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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [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: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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2
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Gao J, Shi X, Sun Y, Liu X, Zhang F, Shi C, Yu X, Yan Z, Liu L, Yu S, Zhang J, Zhang X, Zhang S, Guo W. Deficiency of betaine-homocysteine methyltransferase activates glucose-6-phosphate dehydrogenase (G6PD) by decreasing arginine methylation of G6PD in hepatocellular carcinogenesis. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1648-1665. [PMID: 38679670 DOI: 10.1007/s11427-023-2481-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/11/2023] [Indexed: 05/01/2024]
Abstract
Betaine-homocysteine methyltransferase (BHMT) regulates protein methylation and is correlated with tumorigenesis; however, the effects and regulation of BHMT in hepatocarcinogenesis remain largely unexplored. Here, we determined the clinical significance of BHMT in the occurrence and progression of hepatocellular carcinoma (HCC) using tissue samples from 198 patients. BHMT was to be frequently found (86.6%) expressed at relatively low levels in HCC tissues and was positively correlated with the overall survival of patients with HCC. Bhmt overexpression effectively suppressed several malignant phenotypes in hepatoma cells in vitro and in vivo, whereas complete knockout of Bhmt (Bhmt-/-) produced the opposite effect. We combined proteomics, metabolomics, and molecular biological strategies and detected that Bhmt-/- promoted hepatocarcinogenesis and tumor progression by enhancing the activity of glucose-6-phosphate dehydrogenase (G6PD) and PPP metabolism in DEN-induced HCC mouse and subcutaneous tumor-bearing models. In contrast, restoration of Bhmt with an AAV8-Bhmt injection or pharmacological inhibition of G6PD attenuated hepatocarcinogenesis. Additionally, coimmunoprecipitation identified monomethylated modifications of the G6PD, and BHMT regulated the methylation of G6PD. Protein sequence analysis, generation and application of specific antibodies, and site-directed mutagenesis indicated G6PD methylation at the arginine residue 246. Furthermore, we established bidirectionally regulated BHMT cellular models combined with methylation-deficient G6PD mutants to demonstrate that BHMT potentiated arginine methylation of G6PD, thereby inhibiting G6PD activity, which in turn suppressed hepatocarcinogenesis. Taken together, this study reveals a new methylation-regulatory mechanism in hepatocarcinogenesis owing to BHMT deficiency, suggesting a potential therapeutic strategy for HCC treatment.
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Affiliation(s)
- Jie Gao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Xiaoyi Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Yaohui Sun
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Xudong Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Feng Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Chengcheng Shi
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Zhiping Yan
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Shizhe Yu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
- Cancer Metastasis Institute, Fudan University, Shanghai, 200040, China
| | - Jiacheng Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Xiaodan Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China.
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China.
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Diagnosis & Treatment League for Hepatopathy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Innovative Research Group for Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation, Zhengzhou, 450052, China.
- Henan Organ Transplantation Quality Control Centre, Zhengzhou, 450052, China.
- Henan Engineering Technology Research Center for Organ Transplantation, Zhengzhou, 450052, China.
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3
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Chang C, Li L, Su L, Yang F, Zha Q, Sun M, Tao L, Wang M, Song K, Jiang L, Gao H, Liang Y, Xu C, Yong C, Wang M, Huang J, Liu J, Jin W, Lv W, Dong H, Li Q, Bu F, Yan S, Qi H, Zhao S, Zhu Y, Wang Y, Shi J, Qiao Y, Xu J, Chabot B, Chen J. Intron Retention of DDX39A Driven by SNRPD2 is a Crucial Splicing Axis for Oncogenic MYC/Spliceosome Program in Hepatocellular Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403387. [PMID: 39018261 DOI: 10.1002/advs.202403387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/03/2024] [Indexed: 07/19/2024]
Abstract
RNA splicing is a dynamic molecular process in response to environmental stimuli and is strictly regulated by the spliceosome. Sm proteins, constituents of the spliceosome, are key components that mediate splicing reactions; however, their potential role in hepatocellular carcinoma (HCC) is poorly understood. In the study, SNRPD2 (PD2) is found to be the most highly upregulated Sm protein in HCC and to act as an oncogene. PD2 modulates DDX39A intron retention together with HNRNPL to sustain the DDX39A short variant (39A_S) expression. Mechanistically, 39A_S can mediate MYC mRNA nuclear export to maintain high MYC protein expression, while MYC in turn potentiates PD2 transcription. Importantly, digitoxin can directly interact with PD2 and has a notable cancer-suppressive effect on HCC. The study reveals a novel mechanism by which DDX39A senses oncogenic MYC signaling and undergoes splicing via PD2 to form a positive feedback loop in HCC, which can be targeted by digitoxin.
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Affiliation(s)
- Cunjie Chang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Lina Li
- Medical Molecular Biology Laboratory, Medical College, Jinhua University of Vocational Technology, Jinhua, 321016, P.R. China
| | - Ling Su
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Fan Yang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Quanxiu Zha
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Mengqing Sun
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Lin Tao
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Menglan Wang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Kangli Song
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Liangyu Jiang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Haojin Gao
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Yexin Liang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Chao Xu
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Caiyu Yong
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Minmin Wang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Jiacheng Huang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Jing Liu
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Weiwei Jin
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Wenyuan Lv
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Heng Dong
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Qian Li
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Fangtian Bu
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Shuanghong Yan
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Haoxiang Qi
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Shujuan Zhao
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Yingshuang Zhu
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
- School of Public Health, Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Yu Wang
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
- Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore, 169610, Singapore
| | - Junping Shi
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
| | - Yiting Qiao
- The First Affiliated Hospital, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, 310003, P. R. China
| | - Jian Xu
- Hepatobiliary and Liver transplantation Department of Hainan Digestive Disease Center, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, P. R. China
| | - Benoit Chabot
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Jianxiang Chen
- School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal, University Hangzhou Normal University, Hangzhou, 311121, P. R. China
- Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore, 169610, Singapore
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, P. R. China
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4
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Krenz B, Lee J, Kannan T, Eilers M. Immune evasion: An imperative and consequence of MYC deregulation. Mol Oncol 2024. [PMID: 38957016 DOI: 10.1002/1878-0261.13695] [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: 02/07/2024] [Revised: 05/08/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
MYC has been implicated in the pathogenesis of a wide range of human tumors and has been described for many years as a transcription factor that regulates genes with pleiotropic functions to promote tumorigenic growth. However, despite extensive efforts to identify specific target genes of MYC that alone could be responsible for promoting tumorigenesis, the field is yet to reach a consensus whether this is the crucial function of MYC. Recent work shifts the view on MYC's function from being a gene-specific transcription factor to an essential stress resilience factor. In highly proliferating cells, MYC preserves cell integrity by promoting DNA repair at core promoters, protecting stalled replication forks, and/or preventing transcription-replication conflicts. Furthermore, an increasing body of evidence demonstrates that MYC not only promotes tumorigenesis by driving cell-autonomous growth, but also enables tumors to evade the host's immune system. In this review, we summarize our current understanding of how MYC impairs antitumor immunity and why this function is evolutionarily hard-wired to the biology of the MYC protein family. We show why the cell-autonomous and immune evasive functions of MYC are mutually dependent and discuss ways to target MYC proteins in cancer therapy.
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Affiliation(s)
- Bastian Krenz
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, Würzburg, Germany
| | - Jongkuen Lee
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Toshitha Kannan
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
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5
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Hoang PM, Torre D, Jaynes P, Ho J, Mohammed K, Alvstad E, Lam WY, Khanchandani V, Lee JM, Toh CMC, Lee RX, Anbuselvan A, Lee S, Sebra RP, Martin J Walsh, Marazzi I, Kappei D, Guccione E, Jeyasekharan AD. A PRMT5-ZNF326 axis mediates innate immune activation upon replication stress. SCIENCE ADVANCES 2024; 10:eadm9589. [PMID: 38838142 DOI: 10.1126/sciadv.adm9589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
DNA replication stress (RS) is a widespread phenomenon in carcinogenesis, causing genomic instability and extensive chromatin alterations. DNA damage leads to activation of innate immune signaling, but little is known about transcriptional regulators mediating such signaling upon RS. Using a chemical screen, we identified protein arginine methyltransferase 5 (PRMT5) as a key mediator of RS-dependent induction of interferon-stimulated genes (ISGs). This response is also associated with reactivation of endogenous retroviruses (ERVs). Using quantitative mass spectrometry, we identify proteins with PRMT5-dependent symmetric dimethylarginine (SDMA) modification induced upon RS. Among these, we show that PRMT5 targets and modulates the activity of ZNF326, a zinc finger protein essential for ISG response. Our data demonstrate a role for PRMT5-mediated SDMA in the context of RS-induced transcriptional induction, affecting physiological homeostasis and cancer therapy.
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Affiliation(s)
- Phuong Mai Hoang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Denis Torre
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jessica Ho
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Kevin Mohammed
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erik Alvstad
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Wan Yee Lam
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vartika Khanchandani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jie Min Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chin Min Clarissa Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Rui Xue Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Akshaya Anbuselvan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, South Korea
| | - Robert P Sebra
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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6
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Zhang Y, Xu M, Yuan J, Hu Z, Jiang J, Huang J, Wang B, Shen J, Long M, Fan Y, Montone KT, Tanyi JL, Tavana O, Chan HM, Hu X, Zhang L. Repression of PRMT activities sensitize homologous recombination-proficient ovarian and breast cancer cells to PARP inhibitor treatment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595159. [PMID: 38826355 PMCID: PMC11142138 DOI: 10.1101/2024.05.21.595159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
An "induced PARP inhibitor (PARPi) sensitivity by epigenetic modulation" strategy is being evaluated in the clinic to sensitize homologous recombination (HR)-proficient tumors to PARPi treatments. To expand its clinical applications and identify more efficient combinations, we performed a drug screen by combining PARPi with 74 well-characterized epigenetic modulators that target five major classes of epigenetic enzymes. Both type I PRMT inhibitor and PRMT5 inhibitor exhibit high combination and clinical priority scores in our screen. PRMT inhibition significantly enhances PARPi treatment-induced DNA damage in HR-proficient ovarian and breast cancer cells. Mechanistically, PRMTs maintain the expression of genes associated with DNA damage repair and BRCAness and regulate intrinsic innate immune pathways in cancer cells. Analyzing large-scale genomic and functional profiles from TCGA and DepMap further confirms that PRMT1, PRMT4, and PRMT5 are potential therapeutic targets in oncology. Finally, PRMT1 and PRMT5 inhibition act synergistically to enhance PARPi sensitivity. Our studies provide a strong rationale for the clinical application of a combination of PRMT and PARP inhibitors in patients with HR-proficient ovarian or breast cancer.
