpine IJ, McTigue MA, Xie T, Dillon CP, Wang Y, Yamazaki S, Spiegel N, Shi M, Nemeth A, Miller N, Hendrickson E, Lam H, Sherrill J, Chung CY, McMillan EA, Bryant SK, Palde P, Braganza J, Brooun A, Deng YL, Goshtasbi V, Kephart SE, Kumpf RA, Liu W, Patman RL, Rui E, Scales S, Tran-Dube M, Wang F, Wythes M, Paul TA. SAM Competitive PRMT5 Inhibitor PF-06939999 Demonstrates Antitumor Activity in Splicing Dysregulated NSCLC with Decreased Liability of Drug Resistance. Mol Cancer Ther 2021; 21:3-15. [PMID: 34737197 DOI: 10.1158/1535-7163.mct-21-0620] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/15/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022]
Abstract
Protein arginine methyltransferase 5 (PRMT5) over-expression in hematological and solid tumors methylates arginine residues on cellular proteins involved in important cancer functions including cell cycle regulation, mRNA splicing, cell differentiation, cell signaling, and apoptosis. PRMT5 methyltransferase function has been linked with high rates of tumor cell proliferation and decreased overall survival, and PRMT5 inhibitors are currently being explored as an approach for targeting cancer-specific dependencies due to PRMT5 catalytic function. Here we describe the discovery of potent and selective S-adenosylmethionine (SAM) competitive PRMT5 inhibitors, with in vitro and in vivo characterization of clinical candidate PF-06939999. Acquired resistance mechanisms were explored through the development of drug resistant cell lines. Our data highlight compound-specific resistance mutations in the PRMT5 enzyme that demonstrate structural constraints in the co-factor binding site that prevent emergence of complete resistance to SAM site inhibitors. PRMT5 inhibition by PF-06939999 treatment reduced proliferation of NSCLC cancer cells, with dose-dependent decreases in symmetric dimethyl arginine (SDMA) levels and changes in alternative splicing of numerous pre-mRNAs. Drug sensitivity to PF-06939999 in NSCLC cells associates with cancer pathways including MYC, cell cycle and spliceosome, and with mutations in splicing factors such as RBM10. Translation of efficacy in mouse tumor xenograft models with splicing mutations provides rationale for therapeutic use of PF-06939999 in the treatment of splicing dysregulated NSCLC.
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Affiliation(s)
| | | | | | | | | | - Tao Xie
- Oncology Research Unit, Pfizer Inc
| | | | - Yuli Wang
- Oncology Research Division, Pfizer, Inc
| | - Shinji Yamazaki
- Drug Metabolism & Pharmacokinetics, Johnson & Johnson (United States)
| | | | - Manli Shi
- Oncology Research Division, Pfizer, Inc
| | | | | | | | - Hieu Lam
- Oncology-Rinat Research Units, Pfizer Worldwide Research and Development
| | | | - Chi-Yeh Chung
- Pfizer Oncology Research Unit, Pfizer (United States)
| | | | | | | | | | | | - Ya-Li Deng
- Oncology Medicinal Chemistry, Pfizer, Inc
| | | | | | | | - Wei Liu
- Oncology Medicinal Chemistry, Pfizer, Inc
| | | | - Eugene Rui
- Oncology Medicinal Chemistry, Pfizer, Inc
| | | | | | - Fen Wang
- Oncology Medicinal Chemistry, Pfizer, Inc
| | | | - Thomas A Paul
- Pfizer Oncology Research Unit, Pfizer (United States)
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PRMT5: An Emerging Target for Pancreatic Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13205136. [PMID: 34680285 PMCID: PMC8534199 DOI: 10.3390/cancers13205136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The burden of pancreatic ductal adenocarcinoma (PDAC) increases with rising incidence, yet 5-year overall survival remains poor at 17%. Routine comprehensive genomic profiling of PDAC only finds 2.5% of patients who may benefit and receive matched targeted therapy. Protein arginine methyltransferase 5 (PRMT5) as an anti-cancer target has gained significant interest in recent years and high levels of PRMT5 protein are associated with worse survival outcomes across multiple cancer types. Inhibition of PRMT5 in pre-clinical models can lead to cancer growth inhibition. However, PRMT5 is involved in multiple cellular processes, thus determining its mechanism of action is challenging. While past reviews on PRMT5 have focused on its role in diverse cellular processes and past research studies have focused mainly on haematological malignancies and glioblastoma, this review provides an overview of the possible biological mechanisms of action of PRMT5 inhibition and its potential as a treatment in pancreatic cancer. Abstract The overall survival of pancreatic ductal adenocarcinoma (PDAC) remains poor and its incidence is rising. Targetable mutations in PDAC are rare, thus novel therapeutic approaches are needed. Protein arginine methyltransferase 5 (PRMT5) overexpression is