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Affiliation(s)
- Youyou Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Mu Xu
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Jiao Yuan
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Zhongyi Hu
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Junjie Jiang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Jie Huang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Bingwei Wang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Jianfeng Shen
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Meixiao Long
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, Ohio, 43210, USA
| | - Yi Fan
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Janos L Tanyi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Center for Gynecologic Cancer Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Omid Tavana
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts, 02451, USA
| | - Ho Man Chan
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts, 02451, USA
| | - Xiaowen Hu
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Lin Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Center for Gynecologic Cancer Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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7
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Bouton L, Ecoutin A, Malard F, Campagne S. Small molecules modulating RNA splicing: a review of targets and future perspectives. RSC Med Chem 2024; 15:1109-1126. [PMID: 38665842 PMCID: PMC11042171 DOI: 10.1039/d3md00685a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 04/28/2024] Open
Abstract
In eukaryotic cells, RNA splicing is crucial for gene expression. Dysregulation of this process can result in incorrect mRNA processing, leading to aberrant gene expression patterns. Such abnormalities are implicated in many inherited diseases and cancers. Historically, antisense oligonucleotides, which bind to specific RNA targets, have been used to correct these splicing abnormalities. Despite their high specificity of action, these oligonucleotides have drawbacks, such as lack of oral bioavailability and the need for chemical modifications to enhance cellular uptake and stability. As a result, recent efforts focused on the development of small organic molecules that can correct abnormal RNA splicing event under disease conditions. This review discusses known and potential targets of these molecules, including RNA structures, trans-acting splicing factors, and the spliceosome - the macromolecular complex responsible for RNA splicing. We also rely on recent advances to discuss therapeutic applications of RNA-targeting small molecules in splicing correction. Overall, this review presents an update on strategies for RNA splicing modulation, emphasizing the therapeutic promise of small molecules.
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Affiliation(s)
- Léa Bouton
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Agathe Ecoutin
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
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8
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Rambout X, Maquat LE. Nuclear mRNA decay: regulatory networks that control gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00712-2. [PMID: 38637632 DOI: 10.1038/s41576-024-00712-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 04/20/2024]
Abstract
Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adaptation to internal and environmental cues. Over the past 25 years, it has become clear that the nuclear machineries governing gene transcription, pre-mRNA processing, pre-mRNA and mRNA decay, and mRNA export to the cytoplasm are inextricably linked to control the quality and quantity of mRNAs available for translation. More recently, an ever-expanding diversity of new mechanisms by which nuclear RNA decay factors finely tune the expression of protein-encoding genes have been uncovered. Here, we review the current understanding of how mammalian cells shape their protein-encoding potential by regulating the decay of pre-mRNAs and mRNAs in the nucleus.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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9
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Jablonowski CM, Quarni W, Singh S, Tan H, Bostanthirige DH, Jin H, Fang J, Chang TC, Finkelstein D, Cho JH, Hu D, Pagala V, Sakurada SM, Pruett-Miller SM, Wang R, Murphy A, Freeman K, Peng J, Davidoff AM, Wu G, Yang J. Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing associated with therapeutic response to splicing inhibitor. eLife 2024; 12:RP90993. [PMID: 38488852 PMCID: PMC10942784 DOI: 10.7554/elife.90993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that jumonji domain containing 6, arginine demethylase, and lysine hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven human neuroblastoma. JMJD6 cooperates with MYC in cellular transformation of murine neural crest cells by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a 'molecular glue' that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.
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Affiliation(s)
| | - Waise Quarni
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Shivendra Singh
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | | | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Jie Fang
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - David Finkelstein
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | - Dongli Hu
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | - Sadie Miki Sakurada
- Department of Cell and Molecular Biology, St Jude Children's Research HospitalMemphisUnited States
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St Jude Children's Research HospitalMemphisUnited States
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s HospitalColumbusUnited States
| | - Andrew Murphy
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Kevin Freeman
- Genetics, Genomics & Informatics, The University of Tennessee Health Science Center (UTHSC)MemphisUnited States
| | - Junmin Peng
- Department of Structural Biology, St Jude Children’s Research HospitalMemphisUnited States
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research HospitalMemphisUnited States
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science CenterMemphisUnited States
| | - Gang Wu
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research HospitalMemphisUnited States
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science CenterMemphisUnited States
- College of Graduate Health Sciences, University of Tennessee Health Science CenterMemphisUnited States
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10
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Liu QW, Yang ZW, Tang QH, Wang WE, Chu DS, Ji JF, Fan QY, Jiang H, Yang QX, Zhang H, Liu XY, Xu XS, Wang XF, Liu JB, Fu D, Tao K, Yu H. The power and the promise of synthetic lethality for clinical application in cancer treatment. Biomed Pharmacother 2024; 172:116288. [PMID: 38377739 DOI: 10.1016/j.biopha.2024.116288] [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: 01/04/2024] [Revised: 02/08/2024] [Accepted: 02/17/2024] [Indexed: 02/22/2024] Open
Abstract
Synthetic lethality is a phenomenon wherein the simultaneous deficiency of two or more genes results in cell death, while the deficiency of any individual gene does not lead to cell death. In recent years, synthetic lethality has emerged as a significant topic in the field of targeted cancer therapy, with certain drugs based on this concept exhibiting promising outcomes in clinical trials. Nevertheless, the presence of tumor heterogeneity and the intricate DNA repair mechanisms pose challenges to the effective implementation of synthetic lethality. This review aims to explore the concepts, development, and ethical quandaries surrounding synthetic lethality. Additionally, it will provide an in-depth analysis of the clinical application and underlying mechanism of synthetic lethality.
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Affiliation(s)
- Qian-Wen Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Zhi-Wen Yang
- Department of Pharmacy, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, Shanghai 200050, China
| | - Qing-Hai Tang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region and College of Life Sciences, Hengyang Normal University, Hengyang, Hunan Province 421008, China
| | - Wen-Er Wang
- General Surgery, the Fourth Hospital Of Changsha, Changsha Hospital Of Hunan Normal University, Changsha, Hunan Province 410006, China
| | - Da-Sheng Chu
- Second Cadre Rest Medical and Health Center of Changning District, Shanghai Garrison, Shanghai226631, China
| | - Jin-Feng Ji
- Department of Integrated Traditional Chinese and Western Internal Medicine, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu Province 226631, China
| | - Qi-Yu Fan
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Hong Jiang
- Department of Thoracic Surgery, the 905th Hospital of Chinese People's Liberation Army Navy, Shanghai 200050, China
| | - Qin-Xin Yang
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Hui Zhang
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Xin-Yun Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Xiao-Sheng Xu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Xiao-Feng Wang
- Department of Orthopedics, Xiamen Hospital, Zhongshan Hospital, Fudan University, Xiamen, Fujian Province 361015, China.
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China.
| | - Da Fu
- General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Kun Tao
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
| | - Hong Yu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; Department of Pathology, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province 225300, China.
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11
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Gao Y, Feng C, Ma J, Yan Q. Protein arginine methyltransferases (PRMTs): Orchestrators of cancer pathogenesis, immunotherapy dynamics, and drug resistance. Biochem Pharmacol 2024; 221:116048. [PMID: 38346542 DOI: 10.1016/j.bcp.2024.116048] [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: 11/27/2023] [Revised: 01/15/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Protein Arginine Methyltransferases (PRMTs) are a family of enzymes regulating protein arginine methylation, which is a post-translational modification crucial for various cellular processes. Recent studies have highlighted the mechanistic role of PRMTs in cancer pathogenesis, immunotherapy, and drug resistance. PRMTs are involved in diverse oncogenic processes, including cell proliferation, apoptosis, and metastasis. They exert their effects by methylation of histones, transcription factors, and other regulatory proteins, resulting in altered gene expression patterns. PRMT-mediated histone methylation can lead to aberrant chromatin remodeling and epigenetic changes that drive oncogenesis. Additionally, PRMTs can directly interact with key signaling pathways involved in cancer progression, such as the PI3K/Akt and MAPK pathways, thereby modulating cell survival and proliferation. In the context of cancer immunotherapy, PRMTs have emerged as critical regulators of immune responses. They modulate immune checkpoint molecules, including programmed cell death protein 1 (PD-1), through arginine methylation. Drug resistance is a significant challenge in cancer treatment, and PRMTs have been implicated in this phenomenon. PRMTs can contribute to drug resistance through multiple mechanisms, including the epigenetic regulation of drug efflux pumps, altered DNA damage repair, and modulation of cell survival pathways. In conclusion, PRMTs play critical roles in cancer pathogenesis, immunotherapy, and drug resistance. In this overview, we have endeavored to illuminate the mechanistic intricacies of PRMT-mediated processes. Shedding light on these aspects will offer valuable insights into the fundamental biology of cancer and establish PRMTs as promising therapeutic targets.
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Affiliation(s)
- Yihang Gao
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China
| | - Chongchong Feng
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China.
| | - Jingru Ma
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China
| | - Qingzhu Yan
- Department of Ultrasound Medicine, the Second Hospital of Jilin University, Changchun 130000, China
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12
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Venkatasubramanian M, Schwartz L, Ramachandra N, Bennett J, Subramanian KR, Chen X, Gordon-Mitchell S, Fromowitz A, Pradhan K, Shechter D, Sahu S, Heiser D, Scherle P, Chetal K, Kulkarni A, Myers KC, Weirauch MT, Grimes HL, Starczynowski DT, Verma A, Salomonis N. Broad de-regulated U2AF1 splicing is prognostic and augments leukemic transformation via protein arginine methyltransferase activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578798. [PMID: 38370617 PMCID: PMC10871255 DOI: 10.1101/2024.02.04.578798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The role of splicing dysregulation in cancer is underscored by splicing factor mutations; however, its impact in the absence of such rare mutations is poorly understood. To reveal complex patient subtypes and putative regulators of pathogenic splicing in Acute Myeloid Leukemia (AML), we developed a new approach called OncoSplice. Among diverse new subtypes, OncoSplice identified a biphasic poor prognosis signature that partially phenocopies U2AF1-mutant splicing, impacting thousands of genes in over 40% of adult and pediatric AML cases. U2AF1-like splicing co-opted a healthy circadian splicing program, was stable over time and induced a leukemia stem cell (LSC) program. Pharmacological inhibition of the implicated U2AF1-like splicing regulator, PRMT5, rescued leukemia mis-splicing and inhibited leukemic cell growth. Genetic deletion of IRAK4, a common target of U2AF1-like and PRMT5 treated cells, blocked leukemia development in xenograft models and induced differentiation. These analyses reveal a new prognostic alternative-splicing mechanism in malignancy, independent of splicing-factor mutations.