associated with worse survival and inhibition of PRMT5 results in decreased cancer growth across multiple cancers, including PDAC. Emerging evidence also suggests that altered RNA processing is a driver in PDAC tumorigenesis and creates a partial dependency on this process. PRMT5 inhibition induces altered splicing and this vulnerability can be exploited as a novel therapeutic approach. Three possible biological pathways underpinning the action of PRMT5 inhibitors are discussed; c-Myc regulation appears central to its action in the PDAC setting. Whilst homozygous MTAP deletion and symmetrical dimethylation levels are associated with increased sensitivity to PRMT5 inhibition, neither measure robustly predicts its growth inhibitory response. The immunomodulatory effect of PRMT5 inhibitors on the tumour microenvironment will also be discussed, based on emerging evidence that PDAC stroma has a significant bearing on disease behaviour and response to therapy. Lastly, with the above caveats in mind, current knowledge gaps and the implications and rationales for PRMT5 inhibitor development in PDAC will be explored.
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Chen Y, Shao X, Zhao X, Ji Y, Liu X, Li P, Zhang M, Wang Q. Targeting protein arginine methyltransferase 5 in cancers: Roles, inhibitors and mechanisms. Biomed Pharmacother 2021; 144:112252. [PMID: 34619493 DOI: 10.1016/j.biopha.2021.112252] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 12/31/2022] Open
Abstract
The protein arginine methyltransferase 5 (PRMT5) as the major type II arginine methyltransferase catalyzes the mono- and symmetric dimethylation of arginine residues in both histone and non-histone proteins. Recently, increasing evidence has demonstrated that PRMT5 plays an indispensable role in the occurrence and development of various human cancers by promoting the cell proliferation, invasion, and migration. It has become a promising and valuable target in the cancer epigenetic therapy. This review is to summarize the clinical significance of PRMT5 in the cancers such as lung cancer, breast cancer and colorectal cancer, and the drug discovery targeting PRMT5. Importantly, the existing PRMT5 inhibitors representing different molecular mechanisms, and their pharmacological effect, mechanism of action and biological affinity are analyzed. Clinical status, current problems and future perspective of PRMT5 inhibitors for the treatment of cancers are also discussed, all of which provides crucial help for the future discovery of PRMT5 targeted drugs for cancer treatment.
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Affiliation(s)
- Yingqing Chen
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Xiaomin Shao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Xiangge Zhao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Yuan Ji
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Xiaorong Liu
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Peixuan Li
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Mingyu Zhang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Qianqian Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China.
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Maniaci M, Boffo FL, Massignani E, Bonaldi T. Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach. Front Mol Biosci 2021; 8:688973. [PMID: 34557518 PMCID: PMC8454774 DOI: 10.3389/fmolb.2021.688973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/11/2021] [Indexed: 12/03/2022] Open
Abstract
RNA binding proteins (RBPs) bind RNAs through specific RNA-binding domains, generating multi-molecular complexes known as ribonucleoproteins (RNPs). Various post-translational modifications (PTMs) have been described to regulate RBP structure, subcellular localization, and interactions with other proteins or RNAs. Recent proteome-wide experiments showed that RBPs are the most representative group within the class of arginine (R)-methylated proteins. Moreover, emerging evidence suggests that this modification plays a role in the regulation of RBP-RNA interactions. Nevertheless, a systematic analysis of how changes in protein-R-methylation can affect globally RBPs-RNA interactions is still missing. We describe here a quantitative proteomics approach to profile global changes of RBP-RNA interactions upon the modulation of type I and II protein arginine methyltransferases (PRMTs). By coupling the recently described Orthogonal Organic Phase Separation (OOPS) strategy with the Stable Isotope Labelling with Amino acids in Cell culture (SILAC) and pharmacological modulation of PRMTs, we profiled RNA-protein interaction dynamics in dependence of protein-R-methylation. Data are available via ProteomeXchange with identifier PXD024601.