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Affiliation(s)
- Meenakshi Venkatasubramanian
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
| | - Leya Schwartz
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Nandini Ramachandra
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Joshua Bennett
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Krithika R. Subramanian
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Xiaoting Chen
- Divisions of Human Genetics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Shanisha Gordon-Mitchell
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Ariel Fromowitz
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Kith Pradhan
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - David Shechter
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Srabani Sahu
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Diane Heiser
- Prelude Therapeutics Incorporated, Wilmington, DE
| | | | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Aishwarya Kulkarni
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
| | - Kasiani C. Myers
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Matthew T. Weirauch
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Divisions of Human Genetics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - H. Leighton Grimes
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Daniel T. Starczynowski
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Amit Verma
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
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13
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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14
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Deutzmann A, Sullivan DK, Dhanasekaran R, Li W, Chen X, Tong L, Mahauad-Fernandez WD, Bell J, Mosley A, Koehler AN, Li Y, Felsher DW. Nuclear to cytoplasmic transport is a druggable dependency in MYC-driven hepatocellular carcinoma. Nat Commun 2024; 15:963. [PMID: 38302473 PMCID: PMC10834515 DOI: 10.1038/s41467-024-45128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/12/2024] [Indexed: 02/03/2024] Open
Abstract
The MYC oncogene is often dysregulated in human cancer, including hepatocellular carcinoma (HCC). MYC is considered undruggable to date. Here, we comprehensively identify genes essential for survival of MYChigh but not MYClow cells by a CRISPR/Cas9 genome-wide screen in a MYC-conditional HCC model. Our screen uncovers novel MYC synthetic lethal (MYC-SL) interactions and identifies most MYC-SL genes described previously. In particular, the screen reveals nucleocytoplasmic transport to be a MYC-SL interaction. We show that the majority of MYC-SL nucleocytoplasmic transport genes are upregulated in MYChigh murine HCC and are associated with poor survival in HCC patients. Inhibiting Exportin-1 (XPO1) in vivo induces marked tumor regression in an autochthonous MYC-transgenic HCC model and inhibits tumor growth in HCC patient-derived xenografts. XPO1 expression is associated with poor prognosis only in HCC patients with high MYC activity. We infer that MYC may generally regulate and require altered expression of nucleocytoplasmic transport genes for tumorigenesis.
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Affiliation(s)
- Anja Deutzmann
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Delaney K Sullivan
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Renumathy Dhanasekaran
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
- Division of Gastroenterology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Wei Li
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, 20012, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, 20012, USA
| | - Xinyu Chen
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Ling Tong
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | | | - John Bell
- Stanford Genome Technology Center, Stanford University, Stanford, CA, 94305, USA
| | - Adriane Mosley
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Angela N Koehler
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yulin Li
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Institute for Academic Medicine, Houston Methodist and Weill Cornell Medical College, Houston, TX, 77030, USA.
| | - Dean W Felsher
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA.
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15
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Tompkins VS, Xue Z, Peterson JM, Rouse WB, O’Leary CA, Moss WN. Identification of MYC intron 2 regions that modulate expression. PLoS One 2024; 19:e0296889. [PMID: 38236931 PMCID: PMC10795982 DOI: 10.1371/journal.pone.0296889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024] Open
Abstract
MYC pre-mRNA is spliced with high fidelity to produce the transcription factor known to regulate cellular differentiation, proliferation, apoptosis, and alternative splicing. The mechanisms underpinning the pre-mRNA splicing of MYC, however, remain mostly unexplored. In this study, we examined the interaction of heterogeneous nuclear ribonucleoprotein C (HNRNPC) with MYC intron 2. Building off published eCLIP studies, we confirmed this interaction with poly(U) regions in intron 2 of MYC and found that full binding is correlated with optimal protein production. The interaction appears to be compensatory, as mutational disruption of all three poly(U) regions was required to reduce both HNRNPC binding capacity and fidelity of either splicing or translation. Poly(U) sequences in MYC intron 2 were relatively conserved across sequences from several different species. Lastly, we identified a short sequence just upstream of an HNRNPC binding region that when removed enhances MYC translation.
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Affiliation(s)
- Van S. Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Zheng Xue
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Jake M. Peterson
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Warren B. Rouse
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Collin A. O’Leary
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
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16
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Salib A, Jayatilleke N, Seneviratne JA, Mayoh C, De Preter K, Speleman F, Cheung BB, Carter DR, Marshall GM. MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression. Oncogene 2024; 43:363-377. [PMID: 38049564 PMCID: PMC10824661 DOI: 10.1038/s41388-023-02897-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023]
Abstract
Many of the pro-tumorigenic functions of the oncogene MYCN are attributed to its regulation of global gene expression programs. Alternative splicing is another important regulator of gene expression and has been implicated in neuroblastoma development, however, the molecular mechanisms remain unknown. We found that MYCN up-regulated the expression of the core spliceosomal protein, SNRPD3, in models of neuroblastoma initiation and progression. High mRNA expression of SNRPD3 in human neuroblastoma tissues was a strong, independent prognostic factor for poor patient outcome. Repression of SNRPD3 expression correlated with loss of colony formation in vitro and reduced tumorigenicity in vivo. The effect of SNRPD3 on cell viability was in part dependent on MYCN as an oncogenic co-factor. RNA-sequencing revealed a global increase in the number of genes being differentially spliced when MYCN was overexpressed. Surprisingly, depletion of SNRPD3 in the presence of overexpressed MYCN further increased differential splicing, particularly of cell cycle regulators, such as BIRC5 and CDK10. MYCN directly bound SNRPD3, and the protein arginine methyltransferase, PRMT5, consequently increasing SNRPD3 methylation. Indeed, the PRMT5 inhibitor, JNJ-64619178, reduced cell viability and SNRPD3 methylation in neuroblastoma cells with high SNRPD3 and MYCN expression. Our findings demonstrate a functional relationship between MYCN and SNRPD3, which maintains the fidelity of MYCN-driven alternative splicing in the narrow range required for neuroblastoma cell growth. SNRPD3 methylation and its protein-protein interface with MYCN represent novel therapeutic targets. Hypothetical model for SNRPD3 as a co-factor for MYCN oncogenesis. SNRPD3 and MYCN participate in a regulatory loop to balance splicing fidelity in neuroblastoma cells. First MYCN transactivates SNRPD3 to lead to high-level expression. Second, SNRPD3 and MYCN form a protein complex involving PRMT5. Third, this leads to balanced alterative splicing (AS) activitiy that is favorable to neuroblastoma. Together this forms as a therapeutic vulnerability where SNRPD3 perturbation or PRMT5 inhibitors are selectively toxic to neuroblastoma by conditionally disturbing splicing activity.
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Affiliation(s)
- Alice Salib
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Nisitha Jayatilleke
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Janith A Seneviratne
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Katleen De Preter
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), Ghent, Belgium
| | - Belamy B Cheung
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Daniel R Carter
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia.
- School of Biomedical Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia.
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, 2031, Australia.
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17
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Li Y, Dobrolecki LE, Sallas C, Zhang X, Kerr TD, Bisht D, Wang Y, Awasthi S, Kaundal B, Wu S, Peng W, Mendillo ML, Lu Y, Jeter CR, Peng G, Liu J, Westin SN, Sood AK, Lewis MT, Das J, Yi SS, Bedford MT, McGrail DJ, Sahni N. PRMT blockade induces defective DNA replication stress response and synergizes with PARP inhibition. Cell Rep Med 2023; 4:101326. [PMID: 38118413 PMCID: PMC10772459 DOI: 10.1016/j.xcrm.2023.101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 09/07/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Multiple cancers exhibit aberrant protein arginine methylation by both type I arginine methyltransferases, predominately protein arginine methyltransferase 1 (PRMT1) and to a lesser extent PRMT4, and by type II PRMTs, predominately PRMT5. Here, we perform targeted proteomics following inhibition of PRMT1, PRMT4, and PRMT5 across 12 cancer cell lines. We find that inhibition of type I and II PRMTs suppresses phosphorylated and total ATR in cancer cells. Loss of ATR from PRMT inhibition results in defective DNA replication stress response activation, including from PARP inhibitors. Inhibition of type I and II PRMTs is synergistic with PARP inhibition regardless of homologous recombination function, but type I PRMT inhibition is more toxic to non-malignant cells. Finally, we demonstrate that the combination of PARP and PRMT5 inhibition improves survival in both BRCA-mutant and wild-type patient-derived xenografts without toxicity. Taken together, these results demonstrate that PRMT5 inhibition may be a well-tolerated approach to sensitize tumors to PARP inhibition.
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Affiliation(s)
- Yang Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Christina Sallas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Xudong Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis D Kerr
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharad Awasthi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siqi Wu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiyi Peng
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yiling Lu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Collene R Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shannon N Westin
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jishnu Das
- Center for Systems Immunology, Department of Immunology, and Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA; Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA; Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, USA.
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18
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Kumar D, Jain S, Coulter DW, Joshi SS, Chaturvedi NK. PRMT5 as a Potential Therapeutic Target in MYC-Amplified Medulloblastoma. Cancers (Basel) 2023; 15:5855. [PMID: 38136401 PMCID: PMC10741595 DOI: 10.3390/cancers15245855] [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: 11/06/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
MYC amplification or overexpression is most common in Group 3 medulloblastomas and is positively associated with poor clinical outcomes. Recently, protein arginine methyltransferase 5 (PRMT5) overexpression has been shown to be associated with tumorigenic MYC functions in cancers, particularly in brain cancers such as glioblastoma and medulloblastoma. PRMT5 regulates oncogenes, including MYC, that are often deregulated in medulloblastomas. However, the role of PRMT5-mediated post-translational modification in the stabilization of these oncoproteins remains poorly understood. The potential impact of PRMT5 inhibition on MYC makes it an attractive target in various cancers. PRMT5 inhibitors are a promising class of anti-cancer drugs demonstrating preclinical and preliminary clinical efficacies. Here, we review the publicly available preclinical and clinical studies on PRMT5 targeting using small molecule inhibitors and discuss the prospects of using them in medulloblastoma therapy.
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Affiliation(s)
- Devendra Kumar
- Department of Pediatrics, Division of Hematology and Oncology, University of Nebraska Medical Center, Omaha, NE 69198, USA; (D.K.); (S.J.); (D.W.C.)
| | - Stuti Jain
- Department of Pediatrics, Division of Hematology and Oncology, University of Nebraska Medical Center, Omaha, NE 69198, USA; (D.K.); (S.J.); (D.W.C.)
| | - Don W. Coulter
- Department of Pediatrics, Division of Hematology and Oncology, University of Nebraska Medical Center, Omaha, NE 69198, USA; (D.K.); (S.J.); (D.W.C.)
- Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE 69198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 69198, USA
| | - Shantaram S. Joshi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 69198, USA;
| | - Nagendra K. Chaturvedi
- Department of Pediatrics, Division of Hematology and Oncology, University of Nebraska Medical Center, Omaha, NE 69198, USA; (D.K.); (S.J.); (D.W.C.)
- Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE 69198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 69198, USA
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19
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Jobbins AM, Yu S, Paterson HAB, Maude H, Kefala-Stavridi A, Speck C, Cebola I, Vernia S. Pre-RNA splicing in metabolic homeostasis and liver disease. Trends Endocrinol Metab 2023; 34:823-837. [PMID: 37673766 DOI: 10.1016/j.tem.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
The liver plays a key role in sensing nutritional and hormonal inputs to maintain metabolic homeostasis. Recent studies into pre-mRNA splicing and alternative splicing (AS) and their effects on gene expression have revealed considerable transcriptional complexity in the liver, both in health and disease. While the contribution of these mechanisms to cell and tissue identity is widely accepted, their role in physiological and pathological contexts within tissues is just beginning to be appreciated. In this review, we showcase recent studies on the splicing and AS of key genes in metabolic pathways in the liver, the effect of metabolic signals on the spliceosome, and therapeutic intervention points based on RNA splicing.
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Affiliation(s)
- Andrew M Jobbins
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Sijia Yu
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Helen A B Paterson
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Antonia Kefala-Stavridi
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Christian Speck
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Santiago Vernia
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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20
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Yu T, Xu-Monette ZY, Yu L, Li Y, Young KH. Mechanisms of ferroptosis and targeted therapeutic approaches in lymphoma. Cell Death Dis 2023; 14:771. [PMID: 38007476 PMCID: PMC10676406 DOI: 10.1038/s41419-023-06295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023]
Abstract
Lymphoma is the sixth most common type of cancer worldwide. Under the current treatment standards, patients with lymphoma often fail to respond to treatment or relapse early and require further therapy. Hence, novel therapeutic strategies need to be explored and our understanding of the molecular underpinnings of lymphomas should be expanded. Ferroptosis, a non-apoptotic regulated cell death, is characterized by increased reactive oxygen species and lipid peroxidation due to metabolic dysfunction. Excessive or lack of ferroptosis has been implicated in tumor development. Current preclinical evidences suggest that ferroptosis participates in tumorigenesis, progression, and drug resistance of lymphoma, identifying a potential biomarker and an attractive molecular target. Our review summarizes the core mechanisms and regulatory networks of ferroptosis and discusses existing evidences of ferroptosis induction for the treatment of lymphoma, with intent to provide a framework for understanding the role of ferroptosis in lymphomagenesis and a new perspective of lymphoma treatment.
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Affiliation(s)
- Tiantian Yu
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, USA
- Department of Hematology and Oncology, The Second Affiliated Hospital of NanChang University, Nanchang, China
| | - Zijun Y Xu-Monette
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Li Yu
- Department of Hematology and Oncology, The Second Affiliated Hospital of NanChang University, Nanchang, China
| | - Yong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Ken H Young
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, USA.
- Duke Cancer Institute, Durham, NC, USA.
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21
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Harada K, Carr SM, Shrestha A, La Thangue NB. Citrullination and the protein code: crosstalk between post-translational modifications in cancer. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220243. [PMID: 37778382 PMCID: PMC10542456 DOI: 10.1098/rstb.2022.0243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/05/2023] [Indexed: 10/03/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins are central to epigenetic regulation and cellular signalling, playing an important role in the pathogenesis and progression of numerous diseases. Growing evidence indicates that protein arginine citrullination, catalysed by peptidylarginine deiminases (PADs), is involved in many aspects of molecular and cell biology and is emerging as a potential druggable target in multiple diseases including cancer. However, we are only just beginning to understand the molecular activities of PADs, and their underlying mechanistic details in vivo under both physiological and pathological conditions. Many questions still remain regarding the dynamic cellular functions of citrullination and its interplay with other types of PTMs. This review, therefore, discusses the known functions of PADs with a focus on cancer biology, highlighting the cross-talk between citrullination and other types of PTMs, and how this interplay regulates downstream biological events. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Koyo Harada
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Simon M. Carr
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Amit Shrestha
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Nicholas B. La Thangue
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
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22
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Jablonowski C, Quarni W, Singh S, Tan H, Bostanthirige DH, Jin H, Fang J, Chang TC, Finkelstein D, Cho JH, Hu D, Pagala V, Sakurada SM, Pruett-Miller SM, Wang R, Murphy A, Freeman K, Peng J, Davidoff AM, Wu G, Yang J. Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546606. [PMID: 37425900 PMCID: PMC10327027 DOI: 10.1101/2023.06.26.546606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that Jumonji Domain Containing 6, Arginine Demethylase and Lysine Hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven neuroblastoma. JMJD6 cooperates with MYC in cellular transformation by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a "molecular glue" that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.
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23
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Zhuo Y, Zhang W, Du J, Jiang H, Chen G, Feng X, Gu H. Identification of m6A-associated genes as prognostic and immune-associated biomarkers in Wilms tumor. Discov Oncol 2023; 14:201. [PMID: 37938417 PMCID: PMC10632345 DOI: 10.1007/s12672-023-00817-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
OBJECTIVES Wilms tumor (WT) is a common renal malignant tumor in children. We aimed to investigate the potential prognostic value of m6A-related genes and their relationship to the immune microenvironment in WT. METHODS RNA-seq data and clinical information from 121 WT and 6 normal samples were obtained from the University of California Santa Cruz Xena database. We used various bioinformatics analysis tools to analyze these data and verify the expression level of m6A-related genes by experiments. RESULTS Four m6A-related genes were successfully screened, including ADGRG2, CPD, CTHRC1, and LRTM2. Kaplan-Meier survival curves showed that the four genes were closely related to the prognosis of WT, which was also confirmed by receiver operator characteristic curves. Subsequently, in the immune microenvironment of WT, we discovered that Th1_cells were positively correlated with ADGRG2, CCR was negatively correlated with CPD, CCR was positively correlated with CTHRC1, APC_co_stimulation, CCR, Macrophages, inflammation-promoting cells, Treg, and Type_II_IFN_Reponse were negatively correlated with LRTM2. Finally, qRT-PCR showed that expression levels of the four genes were upregulated in the nephroblastoma cell lines (G-401, SK-NEP-1, and WT-CLS1) compared with the human embryonic kidney cell lines (293T). CONCLUSIONS Taken together, our study first time screened the m6A-related genes and revealed that ADGRG2, CPD, CTHRC1, and LRTM2 are the prognostic and immune-associated biomarkers in WT.
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Affiliation(s)
- Yingquan Zhuo
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Wengqi Zhang
- Department of Anesthesiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jun Du
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Hua Jiang
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Guangtang Chen
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Xiaoyun Feng
- School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Huajian Gu
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, China.
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24
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Kotekar A, Singh AK, Devaiah BN. BRD4 and MYC: power couple in transcription and disease. FEBS J 2023; 290:4820-4842. [PMID: 35866356 PMCID: PMC9867786 DOI: 10.1111/febs.16580] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 01/26/2023]
Abstract
The MYC proto-oncogene and BRD4, a BET family protein, are two cardinal proteins that have a broad influence in cell biology and disease. Both proteins are expressed ubiquitously in mammalian cells and play central roles in controlling growth, development, stress responses and metabolic function. As chromatin and transcriptional regulators, they play a critical role in regulating the expression of a burgeoning array of genes, maintaining chromatin architecture and genome stability. Consequently, impairment of their function or regulation leads to many diseases, with cancer being the most predominant. Interestingly, accumulating evidence indicates that regulation of the expression and functions of MYC are tightly intertwined with BRD4 at both transcriptional and post-transcriptional levels. Here, we review the mechanisms by which MYC and BRD4 are regulated, their functions in governing various molecular mechanisms and the consequences of their dysregulation that lead to disease. We present a perspective of how the regulatory mechanisms for the two proteins could be entwined at multiple points in a BRD4-MYC nexus that leads to the modulation of their functions and disease upon dysregulation.
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Affiliation(s)
- Aparna Kotekar
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Amit Kumar Singh
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
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25
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Bray C, Balcells C, McNeish IA, Keun HC. The potential and challenges of targeting MTAP-negative cancers beyond synthetic lethality. Front Oncol 2023; 13:1264785. [PMID: 37795443 PMCID: PMC10546069 DOI: 10.3389/fonc.2023.1264785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Approximately 15% of cancers exhibit loss of the chromosomal locus 9p21.3 - the genomic location of the tumour suppressor gene CDKN2A and the methionine salvage gene methylthioadenosine phosphorylase (MTAP). A loss of MTAP increases the pool of its substrate methylthioadenosine (MTA), which binds to and inhibits activity of protein arginine methyltransferase 5 (PRMT5). PRMT5 utilises the universal methyl donor S-adenosylmethionine (SAM) to methylate arginine residues of protein substrates and regulate their activity, notably histones to regulate transcription. Recently, targeting PRMT5, or MAT2A that impacts PRMT5 activity by producing SAM, has shown promise as a therapeutic strategy in oncology, generating synthetic lethality in MTAP-negative cancers. However, clinical development of PRMT5 and MAT2A inhibitors has been challenging and highlights the need for further understanding of the downstream mediators of drug effects. Here, we discuss the rationale and methods for targeting the MAT2A/PRMT5 axis for cancer therapy. We evaluate the current limitations in our understanding of the mechanism of MAT2A/PRMT5 inhibitors and identify the challenges that must be addressed to maximise the potential of these drugs. In addition, we review the current literature defining downstream effectors of PRMT5 activity that could determine sensitivity to MAT2A/PRMT5 inhibition and therefore present a rationale for novel combination therapies that may not rely on synthetic lethality with MTAP loss.
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Affiliation(s)
- Chandler Bray
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, London, United Kingdom
| | - Cristina Balcells
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, London, United Kingdom
| | - Iain A. McNeish
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Hector C. Keun
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, London, United Kingdom
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26
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Lu T, Zhang J, Xu-Monette ZY, Young KH. The progress of novel strategies on immune-based therapy in relapsed or refractory diffuse large B-cell lymphoma. Exp Hematol Oncol 2023; 12:72. [PMID: 37580826 PMCID: PMC10424456 DOI: 10.1186/s40164-023-00432-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/30/2023] [Indexed: 08/16/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) can be cured with standard front-line immunochemotherapy, whereas nearly 30-40% of patients experience refractory or relapse. For several decades, the standard treatment strategy for fit relapsed/refractory (R/R) DLBCL patients has been high-dose chemotherapy followed by autologous hematopoietic stem cell transplant (auto-SCT). However, the patients who failed in salvage treatment or those ineligible for subsequent auto-SCT have dismal outcomes. Several immune-based therapies have been developed, including monoclonal antibodies, antibody-drug conjugates, bispecific T-cell engaging antibodies, chimeric antigen receptor T-cells, immune checkpoint inhibitors, and novel small molecules. Meanwhile, allogeneic SCT and radiotherapy are still necessary for disease control for fit patients with certain conditions. In this review, to expand clinical treatment options, we summarize the recent progress of immune-related therapies and prospect the future indirections in patients with R/R DLBCL.
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Affiliation(s)
- Tingxun Lu
- Department of Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu Province, 214122, China
- Division of Hematopathology, Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jie Zhang
- Department of Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu Province, 214122, China
| | - Zijun Y Xu-Monette
- Division of Hematopathology, Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Durham, NC, 27710, USA
| | - Ken H Young
- Division of Hematopathology, Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Cancer Institute, Durham, NC, 27710, USA.
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27
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Han N, Liu Z. Targeting alternative splicing in cancer immunotherapy. Front Cell Dev Biol 2023; 11:1232146. [PMID: 37635865 PMCID: PMC10450511 DOI: 10.3389/fcell.2023.1232146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Tumor immunotherapy has made great progress in cancer treatment but still faces several challenges, such as a limited number of targetable antigens and varying responses among patients. Alternative splicing (AS) is an essential process for the maturation of nearly all mammalian mRNAs. Recent studies show that AS contributes to expanding cancer-specific antigens and modulating immunogenicity, making it a promising solution to the above challenges. The organoid technology preserves the individual immune microenvironment and reduces the time/economic costs of the experiment model, facilitating the development of splicing-based immunotherapy. Here, we summarize three critical roles of AS in immunotherapy: resources for generating neoantigens, targets for immune-therapeutic modulation, and biomarkers to guide immunotherapy options. Subsequently, we highlight the benefits of adopting organoids to develop AS-based immunotherapies. Finally, we discuss the current challenges in studying AS-based immunotherapy in terms of existing bioinformatics algorithms and biological technologies.