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Affiliation(s)
- Marianna Maniaci
- Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, Italy.,European School of Molecular Medicine (SEMM), Milan, Italy
| | - Francesca Ludovica Boffo
- Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, Italy
| | - Enrico Massignani
- Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, Italy.,European School of Molecular Medicine (SEMM), Milan, Italy
| | - Tiziana Bonaldi
- Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, Italy
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Wu Q, Berglund AE, Etame AB. The Impact of Epigenetic Modifications on Adaptive Resistance Evolution in Glioblastoma. Int J Mol Sci 2021; 22:8324. [PMID: 34361090 PMCID: PMC8347012 DOI: 10.3390/ijms22158324] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma (GBM) is a highly lethal cancer that is universally refractory to the standard multimodal therapies of surgical resection, radiation, and chemotherapy treatment. Temozolomide (TMZ) is currently the best chemotherapy agent for GBM, but the durability of response is epigenetically dependent and often short-lived secondary to tumor resistance. Therapies that can provide synergy to chemoradiation are desperately needed in GBM. There is accumulating evidence that adaptive resistance evolution in GBM is facilitated through treatment-induced epigenetic modifications. Epigenetic alterations of DNA methylation, histone modifications, and chromatin remodeling have all been implicated as mechanisms that enhance accessibility for transcriptional activation of genes that play critical roles in GBM resistance and lethality. Hence, understanding and targeting epigenetic modifications associated with GBM resistance is of utmost priority. In this review, we summarize the latest updates on the impact of epigenetic modifications on adaptive resistance evolution in GBM to therapy.
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Affiliation(s)
- Qiong Wu
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA;
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA;
| | - Arnold B. Etame
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA;
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Mehterov N, Kazakova M, Sbirkov Y, Vladimirov B, Belev N, Yaneva G, Todorova K, Hayrabedyan S, Sarafian V. Alternative RNA Splicing-The Trojan Horse of Cancer Cells in Chemotherapy. Genes (Basel) 2021; 12:genes12071085. [PMID: 34356101 PMCID: PMC8306420 DOI: 10.3390/genes12071085] [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: 06/30/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Almost all transcribed human genes undergo alternative RNA splicing, which increases the diversity of the coding and non-coding cellular landscape. The resultant gene products might have distinctly different and, in some cases, even opposite functions. Therefore, the abnormal regulation of alternative splicing plays a crucial role in malignant transformation, development, and progression, a fact supported by the distinct splicing profiles identified in both healthy and tumor cells. Drug resistance, resulting in treatment failure, still remains a major challenge for current cancer therapy. Furthermore, tumor cells often take advantage of aberrant RNA splicing to overcome the toxicity of the administered chemotherapeutic agents. Thus, deciphering the alternative RNA splicing variants in tumor cells would provide opportunities for designing novel therapeutics combating cancer more efficiently. In the present review, we provide a comprehensive outline of the recent findings in alternative splicing in the most common neoplasms, including lung, breast, prostate, head and neck, glioma, colon, and blood malignancies. Molecular mechanisms developed by cancer cells to promote oncogenesis as well as to evade anticancer drug treatment and the subsequent chemotherapy failure are also discussed. Taken together, these findings offer novel opportunities for future studies and the development of targeted therapy for cancer-specific splicing variants.