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Affiliation(s)
- Nan Han
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoqi Liu
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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28
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Prochownik EV, Wang H. Lessons in aging from Myc knockout mouse models. Front Cell Dev Biol 2023; 11:1244321. [PMID: 37621775 PMCID: PMC10446843 DOI: 10.3389/fcell.2023.1244321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Despite MYC being among the most intensively studied oncogenes, its role in normal development has not been determined as Myc-/- mice do not survival beyond mid-gestation. Myc ± mice live longer than their wild-type counterparts and are slower to accumulate many age-related phenotypes. However, Myc haplo-insufficiency likely conceals other important phenotypes as many high-affinity Myc targets genes continue to be regulated normally. By delaying Myc inactivation until after birth it has recently been possible to study the consequences of its near-complete total body loss and thus to infer its normal function. Against expectation, these "MycKO" mice lived significantly longer than control wild-type mice but manifested a marked premature aging phenotype. This seemingly paradoxical behavior was potentially explained by a >3-fold lower lifetime incidence of cancer, normally the most common cause of death in mice and often Myc-driven. Myc loss accelerated the accumulation of numerous "Aging Hallmarks", including the loss of mitochondrial and ribosomal structural and functional integrity, the generation of reactive oxygen species, the acquisition of genotoxic damage, the detrimental rewiring of metabolism and the onset of senescence. In both mice and humans, normal aging in many tissues was accompaniued by the downregulation of Myc and the loss of Myc target gene regulation. Unlike most mouse models of premature aging, which are based on monogenic disorders of DNA damage recognition and repair, the MycKO mouse model directly impacts most Aging Hallmarks and may therefore more faithfully replicate the normal aging process of both mice and humans. It further establishes that the strong association between aging and cancer can be genetically separated and is maintained by a single gene.
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Affiliation(s)
- Edward V. Prochownik
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
- The Department of Microbiology and Molecular Genetics, UPMC, Pittsburgh, PA, United States
- The Hillman Cancer Center of UPMC, Pittsburgh, PA, United States
- The Pittsburgh Liver Research Center, UPMC, Pittsburgh, PA, United States
| | - Huabo Wang
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
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29
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Illi B, Nasi S. Myc beyond Cancer: Regulation of Mammalian Tissue Regeneration. PATHOPHYSIOLOGY 2023; 30:346-365. [PMID: 37606389 PMCID: PMC10443299 DOI: 10.3390/pathophysiology30030027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
Myc is one of the most well-known oncogenes driving tumorigenesis in a wide variety of tissues. From the brain to blood, its deregulation derails physiological pathways that grant the correct functioning of the cell. Its action is carried out at the gene expression level, where Myc governs basically every aspect of transcription. Indeed, in addition to its role as a canonical, chromatin-bound transcription factor, Myc rules RNA polymerase II (RNAPII) transcriptional pause-release, elongation and termination and mRNA capping. For this reason, it is evident that minimal perturbations of Myc function mirror malignant cell behavior and, consistently, a large body of literature mainly focuses on Myc malfunctioning. In healthy cells, Myc controls molecular mechanisms involved in pivotal functions, such as cell cycle (and proliferation thereof), apoptosis, metabolism and cell size, angiogenesis, differentiation and stem cell self-renewal. In this latter regard, Myc has been found to also regulate tissue regeneration, a hot topic in the research fields of aging and regenerative medicine. Indeed, Myc appears to have a role in wound healing, in peripheral nerves and in liver, pancreas and even heart recovery. Herein, we discuss the state of the art of Myc's role in tissue regeneration, giving an overview of its potent action beyond cancer.
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Affiliation(s)
- Barbara Illi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Sergio Nasi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
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30
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Chen X, Yang HT, Zhang B, Phillips JW, Cheng D, Rigo F, Witte ON, Xing Y, Black DL. The RNA-binding proteins hnRNP H and F regulate splicing of a MYC-dependent HRAS exon in prostate cancer cells. Proc Natl Acad Sci U S A 2023; 120:e2220190120. [PMID: 37399401 PMCID: PMC10334793 DOI: 10.1073/pnas.2220190120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/31/2023] [Indexed: 07/05/2023] Open
Abstract
The MYC proto-oncogene contributes to the pathogenesis of more than half of human cancers. Malignant transformation by MYC transcriptionally up-regulates the core pre-mRNA splicing machinery and causes misregulation of alternative splicing. However, our understanding of how splicing changes are directed by MYC is limited. We performed a signaling pathway-guided splicing analysis to identify MYC-dependent splicing events. These included an HRAS cassette exon repressed by MYC across multiple tumor types. To molecularly dissect the regulation of this HRAS exon, we used antisense oligonucleotide tiling to identify splicing enhancers and silencers in its flanking introns. RNA-binding motif prediction indicated multiple binding sites for hnRNP H and hnRNP F within these cis-regulatory elements. Using siRNA knockdown and cDNA expression, we found that both hnRNP H and F activate the HRAS cassette exon. Mutagenesis and targeted RNA immunoprecipitation implicate two downstream G-rich elements in this splicing activation. Analyses of ENCODE RNA-seq datasets confirmed hnRNP H regulation of HRAS splicing. Analyses of RNA-seq datasets across multiple cancers showed a negative correlation of HNRNPH gene expression with MYC hallmark enrichment, consistent with the effect of hnRNP H on HRAS splicing. Interestingly, HNRNPF expression showed a positive correlation with MYC hallmarks and thus was not consistent with the observed effects of hnRNP F. Loss of hnRNP H/F altered cell cycle progression and induced apoptosis in the PC3 prostate cancer cell line. Collectively, our results reveal mechanisms for MYC-dependent regulation of splicing and point to possible therapeutic targets in prostate cancers.
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Affiliation(s)
- Xinyuan Chen
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA90095
| | - Harry Taegyun Yang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA90095
| | - Beatrice Zhang
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - John W. Phillips
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Donghui Cheng
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Frank Rigo
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA92010
| | - Owen N. Witte
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA90095
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Douglas L. Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
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31
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Li S, Qi Y, Yu J, Hao Y, Xu L, Ding X, Zhang M, Geng J. Aurora kinase A regulates cancer-associated RNA aberrant splicing in breast cancer. Heliyon 2023; 9:e17386. [PMID: 37415951 PMCID: PMC10320321 DOI: 10.1016/j.heliyon.2023.e17386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
The contribution of oncogenes to tumor-associated RNA splicing and the relevant molecular mechanisms therein require further elaboration. Here, we show that oncogenic Aurora kinase A (AURKA) promotes breast cancer-related RNA aberrant splicing in a context-dependent manner. AURKA regulated pan-breast cancer-associated RNA splicing events including GOLGA4, RBM4 and UBQLN1. Aberrant splicing of GOLGA4 and RBM4 was closely related to breast cancer development. Mechanistically, AURKA interacted with the splicing factor YBX1 and promoted AURKA-YBX1 complex-mediated GOLGA4 exon inclusion. AURKA binding to the splicing factor hnRNPK promoted AURKA-hnRNPK complex-mediated RBM4 exon skipping. Analysis of clinical data identified an association between the AURKA-YBX1/hnRNPK complex and poor prognosis in breast cancer. Blocking AURKA nuclear translocation with small molecule drugs partially reversed the oncogenic splicing of RBM4 and GOLGA4 in breast cancer cells. In summary, oncogenic AURKA executes its function on modulating breast cancer-related RNA splicing, and nuclear AURKA is distinguished as a hopeful target in the case of treating breast cancer.
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Affiliation(s)
- Sisi Li
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Jiachuan Yu
- Department of Anesthesiology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yuchao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Lingzhi Xu
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xudong Ding
- Department of Pathology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Jingshu Geng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
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32
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Bonner EA, Lee SC. Therapeutic Targeting of RNA Splicing in Cancer. Genes (Basel) 2023; 14:1378. [PMID: 37510283 PMCID: PMC10379351 DOI: 10.3390/genes14071378] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
RNA splicing is a key regulatory step in the proper control of gene expression. It is a highly dynamic process orchestrated by the spliceosome, a macro-molecular machinery that consists of protein and RNA components. The dysregulation of RNA splicing has been observed in many human pathologies ranging from neurodegenerative diseases to cancer. The recent identification of recurrent mutations in the core components of the spliceosome in hematologic malignancies has advanced our knowledge of how splicing alterations contribute to disease pathogenesis. This review article will discuss our current understanding of how aberrant RNA splicing regulation drives tumor initiation and progression. We will also review current therapeutic modalities and highlight emerging technologies designed to target RNA splicing for cancer treatment.
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Affiliation(s)
- Elizabeth A Bonner
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Stanley C Lee
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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33
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Wojtyś W, Oroń M. How Driver Oncogenes Shape and Are Shaped by Alternative Splicing Mechanisms in Tumors. Cancers (Basel) 2023; 15:cancers15112918. [PMID: 37296881 DOI: 10.3390/cancers15112918] [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: 04/28/2023] [Revised: 05/20/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The development of RNA sequencing methods has allowed us to study and better understand the landscape of aberrant pre-mRNA splicing in tumors. Altered splicing patterns are observed in many different tumors and affect all hallmarks of cancer: growth signal independence, avoidance of apoptosis, unlimited proliferation, invasiveness, angiogenesis, and metabolism. In this review, we focus on the interplay between driver oncogenes and alternative splicing in cancer. On one hand, oncogenic proteins-mutant p53, CMYC, KRAS, or PI3K-modify the alternative splicing landscape by regulating expression, phosphorylation, and interaction of splicing factors with spliceosome components. Some splicing factors-SRSF1 and hnRNPA1-are also driver oncogenes. At the same time, aberrant splicing activates key oncogenes and oncogenic pathways: p53 oncogenic isoforms, the RAS-RAF-MAPK pathway, the PI3K-mTOR pathway, the EGF and FGF receptor families, and SRSF1 splicing factor. The ultimate goal of cancer research is a better diagnosis and treatment of cancer patients. In the final part of this review, we discuss present therapeutic opportunities and possible directions of further studies aiming to design therapies targeting alternative splicing mechanisms in the context of driver oncogenes.