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Affiliation(s)
- Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Yordan Sbirkov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Nikolay Belev
- Medical Simulation and Training Center, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Galina Yaneva
- Department of Biology, Faculty of Pharmacy, Medical University of Varna, 9002 Varna, Bulgaria;
| | - Krassimira Todorova
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Soren Hayrabedyan
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +359-882-512-952
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63
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Barekatain Y, Ackroyd JJ, Yan VC, Khadka S, Wang L, Chen KC, Poral AH, Tran T, Georgiou DK, Arthur K, Lin YH, Satani N, Ballato ES, Behr EI, deCarvalho AC, Verhaak RGW, de Groot J, Huse JT, Asara JM, Kalluri R, Muller FL. Homozygous MTAP deletion in primary human glioblastoma is not associated with elevation of methylthioadenosine. Nat Commun 2021; 12:4228. [PMID: 34244484 PMCID: PMC8270912 DOI: 10.1038/s41467-021-24240-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/04/2021] [Indexed: 02/07/2023] Open
Abstract
Homozygous deletion of methylthioadenosine phosphorylase (MTAP) in cancers such as glioblastoma represents a potentially targetable vulnerability. Homozygous MTAP-deleted cell lines in culture show elevation of MTAP’s substrate metabolite, methylthioadenosine (MTA). High levels of MTA inhibit protein arginine methyltransferase 5 (PRMT5), which sensitizes MTAP-deleted cells to PRMT5 and methionine adenosyltransferase 2A (MAT2A) inhibition. While this concept has been extensively corroborated in vitro, the clinical relevance relies on exhibiting significant MTA accumulation in human glioblastoma. In this work, using comprehensive metabolomic profiling, we show that MTA secreted by MTAP-deleted cells in vitro results in high levels of extracellular MTA. We further demonstrate that homozygous MTAP-deleted primary glioblastoma tumors do not significantly accumulate MTA in vivo due to metabolism of MTA by MTAP-expressing stroma. These findings highlight metabolic discrepancies between in vitro models and primary human tumors that must be considered when developing strategies for precision therapies targeting glioblastoma with homozygous MTAP deletion. The metabolite methylthioadenosine (MTA) inhibits PRMT5. Therefore, MTA accumulation due to MTA phosphorylase (MTAP) deletion has been proposed as a vulnerability for PRMT5-targeted therapy in cancer. Here, the authors show that MTA does not accumulate in MTAP-deficient cancer cells but is secreted and metabolized by MTAP-intact cells in the tumour microenvironment.
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Affiliation(s)
- Yasaman Barekatain
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX, USA.
| | - Jeffrey J Ackroyd
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Victoria C Yan
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Sunada Khadka
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Lin Wang
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ko-Chien Chen
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Anton H Poral
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Theresa Tran
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dimitra K Georgiou
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenisha Arthur
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu-Hsi Lin
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nikunj Satani
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elliot S Ballato
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eliot I Behr
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana C deCarvalho
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - John de Groot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason T Huse
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John M Asara
- Department of Medicine, Harvard Medical School, and Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Raghu Kalluri
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Florian L Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,SPOROS Bioventures, Houston, TX, USA.
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64
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Protein arginine methylation: from enigmatic functions to therapeutic targeting. Nat Rev Drug Discov 2021; 20:509-530. [PMID: 33742187 DOI: 10.1038/s41573-021-00159-8] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
Protein arginine methyltransferases (PRMTs) are emerging as attractive therapeutic targets. PRMTs regulate transcription, splicing, RNA biology, the DNA damage response and cell metabolism; these fundamental processes are altered in many diseases. Mechanistically understanding how these enzymes fuel and sustain cancer cells, especially in specific metabolic contexts or in the presence of certain mutations, has provided the rationale for targeting them in oncology. Ongoing inhibitor development, facilitated by structural biology, has generated tool compounds for the majority of PRMTs and enabled clinical programmes for the most advanced oncology targets, PRMT1 and PRMT5. In-depth mechanistic investigations using genetic and chemical tools continue to delineate the roles of PRMTs in regulating immune cells and cancer cells, and cardiovascular and neuronal function, and determine which pathways involving PRMTs could be synergistically targeted in combination therapies for cancer. This research is enhancing our knowledge of the complex functions of arginine methylation, will guide future clinical development and could identify new clinical indications.