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Affiliation(s)
- Weronika Wojtyś
- Laboratory of Human Disease Multiomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Magdalena Oroń
- Laboratory of Human Disease Multiomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
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34
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Guo L, Xu CE. Integrated bioinformatics and machine learning algorithms reveal the critical cellular senescence-associated genes and immune infiltration in heart failure due to ischemic cardiomyopathy. Front Immunol 2023; 14:1150304. [PMID: 37234159 PMCID: PMC10206252 DOI: 10.3389/fimmu.2023.1150304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Heart failure (HF) is the final stage of many cardiovascular illnesses and the leading cause of death worldwide. At the same time, ischemic cardiomyopathy has replaced valvular heart disease and hypertension as the primary causes of heart failure. Cellular senescence in heart failure is currently receiving more attention. In this paper, we investigated the correlation between the immunological properties of myocardial tissue and the pathological mechanisms of cellular senescence during ischemic cardiomyopathy leading to heart failure (ICM-HF) using bioinformatics and machine learning methodologies. Our goals were to clarify the pathogenic causes of heart failure and find new treatment options. First, after obtaining GSE5406 from the Gene Expression Omnibus (GEO) database and doing limma analysis, differential genes (DEGs) among the ICM-HF and control groups were identified. We intersected these differential genes with cellular senescence-associated genes (CSAG) via the CellAge database to obtain 39 cellular senescence-associated DEGs (CSA-DEGs). Then, a functional enrichment analysis was performed to elucidate the precise biological processes by which the hub genes control cellular senescence and immunological pathways. Then, the respective key genes were identified by Random Forest (RF) method, LASSO (Least Absolute Shrinkage and Selection Operator) algorithms, and Cytoscape's MCODE plug-in. Three sets of key genes were taken to intersect to obtain three CSA-signature genes (including MYC, MAP2K1, and STAT3), and these three CSA-signature genes were validated in the test gene set (GSE57345), and Nomogram analysis was done. In addition, we assessed the relationship between these three CSA- signature genes and the immunological landscape of heart failure encompassing immunological infiltration expression profiles. This work implies that cellular senescence may have a crucial role in the pathogenesis of ICM-HF, which may be closely tied to its effect on the immune microenvironment. Exploring the molecular underpinnings of cellular senescence during ICM-HF is anticipated to yield significant advances in the disease's diagnosis and therapy.
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Affiliation(s)
- Ling Guo
- Department of Cardiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Chong-En Xu
- Department of Cardiac Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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35
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Wu B, Chen X, Pan X, Deng X, Li S, Wang Z, Wang J, Liao D, Xu J, Chen M, Zhao C, Xue Z, Wang Y, Niu T, Lin J, Chen L, Liu Y, Chen C. Single-cell transcriptome analyses reveal critical roles of RNA splicing during leukemia progression. PLoS Biol 2023; 21:e3002088. [PMID: 37130348 PMCID: PMC10154039 DOI: 10.1371/journal.pbio.3002088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/21/2023] [Indexed: 05/04/2023] Open
Abstract
Leukemogenesis is proposed to be a multistep process by which normal hematopoietic stem and progenitor cells are transformed into full-blown leukemic cells, the details of which are not fully understood. Here, we performed serial single-cell transcriptome analyses of preleukemic and leukemic cells (PLCs) and constructed the cellular and molecular transformation trajectory in a Myc-driven acute myeloid leukemia (AML) model in mice, which represented the transformation course in patients. We found that the Myc targets were gradually up-regulated along the trajectory. Among them were splicing factors, which showed stage-specific prognosis for AML patients. Furthermore, we dissected the detailed gene network of a tipping point for hematopoietic stem and progenitor cells (HSPCs) to generate initiating PLCs, which was characterized by dramatically increased splicing factors and unusual RNA velocity. In the late stage, PLCs acquired explosive heterogeneity through RNA alternative splicing. Among them, the Hsp90aa1hi subpopulation was conserved in both human and mouse AML and associated with poor prognosis. Exon 4 skipping of Tmem134 was identified in these cells. While the exon skipping product Tmem134β promoted the cell cycle, full-length Tmem134α delayed tumorigenesis. Our study emphasized the critical roles of RNA splicing in the full process of leukemogenesis.
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Affiliation(s)
- Baohong Wu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xuelan Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiangyu Pan
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xintong Deng
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shujun Li
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhongwang Wang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian Wang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dan Liao
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Xu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mei Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chengjian Zhao
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Zhihong Xue
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Yuan Wang
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Ting Niu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingwen Lin
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Lu Chen
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yu Liu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Chong Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
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Xie F, Zhang H, Zhu K, Jiang C, Zhang X, Chang H, Qiao Y, Sun M, Wang J, Wang M, Tan J, Wang T, Zhao L, Zhang Y, Lin J, Zhang C, Liu S, Zhao J, Luo C, Zhang S, Shan C. PRMT5 promotes ovarian cancer growth through enhancing Warburg effect by methylating ENO1. MedComm (Beijing) 2023; 4:e245. [PMID: 36999124 PMCID: PMC10044308 DOI: 10.1002/mco2.245] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) is a major type II enzyme responsible for symmetric dimethylation of arginine (SDMA), and plays predominantly roles in human cancers, including in ovarian cancer. However, the exactly roles and underlying mechanisms of PRMT5 contributing to the progression of ovarian cancer mediated by reprogramming cell metabolism remain largely elusive. Here, we report that PRMT5 is highly expressed and correlates with poor survival in ovarian cancer. Knockdown or pharmaceutical inhibition of PRMT5 is sufficient to decrease glycolysis flux, attenuate tumor growth, and enhance the antitumor effect of Taxol. Mechanistically, we find that PRMT5 symmetrically dimethylates alpha‐enolase (ENO1) at arginine 9 to promotes active ENO1 dimer formation, which increases glycolysis flux and accelerates tumor growth. Moreover, PRMT5 signals high glucose to increase the methylation modification of ENO1. Together, our data reveal a novel role of PRMT5 in promoting ovarian cancer growth by controlling glycolysis flux mediated by methylating ENO1, and highlights that PRMT5 may represent a promising therapeutic target for treating ovarian cancer.
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Affiliation(s)
- Fei Xie
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Han Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Kongkai Zhu
- Advanced Medical Research InstituteShandong UniversityJinanChina
| | - Cheng‐Shi Jiang
- School of Biological Science and TechnologyUniversity of JinanJinanChina
| | - Xiaoya Zhang
- Biomedical Translational Research InstituteJinan UniversityGuangzhouGuangdongChina
| | - Hongkai Chang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Yaya Qiao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Mingming Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Jiyan Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Mukuo Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Junzhen Tan
- School of Integrative MedicineTianjin University of Traditional Chinese MedicineTianjinChina
| | - Tao Wang
- Tianjin Key Laboratory of human development and reproductive regulationTianjin Central Hospital of Obstetrics and GynecologyTianjinChina
| | - Lianmei Zhao
- Research CenterThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Yuan Zhang
- The Sixth Affiliated Hospital of Guangzhou Medical UniversityQingyuanGuangdongChina
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
| | - Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical CenterNankai UniversityTianjinChina
| | - Shuangping Liu
- Department of Pathology, Medical SchoolDalian UniversityDalianLiaoningChina
| | - Jianguo Zhao
- Tianjin Key Laboratory of human development and reproductive regulationTianjin Central Hospital of Obstetrics and GynecologyTianjinChina
| | - Cheng Luo
- State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Shuai Zhang
- School of Integrative MedicineTianjin University of Traditional Chinese MedicineTianjinChina
| | - Changliang Shan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug ResearchNankai UniversityTianjinChina
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Fackenthal JD. Alternative mRNA Splicing and Promising Therapies in Cancer. Biomolecules 2023; 13:biom13030561. [PMID: 36979496 PMCID: PMC10046298 DOI: 10.3390/biom13030561] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/09/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer is among the leading causes of mortality worldwide. While considerable attention has been given to genetic and epigenetic sources of cancer-specific cellular activities, the role of alternative mRNA splicing has only recently received attention as a major contributor to cancer initiation and progression. The distribution of alternate mRNA splicing variants in cancer cells is different from their non-cancer counterparts, and cancer cells are more sensitive than non-cancer cells to drugs that target components of the splicing regulatory network. While many of the alternatively spliced mRNAs in cancer cells may represent "noise" from splicing dysregulation, certain recurring splicing variants have been shown to contribute to tumor progression. Some pathogenic splicing disruption events result from mutations in cis-acting splicing regulatory sequences in disease-associated genes, while others may result from shifts in balance among naturally occurring alternate splicing variants among mRNAs that participate in cell cycle progression and the regulation of apoptosis. This review provides examples of cancer-related alternate splicing events resulting from each step of mRNA processing and the promising therapies that may be used to address them.
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Affiliation(s)
- James D Fackenthal
- Department of Biological Sciences, College of Science and Health, Benedictine University, Lisle, IL 60532, USA
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38
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Smith BAH, Deutzmann A, Correa KM, Delaveris CS, Dhanasekaran R, Dove CG, Sullivan DK, Wisnovsky S, Stark JC, Pluvinage JV, Swaminathan S, Riley NM, Rajan A, Majeti R, Felsher DW, Bertozzi CR. MYC-driven synthesis of Siglec ligands is a glycoimmune checkpoint. Proc Natl Acad Sci U S A 2023; 120:e2215376120. [PMID: 36897988 PMCID: PMC10089186 DOI: 10.1073/pnas.2215376120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/06/2022] [Indexed: 03/12/2023] Open
Abstract
The Siglecs (sialic acid-binding immunoglobulin-like lectins) are glycoimmune checkpoint receptors that suppress immune cell activation upon engagement of cognate sialoglycan ligands. The cellular drivers underlying Siglec ligand production on cancer cells are poorly understood. We find the MYC oncogene causally regulates Siglec ligand production to enable tumor immune evasion. A combination of glycomics and RNA-sequencing of mouse tumors revealed the MYC oncogene controls expression of the sialyltransferase St6galnac4 and induces a glycan known as disialyl-T. Using in vivo models and primary human leukemias, we find that disialyl-T functions as a "don't eat me" signal by engaging macrophage Siglec-E in mice or the human ortholog Siglec-7, thereby preventing cancer cell clearance. Combined high expression of MYC and ST6GALNAC4 identifies patients with high-risk cancers and reduced tumor myeloid infiltration. MYC therefore regulates glycosylation to enable tumor immune evasion. We conclude that disialyl-T is a glycoimmune checkpoint ligand. Thus, disialyl-T is a candidate for antibody-based checkpoint blockade, and the disialyl-T synthase ST6GALNAC4 is a potential enzyme target for small molecule-mediated immune therapy.
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Affiliation(s)
- Benjamin A. H. Smith
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA94305
| | - Anja Deutzmann
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | | | - Corleone S. Delaveris
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Renumathy Dhanasekaran
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Christopher G. Dove
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Delaney K. Sullivan
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Simon Wisnovsky
- Faculty of Pharmaceutical Sciences, University of British Columbia, British Columbia, BC V6T 1Z3, Canada
| | - Jessica C. Stark
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - John V. Pluvinage
- Department of Neurology, University of California, San Francisco, CA94143
| | - Srividya Swaminathan
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA91016
- Department of Pediatrics, Beckman Research Institute of City of Hope, Duarte, CA91010
| | | | - Anand Rajan
- Department of Pathology, University of Iowa, Iowa City, IA52242
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Dean W. Felsher
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Carolyn R. Bertozzi
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Chemistry, Stanford University, Stanford, CA94305
- Howard Hughes Medical Institute, Stanford University, Stanford, CA94305
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Miao X, Luo Q, Zhao H, Qin X. Comparison of alternative splicing (AS) events in adipose tissue of polled dorset versus small tail han sheep. Heliyon 2023; 9:e14938. [PMID: 37095997 PMCID: PMC10121611 DOI: 10.1016/j.heliyon.2023.e14938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Background During the alternative splicing (AS), the exons of primary transcripts are spliced in various arrangements, resulting in structurally and functionally distinct mRNAs and proteins. This study aimed to examine genes with AS events from Small Tail Han sheep and Dorset sheep to explore the mechanism of adipose developments. Methods This study identified the genes with AS events in adipose tissues of two different sheep with next-generation sequencing. In this paper, genes with significantly different AS events were performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Results 364 genes with 411 A S events showed significant differences in adipose tissues between the two breeds; 108 genes with 120 A S events were extremely significant differences between the two breeds. We identified several novel genes that are related with adipose growth and development. The results of KEGG and GO analysis indicated that oocyte meiosis, mitogen-activated protein kinase (Wnt), mitogen-activated protein kinase (MAPK) signaling pathway, etc. Were closely related to the adipose tissue developments. Conclusions This paper revealed that the genes with AS events are important for adipose tissues in sheep, exploring the mechanisms of AS events associated with adipose tissue developments in sheep of different breeds.
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40
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Abstract
Dysregulated RNA splicing is a molecular feature that characterizes almost all tumour types. Cancer-associated splicing alterations arise from both recurrent mutations and altered expression of trans-acting factors governing splicing catalysis and regulation. Cancer-associated splicing dysregulation can promote tumorigenesis via diverse mechanisms, contributing to increased cell proliferation, decreased apoptosis, enhanced migration and metastatic potential, resistance to chemotherapy and evasion of immune surveillance. Recent studies have identified specific cancer-associated isoforms that play critical roles in cancer cell transformation and growth and demonstrated the therapeutic benefits of correcting or otherwise antagonizing such cancer-associated mRNA isoforms. Clinical-grade small molecules that modulate or inhibit RNA splicing have similarly been developed as promising anticancer therapeutics. Here, we review splicing alterations characteristic of cancer cell transcriptomes, dysregulated splicing's contributions to tumour initiation and progression, and existing and emerging approaches for targeting splicing for cancer therapy. Finally, we discuss the outstanding questions and challenges that must be addressed to translate these findings into the clinic.
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Affiliation(s)
- Robert K Bradley
- Computational Biology Program, Public Health Sciences Division and Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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41
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The "Superoncogene" Myc at the Crossroad between Metabolism and Gene Expression in Glioblastoma Multiforme. Int J Mol Sci 2023; 24:ijms24044217. [PMID: 36835628 PMCID: PMC9966483 DOI: 10.3390/ijms24044217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The concept of the Myc (c-myc, n-myc, l-myc) oncogene as a canonical, DNA-bound transcription factor has consistently changed over the past few years. Indeed, Myc controls gene expression programs at multiple levels: directly binding chromatin and recruiting transcriptional coregulators; modulating the activity of RNA polymerases (RNAPs); and drawing chromatin topology. Therefore, it is evident that Myc deregulation in cancer is a dramatic event. Glioblastoma multiforme (GBM) is the most lethal, still incurable, brain cancer in adults, and it is characterized in most cases by Myc deregulation. Metabolic rewiring typically occurs in cancer cells, and GBM undergoes profound metabolic changes to supply increased energy demand. In nontransformed cells, Myc tightly controls metabolic pathways to maintain cellular homeostasis. Consistently, in Myc-overexpressing cancer cells, including GBM cells, these highly controlled metabolic routes are affected by enhanced Myc activity and show substantial alterations. On the other hand, deregulated cancer metabolism impacts Myc expression and function, placing Myc at the intersection between metabolic pathway activation and gene expression. In this review paper, we summarize the available information on GBM metabolism with a specific focus on the control of the Myc oncogene that, in turn, rules the activation of metabolic signals, ensuring GBM growth.
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42
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Scagnoli F, Palma A, Favia A, Scuoppo C, Illi B, Nasi S. A New Insight into MYC Action: Control of RNA Polymerase II Methylation and Transcription Termination. Biomedicines 2023; 11:biomedicines11020412. [PMID: 36830948 PMCID: PMC9952900 DOI: 10.3390/biomedicines11020412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
MYC oncoprotein deregulation is a common catastrophic event in human cancer and limiting its activity restrains tumor development and maintenance, as clearly shown via Omomyc, an MYC-interfering 90 amino acid mini-protein. MYC is a multifunctional transcription factor that regulates many aspects of transcription by RNA polymerase II (RNAPII), such as transcription activation, pause release, and elongation. MYC directly associates with Protein Arginine Methyltransferase 5 (PRMT5), a protein that methylates a variety of targets, including RNAPII at the arginine residue R1810 (R1810me2s), crucial for proper transcription termination and splicing of transcripts. Therefore, we asked whether MYC controls termination as well, by affecting R1810me2S. We show that MYC overexpression strongly increases R1810me2s, while Omomyc, an MYC shRNA, or a PRMT5 inhibitor and siRNA counteract this phenomenon. Omomyc also impairs Serine 2 phosphorylation in the RNAPII carboxyterminal domain, a modification that sustains transcription elongation. ChIP-seq experiments show that Omomyc replaces MYC and reshapes RNAPII distribution, increasing occupancy at promoter and termination sites. It is unclear how this may affect gene expression. Transcriptomic analysis shows that transcripts pivotal to key signaling pathways are both up- or down-regulated by Omomyc, whereas genes directly controlled by MYC and belonging to a specific signature are strongly down-regulated. Overall, our data point to an MYC/PRMT5/RNAPII axis that controls termination via RNAPII symmetrical dimethylation and contributes to rewiring the expression of genes altered by MYC overexpression in cancer cells. It remains to be clarified which role this may have in tumor development.
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Affiliation(s)
- Fiorella Scagnoli
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
| | - Alessandro Palma
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
| | - Annarita Favia
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
| | - Claudio Scuoppo
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Barbara Illi
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
| | - Sergio Nasi
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
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Hing ZA, Walker JS, Whipp EC, Brinton L, Cannon M, Zhang P, Sher S, Cempre CB, Brown F, Smith PL, Agostinelli C, Pileri SA, Skinner JN, Williams K, Phillips H, Shaffer J, Beaver LP, Pan A, Shin K, Gregory CT, Ozer GH, Yilmaz SA, Harrington BK, Lehman AM, Yu L, Coppola V, Yan P, Scherle P, Wang M, Pitis P, Xu C, Vaddi K, Chen-Kiang S, Woyach J, Blachly JS, Alinari L, Yang Y, Byrd JC, Baiocchi RA, Blaser BW, Lapalombella R. Dysregulation of PRMT5 in chronic lymphocytic leukemia promotes progression with high risk of Richter's transformation. Nat Commun 2023; 14:97. [PMID: 36609611 PMCID: PMC9823097 DOI: 10.1038/s41467-022-35778-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 12/22/2022] [Indexed: 01/08/2023] Open
Abstract
Richter's Transformation (RT) is a poorly understood and fatal progression of chronic lymphocytic leukemia (CLL) manifesting histologically as diffuse large B-cell lymphoma. Protein arginine methyltransferase 5 (PRMT5) is implicated in lymphomagenesis, but its role in CLL or RT progression is unknown. We demonstrate herein that tumors uniformly overexpress PRMT5 in patients with progression to RT. Furthermore, mice with B-specific overexpression of hPRMT5 develop a B-lymphoid expansion with increased risk of death, and Eµ-PRMT5/TCL1 double transgenic mice develop a highly aggressive disease with transformation that histologically resembles RT; where large-scale transcriptional profiling identifies oncogenic pathways mediating PRMT5-driven disease progression. Lastly, we report the development of a SAM-competitive PRMT5 inhibitor, PRT382, with exclusive selectivity and optimal in vitro and in vivo activity compared to available PRMT5 inhibitors. Taken together, the discovery that PRMT5 drives oncogenic pathways promoting RT provides a compelling rationale for clinical investigation of PRMT5 inhibitors such as PRT382 in aggressive CLL/RT cases.
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Affiliation(s)
- Zachary A Hing
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Janek S Walker
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Ethan C Whipp
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Lindsey Brinton
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Matthew Cannon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Pu Zhang
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Steven Sher
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Casey B Cempre
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Fiona Brown
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Porsha L Smith
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Claudio Agostinelli
- Haematopathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Stefano A Pileri
- European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Department of Specialized, Experimental and Diagnostic Medicine, University of Bologna, Bologna, Italy
| | - Jordan N Skinner
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Katie Williams
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Hannah Phillips
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Jami Shaffer
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Larry P Beaver
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Alexander Pan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Kyle Shin
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Charles T Gregory
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Gulcin H Ozer
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Selen A Yilmaz
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Bonnie K Harrington
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Amy M Lehman
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Lianbo Yu
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Pearlly Yan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Min Wang
- Prelude Therapeutics, Wilmington, DE, USA
| | | | - Chaoyi Xu
- Prelude Therapeutics, Wilmington, DE, USA
| | - Kris Vaddi
- Prelude Therapeutics, Wilmington, DE, USA
| | - Selina Chen-Kiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jennifer Woyach
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Yiping Yang
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Robert A Baiocchi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Bradley W Blaser
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Rosa Lapalombella
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.
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Winkler R, Piskor EM, Kosan C. Lessons from Using Genetically Engineered Mouse Models of MYC-Induced Lymphoma. Cells 2022; 12:cells12010037. [PMID: 36611833 PMCID: PMC9818924 DOI: 10.3390/cells12010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Oncogenic overexpression of MYC leads to the fatal deregulation of signaling pathways, cellular metabolism, and cell growth. MYC rearrangements are found frequently among non-Hodgkin B-cell lymphomas enforcing MYC overexpression. Genetically engineered mouse models (GEMMs) were developed to understand MYC-induced B-cell lymphomagenesis. Here, we highlight the advantages of using Eµ-Myc transgenic mice. We thoroughly compiled the available literature to discuss common challenges when using such mouse models. Furthermore, we give an overview of pathways affected by MYC based on knowledge gained from the use of GEMMs. We identified top regulators of MYC-induced lymphomagenesis, including some candidates that are not pharmacologically targeted yet.
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45
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Aktas Samur A, Fulciniti M, Avet-Loiseau H, Lopez MA, Derebail S, Corre J, Minvielle S, Magrangeas F, Moreau P, Anderson KC, Parmigiani G, Samur MK, Munshi NC. In-depth analysis of alternative splicing landscape in multiple myeloma and potential role of dysregulated splicing factors. Blood Cancer J 2022; 12:171. [PMID: 36535935 PMCID: PMC9763261 DOI: 10.1038/s41408-022-00759-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Splicing changes are common in cancer and are associated with dysregulated splicing factors. Here, we analyzed RNA-seq data from 323 newly diagnosed multiple myeloma (MM) patients and described the alternative splicing (AS) landscape. We observed a large number of splicing pattern changes in MM cells compared to normal plasma cells (NPC). The most common events were alterations of mutually exclusive exons and exon skipping. Most of these events were observed in the absence of overall changes in gene expression and often impacted the coding potential of the alternatively spliced genes. To understand the molecular mechanisms driving frequent aberrant AS, we investigated 115 splicing factors (SFs) and associated them with the AS events in MM. We observed that ~40% of SFs were dysregulated in MM cells compared to NPC and found a significant enrichment of SRSF1, SRSF9, and PCB1 binding motifs around AS events. Importantly, SRSF1 overexpression was linked with shorter survival in two independent MM datasets and was correlated with the number of AS events, impacting tumor cell proliferation. Together with the observation that MM cells are vulnerable to splicing inhibition, our results may lay the foundation for developing new therapeutic strategies for MM. We have developed a web portal that allows custom alternative splicing event queries by using gene symbols and visualizes AS events in MM and subgroups. Our portals can be accessed at http://rconnect.dfci.harvard.edu/mmsplicing/ and https://rconnect.dfci.harvard.edu/mmleafcutter/ .