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65
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Mazor G, Smirnov D, Ben David H, Khrameeva E, Toiber D, Rotblat B. TP73-AS1 is induced by YY1 during TMZ treatment and highly expressed in the aging brain. Aging (Albany NY) 2021; 13:14843-14861. [PMID: 34115613 PMCID: PMC8221307 DOI: 10.18632/aging.203182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022]
Abstract
Aging is a factor associated with poor prognosis in glioblastoma (GBM). It is therefore important to understand the molecular features of aging contributing to GBM morbidity. TP73-AS1 is a long noncoding RNA (lncRNA) over expressed in GBM tumors shown to promote resistance to the chemotherapeutic temozolomide (TMZ), and tumor aggressiveness. How the expression of TP73-AS1 is regulated is not known, nor is it known if its expression is associated with aging. By analyzing transcriptional data obtained from natural and pathological aging brain, we found that the expression of TP73-AS1 is high in pathological and naturally aging brains. YY1 physically associates with the promoter of TP73-AS1 and we found that along with TP73-AS1, YY1 is induced by TMZ. We found that the TP73-AS1 promoter is activated by TMZ, and by YY1 over expression. Using CRISPRi to deplete YY1, we found that YY1 promotes up regulation of TP73-AS1 and the activation of its promoter during TMZ treatment. In addition, we identified two putative YY1 binding sites within the TP73-AS1 promoter, and used mutagenesis to find that they are essential for TMZ mediated promoter activation. Together, our data positions YY1 as an important TP73-AS1 regulator, demonstrating that TP73-AS1 is expressed in the natural and pathological aging brain, including during neurodegeneration and cancer. Our findings advance our understanding of TP73-AS1 expression, bringing forth a new link between TMZ resistance and aging, both of which contribute to GBM morbidity.
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Affiliation(s)
- Gal Mazor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Dmitri Smirnov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Hila Ben David
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Ekaterina Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Debra Toiber
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Barak Rotblat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 8410501, Israel
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66
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Miller JJ. Targeting protein arginine methylation to death. Neuro Oncol 2021; 23:1421-1422. [PMID: 34037795 DOI: 10.1093/neuonc/noab123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Julie J Miller
- Pappas Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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67
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Sulman EP, Eisenstat DD. World Cancer Day 2021 - Perspectives in Pediatric and Adult Neuro-Oncology. Front Oncol 2021; 11:659800. [PMID: 34041027 PMCID: PMC8142853 DOI: 10.3389/fonc.2021.659800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022] Open
Abstract
Significant advances in our understanding of the molecular genetics of pediatric and adult brain tumors and the resulting rapid expansion of clinical molecular neuropathology have led to improvements in diagnostic accuracy and identified new targets for therapy. Moreover, there have been major improvements in all facets of clinical care, including imaging, surgery, radiation and supportive care. In selected cohorts of patients, targeted and immunotherapies have resulted in improved patient outcomes. Furthermore, adaptations to clinical trial design have facilitated our study of new agents and other therapeutic innovations. However, considerable work remains to be done towards extending survival for all patients with primary brain tumors, especially children and adults with diffuse midline gliomas harboring Histone H3 K27 mutations and adults with isocitrate dehydrogenase (IDH) wild-type, O6 guanine DNA-methyltransferase gene (MGMT) promoter unmethylated high grade gliomas. In addition to improvements in therapy and care, access to the advances in technology, such as particle radiation or biologic therapy, neuroimaging and molecular diagnostics in both developing and developed countries is needed to improve the outcome of patients with brain tumors.
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Affiliation(s)
- Erik P. Sulman
- Section of Neuro-oncology & Neurosurgical Oncology, Frontiers in Oncology and Frontiers in Neurology, Lausanne, Switzerland
- Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, United States
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, New York, NY, United States
- NYU Langone Health, New York, NY, United States
| | - David D. Eisenstat
- Section of Neuro-oncology & Neurosurgical Oncology, Frontiers in Oncology and Frontiers in Neurology, Lausanne, Switzerland
- Children’s Cancer Centre, Royal Children’s Hospital, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
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