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Affiliation(s)
- Anil Aktas Samur
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health Boston, Boston, MA, 02115, USA
| | - Mariateresa Fulciniti
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Herve Avet-Loiseau
- University Cancer Center of Toulouse Institut National de la Santé, Toulouse, France
| | - Michael A Lopez
- Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Sanika Derebail
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jill Corre
- University Cancer Center of Toulouse Institut National de la Santé, Toulouse, France
| | - Stephane Minvielle
- Inserm UMR892, CNRS 6299, Université de Nantes; Centre Hospitalier Universitaire de Nantes, Unité Mixte de Genomique du Cancer, Nantes, France
| | - Florence Magrangeas
- Inserm UMR892, CNRS 6299, Université de Nantes; Centre Hospitalier Universitaire de Nantes, Unité Mixte de Genomique du Cancer, Nantes, France
| | - Philippe Moreau
- Inserm UMR892, CNRS 6299, Université de Nantes; Centre Hospitalier Universitaire de Nantes, Unité Mixte de Genomique du Cancer, Nantes, France
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Giovanni Parmigiani
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health Boston, Boston, MA, 02115, USA.
| | - Mehmet K Samur
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health Boston, Boston, MA, 02115, USA.
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
- VA Boston Healthcare System, Boston, MA, 02115, USA.
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46
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Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol 2022; 12:1051487. [PMID: 36505834 PMCID: PMC9730332 DOI: 10.3389/fonc.2022.1051487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer-specific alternatively spliced events (ASE) play a role in cancer pathogenesis and can be targeted by immunotherapy, oligonucleotide therapy, and small molecule inhibition. However, identifying actionable ASE targets remains challenging due to the uncertainty of its protein product, structure impact, and proteoform (protein isoform) function. Here we argue that an integrated multi-omics profiling strategy can overcome these challenges, allowing us to mine this untapped source of targets for therapeutic development. In this review, we will provide an overview of current multi-omics strategies in characterizing ASEs by utilizing the transcriptome, proteome, and state-of-art algorithms for protein structure prediction. We will discuss limitations and knowledge gaps associated with each technology and informatics analytics. Finally, we will discuss future directions that will enable the full integration of multi-omics data for ASE target discovery.
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Affiliation(s)
- Timothy I. Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States,*Correspondence: Timothy I. Shaw,
| | - Bi Zhao
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Brandon Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Paul A. Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Aleksandra Karolak
- Department of Machine Learning, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
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47
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Markouli M, Strepkos D, Piperi C. Impact of Histone Modifications and Their Therapeutic Targeting in Hematological Malignancies. Int J Mol Sci 2022; 23:13657. [PMID: 36362442 PMCID: PMC9654260 DOI: 10.3390/ijms232113657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Hematologic malignancies are a large and heterogeneous group of neoplasms characterized by complex pathogenetic mechanisms. The abnormal regulation of epigenetic mechanisms and specifically, histone modifications, has been demonstrated to play a central role in hematological cancer pathogenesis and progression. A variety of epigenetic enzymes that affect the state of histones have been detected as deregulated, being either over- or underexpressed, which induces changes in chromatin compaction and, subsequently, affects gene expression. Recent advances in the field of epigenetics have revealed novel therapeutic targets, with many epigenetic drugs being investigated in clinical trials. The present review focuses on the biological impact of histone modifications in the pathogenesis of hematologic malignancies, describing a wide range of therapeutic agents that have been discovered to target these alterations and are currently under investigation in clinical trials.
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Affiliation(s)
| | | | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.M.); (D.S.)
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48
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Sauter C, Simonet J, Guidez F, Dumétier B, Pernon B, Callanan M, Bastie JN, Aucagne R, Delva L. Protein Arginine Methyltransferases as Therapeutic Targets in Hematological Malignancies. Cancers (Basel) 2022; 14:5443. [PMID: 36358861 PMCID: PMC9657843 DOI: 10.3390/cancers14215443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 08/02/2023] Open
Abstract
Arginine methylation is a common post-translational modification affecting protein activity and the transcription of target genes when methylation occurs on histone tails. There are nine protein arginine methyltransferases (PRMTs) in mammals, divided into subgroups depending on the methylation they form on a molecule of arginine. During the formation and maturation of the different types of blood cells, PRMTs play a central role by controlling cell differentiation at the transcriptional level. PRMT enzymatic activity is necessary for many cellular processes in hematological malignancies, such as the activation of cell cycle and proliferation, inhibition of apoptosis, DNA repair processes, RNA splicing, and transcription by methylating histone tails' arginine. Chemical tools have been developed to inhibit the activity of PRMTs and have been tested in several models of hematological malignancies, including primary samples from patients, xenografts into immunodeficient mice, mouse models, and human cell lines. They show a significant effect by reducing cell viability and increasing the overall survival of mice. PRMT5 inhibitors have a strong therapeutic potential, as phase I clinical trials in hematological malignancies that use these molecules show promising results, thus, underlining PRMT inhibitors as useful therapeutic tools for cancer treatment in the future.
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Affiliation(s)
- Camille Sauter
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - John Simonet
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Fabien Guidez
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Baptiste Dumétier
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Baptiste Pernon
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Mary Callanan
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
- Unit for Innovation in Genetics and Epigenetic in Oncology (IGEO)/CRIGEN Core Facility, University Hospital François Mitterrand, 21000 Dijon, France
| | - Jean-Noël Bastie
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
- Department of Clinical Hematology, University Hospital François Mitterrand, 21000 Dijon, France
| | - Romain Aucagne
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
- Unit for Innovation in Genetics and Epigenetic in Oncology (IGEO)/CRIGEN Core Facility, University Hospital François Mitterrand, 21000 Dijon, France
| | - Laurent Delva
- Inserm U1231, Team Epi2THM, LipSTIC Labex, UFR des Sciences de Santé, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
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49
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Schwarz M, Torre D, Lozano-Ojalvo D, Tan AT, Tabaglio T, Mzoughi S, Sanchez-Tarjuelo R, Le Bert N, Lim JME, Hatem S, Tuballes K, Camara C, Lopez-Granados E, Paz-Artal E, Correa-Rocha R, Ortiz A, Lopez-Hoyos M, Portoles J, Cervera I, Gonzalez-Perez M, Bodega-Mayor I, Conde P, Oteo-Iglesias J, Borobia AM, Carcas AJ, Frías J, Belda-Iniesta C, Ho JSY, Nunez K, Hekmaty S, Mohammed K, Marsiglia WM, Carreño JM, Dar AC, Berin C, Nicoletti G, Della Noce I, Colombo L, Lapucci C, Santoro G, Ferrari M, Nie K, Patel M, Barcessat V, Gnjatic S, Harris J, Sebra R, Merad M, Krammer F, Kim-Schulze S, Marazzi I, Bertoletti A, Ochando J, Guccione E. Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR. Nat Biotechnol 2022; 40:1680-1689. [PMID: 35697804 PMCID: PMC10603792 DOI: 10.1038/s41587-022-01347-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 05/02/2022] [Indexed: 12/30/2022]
Abstract
Fast, high-throughput methods for measuring the level and duration of protective immune responses to SARS-CoV-2 are needed to anticipate the risk of breakthrough infections. Here we report the development of two quantitative PCR assays for SARS-CoV-2-specific T cell activation. The assays are rapid, internally normalized and probe-based: qTACT requires RNA extraction and dqTACT avoids sample preparation steps. Both assays rely on the quantification of CXCL10 messenger RNA, a chemokine whose expression is strongly correlated with activation of antigen-specific T cells. On restimulation of whole-blood cells with SARS-CoV-2 viral antigens, viral-specific T cells secrete IFN-γ, which stimulates monocytes to produce CXCL10. CXCL10 mRNA can thus serve as a proxy to quantify cellular immunity. Our assays may allow large-scale monitoring of the magnitude and duration of functional T cell immunity to SARS-CoV-2, thus helping to prioritize revaccination strategies in vulnerable populations.
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Affiliation(s)
- Megan Schwarz
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Denis Torre
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Lozano-Ojalvo
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anthony T Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology, IMCB, A*STAR, Singapore, Singapore
| | - Slim Mzoughi
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rodrigo Sanchez-Tarjuelo
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- National Center for Microbiology, Carlos III Health Institute, Madrid, Spain
| | - Nina Le Bert
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Joey Ming Er Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Sandra Hatem
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Camara
- Department of Immunology, University Hospital La Paz-IdiPAZ, Madrid, Spain
| | | | - Estela Paz-Artal
- Department of Immunology, Research Institution, Sanitaria Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, Complutense University of Madrid, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Rafael Correa-Rocha
- Laboratory of Immune-Regulation, Research Institute Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Alberto Ortiz
- Department of Nephrology, IIS-Fundación Jimenez Díaz, Madrid, Spain
| | - Marcos Lopez-Hoyos
- Department of Immunology, Hospital University of Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Jose Portoles
- Department of Nephrology, Hospital of Puerta de Hierro, Madrid, Spain
| | - Isabel Cervera
- National Center for Microbiology, Carlos III Health Institute, Madrid, Spain
| | | | - Irene Bodega-Mayor
- National Center for Microbiology, Carlos III Health Institute, Madrid, Spain
| | - Patricia Conde
- National Center for Microbiology, Carlos III Health Institute, Madrid, Spain
| | - Jesús Oteo-Iglesias
- National Center for Microbiology, Carlos III Health Institute, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
| | - Alberto M Borobia
- Clinical Pharmacology, University Hospital La Paz-IDIPAZ, Platform of Clinical Research Units and Clinical Trials, Spain Faculty of Medicine Autonomous University of Madrid, Madrid, Spain
| | - Antonio J Carcas
- Clinical Pharmacology, University Hospital La Paz-IDIPAZ, Platform of Clinical Research Units and Clinical Trials, Spain Faculty of Medicine Autonomous University of Madrid, Madrid, Spain
| | - Jesús Frías
- Clinical Pharmacology, University Hospital La Paz-IDIPAZ, Platform of Clinical Research Units and Clinical Trials, Spain Faculty of Medicine Autonomous University of Madrid, Madrid, Spain
| | | | - Jessica S Y Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kemuel Nunez
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saboor Hekmaty
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Mohammed
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - William M Marsiglia
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arvin C Dar
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cecilia Berin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | | | | | | | - Kai Nie
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vanessa Barcessat
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jocelyn Harris
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Antonio Bertoletti
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Jordi Ochando
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- National Center for Microbiology, Carlos III Health Institute, Madrid, Spain.
| | - Ernesto Guccione
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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50
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Urbanski L, Brugiolo M, Park S, Angarola BL, Leclair NK, Yurieva M, Palmer P, Sahu SK, Anczuków O. MYC regulates a pan-cancer network of co-expressed oncogenic splicing factors. Cell Rep 2022; 41:111704. [DOI: 10.1016/j.celrep.2022.111704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/16/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
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